Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples

BACKGROUND

Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples.

METHODS AND RESULTS

The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System.

CONCLUSIONS

We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.

WFA-GPU: gap-affine pairwise read-alignment using GPUs

MOTIVATION

Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like those produced by PacBio and Nanopore technologies. The recently proposed wavefront alignment (WFA) algorithm paves the way for more efficient alignment tools, improving time and memory complexity over previous methods. However, high-performance computing (HPC) platforms require efficient parallel algorithms and tools to exploit the computing resources available on modern accelerator-based architectures.

RESULTS

This paper presents WFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute exact gap-affine alignments based on the WFA algorithm. We present the algorithmic adaptations and performance optimizations that allow exploiting the massively parallel capabilities of modern GPU devices to accelerate the alignment computations. In particular, we propose a CPU-GPU co-design capable of performing inter-sequence and intra-sequence parallel sequence alignment, combining a succinct WFA-data representation with an efficient GPU implementation. As a result, we demonstrate that our implementation outperforms the original multi-threaded WFA implementation by up to 4.3× and up to 18.2× when using heuristic methods on long and noisy sequences. Compared to other state-of-the-art tools and libraries, the WFA-GPU is up to 29× faster than other GPU implementations and up to four orders of magnitude faster than other CPU implementations. Furthermore, WFA-GPU is the only GPU solution capable of correctly aligning long reads using a commodity GPU.

AVAILABILITY AND IMPLEMENTATION

WFA-GPU code and documentation are publicly available at https://github.com/quim0/WFA-GPU.

Non-Invasive Wildlife Disease Surveillance Using Real Time PCR Assays: The Case of the Endangered Galemys pyrenaicus Populations from the Central System Mountains (Extremadura, Spain)

The Iberian desman (Galemys pyrenaicus) is a small semi-aquatic mammal that inhabits mountainous areas from the centre to the north of the Iberian Peninsula and the Pyrenees and is listed as endangered because it has suffered a serious decline. Since 1960, only three species of digeneans (Omphalometra flexuosa, Maritrema pyrenaica and Mathovius galemydis) and two nematodes (Aonchotheca galemydis and Paracuaria hispanica) have been reported from the desman, but no further information on health status and no data from Extremadura has been available. The aim of our study was to characterise the diversity and distribution of parasites and microbiomes of desmans in different areas of the Central System of Extremadura. Between 2019 and 2021 we collected 238 fecal samples and one tissue (intestine) sample that was obtained from a dead desman. DNA templates were processed by commercial or customised real-time PCR using TaqMan probes. Representative data were obtained for Cryptosporidium spp., Omphalometra spp., Eimeria spp., Salmonella spp., Staphylococcus spp. and Leptospira spp. Omphalometra spp. was studied using a newly developed PCR test. The screening of the dead desman allowed us to obtain, for the first time, a partial sequence of the 18SrDNA. This study is the most complete study of the desman, allowing us to identify parasites and the microbiome in populations of G. pyrenaicus using non-invasive sampling.

Fabrication of paper-based microfluidic devices using a 3D printer and a commercially-available wax filament

In this work, we developed an alternative manufacturing paper-based microfluidics method through 3D printing and wax filament. Microfluidic paper-based analytical devices (μPADs) are low-cost and easy-to-manufacture tools used for various chemical and biological analyses and studies. Paper-based microfluidics with wax has been limited as the manufacturers have discontinued most wax printing equipment. We aim to develop a low-cost and accessible manufacturing method that can replace conventional wax-on paper-based microfluidic manufacturing methods. Using highly available commercial 3D printing technology and wax filament, we could create hydrophobic wax barriers on the surface of different paper types. The properties and limits of this manufacturing method were characterized. Moreover, using this paper-based microfluidic manufacturing method, we were able to measure dopamine electrochemically using μPAD as a passive flow-based method in concentrations as low as 1 nM using injections as small as 15 μL.

Mental health and COVID-19 in a general population cohort in Spain (COVICAT study)

PURPOSE

Mental health conditions may affect outcome of COVID-19 disease, while exposure to stressors during the pandemic may impact mental health. The purpose of this study was to examine these factors in relation to ocurrence of depression and anxiety after the first outbreak in Spain.

