Volatile N-nitrosamines in processed meat products: An approach for monitoring dietary exposure, assessing human risk, and evaluating variable correlations by principal component analysis and heat map

Several epidemiological studies have reported a positive association between the consumption of processed meats containing N-nitrosamines (NAs) and the incidence of hepatocellular and colon cancer. The health risk assessment in this investigation was based on the concentration of six volatile N-nitrosamines (VNAs) (N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosomethylethylamine, N-nitrosopiperidine, N-nitrosodibutylamine, and N-nitrosodi-n-propylamine) found in processed meat products (sausage and kielbasa) in the Iranian market. Direct supported liquid membrane two-phase hollow fiber electromembrane extraction coupled to gas chromatography/mass spectrometry was used to analyse six VNAs. The mean concentration of the six VNAs in sausages and kielbasa was 38.677 ± 27.56 and 48.383 ± 35.76 μg/kg, respectively. The 95th percentile for the chronic daily intake of total VNAs for children (3-14 years) and adults (15-70 years) were calculated to be 5.06 × 10-4 and 1.09 × 10-4 mg/kg bw/day, respectively. The cancer risk assessment showed that the risk associated with NDEA was the highest among the other VNAs studied in Iranian processed meat, with a 95th percentile for the child and adult groups. Based on an incremental lifetime cancer risk (ILCR) value of ≤10-4 for the carcinogenic effects of exposure to a total of six VNAs, it indicates low concern for all age groups.

Quadrilateral plate classification program of acetabular fractures based on three-column classification: a three-dimensional fracture mapping study

BACKGROUND

A new classification system for acetabular fractures has been proposed in recent years, which is called the 3-column classification. However, this system does not provide information regarding quadrilateral plate fractures. To address this issue, we utilized three-dimensional (3D) fracture line mapping and heat map to analyze the link between the 3-column classification and quadrilateral plate fractures.

METHODS

We collected CT scan data from 177 patients who had been diagnosed with acetabular fractures. Additionally, we utilized a CT scan of a healthy adult to generate a standard acetabular model. We utilized the collected CT data of the fracture to create a 3D model and subsequently reduced it. We then matched each acetabular fracture model with the standard acetabular model and mapped all of the fracture lines to the standard model. 3D fracture lines and heat maps were created by overlapping all fracture lines. Fracture characteristics were then summarized using these maps.

RESULTS

This study analyzed a total of 221 acetabular fractures. The most frequently observed fracture type, based on the three-column classification, was A1.2, which corresponds to fractures of the anterior column. In contrast, the least common type of fracture was A4, which represents fractures of the central wall. It was noted that quadrilateral plate fractures were frequently observed in fractures classified as type B and C according to the three-column classification.

CONCLUSIONS

Among the three-column classification, the QLP fractures are commonly observed in type B and C. It is important to carefully identify these fractures during the diagnostic process. Therefore, based on the three-column classification, we have amalgamated quadrilateral plate fractures and formulated a classification program for acetabular fractures.

BarlowTwins-CXR: enhancing chest X-ray abnormality localization in heterogeneous data with cross-domain self-supervised learning

BACKGROUND

Chest X-ray imaging based abnormality localization, essential in diagnosing various diseases, faces significant clinical challenges due to complex interpretations and the growing workload of radiologists. While recent advances in deep learning offer promising solutions, there is still a critical issue of domain inconsistency in cross-domain transfer learning, which hampers the efficiency and accuracy of diagnostic processes. This study aims to address the domain inconsistency problem and improve autonomic abnormality localization performance of heterogeneous chest X-ray image analysis, particularly in detecting abnormalities, by developing a self-supervised learning strategy called "BarlwoTwins-CXR".

METHODS

We utilized two publicly available datasets: the NIH Chest X-ray Dataset and the VinDr-CXR. The BarlowTwins-CXR approach was conducted in a two-stage training process. Initially, self-supervised pre-training was performed using an adjusted Barlow Twins algorithm on the NIH dataset with a Resnet50 backbone pre-trained on ImageNet. This was followed by supervised fine-tuning on the VinDr-CXR dataset using Faster R-CNN with Feature Pyramid Network (FPN). The study employed mean Average Precision (mAP) at an Intersection over Union (IoU) of 50% and Area Under the Curve (AUC) for performance evaluation.

RESULTS

Our experiments showed a significant improvement in model performance with BarlowTwins-CXR. The approach achieved a 3% increase in mAP50 accuracy compared to traditional ImageNet pre-trained models. In addition, the Ablation CAM method revealed enhanced precision in localizing chest abnormalities. The study involved 112,120 images from the NIH dataset and 18,000 images from the VinDr-CXR dataset, indicating robust training and testing samples.

CONCLUSION

BarlowTwins-CXR significantly enhances the efficiency and accuracy of chest X-ray image-based abnormality localization, outperforming traditional transfer learning methods and effectively overcoming domain inconsistency in cross-domain scenarios. Our experiment results demonstrate the potential of using self-supervised learning to improve the generalizability of models in medical settings with limited amounts of heterogeneous data. This approach can be instrumental in aiding radiologists, particularly in high-workload environments, offering a promising direction for future AI-driven healthcare solutions.

Three-dimensional Mapping Analysis of Talus Fractures and Demonstration of Different Surgical Approaches for Talus Fractures

OBJECTIVE

The talus is an important component in the ankle, and its treatment after injury is crucial. However, complications and adverse events due to incomplete traditional classifications may still occur, and these classifications fail to analyze the patterns and distribution of fractures from a three-dimensional perspective. Therefore, in this study, we aimed to analyze the location and distribution of fracture lines in different types of talus fractures using three-dimensional (3D) and heat mapping techniques. Additionally, we aimed to determine the surface area of the talus that can be utilized for different approaches of internal fixation, aiding in the planning of surgical procedures.

METHODS

We retrospectively analyzed data from CT scans from 126 patients diagnosed with talus fractures at our two hospitals. We extracted the CT data of a healthy adult and created a standard talus model. We performed 3D reconstruction using patients' CT images and superimposed the fracture model onto the standard model for drawing fracture lines. Subsequently, we converted the fracture lines into a heat map for visualization. Additionally, we measured 20 specimens to determine the boundary for various ligaments attached to the talus. We determined the surface area of the talus available for different surgical approaches by integrating the boundary data with previously reported data on area of exposure.

