Comparative evaluation of different techniques for herniorrhaphy in calves

Umbilical hernia is one of the most common problems in young calves. This problem occurs in dairy sector as well as in the local farmers. Present study was conducted to compare outcomes of four different techniques of herniorrhaphy. Twenty four young calves (n=24) were divided in 4 groups (A, B, C, and D) which underwent four different surgical techniques. Group A underwent vicryl plus suture material and pants-over-west technique, Group B underwent mesh application with Dexon suture material by using simple interrupted suture pattern, Group C underwent closed method with Nylon No. 3 suture material by using vertical mattress suture pattern and Group D underwent clamp application method with Silk No. 2 suture material by using simple interrupted suture pattern. The result showed that mesh application method was comparatively better with respect to feed intake, body weight gain and healing time. There was no reoccurrence with non-significant hematological changes (p≤0.05). It is concluded that mesh application method is safer than other three techniques and there are no systemic effects of this surgical intervention on calves' health.

A comparative assessment of air pollutants of smog in wagah border and other sites in Lahore, Pakistan

Smog has become the fifth season of Pakistan especially in Lahore city. Increased level of air pollutants (primary and secondary) are thought to be responsible for the formation of smog in Lahore. Therefore, the current study was carried out for the evaluation of air pollutants (primary and secondary) of smog in Wagah border particularly and other sites (Jail road, Gulburg) Lahore. For this purpose, baseline data on winter smog from March to December on primary and secondary air pollutants and meteorological parameters was collected from Environmental Protection Department and Pakistan Meteorological Department respectively. Devices being used in both departments for analysis of parameters were also studied. Collected data was further statistically analyzed to determine the correlation of parameters with meteorological conditions and was subjected to air quality index. According to results, PM 10 and PM 2.5 were found very high above the NEQS. NOx concentrations were also high above the permissible limits whereas SO2 and O3 were found below the NEQS thus have no roles in smog formation. Air Quality Index (AQI) of pollutants was PM 2.5(86-227), PM 10 (46-332), NOx (26-110), O3 (19-84) and SO2 (10-95). AQI of PM 2.5 remained between moderate to very unhealthy levels. AQI of PM 10 remained between good to hazardous levels. AQI of NOx remained between good to unhealthy for sensitive groups' levels. AQI of O3 and SO2 remained between good to moderate levels. Pearson correlation showed that every pollutant has a different relation with different or same parameters in different areas. It is concluded from the present study that particulate matter was much more responsible for smog formation. Although NOx also played role in smog formation. So there is need to reduce sources of particulate matter and NOx specifically in order to reduce smog formation in Lahore.

Identification of locally isolated entomopathogenic Fusarium species from the soil of Changa Manga Forest, Pakistan and evaluation of their larvicidal efficacy against Aedes aegypti

Dengue fever vectored by the mosquito Aedes aegypti is one of the most rapidly spreading insect-borne diseases. Current reliance of dengue vector control is mostly on chemical insecticides. Growing insecticide resistance in the primary mosquito vector, Aedes aegypti, limits the effectiveness of vector control through chemical insecticides. These chemical insecticides also have negative environmental impacts on animals, plants and human health. Myco-biocontrol agents are naturally occurring organisms and are found to be less damaging to the environment as compared to chemical insecticides. In the present study, entomopathogenic potential of local strains of fungi isolated from soil was assessed for the control of dengue vector. Local fungal isolates presents better alternative to introducing a foreign biocontrol strain, as they may be better adapted to environmental conditions of the area to survive and may have more entomopathogenic efficacy against target organism. Larvicidal efficacy of Fusarium equiseti and Fusarium proliferatum was evaluated against Aedes aegypti. Local strains of F. equiseti (MK371718) and F. proliferatum (MK371715) were isolated from the soil of Changa Manga Forest, Pakistan by using insect bait method. Larvicidal activity of two Fusarium spp. was tested against forth instar larvae of A. aegypti in the laboratory, using concentrations 105, 106, 107 and 108 conidia /ml. LC50 values for F. equiseti after 24h, 48h, 72h and 96h of exposure were recorded as 3.8x 108, 2.9x107, 2.0x107, and 7.1x106 conidia /ml respectively while LC50 values for F. proliferatum were recorded as 1.21x108, 9.6x107, 4.2x107, 2.6x107 conidia /ml respectively after 24h, 48h, 72h and 96h of exposure. The results indicate that among two fungal strains F. equiseti was found to be more effective in terms of its larvicidal activity than F. proliferatum against larvae of A. aegypti.