METHODS

We contacted 9515 participants from a population-based cohort study in Catalonia between May and October 2020. We drew blood samples to establish infection to the virus. Pre-pandemic mental health conditions were confirmed through Electronic Health Registries. We used the Hospital Anxiety and Depression Scale to assess severe depression and anxiety post-pandemic. Exposure to proximal, financial and wider environment stressors during the lockdown were collected. We calculated Relative Risks (RR), adjusting for individual- and contextual covariates.

RESULTS

Pre-pandemic mental health disorders were not associated with SARS-CoV-2 infection , but were associated with severity of COVID-19 disease. People with pre-existing mental health disorders showed higher prevalence of severe depression (25.4%) and anxiety (37.8%) than those without prior mental disorders (4.9% and 10.1%). Living alone was a strong predictor of severe depression among mental health patients (RR = 1.6, 95% CI 1.2-2.2). Among those without prior mental health disorders, post-lockdown depression and anxiety were associated with household interpersonal conflicts (RR = 2.6, 95% CI 2.1-3.1; RR = 2.1, 95% CI 1.9-2.4) and financial instability (RR = 2.2, 95% CI 1.8-2.9; 1.9, 95% CI 1.6-2.2).

CONCLUSIONS

The COVID-19 pandemic and the lockdown were associated with increased post-lockdown depression and anxiety. Patients with pre-existing mental health conditions are a vulnerable group for severe COVID-19 disease.

Combination of white matter hyperintensities and Aβ burden is related to cognitive composites domain scores in subjective cognitive decline: the FACEHBI cohort

BACKGROUND

To explore whether the combination of white matter hyperintensities (WMHs) and amyloid-beta (Aβ) deposition is associated with worse cognitive performance on cognitive composites (CCs) domain scores in individuals with subjective cognitive decline (SCD).

METHODS

Two hundred participants from the FACEHBI cohort underwent structural magnetic resonance imaging (MRI), 18F-florbetaben positron emission tomography (FBB-PET), and neuropsychological assessment. WMHs were addressed through the Fazekas scale, the Age-Related White Matter Changes (ARWMC) scale, and the FreeSurfer pipeline. Eight CCs domain scores were created using the principal component analysis (PCA). Age, sex, education, and apolipoprotein E (APOE) were used as adjusting variables.

RESULTS

Adjusted multiple linear regression models showed that FreeSurfer (B - .245; 95% CI - .1.676, - .393, p = .016) and β burden (SUVR) (B - .180; 95% CI - 2.140, - .292; p = .070) were associated with face-name associative memory CCs domain score, although the latest one was not statistically significant after correction for multiple testing (p = .070). There was non-significant interaction of these two factors on this same CCs domain score (p = .54). However, its cumulative effects on face-name associative performance indicated that those individuals with either higher WMH load or higher Aβ burden showed the worst performance on the face-name associative memory CCs domain score.

CONCLUSIONS

Our results suggest that increased WMH load and increased Aβ are independently associated with poorer episodic memory performance in SCD individuals, indicating a cumulative effect of the combination of these two pathological conditions in promoting lower cognitive performance, an aspect that could help in terms of treatment and prevention.

Fast gap-affine pairwise alignment using the wavefront algorithm

MOTIVATION

Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields.

RESULTS

In this article, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory. Furthermore, our algorithm exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code. We evaluate the performance of our algorithm, together with other state-of-the-art implementations. As a result, we demonstrate that the WFA runs 20-300× faster than other methods aligning short Illumina-like sequences, and 10-100× faster using long noisy reads like those produced by Oxford Nanopore Technologies.

AVAILABILITY AND IMPLEMENTATION

The WFA algorithm is implemented within the wavefront-aligner library, and it is publicly available at https://github.com/smarco/WFA.

A fatal case of acute hemolytic transfusion reaction caused by anti-Wra: case report and review of the literature

The red blood cell (RBC) antigen Wr^a is a low-prevalence antigen first described in 1953 by Holman and assigned to the Diego system in 1995. Because of its low prevalence, Wr^a is usually absent on commercial screening RBCs and antibody identification panels. When Wr(a+) screening RBCs are available, the corresponding antibody, anti-Wr^a, is often found in sera from healthy individuals, patients, and pregnant women. Anti-Wr^a can cause both hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. We describe a fatal acute hemolytic transfusion reaction caused by anti-Wr^a in a patient with no other RBC alloantibodies. Serologic investigation showed that one of the RBC units the patient received was Wr(a+). Immunohematology 2021;37:20-24.