RESULTS

Without considering the displacement distance of the fracture, fracture types were classified as follows, by combining Hawkins and Sneppen classifications: talar neck, 41.3%; posterior talar tubercle, 22.2%; body for the talus and comminuted, 17.5%; lateral talar tubercle, 11.9%; and talar head, 7.1%. We established fracture line and heat maps using this classification. Additionally, we demonstrated the available area for anteromedial, anterolateral, posteromedial, posterolateral, and medial malleolus osteotomy and Chaput osteotomy approaches.

CONCLUSION

Fracture line and heat map analyses can aid surgeons in planning a single or combined surgical approach for the reduction and internal fixation of talus fractures. Demonstrating the different surgical approaches can help surgeons choose the most effective technique for individual cases.

Neurofibromatosis type 1-associated plexiform neurofibromas of the neck: topography of lesions and surgical treatment data of 69 patients

PURPOSE

Plexiform neurofibromas (PNF) are rare tumors arising from peripheral nerve sheath cells. PNF are a hallmark in patients with neurofibromatosis type 1 (NF1), a tumor predisposition syndrome. PNF often grow invasively and destructively, what may complicate surgical treatment. Data on frequency, location, and surgical procedures of patients with NF1-associated FPNF are scarce. This study provides treatment data of NF1 patients.

METHODS

Localization and treatment data of 69 NF1 patients with neck PNF were analyzed. Frequency of lesions was recorded in coded colors on schematic neck drawings.

RESULTS

The tumors showed no side preference, were located in the entire area under investigation, and did not respect anatomical units/dermatomes. However, the sternocleidomastoid region was particularly frequently affected. The mean number of surgical measures per patient was 1.33. Complications were extensive swelling, hematoma, and bleeding. Histological assessment usually confirmed the clinical assessment of neoplasm. However, histologic differentiation of PNST reveals differences in between tumors that have been unified in clinical assessment as PNF.

CONCLUSION

The color-coded, schematic overview of the frequency distribution of surgical neck interventions in NF1 patients with PNF proved a useful tool to gain assessment of preferred treatment needs. The imaging procedure may be suitable for controlling the external aspect of natural tumor development (growth, effects of aging) in the same way as the documentation of the post-surgical course. Treatment plans for patients with these tumors should consider that repeated interventions may be necessary to achieve a longer-term stable result.

Non-targeted Profiling of Sea Buckthorn Fruit Oil Fingerprints from 3 Regions and Study on Its Antioxidant Activity

This study investigated the chemical and volatile characteristics of sea buckthorn fruits from three different regions in China. The chemical composition of the volatile oil was determined by using a non-targeted gas chromatography and mass spectrometry (GC/MS) method and the differences in chemical composition among the three producing areas were compared by heatmap providing a visual basis for researchers. A total of 93 compounds were identified, including 52 compounds from the Northeast China, 51 from the Xinjiang region, and 37 from Inner Mongolia region. Then, the in vitro antioxidant activity of sea buckthorn fruit oil was measured using DPPH, ABTS, and SOD inhibition tests, and the results showed that sea buckthorn fruit oil in northeast China was the strongest antioxidant, followed by Inner Mongolia and Xinjiang. The results of the CCK-8 experiment indicated that within the tested concentration, there is no cell cytotoxicity of the essential oil in human umbilical vein endothelial cells (HUVECs) cells. The results could supply reference to distinguish sea buckthorn fruit from different production areas and, meanwhile, clarify the activity and safety of sea buckthorn oil.

Neurofibromatosis Type 1-Associated Plexiform Neurofibromas of the Face and Adjacent Head Regions: Topography of Lesions and Surgical Treatment Data of 179 Patients

Introduction

Facial plexiform neurofibromas (FPNF) are rare tumors frequently diagnosed in patients with neurofibromatosis type 1 (NF1), a tumor predisposition syndrome. FPNF often grows invasively and destructively, which may complicate surgical treatment. Data on the frequency, location, and surgical procedures of patients with NF1-associated FPNF are scarce. This study provides treatment data from a nationally networked reference center for the treatment of NF1 patients.

Material and Methods

The localization and treatment data of 179 NF1 patients with FPNF were analyzed. Photographically documented tumors of the study area, further determined by imaging, were manually transferred to a facial scheme and digitized. The digitized registrations of the facial extensions of the tumors of each patient were overlaid in a single image (Photoshop™), so that the file of the facial scheme contained the sum of the tumor localization. Finally, the frequency of tumor localization was indicated with a color code. The frequency of tumor extension-related coded colors was applied to outline the lesions' topography on schematic face drawings (heat map).

Results

The distribution of the tumors showed no side preference. The need for the treatment of patients with orbital/periorbital manifestations became evident in the graphic representations. Tumors do not respect anatomical units. However, the classification of the face according to dermatomes, especially the trigeminal nerve, offers indications of tumor spread and guides treatment planning. The mean number of surgical measures per patient was 2.21 (median: 1). Extensive swelling, hematoma, and delayed wound healing were all common postoperative complications.

Conclusion

The color-coded, schematic overview of the frequency distribution of cutaneous tumor spread in NF1 patients with FPNF illustrates the importance of orbital/periorbital and cheek tumor manifestations in patients' treatment needs. The imaging procedure is suitable for controlling natural tumor growth in the same way as the documentation of the post-surgical course. Repeated interventions in the region are included in surgical planning of the progressing tumor disease.

Hand wounds: An analysis of topography and related damage to underlying structures

INTRODUCTION

Hand wounds account for 35 to 51% of hand traumas. Damage to underlying anatomical structures depends on the location of the wound. The objective of this study is to describe the topographic distribution of hand wounds allowing for subsequent evaluation of the link between affected surface area and underlying lesion.

METHODS

We retrospectively reviewed the medical records of 1058 patients with a total of 1319 wounds over a period of 2 years. Wound location was described according to the cutaneous projection of IFSSH zones for flexors and extensors. Any associated deep lesions were evaluated. Topographical distribution was modeled graphically using a heat-map. We compared the proportion of underlying lesions between each cutaneous zone. Sub-group analysis for lesions' rate regarding zone groups were performed.

RESULTS

58.9% of wounds were located on the palmar surface and 41.1% on the dorsal surface. 71% of wounds affected only the digits. The index finger was the most affected. The most damaged region was zone 2 for palmar wounds and zone 3 for dorsal wounds. 45.5% of wounds resulted in injury to a significant underlying anatomical structure. This frequency was 36.4% and 58.5% for palmar and dorsal wounds respectively. More than 50% of wounds in palmar zone 5 and dorsal zones 1, 3, 5, 6 and 7 presented at least one lesion. A lesion of major structure was more frequently found in palmar zone 5 (p <0.001). Dorsally, no zone predominated. Subgroup analysis for dorsal wounds revealed that wounds overlying joints had more major lesions including more tendons injuries and more articular violations with zone 3 presenting a rate of 68%.