Learning anatomy before and during COVID-19 pandemic: Students' perceptions and exam performance

The objective of our study was to explore the impact of COVID-19 pandemic on learning anatomy and to compare the students’ perceptions of “face-to-face” and “online” anatomy teaching, and to assess their impact on student's performance. We used a descriptive, cross-sectional, questionnaire-based study that focused on a single cohort of undergraduate medial students who attended anatomy demonstrations, at the College of Medicine and Medical Sciences, Arabian Gulf University (CMMS-AGU), both pre-pandemic (face-to-face) during 2019-2020 and the pandemic (online) during 2020-2021. Students who participated in this study responded in favor of face-to-face demonstrations for better understanding of the spatial orientation of body organs and systems, the visualization of the anatomical relations between structures, understanding the difficult anatomical structures, understanding the clinical correlations, and making them more confident about their practical exams. On the other hand, students were in favor of online demonstrations for retaining key information, confidence levels on discussing anatomy learning needs, effective utilization of demonstration time, and lower stress associated with the online learning. Regarding anatomy exam scores, statistically significant difference was found between mean scores of online and onsite exams in one of the two analyzed multiple choice questions tests. However, there was a statistically significant difference between the mean scores of objective structured practical examination of online and onsite exams in the two analyzed tests. Furthermore, the majority of the students who participated in the survey prefer a mixture of both face-to-face and online anatomy demonstrations during the pandemic and also in the post-COVID-19 era.

In silico screening of Allium cepa phytochemicals for their binding abilities to SARS and SARS-CoV-2 3C-like protease and COVID-19 human receptor ACE-2

Corona virus SARS-CoV-2-induced viral disease (COVID-19) is a zoonotic disease that was initially transmitted from animals to humans. The virus surfaced towards the end of December 2019 in Wuhan, China where earlier SARS (Severe Acute Respiratory Syndrome) had also surfaced in 2003. Unlike SARS, SARS-CoV-2 (a close relative of the SARS virus) created a pandemic, and as of February 24 2021, caused 112,778,672 infections and 2,499,252 deaths world-wide. Despite the best efforts of scientists, no drugs against COVID-19 are yet in sight; five vaccines have received emergency approval in various countries, but it would be a difficult task to vaccinate twice the world population of 8 billion. The objective of the present study was to evaluate through in silico screening a number of phytochemicals in Allium cepa (onion) regarding their ability to bind to the main protease of COVID-19 known as the 3C-like protease or 3CL^pro, (PDB ID: 6LU7), 3CL^pro of SARS (PDB ID: 3M3V), and human angiotensin converting enzyme-2 (ACE-2), [PDB ID: 1R42], which functions as a receptor for entry of the virus into humans. Molecular docking (blind docking, that is docking not only against any target pocket) were done with the help of AutoDockVina. It was observed that of the twenty-two phytochemicals screened, twelve showed good binding affinities to the main protease of SARS-CoV-2. Surprisingly, the compounds also demonstrated good binding affinities to ACE-2. It is therefore very likely that the binding affinities shown by these compounds against both 3CL^pro and ACE-2 merit further study for their potential use as therapeutic agents.

COVID-19 révélée par un érythème noueux

Introduction

Observation

Discussion

Conclusion

Super-resolution time-resolved imaging using computational sensor fusion

Imaging across both the full transverse spatial and temporal dimensions of a scene with high precision in all three coordinates is key to applications ranging from LIDAR to fluorescence lifetime imaging. However, compromises that sacrifice, for example, spatial resolution at the expense of temporal resolution are often required, in particular when the full 3-dimensional data cube is required in short acquisition times. We introduce a sensor fusion approach that combines data having low-spatial resolution but high temporal precision gathered with a single-photon-avalanche-diode (SPAD) array with data that has high spatial but no temporal resolution, such as that acquired with a standard CMOS camera. Our method, based on blurring the image on the SPAD array and computational sensor fusion, reconstructs time-resolved images at significantly higher spatial resolution than the SPAD input, upsampling numerical data by a factor \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$12 \times 12$$\end{document}12×12, and demonstrating up to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$4 \times 4$$\end{document}4×4 upsampling of experimental data. We demonstrate the technique for both LIDAR applications and FLIM of fluorescent cancer cells. This technique paves the way to high spatial resolution SPAD imaging or, equivalently, FLIM imaging with conventional microscopes at frame rates accelerated by more than an order of magnitude.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Poverty-associated emerging infection of Cystic Echinococcosis in population of Northern Pakistan: A hospital based study