The red blood cell (RBC) antigen Wr^a is a low-prevalence antigen first described in 1953 by Holman and assigned to the Diego system in 1995. Because of its low prevalence, Wr^a is usually absent on commercial screening RBCs and antibody identification panels. When Wr(a+) screening RBCs are available, the corresponding antibody, anti-Wr^a, is often found in sera from healthy individuals, patients, and pregnant women. Anti-Wr^a can cause both hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. We describe a fatal acute hemolytic transfusion reaction caused by anti-Wr^a in a patient with no other RBC alloantibodies. Serologic investigation showed that one of the RBC units the patient received was Wr(a+). Immunohematology 2021;37:20–24.

Introduction to Nanomaterials Applied to Life Sciences

A. Espinosa, F. J. Teran and D. Ortega introduce the Nanoscale Advances themed collection on Nanomaterials Applied to Life Sciences.

Correlations between plasma and PET beta-amyloid levels in individuals with subjective cognitive decline: the Fundació ACE Healthy Brain Initiative (FACEHBI)

BACKGROUND

Peripheral biomarkers that identify individuals at risk of developing Alzheimer's disease (AD) or predicting high amyloid beta (Aβ) brain burden would be highly valuable. To facilitate clinical trials of disease-modifying therapies, plasma concentrations of Aβ species are good candidates for peripheral AD biomarkers, but studies to date have generated conflicting results.

METHODS

The Fundació ACE Healthy Brain Initiative (FACEHBI) study uses a convenience sample of 200 individuals diagnosed with subjective cognitive decline (SCD) at the Fundació ACE (Barcelona, Spain) who underwent amyloid florbetaben(18F) (FBB) positron emission tomography (PET) brain imaging. Baseline plasma samples from FACEHBI subjects (aged 65.9 ± 7.2 years) were analyzed using the ABtest (Araclon Biotech). This test directly determines the free plasma (FP) and total plasma (TP) levels of Aβ40 and Aβ42 peptides. The association between Aβ40 and Aβ42 plasma levels and FBB-PET global standardized uptake value ratio (SUVR) was determined using correlations and linear regression-based methods. The effect of the APOE genotype on plasma Aβ levels and FBB-PET was also assessed. Finally, various models including different combinations of demographics, genetics, and Aβ plasma levels were constructed using logistic regression and area under the receiver operating characteristic curve (AUROC) analyses to evaluate their ability for discriminating which subjects presented brain amyloidosis.

RESULTS

FBB-PET global SUVR correlated weakly but significantly with Aβ42/40 plasma ratios. For TP42/40, this observation persisted after controlling for age and APOE ε4 allele carrier status (R2 = 0.193, p = 1.01E-09). The ROC curve demonstrated that plasma Aβ measurements are not superior to APOE and age in combination in predicting brain amyloidosis. It is noteworthy that using a simple preselection tool (the TP42/40 ratio with an empirical cut-off value of 0.08) optimizes the sensitivity and reduces the number of individuals subjected to Aβ FBB-PET scanners to 52.8%. No significant dependency was observed between APOE genotype and plasma Aβ measurements (p value for interaction = 0.105).

CONCLUSION

Brain and plasma Aβ levels are partially correlated in individuals diagnosed with SCD. Aβ plasma measurements, particularly the TP42/40 ratio, could generate a new recruitment strategy independent of the APOE genotype that would improve identification of SCD subjects with brain amyloidosis and reduce the rate of screening failures in preclinical AD studies. Independent replication of these findings is warranted.

FACEHBI: A Prospective Study of Risk Factors, Biomarkers and Cognition in a Cohort of Individuals with Subjective Cognitive Decline. Study Rationale and Research Protocols

BACKGROUND

Long-term longitudinal studies with multimodal biomarkers are needed to delve into the knowledge of preclinical AD. Subjective cognitive decline has been proposed as a risk factor for the development of cognitive impairment. Thus, including individuals with SCD in observational studies may be a cost-effective strategy to increase the prevalence of preclinical AD in the sample.

OBJECTIVES

To describe the rationale, research protocols and baseline characteristics of participants in the Fundació ACE Healthy Brain Initiative (FACEHBI).