CONCLUSION

We provided the first graphical representation for the topographical distribution of hand wounds. Dorsal wounds have a higher association with injury to underlying structures. These results generally support surgical exploration of all hand wounds regardless of their location.

LEVEL OF EVIDENCE

IV Study type: Epidemiological study.

Is the T-shaped acetabular fracture really likes a "T"? A study based on three-dimensional fracture mapping

OBJECTIVES

To explore the morphological pattern of T-shaped acetabular fractures (T-SAFs) by mapping the fracture line using 3D software.

MATERIAL AND METHODS

We retrospectively reviewed 1298 consecutive patients with acetabular fractures, and a total of 56 T-SAF patients were enrolled. After the simulated reduction of each fracture in the software, the fracture lines of all patients were overlaid and plotted on a template. A frequency heat map was generated according to the differences in fracture line density distribution. According to the location of fracture lines, all cases were divided into three groups: posterior group, anterior group, extra-posterior group. In surgically treated patients, the surgical approach, fixation methods, and reduction quality were recorded or evaluated.

RESULTS

The transverse fracture line was sinuous without involving the acetabular roof, and the longitudinal fracture line sloped forward or backward along the edge of the acetabular fossa to split the obturator foramen. The anterior and posterior edges of the acetabular fossa, the transition zone of the acetabular roof and anterior wall, the transition zone of the superior pubic ramus and anterior wall, and the posterior wall near the greater sciatic notch were areas with high rates of fracture incidence. The posterior group included 26 patients (46.4%) and the distribution of fracture lines resembled a "T" or "Y". The anterior group included 25 patients (44.6%) and the distribution of fracture lines resembled a "7″. The extra-posterior group included 5 patients (8.9%) and the fracture lines run through the ischial body. The surgical strategies vary among different groups of T-SAF patients.

CONCLUSION

Our findings shed light on the characteristics of fracture lines for T-SAFs and provide a reference for surgical treatment strategies.

Foliar-applied magnesium nanoparticles modulate drought stress through changes in physio-biochemical attributes and essential oil profile of yarrow (Achillea millefolium L.)

Nanoparticles (NPs) are an emerging tool for mitigating environmental stresses. Although beneficial roles of NPs have been reported in some plants, there is little data on magnesium (Mg)-NPs in alleviating drought stress. Therefore, the field experiment was conducted to study changes in biochemical attributes and essential oil (EO) compositions of yarrow (Achillea millefolium L.) plants under drought stress and Mg-NPs in 2016 and 2017. Irrigation regimes were used in two levels as well-watered (irrigation intervals of 7 days) and drought stress (irrigation intervals of 14 days) conditions, and Mg-NPs were sprayed on leaves in four levels (0, 0.1, 0.3, and 0.5 g L-1). The results showed drought stress led to increased electrolyte leakage (EL), proline, carotenoid, anthocyanin, and total flavonoid content (TFC). However, flowers yield and EO yield were lower in plants exposed to drought stress as compared to well-watered conditions. The 0.3 and 0.5 g L-1 Mg-NPs were more effective in alleviating drought stress by enhancing these traits. Heat map results showed that EL and TSS represented the high variability upon different treatments. The GC and GC/MS results represented that α-pinene (8.60-12.20%), 1,8-cineol (9.03-14.02%), camphor (6.84-9.80%), α-bisabolol (8.54-18.81%), chamazulene (14.23-22.50%), and caryophyllene oxide (7.20-9.80%) were the min EO constitutes of yarrow plants. Totally, drought decreased monopertens but increased sesquiterpenes of EO. To sum up, foliar applied Mg-NPs in a range of 0.3-0.5 g L-1 can be recommended as effective tool to improve plant yield through changes in biochemical attributes of yarrow plants.

Cold plasma can alleviate cadmium stress by optimizing growth and yield of wheat (Triticum aestivum L.) through changes in physio-biochemical properties and fatty acid profile

Cold plasma (CP) application has increasing interest due to its environmental-friendly, high efficient, and low cost aspects to mitigate deletion effects of heavy metals on plants. A pot experiment was carried out to evaluate the CP application on yield, physiological, and fatty acid profile of wheat (Triticum aestivum L.) in a completely randomized design (CRD) with five replicates. Cadmium (Cd) was applied at four levels (0, 50, 100, and 150 μM), and CP were used on germinated seeds at three levels (0, 60, and 120 s) in a hydroponic system. The results showed CP alleviated the Cd accumulation in roots, shoots, and grains. The significant reduction of grain yield (GY) and thousand grain yield (TGY) was observed in plants exposed to 100 and 150 μM compared with the control plants; however, CP improved GY and TGY particularly at severe Cd stress. The minimum chlorophyll (Chl) and relative water content (RWC) were observed in plants exposed in 100 μM Cd and non-CP treatments. Proline increased by Cd stress but decreased with CP in most treatments. Unlike proline, methionine showed significant reduction under Cd stress. The fatty acid profile of wheat represented that severe Cd stress decreased monounsaturated fatty acid (MUFA) but increased polyunsaturated fatty acid (PUFA). Heat map (HM) showed that GY and methionine were the most sensitive traits under treatments of Cd and CP. Totally, we suggest the use of 120 s of CP to mitigate Cd stress on wheat plants.

Using GraphPad Prism's Heat Maps for Efficient, Fine-Grained Analyses of Single-Case Data

Behavior analysts sometimes consider various forms of data analysis when making clinical decisions and when attempting to illuminate interesting relations in existing datasets. For example, an ongoing plot of when problem behavior occurs across days and times can yield useful information regarding the function(s) of problem behavior. In a post-hoc analysis, a plot of within-session error patterns can reveal which variables may be contributing to faulty stimulus control. Such analyses can be burdensome to conduct manually (e.g., changing the color of individual data points based on error type), and more efficient methods (e.g., using conditional formatting in Microsoft Excel data tables) might not be conducive for producing publication-quality figures. In the present article, we provide an overview of how behavior analysts can use GraphPad Prism's heat-map feature to efficiently populate fine-grained graphs of behavior with data points that are coded automatically (e.g., with categorical colors or gradients). Implications for clinical utility and research production are discussed.