Cystic Echinococcosis (CE) is one of the most important zoonotic parasitic diseases in human, livestock, and wildlife globally. The prevalence of CE depends upon human behavioral risk factors, the diversity and ecology of animal host interactions and the genetic diversity within Echinococcus species which differ in their zoonotic potential and pathogenicity. It is a neglected, economic and socio-cultural problem in Pakistan. The available data about the incidence of CE is very limited and no extensive study has been reported in Pakistan. The current study was aimed to analyze the hospital reported cases of CE and the associated risk factors related to the incidence of CE. The hospital-based data of CE for the time period of January 2012-December 2017 was collected from Islamabad, Rawalpindi and Peshawar. The data covered demographic characteristics including age, gender, and cyst localization of infected individuals and socioeconomic determinants. The data was analyzed based upon different risk factors along with the different socioeconomic parameters that has an important impact on the distribution of disease. A total of 228 cases were presented in the selected hospitals of different cities during the study period. Out of total 228 patients, 59.21% were males and 40.78% were females (P<0.001). Most infections have been recorded in young adults (>20-30) showing 22.8% of total infected individuals followed by children (0-10) showing 10.5% (n=24), respectively (P<0.001). Liver was the most vulnerable organ (58.77%, n=134) followed by lungs (14.47%, n=33) (P<0.001). The infection was higher among rural communities (84.2%) than urban (12.8%) (P<0.001). Socioeconomic and demographic factors had an important impact on the intensity of disease (P<0.001). The occurrence of cases in children and young adults was an important finding as it indicated an active transmission of the parasite in Pakistan along with the poverty index. Emergence of echinococcosis in Pakistan showed that emerging health issues in Pakistan could bring the disease to limelight for future research. This finding, together with the fact that 1 hospital reported 214 cases over 6 years 325 underlines the need for a program for prevention/control of this disease in Pakistan. The timely measure needs to be taken to hamper the disease development and establishment. In order to control the disease, complete surveillance should be done which in turn weighs down the disease progress.

3D spatial distribution of ore mineral phases using high resolution synchrotron micro-computed tomography (μCT) combined with optical microscopy

Ore minerals in dolomites and Graphite Mica Schist (GMS) were studied by synchrotron radiation micro-computed tomography (SR-μCT) and optical microscopy. High resolution μCT images of ore minerals were obtained at Imaging Beamline (BL-4), Indus-2 synchrotron radiation source for the comprehensive volume characterization of minerals. Optical microscopy was used for mineral identification, mineral/rock characterization and quantification of ore mineral assemblages was also confirmed by XRD. 3D images from SR-μCT have shown spatial distribution of major minerals and crystals of different minerals in the volume of samples. The results obtained shows that the GMS and dolomitic hosted rocks mined from region near Udaipur, Rajasthan contains sulfide mineral phases. SR-μCT facilitates visualization of the association of the various metallic minerals with the host rock. The presence of economically important metallic minerals galena, sphalerite and pyrite found in the samples through SR-μCT has implications on exploration and processing of ores.

Interaction between blood and solid particles propagating through a capillary with slip effects

This article describes the interaction between solid particles and blood propagating through a capillary. A slip condition is considered on the walls of the capillary. The rheological features of the blood are discussed by considering as a two-phase Newtonian fluid model, i.e., the suspension of cells in plasma. A perturbation method is successfully applied to obtain the series solution of the governing coupled differential equations. The series solution for both fluid and particle phase are presented up to second order approximation. The expressions for the velocity and pressure distributions under slip effects are determined within a tube. Furthermore, the current results are beneficial to understand the rheological features of blood which will be helpful to interpret and analyze more complex blood flow models.

A systemic review of existing serological possibilities to diagnose canine osteoarthritis with a particular focus on extracellular matrix proteoglycans and protein

Extra-cellular matrix (ECM) components are important and their stabilization is significant in maintaining normal healthy joint environment. In osteoarthritis (OA), ECM components are altered and indicate disease progression. The joint ECM is composed of proteoglycans (aggrecan, perlecan, inter α-trypsin inhibitor), glycoproteins (fibronectin, lubricin, COMP) and collagen types (most abundantly collagen type II) which represent structural and functional transformation during disease advancement. ECM investigation revealed significant biomarkers of OA that could be used as a diagnostic and therapeutic tool in different canine orthopedic diseases. This review deliberates our current findings of how the components of ECM change at the molecular level during disease progression in canine OA.

Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean

Experiments were conducted to study the effects of static magnetic fields (SMFs) on the venation network of soybean leaves using the synchrotron-based X-ray micro-imaging technique. The seeds of soybean (Glycine max, variety JS-335) were pretreated with different SMFs from 50 to 300 mT in steps of 50 mT for 1 h. The phase-contrast images obtained showed that, as the strength of the SMF increased, the area, width of the midrib, area of the midrib and minor vein of the middle leaflets of third trifoliate leaves also increased up to the SMF strength of 200 mT (1 h) and decreased thereafter. Quantification of the major conducting vein also showed the differences in the major and minor vein structures of the soybean leaves as compared with control leaves. Further, the phase-retrieval technique has been applied to make the segmentation process easy and to quantify the major and minor veins in the venation network. The width and area of midrib enhancement by pre-treatment with SMF implies an enhancement in the uptake of water, which in turn causes an increased rate of photosynthesis and stomatal conductance.

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration

A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer

Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.

•

Greater transcriptional activity in cancer than stromal cells, particularly when ER-ve

•

Intron mutations only infrequently affect splicing, even at essential splice sites

•

Distinctive RNA effects of sense-to-antisense and gene-to-intergenic rearrangements

•

Exhaustive pipeline for identifying aberrant transcripts from RNA-sequencing data

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

Synchrotron X-ray phase contrast imaging of leaf venation in soybean (Glycine max) after exclusion of solar UV (280-400 nm) radiation

The hydraulic efficiency of a leaf depends on its vascular structure as this is responsible for transport activities. To investigate the effect of exclusion of UVAB and UVB radiation from the solar spectrum on the micro-structure of leaves of soybean (Glycine max, variety JS-335), a field experiment was conducted using synchrotron-based phase contrast imaging (PCI). Plants were grown in specially designed UV exclusion chambers, and wrapped with filters that excluded UVB (280-315 nm) or UVAB (280-400 nm), or transmitted all the ambient solar UV (280-400 nm) radiation (filter control). Qualitative observation of high-resolution X-ray PCI images obtained at 10 keV has shown the differences in major and minor vein structures of the leaves. The mid-rib width of the middle leaflet of third trifoliate leaves, for all treatments, were obtained using quantitative image analysis. The width of the mid-rib of the middle leaflet of third trifoliate leaves of UVB excluded plants was found to be more compared to leaves of filter control plants, which are exposed to ambient UV. The mid-rib or the main conducting vein transports water and sugars to the whole plant; therefore, mid-rib enhancement by the exclusion of solar UV radiation possibly implies enhancement in the leaf area which in turn causes an increased rate of photosynthesis.

Non-destructive evaluation of teeth restored with different composite resins using synchrotron based micro-imaging

BACKGROUND

Application of high resolution synchrotron micro-imaging in microdefects studies of restored dental samples.

OBJECTIVE

The purpose of this study was to identify and compare the defects in restorations done by two different resin systems on teeth samples using synchrotron based micro-imaging techniques namely Phase Contrast Imaging (PCI) and micro-computed tomography (MCT). With this aim acquired image quality was also compared with routinely used RVG (Radiovisiograph).

METHODS

Crowns of human teeth samples were fractured mechanically involving only enamel and dentin, without exposure of pulp chamber and were divided into two groups depending on the restorative composite materials used. Group A samples were restored using a submicron Hybrid composite material and Group B samples were restored using a Nano-Hybrid restorative composite material. Synchrotron based PCI and MCT was performed with the aim of visualization of tooth structure, composite resin and their interface.

RESULTS

The quantitative and qualitative comparison of phase contrast and absorption contrast images along with MCT on the restored teeth samples shows comparatively large number of voids in Group A samples.

CONCLUSIONS

Quality assessment of dental restorations using synchrotron based micro-imaging suggests Nano-Hybrid resin restorations (Group B) are better than Group A.

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

The sequencing of cancer genomes may enable tailoring of therapeutics to the underlying biological abnormalities driving a particular patient's tumor. However, sequencing-based strategies rely heavily on representative sampling of tumors. To understand the subclonal structure of primary breast cancer, we applied whole-genome and targeted sequencing to multiple samples from each of 50 patients' tumors (303 samples in total). The extent of subclonal diversification varied among cases and followed spatial patterns. No strict temporal order was evident, with point mutations and rearrangements affecting the most common breast cancer genes, including PIK3CA, TP53, PTEN, BRCA2 and MYC, occurring early in some tumors and late in others. In 13 out of 50 cancers, potentially targetable mutations were subclonal. Landmarks of disease progression, such as resistance to chemotherapy and the acquisition of invasive or metastatic potential, arose within detectable subclones of antecedent lesions. These findings highlight the importance of including analyses of subclonal structure and tumor evolution in clinical trials of primary breast cancer.