DESIGN

FACEHBI is a clinical trial (EudraCT: 2014-000798-38) embedded within a long-term observational study of individuals with SCD.

SETTING

Participants have been recruited at the memory clinic of Fundació ACE (Barcelona) from two different sources: patients referred by a general practitioner and individuals from an Open House Initiative.

PARTICIPANTS

200 individuals diagnosed with SCD with a strictly normal performance in a comprehensive neuropsychological battery.

MEASUREMENTS

Individuals will undergo an extensive neuropsychological protocol, risk factor assessment and a set of multimodal biomarkers including florbetaben PET, structural and functional MRI, diffusion tensor imaging, determination of amyloid species in plasma and neurophthalmologic assessment with optical coherence tomography.

RESULTS

Two hundred individuals have been recruited in 15 months. Mean age was 65.9 years; mean MMSE was 29.2 with a mean of 14.8 years of education.

CONCLUSIONS

FACEHBI is a long-term study of cognition, biomarkers and lifestyle that has been designed upon an innovative symptom-based approach using SCD as target population. It will shed light on the pathophysiology of preclinical AD and the role of SCD as a risk marker for the development of cognitive impairment.

Reduction of high-fat diet-induced liver proinflammatory state by eicosapentaenoic acid plus hydroxytyrosol supplementation: involvement of resolvins RvE1/2 and RvD1/2

High-fat diet (HFD)-fed mice show obesity with development of liver steatosis and a proinflammatory state without establishing an inflammatory reaction. The aim of this work was to assess the hypothesis that eicosapentaenoic acid (EPA) plus hydroxytyrosol (HT) supplementation prevents the inflammatory reaction through enhancement in the hepatic resolvin content in HFD-fed mice. Male C57BL/6J mice were fed an HFD or a control diet and supplemented with EPA (50 mg/kg/day) and HT (5 mg/kg/day) or their respective vehicles for 12 weeks. Measurements include liver levels of EPA, DHA and palmitate (gas chromatography), liver resolvins and triglyceride (TG) and serum aspartate transaminase (AST) (specific kits) and hepatic and serum inflammatory markers (quantitative polymerase chain reaction and enzyme-linked immunosorbent assay). Compared to CD, HFD induced body weight gain, liver steatosis and TG accumulation, with up-regulation of proinflammatory markers in the absence of histological inflammation or serum AST changes; these results were accompanied by higher hepatic levels of resolvins RvE1, RvE2, RvD1 and RvD2, with decreases in EPA and DHA contents. EPA+HT supplementation in HFD feeding synergistically reduced the steatosis score over individual treatments and increased the hepatic levels of EPA, DHA and resolvins, with attenuation of proinflammatory markers. Lack of progression of HFD-induced proinflammatory state into overt inflammation is associated with resolvin up-regulation, which is further increased by EPA+HT supplementation eliciting steatosis attenuation. These findings point to the importance of combined protocols in hepatoprotection due to the involvement of cross-talk mechanisms, which increase effectiveness and diminish dosages, avoiding undesirable effects.

The rheumatic disease-associated FAM167A-BLK locus encodes DIORA-1, a novel disordered protein expressed highly in bronchial epithelium and alveolar macrophages

Triggering of autoimmunity that leads to rheumatic disease has been suggested to depend upon gene-environment interactions occurring in epithelial barriers and associated immune cells. Genetic studies have identified associations of the FAM167A-BLK locus with rheumatoid arthritis, systemic lupus erythematosus (SLE) and Sjögren's syndrome. While BLK (B lymphocyte kinase) has a well-established role in B cells, family with sequence similarity to 167 member A (FAM167A) and its gene family remain uncharacterized. To begin to understand the role of FAM167A in rheumatic disease pathogenesis, we explored this gene family and cloned and investigated the gene products. Expression of quantitative trait locus analysis was performed in immune cells. FAM167A and FAM167B were cloned from human peripheral blood mononuclear cells (PBMC). Gene conservation and protein properties were analysed by online tools, mRNA expression measured in mouse organs by quantitative polymerase chain reaction (qPCR) and protein expression investigated in human tissues by immunohistochemistry. We found that autoimmune risk genotypes within the FAM167A-BLK locus lead to increased expression of FAM167A. The FAM167 gene family includes two members, FAM167A and FAM167B, which are not homologous to any other annotated gene but are evolutionarily conserved. The encoded proteins, which we denote 'disordered autoimmunity' (DIORA)-1 and DIORA-2, respectively, are characterized by a high content of intrinsic disorder. Notably, DIORA-1 has its highest expression in the lung, detectable in both bronchial epithelium and alveolar macrophages with an endosomal localization pattern. In summary, the FAM167A gene is associated with several rheumatic diseases and encodes a novel disordered protein, DIORA-1, which is expressed highly in the lung, consistent with a potential role in disease pathogenesis.