Towards high light conversion efficiency from photo-fermentative hydrogen production of Arundo donax L. By light-dark duration alternation strategy

Suitable illumination project would help in achieving high light conversion efficiency (LCE) for photo-fermentation. This study proposed an improvement strategy for LCE of photo-fermentative hydrogen production (PFHP) with a photosynthetic consortium by adopting light-dark duration alternation. For this purpose, 6 projects (continues light, 24 h light + 24 h dark, 24 h dark + 24 h light, 48 h light + 48 h light, 48 h dark + 48 h light, and continues dark) light disturbances were carried out to estimate the strategy. The fluctuation of cell growth (OD660) was corresponded to the light-dark alternation. 24 h dark + 24 h light alternation achieved the maximum hydrogen yield (HY) of 390.9 mL/g TS cell (6.7 % higher than continuous light) and maximum improvement of LCE of 114.7%. Moreover, heat map analysis revealed that the light period after inoculation had the closest relation (Pearson's r = 1) with the average hydrogen production rate (HPR) of photo-fermentation. Besides, decreased dark period after inoculation would increase the hydrogen yield of photo-fermentation.

The Social Exclusion Bench Tool (SEBT): A visual way of assessing interpersonal social exclusion

People usually prefer to appear with an inclusive and positive attitude to others’ eyes. For this reason, the self-report scales assessing social exclusion intentions are often biased by social desirability. In this work, we present an innovative graphical tool, named Social Exclusion Bench Tool (SEBT), for assessing social exclusion not influenced by social desirability. The tool is based on the consistency between social distance and physical distance evaluation. The results showed that in two samples of adults from Italy (N = 252) and the UK (N = 254), the SEBT positively correlated with self-report measures of social exclusion, but not with the social desirability measure. The tool has been preliminarily evaluated in the context of social exclusion toward migrant people, but it appears a promising instrument for assessing social exclusion intentions toward different social groups.•

The self-report scales assessing social exclusion intentions are often biased by social desirability.

•

The Social Exclusion Bench Tool (SEBT) is an innovative visual instrument for assessing social exclusion that seems not to be influenced by social desirability.

•

The tool appears a promising instrument for assessing social exclusion intentions toward different social groups.

Three-dimensional mapping of distal humerus fracture

Background

Distal humerus fractures (DHFs) constitute one-third of elbow fractures approximately. In this study, we aim to define and analyze the fracture lines and morphological features of DHFs using mapping technique.

Methods

One hundred and two DHFs were retrospectively reviewed. All the computed tomography (CT) data were used to manually reconstruct and virtually reduce the DHF fragments to fit a standard 3D model. Smooth curves were depicted accurately onto the surface of the template to represent the fracture lines. All the curves were overlapped onto the model to create the 3D fracture map and heat map.

Results

Our analysis was based on 102 CT images of DHFs, contributed by 59 male and 43 female patients (mean age, 46 years; range, 18-93 years), and included 15 type A, 25 type B, and 62 type C fractures. On mapping, the hot zones were located in the radial fossa, coronoid fossa, olecranon fossa, and the external part of the trochlear. Conversely, the cold zones were noted in medial condyle, the medial side of the trochlear, and the anterolateral area on the supracondylar ridge.

Conclusions

Our study firstly shows the fracture lines and morphological features of distal humeral fractures by three-dimensional mapping technology. Distal humerus fracture lines are characteristic and highly related to the micro-architecture difference of distal humerus, which may provide some guidance for the treatment plan selection and surgical fixation design.

Improve teaching with modalities and collaborative groups in an LMS: an analysis of monitoring using visualisation techniques

Monitoring students in Learning Management Systems (LMS) throughout the teaching-learning process has been shown to be a very effective technique for detecting students at risk. Likewise, the teaching style in the LMS conditions, the type of student behaviours on the platform and the learning outcomes. The main objective of this study was to test the effectiveness of three teaching modalities (all using Online Project-based Learning -OPBL- and Flipped Classroom experiences and differing in the use of virtual laboratories and Intelligent Personal Assistant -IPA-) on Moodle behaviour and student performance taking into account the covariate "collaborative group". Both quantitative and qualitative research methods were used. With regard to the quantitative analysis, differences were found in student behaviour in Moodle and in learning outcomes, with respect to teaching modalities that included virtual laboratories. Similarly, the qualitative study also analysed the behaviour patterns found in each collaborative group in the three teaching modalities studied. The results indicate that the collaborative group homogenises the learning outcomes, but not the behaviour pattern of each member. Future research will address the analysis of collaborative behaviour in LMSs according to different variables (motivation and metacognitive strategies in students, number of members, interactions between students and teacher in the LMS, etc.).

Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis

Background

Genetic disposition is considered critical for identifying subjects at high risk for disease development. Investigating disease-causing and high and low expressed genes can support finding the root causes of uncertainties in patient care. However, independent and timely high-throughput next-generation sequencing data analysis is still a challenge for non-computational biologists and geneticists.

Results

In this manuscript, we present a findable, accessible, interactive, and reusable (FAIR) bioinformatics platform, i.e., GVViZ (visualizing genes with disease-causing variants). GVViZ is a user-friendly, cross-platform, and database application for RNA-seq-driven variable and complex gene-disease data annotation and expression analysis with a dynamic heat map visualization. GVViZ has the potential to find patterns across millions of features and extract actionable information, which can support the early detection of complex disorders and the development of new therapies for personalized patient care. The execution of GVViZ is based on a set of simple instructions that users without a computational background can follow to design and perform customized data analysis. It can assimilate patients’ transcriptomics data with the public, proprietary, and our in-house developed gene-disease databases to query, easily explore, and access information on gene annotation and classified disease phenotypes with greater visibility and customization. To test its performance and understand the clinical and scientific impact of GVViZ, we present GVViZ analysis for different chronic diseases and conditions, including Alzheimer’s disease, arthritis, asthma, diabetes mellitus, heart failure, hypertension, obesity, osteoporosis, and multiple cancer disorders. The results are visualized using GVViZ and can be exported as image (PNF/TIFF) and text (CSV) files that include gene names, Ensembl (ENSG) IDs, quantified abundances, expressed transcript lengths, and annotated oncology and non-oncology diseases.

Conclusions

We emphasize that automated and interactive visualization should be an indispensable component of modern RNA-seq analysis, which is currently not the case. However, experts in clinics and researchers in life sciences can use GVViZ to visualize and interpret the transcriptomics data, making it a powerful tool to study the dynamics of gene expression and regulation. Furthermore, with successful deployment in clinical settings, GVViZ has the potential to enable high-throughput correlations between patient diagnoses based on clinical and transcriptomics data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40246-021-00336-1.