Maternal and fetal genetic contribution to gestational weight gain

BACKGROUND

Clinical recommendations to limit gestational weight gain (GWG) imply high GWG is causally related to adverse outcomes in mother or offspring, but GWG is the sum of several inter-related complex phenotypes (maternal fat deposition and vascular expansion, placenta, amniotic fluid and fetal growth). Understanding the genetic contribution to GWG could help clarify the potential effect of its different components on maternal and offspring health. Here we explore the genetic contribution to total, early and late GWG.

PARTICIPANTS AND METHODS

A genome-wide association study was used to identify maternal and fetal variants contributing to GWG in up to 10 543 mothers and 16 317 offspring of European origin, with replication in 10 660 mothers and 7561 offspring. Additional analyses determined the proportion of variability in GWG from maternal and fetal common genetic variants and the overlap of established genome-wide significant variants for phenotypes relevant to GWG (for example, maternal body mass index (BMI) and glucose, birth weight).

RESULTS

Approximately 20% of the variability in GWG was tagged by common maternal genetic variants, and the fetal genome made a surprisingly minor contribution to explain variation in GWG. Variants near the pregnancy-specific beta-1 glycoprotein 5 (PSG5) gene reached genome-wide significance (P=1.71 × 10-8) for total GWG in the offspring genome, but did not replicate. Some established variants associated with increased BMI, fasting glucose and type 2 diabetes were associated with lower early, and higher later GWG. Maternal variants related to higher systolic blood pressure were related to lower late GWG. Established maternal and fetal birth weight variants were largely unrelated to GWG.

CONCLUSIONS

We found a modest contribution of maternal common variants to GWG and some overlap of maternal BMI, glucose and type 2 diabetes variants with GWG. These findings suggest that associations between GWG and later offspring/maternal outcomes may be due to the relationship of maternal BMI and diabetes with GWG.

Intranasal delivery of dexamethasone efficiently controls LPS-induced murine neuroinflammation

Neuroinflammation is the hallmark of several infectious and neurodegenerative diseases. Synthetic glucocorticoids (GCs) are the first-line immunosuppressive drugs used for controlling neuroinflammation. A delayed diffusion of GCs molecules and the high systemic doses required for brain-specific targeting lead to severe undesirable effects, particularly when lifelong treatment is required. Therefore, there is an urgent need for improving this current therapeutic approach. The intranasal (i.n.) route is being employed increasingly for drug delivery to the brain via the olfactory system. In this study, the i.n. route is compared to the intravenous (i.v.) administration of GCs with respect to their effectiveness in controlling neuroinflammation induced experimentally by systemic lipopolysaccharide (LPS) injection. A statistically significant reduction in interleukin (IL)-6 levels in the central nervous system (CNS) in the percentage of CD45⁺ /CD11b⁺ /lymphocyte antigen 6 complex locus G6D [Ly6G⁺ and in glial fibrillary acidic protein (GFAP) immunostaining was observed in mice from the i.n.-dexamethasone (DX] group compared to control and i.v.-DX-treated animals. DX treatment did not modify the percentage of microglia and perivascular macrophages as determined by ionized calcium binding adaptor molecule 1 (Iba1) immunostaining of the cortex and hippocampus. The increased accumulation of DX in brain microvasculature in DX-i.n.-treated mice compared with controls and DX-IV-treated animals may underlie the higher effectiveness in controlling neuroinflammation. Altogether, these results indicate that IN-DX administration may offer a more efficient alternative than systemic administration to control neuroinflammation in different neuropathologies.