Optimization of Micropropagation and Genetic Transformation Protocols for Paulownia elongata : A Short Rotation Fast Growing Bioenergy Tree

Various steps of micropropagation include selection of suitable explant, establishment of adventitious shoot induction cultures, proliferation, rooting, and acclimatization of the resulting plantlets. A systematic protocol is provided for the micropropagation and Agrobacterium tumefaciens-mediated genetic transformation of a fast growing, multipurpose tree, Paulownia elongata. Our studies show that optimum shoot induction is on half leaf with petiole explant on MS medium supplemented with 25 μM thidiazuron and 10 μM indole-3 acetic acid. Micropropagation protocols provided here are applicable to explants collected from the primed in vitro raised seedlings on MS medium containing 2.5 μM 6-benzylaminopurine (BAP) or actively growing shoots collected from greenhouse or field growing plants. We also discuss a possible role of "Python" script guided protocol optimization for higher and consistent multiplication of shoots that can be very helpful for scaled up production in commercial settings. To facilitate future plant improvement and gene editing possibilities, an A. tumefaciens based genetic transformation protocol and molecular identification of transgenic plants using Polymerase Chain Reaction (PCR) and Reverse Transcriptase-PCR (RT-PCR) techniques have also been optimized.

Socioeconomic disparities and COVID-19 vaccination acceptance: a nationwide ecologic study

Objective

To analyse the correlation between COVID-19 vaccination percentage and socioeconomic status (SES).

Methods

A nationwide ecologic study based on open-sourced, anonymized, aggregated data provided by the Israel Ministry of Health. The correlations between municipal SES, vaccination percentage and active COVID-19 cases during the vaccination campaign were analysed by using weighted Pearson correlations. To assess the adequacy of first dose vaccination rollout relative to the municipality COVID-19 disease burden, a metric termed the vaccination need ratio was devised by dividing the total number of active cases (per 10 000 people) by the vaccination percentage of the population over 60 in each municipality, and its correlation with the SES was examined.

Results

23 days after initiation of the vaccination campaign, 760 916 (56.8%) individuals over the age of 60 were vaccinated in Israel with the first dose of the BNT162b2 COVID-19 vaccine. A negative correlation was found between the COVID-19 active case burden and the vaccination percentage of the study population in each municipality (r = –0.47, 95% CI –0.59 to –0.30). The vaccination percentage significantly correlated with the municipal SES (r = 0.83, 95% CI 0.79 to 0.87). This finding persisted but was attenuated over a 5-week period. A negative correlation between the vaccination need ratio and municipal SES (r = –0.80, 95% CI –0.88 to –0.66) was found.

Discussion

Lower COVID-19 vaccination percentage was associated with lower SES and high active disease burden. Vaccination efforts should focus on areas with lower SES and high disease burden to assure equality of vaccine allocation and potentially provide a more diligent disease mitigation.

Antifungal potential of zinc against leaf spot disease in chili pepper caused by Alternaria alternata

The fungal pathogen, Alternaria alternata is responsible for causing leaf spot disease in many plants, including chili pepper. Zinc (Zn) an essential micronutrient for plant growth, also increases resistance in plants against diseases, and also acts as an antifungal agent. Here, in vitro effects of ZnSO4 on the propagation of A. alternata were investigated, and also in vivo, the effect of foliar application of ZnSO4 was investigated in chili pepper plants under disease stress. In vitro, ZnSO4 inhibited fungal growth in a dose-dependent manner, with complete inhibition being observed at the concentration of 8.50 mM. Hyphae and conidial damage were observed along with abnormal activity of antioxidant enzymes, Fourier-transform infrared spectroscopy confirmed the major changes in the protein structure of the fungal biomass after Zn accumulation. In vivo, pathogen infection caused the highest leaf spot disease incidence, and cumulative disease index, which resulted in a significant reduction in the plant's growth (length and biomass), and physiochemical traits (photosynthetic pigment, activity of catalase, peroxidase, polyphenol oxidase, and phenylalanine ammonia lyase). The heat map and principal component analysis based on disease, growth and, physico-chemical variables generated useful information regarding the best treatment useful for disease management. Foliar Zn (0.036 mM) acted as a resistance inducer in chili pepper plants that improved activities of antioxidants (CAT and POX), and defense compounds (PPO and PAL), while managing 77% of disease. The study indicated foliar ZnSO4 as an effective and sustainable agriculture practice to manage Alternaria leaf spot disease in chili pepper plants.

A novel machine learning-based algorithm to identify and classify lesions and anatomical landmarks in colonoscopy images

OBJECTIVES

Computer-aided diagnosis (CAD)-based artificial intelligence (AI) has been shown to be highly accurate for detecting and characterizing colon polyps. However, the application of AI to identify normal colon landmarks and differentiate multiple colon diseases has not yet been established. We aimed to develop a convolutional neural network (CNN)-based algorithm (GUTAID) to recognize different colon lesions and anatomical landmarks.

METHODS

Colonoscopic images were obtained to train and validate the AI classifiers. An independent dataset was collected for verification. The architecture of GUTAID contains two major sub-models: the Normal, Polyp, Diverticulum, Cecum and CAncer (NPDCCA) and Narrow-Band Imaging for Adenomatous/Hyperplastic polyps (NBI-AH) models. The development of GUTAID was based on the 16-layer Visual Geometry Group (VGG16) architecture and implemented on Google Cloud Platform.

RESULTS

In total, 7838 colonoscopy images were used for developing and validating the AI model. An additional 1273 images were independently applied to verify the GUTAID. The accuracy for GUTAID in detecting various colon lesions/landmarks is 93.3% for polyps, 93.9% for diverticula, 91.7% for cecum, 97.5% for cancer, and 83.5% for adenomatous/hyperplastic polyps.

CONCLUSIONS

A CNN-based algorithm (GUTAID) to identify colonic abnormalities and landmarks was successfully established with high accuracy. This GUTAID system can further characterize polyps for optical diagnosis. We demonstrated that AI classification methodology is feasible to identify multiple and different colon diseases.

Mapping the amelogenin protein expression during porcine molar crown development

INTRODUCTION

Amelogenin (AMEL) plays critical roles during enamel and dentin matrix deposition and mineralization. Most studies focused on the expression patterns of AMEL through the bud, cap, and bell stages. The spatial-temporal expression of AMEL protein during different mineralization stages, especially from presence of crypts to crown completed stages, remains unknown. Thus, the distribution pattern of AMEL in tooth crown formation from Nolla Stage 1 to 6 was investigated.

METHODS

Porcine mandibular molar tooth germs from Nolla Stage 1 to 6 were obtained. The dynamic morphologic changes of tooth germs were examined by X-ray and surgical operating microscope. The AMEL protein expression was evaluated immunohistochemically, then analyzed semi-quantitatively, and further visualized via heat map.