School attendance and daily respiratory symptoms in children: influence of moisture damage

We investigated the effect of weekends and school holidays on the daily frequency and severity of respiratory and other symptoms among children attending schools with (index) or without (reference) moisture damage in Spain, the Netherlands, and Finland. Throughout 1 year, parents of 419 children with a respiratory condition attending index (n=15) or reference (n=10) primary schools completed three symptom diaries. We assessed associations between lower respiratory tract, upper respiratory tract or allergy, and other symptom scores and school day, weekend, or summer holiday using mixed regression models stratified by country and moisture damage. We evaluated interactions between moisture damage and type of day. We combined country-specific estimates (incidence rate ratios [IRRs] and 95% confidence interval [CI]) in meta-analyses. Symptom scores were lower during weekends and holiday. Lower respiratory tract symptoms were statistically significantly less common during holiday with strongest effect in index schools (IRR=0.7; CI=0.6-0.8). Reporting of other symptoms was more reduced during holiday in index (IRR=0.6; CI=0.4-0.9) than in reference (IRR=0.95; CI=0.8-1.2) schools (interaction P<.01). In conclusion, symptoms were less frequent and/or severe during summer holiday and weekends. This pattern was stronger among children attending moisture-damaged schools, suggesting potential improvement in moisture damage-related symptoms during school breaks.

Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS

The msParSm application is an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence. This work introduces msParSm, describes its significant performance improvements over msPar and its shared memory parallelization details, and shows how it can get better, if not similar, execution times than MaCS. Two case studies with different mutation rates were analyzed, one approximating the human average and the other approximating the Drosophila melanogaster average. Source code is available at https://github.com/cmontemuino/msparsm.

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next‐generation sequencing as standard practice in research and diagnostics. However, computing cost–performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state‐of‐the‐art read aligners (BWA‐MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample. Results have been compared between them and against the NIST Genome in a Bottle (GIAB) variants reference dataset. We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome. SNV, and especially InDel, detection is less reliable in 20% of the genome, and almost unfeasible in the remaining 10%. These findings will aid in choosing the appropriate tools bearing in mind objectives, workload, and computing infrastructure available.

Sustentabilidad social de agroecosistemas bovinos de doble propósito en México

El objetivo de este estudio fue identificar las diferencias existentes en la sustentabilidad social, de los pequeños productores de ganado de doble propósito en el trópico mexicano. En dos zonas ecológicas definidas: Trópico Seco (TS) y Húmedo (TH). Para ello se analizaron las variables socioeconómicas y los indicadores de desarrollo humano establecidos por el Programa de las Naciones Unidas para el Desarrollo (PNUD). Se encontraron diferencias significativas; tanto en los objetivos de la producción (carne y leche) y en los indicadores de desarrollo humano y marginación (p<0,05). Las diferencias encontradas han de ser consideradas para establecer distintas estrategias y políticas públicas para cada una de las zonas ecológicas del trópico mexicano.

Goal directed hemodynamic therapy based in esophageal Doppler flow parameters: A systematic review, meta-analysis and trial sequential analysis

BACKGROUND

Numerous studies have compared perioperative esophageal doppler monitoring (EDM) guided intravascular volume replacement strategies with conventional clinical volume replacement in surgical patients. The use of the EDM within hemodynamic algorithms is called 'goal directed hemodynamic therapy' (GDHT).

METHODS

Meta-analysis of the effects of EDM guided GDHT in adult non-cardiac surgery on postoperative complications and mortality using PRISMA methodology. A systematic search was performed in Medline, PubMed, EMBASE, and the Cochrane Library (last update, March 2015).

INCLUSION CRITERIA

Randomized clinical trials (RCTs) in which perioperative GDHT was compared to other fluid management.

PRIMARY OUTCOMES

Overall complications.

SECONDARY OUTCOMES

Mortality; number of patients with complications; cardiac, renal and infectious complications; incidence of ileus. Studies were subjected to quantifiable analysis, pre-defined subgroup analysis (stratified by surgery, type of comparator and risk); pre-defined sensitivity analysis and trial sequential analysis (TSA).

RESULTS

Fifty six RCTs were initially identified, 15 fulfilling the inclusion criteria, including 1,368 patients. A significant reduction was observed in overall complications associated with GDHT compared to other fluid therapy (RR=0.75; 95%CI: 0.63-0.89; P=0.0009) in colorectal, urological and high-risk surgery compared to conventional fluid therapy. No differences were found in secondary outcomes, neither in other subgroups. The impact on preventing the development of complications in patients using EDM is high, causing a relative risk reduction (RRR) of 50% for a number needed to treat (NNT)=6.