RESULTS

Tooth germs continuously increased in size from Nolla Stage 1 to 6. AMEL expression in the newly formed enamel kept negative, but presented intensively positive in the previously formed enamel from Stage 1 to 3. The adjacent enamel-dentin junction (EDJ) was strongly positive during the whole process. In predentin, AMEL was weakly seen at Stage 1 and then dramatically up-regulated from Stage 2 to Stage 3, then down-regulated but was still apparently seen in the whole process. AMEL expression in dentin was decreased during dentin matrix secretion and mineralization.

CONCLUSIONS

This study identified the dynamic distribution of AMEL during porcine tooth crown formation. Semi-quantitative analysis and heat map emerged as reliable indicators in demonstrating AMEL distribution pattern.

Estimating the cumulative risk of postnatal depressive symptoms: the role of insomnia symptoms across pregnancy

PURPOSE

Insomnia symptoms during late pregnancy are a known risk for postnatal depressive symptoms (PDS). However, the cumulative effect of various risk factors throughout pregnancy has not been explored. Our aim was to test how various insomnia symptoms (sleep latency, duration, quality, frequent night awakenings, early morning awakenings) and other risk factors (e.g., history of depression, symptoms of depression and anxiety, as well as sociodemographic factors) in early, mid-, and late pregnancy predict PDS.

METHODS

Using data from the FinnBrain Birth Cohort Study and logistic regression analyses, we investigated the associations of distinct insomnia symptoms at gw 14, 24, and 34 with depressive symptoms (Edinburgh Postnatal Depression Scale score ≥ 11) 3 months postnatally. We also calculated separate and combined predictive models of PDS for each pregnancy time point and reported the odds ratios for each risk group.

RESULTS

Of the 2224 women included in the study, 7.1% scored EPDS ≥ 11 3 months postnatally. Our predictive models indicated that sleep latency of ≥ 20 min, anxiety in early pregnancy, and insufficient sleep during late pregnancy predicted the risk of PDS. Furthermore, we found highly elevated odds ratios in early, mid-, and late pregnancy for women with multiple PDS risk factors.

CONCLUSION

Screening of long sleep latency and anxiety during early pregnancy, in addition to depression screening, could be advisable. Odds ratios of risk factor combinations demonstrate the magnitude of cumulating risk of PDS when multiple risk factors are present.

Heat map visualization for electrocardiogram data analysis

BACKGROUND

Most electrocardiogram (ECG) studies still take advantage of traditional statistical functions, and the results are mostly presented in tables, histograms, and curves. Few papers display ECG data by visual means. The aim of this study was to analyze and show data for electrocardiographic left ventricular hypertrophy (LVH) with ST-segment elevation (STE) by a heat map in order to explore the feasibility and clinical value of heat mapping for ECG data visualization.

METHODS

We sequentially collected the electrocardiograms of inpatients in the First Affiliated Hospital of Shantou University Medical College from July 2015 to December 2015 in order to screen cases of LVH with STE. HemI 1.0 software was used to draw heat maps to display the STE of each lead of each collected ECG. Cluster analysis was carried out based on the heat map and the results were drawn as tree maps (pedigree maps) in the heat map.

RESULTS

In total, 60 cases of electrocardiographic LVH with STE were screened and analyzed. STE leads were mainly in the V₁, V₂ and V₃ leads. The ST-segment shifts of each lead of each collected ECG could be conveniently visualized in the heat map. According to cluster analysis in the heat map, STE leads were clustered into two categories, comprising of the right precordial leads (V₁, V₂, V₃) and others (V₄, V₅, V₆, I, II, III, aVF, aVL, aVR). Moreover, the STE amplitude in 40% (24 out of 60) of cases reached the threshold specified in the STEMI guideline. These cases also could be fully displayed and visualized in the heat map. Cluster analysis in the heat map showed that the III, aVF and aVR leads could be clustered together, the V₁, V₂, V₃ and V₄ leads could be clustered together, and the V₅, V₆, I and aVL leads could be clustered together.

CONCLUSION

Heat maps and cluster analysis can be used to fully display every lead of each electrocardiogram and provide relatively comprehensive information.

Creating 2D Occupancy Plots Using plot2DO

Chromatin organization and epigenetic marks play a critical role in stem cell pluripotency and differentiation. Chromatin digestion by micrococcal nuclease (MNase) followed by high-throughput sequencing (MNase-seq) is the most widely used genome-wide method for studying nucleosome organization, that is, the first level of DNA packaging into chromatin. Combined with chromatin immunoprecipitation (ChIP), MNase-ChIP-seq represents a high-resolution method for investigating both chromatin organization and the distribution of epigenetic marks and histone variants. The plot2DO package presented here is a flexible tool for evaluating the quality of MNase-seq and MNase-ChIP-seq data, and for visualizing the distribution of nucleosomes near the functional regions of the genome. The plot2DO package is open-source software, and it is freely available from https://github.com/rchereji/plot2DO under the MIT license.

Systematic data analysis and data mining in CatWalk gait analysis by heat mapping exemplified in rodent models for neurodegenerative diseases

BACKGROUND

Motor impairment appears as a characteristic symptom of several diseases and injuries. Therefore, tests for analyzing motor dysfunction are widely applied across preclinical models and disease stages. Among those, gait analysis tests are commonly used, but they generate a huge number of gait parameters. Thus, complications in data analysis and reporting raise, which often leads to premature parameter selection.

NEW METHODS

In order to avoid arbitrary parameter selection, we present here a systematic initial data analysis by utilizing heat-maps for data reporting. We exemplified this approach within an intervention study, as well as applied it to two longitudinal studies in rodent models related to Parkinson's disease (PD) and Huntington disease (HD).

RESULTS

The systematic initial data analysis (IDA) is feasible for exploring gait parameters, both in experimental and longitudinal studies. The resulting heat maps provided a visualization of gait parameters within a single chart, highlighting important clusters of differences.

COMPARISON WITH EXISTING METHOD

Often, premature parameter selection is practiced, lacking comprehensiveness. Researchers often use multiple separated graphs on distinct gait parameters for reporting. Additionally, negative results are often not reported.

CONCLUSIONS

Heat mapping utilized in initial data analysis is advantageous for reporting clustered gait parameter differences in one single chart and improves data mining.

The Fundamentals of Constructing and Interpreting Heat Maps

This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope includes describing the general features of heat maps, how their components are designed, the meaning of parameters such as "distance method" and "linkage method," and the influence of manipulations such as row-scaling and logarithmic transformations on data interpretation and presentation. This chapter may serve as a guide to understanding the use of heat maps in published analyses or to aid in their design, allowing efficient interpretations of high-throughput experiments, exploration of hypotheses, or clear communications of findings.

PLGA microsphere/PVA hydrogel coatings suppress the foreign body reaction for 6 months

The application of dexamethasone releasing poly (lactic-co-glycolic acid) (PLGA) microspheres embedded in a poly vinyl alcohol (PVA) hydrogel coatings have been successfully used in the suppression of the foreign body response (FBR) to implantable glucose sensors. In the current study, dexamethasone-loaded PLGA microspheres were prepared by blending two types of PLGA polymers (RG503H and DLG7E with MW of ca. 25 kDa and 113 kDa, respectively) to achieve long-term (6 months) inhibition of the FBR. The microsphere composition was optimized according to the in vitro drug release profiles. Microspheres with DLG7E/RG503H/dexamethasone = 70/13.3/16.7 wt% composition, when embedded in a PVA hydrogel, provided a continuous drug release for 6 months. By combining the aforementioned microspheres with microspheres composed solely of the DLG7E polymer within a similar PVA hydrogel realized an even longer (>7 months) in vitro drug release. A heat map was constructed to depict the daily in vitro drug released and elucidate possible lag phases that could affect the pharmacodynamic response. These drug-loaded implant coatings were investigated in vivo (rat model) and showed inhibition of the foreign body response for 6 months. These results suggest that the minimum effective daily dose to counter chronic inflammation is ca. 0.1 μg per mg of coating surrounding a 0.5 × 0.5 × 5 mm silicon implant (dummy sensor). Accordingly, these drug-eluting composite coatings can ensure long-term inflammation control for miniaturized implantable devices.

Survival Patterns for Patients with Resected N2 Non-Small Cell Lung Cancer and Postoperative Radiotherapy: A Prognostic Scoring Model and Heat Map Approach

INTRODUCTION

The positive-to-resected lymph node ratio (LNR) predicts survival in many cancers, but little information is available on its value for patients with N2 NSCLC who receive postoperative radiotherapy (PORT) after resection. We tested the applicability of prognostic scoring models and heat mapping to predict overall survival (OS) and cancer-specific survival (CSS) in patients with resected N2 NSCLC and PORT.

METHODS

Our test cohort comprised patients identified from the Surveillance, Epidemiology, and End Results database with N2 NSCLC who received resection and PORT in 2000-2014. Prognostic scoring models were developed to predict OS and CSS using Cox regression; heat maps were constructed with corresponding survival probabilities. Recursive partitioning analysis was applied to the Surveillance, Epidemiology, and End Results data to identify the optimal LNR cutoff point. Models and cutoff points were further tested in 183 similar patients treated at The University of Texas M. D. Anderson Cancer Center in 2000-2015.

RESULTS

Multivariate analyses revealed that low LNR independently predicted better OS and CSS in patients with resected N2 NSCLC who received PORT.

CONCLUSIONS

LNR can be used to predict survival of patients with resected N2 NSCLC followed by PORT. This approach, which to our knowledge is the first application of heat mapping of positive and negative lymph nodes, was effective in estimating 3-, 5-, and 10-year OS probabilities.

Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa

74 phytocyanin genes were identified in the Populus trichocarpa genome. Phylogenetic analysis grouped the PC proteins into four subfamilies (UCs, PLCs, SCs, and ENODLs). Closely related PC proteins share similar motifs, implying similar functions. Expression profiles of PtPC genes were analyzed in response to drought and salt-stress. Phytocyanins (PCs) are blue copper proteins associated with electron carrier activity that have a large influence on plant growth and resistance. The majority of PCs are chimeric arabinogalactan proteins (AGPs). In this work, we identified 74 PC genes in Populus trichocarpa and analyzed them comprehensively. Based on the ligands composition of copper-binding sites, glycosylation state, the domain structure and spectral characteristics of PC genes, PCs were divided into four subfamilies [uclacyanins (UCs), plantacyanins (PLCs), stellacyanins (SCs) and early nodulin-like proteins (ENODLs)], and phylogenetic relationship analysis classified them into seven groups. All PtPCs are randomly distributed on 17 of the 19 poplar chromosomes, and they appear to have undergone expansion via segmental duplication. Eight PtPCs do not contain introns, and each group has a similar conserved motif structure. Promoter analysis revealed cis-elements related to growth, development and stress responses, and established orthology relationships of PCs between Arabidopsis and poplar by synteny analysis. Expression profile analysis and qRT-PCR analysis showed that PtPCs were expressed widely in various tissues. Quantitative real-time RT-PCR analysis of PC genes expression in response to salt and drought stress revealed their stress-responses profiles. This work provides a theoretical basis for a further study of stress resistance mechanisms and the function of PC genes in poplar growth and development.

Using heat maps to assess the multidimensional association of comorbidities with survival in older cancer patients treated with chemotherapy

OBJECTIVE

To date, most comorbidity studies have analyzed either a subgroup of frequent diseases, or used summary instruments such as the Charlson score or the Cumulative Illness Rating Scale-Geriatric (CIRS-G). Yet, comorbidity is a multidimensional construct and impacts function, treatment tolerance, and survival. We assessed how heat maps can unveil specific patterns of comorbidities associated with overall survival (OS) in older cancer patients treated with chemotherapy.

MATERIAL AND METHODS

We reviewed four trials that prospectively evaluated comorbidities using CIRS-G. Eligible patients were 65years or older and had solid tumors with 30 or more patients per tumor site. Heat maps were constructed based on CIRS-G scores and correlated with OS.

RESULTS

Among 818 patients accrued, 399 were eligible: Median follow-up was 53.4months and median OS was 19.6months (95% CI: 16.5-24.2). In the univariate model for OS, patients with a severe CIRS-G score in 6 organ categories (3-4 in heart, hematopoietic, respiratory, and musculoskeletal-integument and 2-4 in upper GI and liver) had statistically worse OS than those with lower scores. According to a total risk score (TRS) based on hazard ratios for OS, OS of the low risk group (N=309, TRS<2) was significantly higher (24.3m vs. 10.8m, HR=2.05, 95% CI: 1.58-2.66). TRS was a predictor for OS independently from stage, primary site, prior chemotherapy, ECOG performance status, and IADL (HR=1.94, 95% CI: 1.47-2.57).

CONCLUSIONS

High TRS was a predictor of poor survival. Comorbidity heat maps appear promising to identify diseases most affecting the OS of older cancer patients.