CONCLUSIONS

GDHT guided by EDM decreases postoperative complications, especially in patients undergoing colorectal surgery and high-risk surgery. However, no differences versus restrictive fluid therapy and in intermediate-risk patients were found.

Implementing a patient blood management program in Norway: Where to start?

Norway has recently established a working group to implement a national patient blood management (PBM) program. Although benchmarking regarding blood usage is challenging in Norway due to legal barriers, a survey was sent to different hospitals to identify possible areas to be prioritized in the first phase of the PBM program. Among them, optimizing the patient's hemoglobin level before elective surgery and implementing electronic check-lists for the indication of transfusion when ordering blood products are two measures that may have a considerable impact on blood usage. The results of the survey also showed that patients may receive a red blood cell transfusion at hemoglobin levels that are higher than those internationally recommended. Since there are no national guidelines for the use of blood products, agreement regarding hemoglobin thresholds is essential to reduce variation in transfusion practice. To achieve these goals, the transfusion specialist plays a key role in promoting the principles behind the PBM concept at the local hospital.

Olfactory reference syndrome

Introduction

The term “olfactory reference syndrome” (ORS), introduced by Pryse-Phillips in 1971, is a persistent false belief and preoccupation with body odor accompanied by significant distress and functional impairment. Nowadays, it is not a distinct syndrome and it is currently classified as a delusional or obsessive-compulsive disorder.

Objectives and aims

Review the history of ORSs classification and discuss why it should be considered as a separate diagnostic in the current health care classification systems.

Methods

Description of a clinical case of a 36-year-old man and review the published articles on ORS by using PubMed database with the keywords: “olfactory reference syndrome”, “chronic olfactory paranoid syndrome”, “hallucinations of smell”, “chronic olfactory paranoid syndrome”, “delusions of bromosis” and “taijin kyofusho”.

Results

The published literature on ORS spans more than a century and provides consistent descriptions of its clinical features but nowadays is not explicitly mentioned in current classification systems as Diagnostic and Statistical Manual of Mental Disorders (DSM) or International Statistical Classification of Diseases and Related Health Problems (ICD). ORS is overlap with different diagnostics such as delusional disorder, body dysmorphic disorder, obsessive-compulsive disorder, and hypochondriasis.

Conclusions

Right now, it is not clear how the ORSs should best be classified so we consider interesting to include it as a separate diagnosis in our set classifications, since we understand that an adjusted diagnosis is important in order to help patients and therapists to work on a treatment and to establish a more accurate prognosis.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

A systematic review of sugammadex vs neostigmine for reversal of neuromuscular blockade

We reviewed systematically sugammadex vs neostigmine for reversing neuromuscular blockade. We included 17 randomised controlled trials with 1553 participants. Sugammadex reduced all signs of residual postoperative paralysis, relative risk (95% CI) 0.46 (0.29-0.71), p = 0.0004 and minor respiratory events, relative risk (95% CI) 0.51 (0.32-0.80), p = 0.0034. There was no difference in critical respiratory events, relative risk (95% CI) 0.13 (0.02-1.06), p = 0.06. Sugammadex reduced drug-related side-effects, relative risk (95% CI) 0.72 (0.54-0.95), p = 0.02. There was no difference in the rate of postoperative nausea or the rate of postoperative vomiting, relative risk (95% CI) 0.94 (0.79-1.13), p = 0.53, and 0.87 (0.65-1.17), p = 0.36 respectively.

Non-covalent stacking interactions directing the structural and photophysical features of mono- and dinuclear cyclometalated palladium(ii) complexes

Cyclometallated Pd(ii) complexes with different stackings show emission in solid state in relationship to them.

Design of magnetic molecularly imprinted polymer nanoparticles for controlled release of doxorubicin under an alternative magnetic field in athermal conditions

An innovative magnetic delivery nanomaterial for triggered cancer therapy showing active control over drug release by using an alternative magnetic field is proposed. In vitro and In vivo release of doxorubicin (DOX) were investigated and showed a massive DOX release under an alternative magnetic field without temperature elevation of the medium.

Formation of biomineral iron oxides compounds in a Fe hyperaccumulator plant: Imperata cylindrica (L.) P. Beauv

We report a detailed work of composition and location of naturally formed iron biominerals in plant cells tissues grown in iron rich environments as Imperata cylindrica. This perennial grass grows on the Tinto River banks (Iberian Pyritic Belt) in an extreme acidic ecosystem (pH∼2.3) with high concentration of dissolved iron, sulphate and heavy metals. Iron biominerals were found at the cellular level in tissues of root, stem and leaf both in collected and laboratory-cultivated plants. Iron accumulated in this plant as a mix of iron compounds (mainly as jarosite, ferrihydrite, hematite and spinel phases) was characterized by X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), Mössbauer spectroscopy (MS), magnetometry (SQUID), electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX; TEM-EDX; HRSTEM). A low fraction of phosphorous was detected in this iron hyperaccumulator plant. Root and rhizomes tissues present a high proportion of ferromagnetic iron oxide compounds. Iron oxides-rich zones are localized in electron dense intra and inter-cellular aggregates that appear as dark deposits covering the inner membrane and organelles of the cell. This study aims to contribute to a better understanding of the mechanisms of accumulation, transport, distribution of iron in Imperata cylindrica.

Diversity of solitons in a generalized nonlinear Schrödinger equation with self-steepening and higher-order dispersive and nonlinear terms

In this article, we show that if the nonlinear Schrödinger (NLS) equation is generalized by simultaneously taking into account higher-order dispersion, a quintic nonlinearity, and self-steepening terms, the resulting equation is interesting as it has exact soliton solutions which may be (depending on the values of the coefficients) stable or unstable, standard or "embedded," fixed or "moving" (i.e., solitons which advance along the retarded-time axis). We investigate the stability of these solitons by means of a modified version of the Vakhitov-Kolokolov criterion, and numerical tests are carried out to corroborate that these solitons respond differently to perturbations. It is shown that this generalized NLS equation can be derived from a Lagrangian density which contains an auxiliary variable, and Noether's theorem is then used to show that the invariance of the action integral under infinitesimal gauge transformations generates a whole family of conserved quantities. Finally, we study if this equation has the Painlevé property.

Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access

The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8 × faster than a comparable multi-core CPU version, and about 3 × to 5 × faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.

Radiating subdispersive fractional optical solitons

It was recently found [Fujioka et al., Phys. Lett. A 374, 1126 (2010)] that the propagation of solitary waves can be described by a fractional extension of the nonlinear Schrödinger (NLS) equation which involves a temporal fractional derivative (TFD) of order α > 2. In the present paper, we show that there is also another fractional extension of the NLS equation which contains a TFD with α < 2, and in this case, the new equation describes the propagation of radiating solitons. We show that the emission of the radiation (when α < 2) is explained by resonances at various frequencies between the pulses and the linear modes of the system. It is found that the new fractional NLS equation can be derived from a suitable Lagrangian density, and a fractional Noether's theorem can be applied to it, thus predicting the conservation of the Hamiltonian, momentum and energy.

Follow-up of loci from the International Genomics of Alzheimer's Disease Project identifies TRIP4 as a novel susceptibility gene

To follow-up loci discovered by the International Genomics of Alzheimer's Disease Project, we attempted independent replication of 19 single nucleotide polymorphisms (SNPs) in a large Spanish sample (Fundació ACE data set; 1808 patients and 2564 controls). Our results corroborate association with four SNPs located in the genes INPP5D, MEF2C, ZCWPW1 and FERMT2, respectively. Of these, ZCWPW1 was the only SNP to withstand correction for multiple testing (P=0.000655). Furthermore, we identify TRIP4 (rs74615166) as a novel genome-wide significant locus for Alzheimer's disease risk (odds ratio=1.31; confidence interval 95% (1.19-1.44); P=9.74 × 10(-)(9)).

1H, 13C NMR studies of new 3-aminophenol isomers linked to pyridinium salts

(1)H and (13)C NMR spectroscopic data of 20 new non-symmetrical compounds were assigned by a combination of 1D and 2D NMR experiments (DEPT, HSQC, and HMBC). These compounds contain a 4-(N,N-dimethylamino)- or 4-(pyrrolidin-1-yl)pyridinium moiety and a 3-nitro-, 3-amino-, or 3-hydroxyphenyl ring, linked by p-xylene, 4,4'-dimethylbiphenyl, 1,2-bis(p-tolyl)ethane, or 1,4-bis(p-tolyl)butane.

The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor

Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.