Heat map for data visualization in infection control epidemiology: An application describing the relationship between hospital-acquired infections, Simplified Acute Physiological Score II, and length of stay in adult intensive care units

BACKGROUND

Hospital-acquired infections (HAIs) in intensive care units (ICUs) are associated with increased length of stay (LOS). The objective of this study was to graphically describe by heat mapping LOS of patients hospitalized in ICUs related to the occurrence of HAI and severity at admission measured by the Simplified Acute Physiological Score II (SAPSII).

METHODS

Adult patients hospitalized in ICUs of Lyon University Hospitals (France) were included in an active standardized surveillance study of HAI from January 1, 1995-December 31, 2012. Surveillance included adult patients aged ≥18 years hospitalized ≥2 days. Patient follow-up ended at ICU discharge or death. LOS was calculated in days from differences between dates of entry and discharge from ICUs. HAIs recorded were pneumonia, bacteremia, and urinary tract infection. The heat map was designed with a spreadsheet software.

RESULTS

A total of 34,694 patients were analyzed. Among infected patients, 72.3% had 1 infected site (IS), 23% had 2 ISs, and 4.7% had 3 ISs. Median LOS was 24 days in infected patients (20.4 days among patients with 1 IS, 34.2 days among patients with 2 ISs, and 45.3 days among patients with 3 ISs) and 5 days in noninfected patients (P < .001). Two groups of multi-infected patients with long LOSs were identified with the heat map.

CONCLUSIONS

The heat map facilitated easy-to-implement semi-quantitative visualization of increasing LOS through the SAPSIIs and number of ISs.

Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)

29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo (Phyllostachys edulis). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I-VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K _s analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.

Multiplexed Protease Specificity Profiling Using Isobaric Labeling

The determination of a protease's cleavage site specificity is one of the major goals in degradomics. In the last years, the use of proteome-derived peptide libraries and liquid chromatography-mass spectrometry (LC-MS) in a proteomic identification of protease cleavage sites (PICS) experiment became popular for that purpose.In this chapter, we offer a step-by-step protocol for the execution of a quantitative proteomic identification of protease cleavage sites (Q-PICS) experiment, which enables the relative quantification of proteolytic events by isobaric labeling, e.g., with tandem mass tags (TMT). In this way, the cleavage site specificity and activity of a protease can be compared under different reaction conditions (e.g., buffer, pH, temperature, inhibitor). Multiplexing can further be used to analyze replicate experiments in parallel, decreasing instrument times and work effort significantly, or to perform internal controls.

Age of onset of bipolar disorder: Combined effect of childhood adversity and familial loading of psychiatric disorders

BACKGROUND

Family history and adversity in childhood are two replicated risk factors for early onset bipolar disorder. However, their combined impact has not been adequately studied.

METHODS

Based on questionnaire data from 968 outpatients with bipolar disorder who gave informed consent, the relationship and interaction of: 1) parental and grandparental total burden of psychiatric illness; and 2) the degree of adversity the patient experienced in childhood on their age of onset of bipolar disorder was examined with multiple regression and illustrated with a heat map.

RESULTS

The familial loading and child adversity vulnerability factors were significantly related to age of onset of bipolar and their combined effect was even larger. A heat map showed that at the extremes (none of each factor vs high amounts of both) the average age of onset differed by almost 20 years (mean = 25.8 vs 5.9 years of age).

LIMITATIONS

The data were not based on interviews of family members and came from unverified answers on a patient questionnaire.

CONCLUSIONS

Family loading for psychiatric illness and adversity in childhood combine to have a very large influence on age of onset of bipolar disorder. These variables should be considered in assessment of risk for illness onset in different populations, the need for early intervention, and in the design of studies of primary and secondary prevention.

Cadmium toxicity in diazotrophic Anabaena spp. adjudged by hasty up-accumulation of transporter and signaling and severe down-accumulation of nitrogen metabolism proteins

Present study demonstrates interspecies variation in proteome and survival strategy of three Anabaena species i.e., Anabaena L31, Anabaena sp. PCC 7120 and Anabaena doliolum subjected to respective LC50 doses of Cd at 0, 1, 3, 5 and 7day intervals. The proteome coverage with 452 differentially accumulated proteins unveiled species and time specific expression and interaction network of proteins involved in important cellular functions. Statistical analysis of protein abundance across Cd-treated proteomes clustered their co-expression pattern into four groups viz., (i) early (days 1 and 3) accumulated proteins, (ii) proteins up-accumulated for longer duration, (iii) late (days 5 and 7) accumulated proteins, and (iv) mostly down-accumulated proteins. Appreciable growth of Cd treated A L31 over other two species may be ascribed to proteins contained in the first and second groups (belonging to energy and carbohydrate metabolism (TK, G6-PI, PGD, FBA, PPA, ATP synthase)), sulfur metabolism (GR, GST, PGDH, PAPS reductase, GDC-P, and SAM synthetase), fatty acid metabolism (AspD, PspA, SQD-1), phosphorous metabolism (PhoD, PstB and SQD1), molecular chaperones (Gro-EL, FKBP-type peptidylprolyl isomerase), and antioxidative defense enzymes (SOD-A, catalase). Anabaena sp. PCC 7120 harboring proteins largely from the third group qualified as a late accumulator and A. doliolum housing majority of proteins from the fourth group emerged as the most sensitive species. Thus early up-accumulation of transporter and signaling category proteins and drastic reduction of nitrogen assimilation proteins could be taken as a vital indicator of cadmium toxicity in Anabaena spp. This article is part of a Special Issue entitled: Proteomics in India.

Feature-expression heat maps--a new visual method to explore complex associations between two variable sets

INTRODUCTION

Existing methods such as correlation plots and cluster heat maps are insufficient in the visual exploration of multiple associations between genetics and phenotype, which is of importance to achieve a better understanding of the pathophysiology of psychiatric and other illnesses. The implementation of a combined presentation of effect size and statistical significance in a graphical method, added to the ordering of the variables based on the effect-ordered data display principle was deemed useful by the authors to facilitate in the process of recognizing meaningful patterns in these associations.

MATERIALS AND METHODS

The requirements, analyses and graphical presentation of the feature-expression heat map are described. The graphs display associations of two sets of ordered variables where a one-way direction is assumed. The associations are depicted as circles representing a combination of effect size (color) and statistical significance (radius).

RESULTS

An example dataset is presented and relation to other methods, limitations, areas of application and possible future enhancements are discussed.

CONCLUSION

The feature-expression heat map is a useful graphical instrument to explore associations in complex biological systems where one-way direction is assumed, such as genotype-phenotype pathophysiological models.