bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selectivity of afferent microstimulation at the DRG using epineural and penetrating electrode arrays
Authors: Nanivadekar Ameya C , Ayers Christopher A , Gaunt Robert A , Weber Douglas J , Fisher Lee E 
Published: October 2019

Abstract

Objective. We have shown previously that microstimulation of the lumbar dorsal root ganglia (L5-L7 DRG) using penetrating microelectrodes, selectively recruits distal branches of the sciatic and femoral nerves in an acute preparation. However, a variety of challenges limit the clinical translatability of DRG microstimulation via penetrating electrodes. For clinical translation of a DRG somatosensory neural interface, electrodes placed on the epineural surface of the DRG may be a viable path forward. The goal of this study was to evaluate the recruitment properties of epineural electrodes and compare their performance with that of penetrating electrodes. Here, we compare the number of selectively recruited distal nerve branches and the threshold stimulus intensities between penetrating and epineural electrode arrays. Approach. Antidromically propagating action potentials were recorded from multiple distal branches of the femoral and sciatic nerves in response to epineural stimulation on 11 ganglia in four cats to quantify the selectivity of DRG stimulation. Compound action potentials (CAPs) were recorded using nerve cuff electrodes implanted around up to nine distal branches of the femoral and sciatic nerve trunks. We also tested stimulation selectivity with penetrating microelectrode arrays implanted into ten ganglia in four cats. A binary search was carried out to identify the minimum stimulus intensity that evoked a response at any of the distal cuffs, as well as whether the threshold response selectively occurred in only a single distal nerve branch. Main results. Stimulation evoked activity in just a single peripheral nerve through 67% of epineural electrodes (35/52) and through 79% of the penetrating microelectrodes (240/308). The recruitment threshold (median  =  9.67 nC/phase) and dynamic range of epineural stimulation (median  =  1.01 nC/phase) were significantly higher than penetrating stimulation (0.90 nC/phase and 0.36 nC/phase, respectively). However, the pattern of peripheral nerves recruited for each DRG were similar for stimulation through epineural and penetrating electrodes. Significance. Despite higher recruitment thresholds, epineural stimulation provides comparable selectivity and superior dynamic range to penetrating electrodes. These results suggest that it may be possible to achieve a highly selective neural interface with the DRG without penetrating the epineurium.
Annual effective dose of radon in groundwater samples for different age groups in Obuasi and Offinso in the Ashanti Region, Ghana
Authors: Opoku-Ntim Irene , Andam Aba Bentil , Akiti Tetteh T , Flectcher J J , Roca Vicenzo 
Published: October 2019

AbstractThe study presents radon (222Rn) activity concentration in the groundwater samples and their annual effective dose exposure in Offinso and Obuasi in the Ashanti, Region for different age groups. Radon measurement was made using Durridge RAD-7 H2O technique. In Obuasi, mean222Rn concentration in groundwater was 0.09 ± 0.01 Bq l−1, mean annual effective dose due to ingestion for adult, child and infant were 0.64 ± 0.11μSv yr−1, 1.28 ± 0.21μSv yr−1and 4.46 ± 0.73μSv yr−1respectively and the mean annual effective dose due to inhalation was 0.28 ± 0.05 mSv yr−1for the dry season whiles in the rainy season the mean222Rn concentration in groundwater was 0.08 ± 0.01 Bq l−1, the mean annual effective dose due to ingestion for adult, child and infant was 0.56 ± 0.09μSv yr−1, 1.13 ± 0.18μSv yr−1, 3.94 ± 0.62μSv yr−1respectively and the annual effective dose due to inhalation was 0.24 ± 0.04 mSv yr−1. In Offinso , the mean222Rn concentration in groundwater was 0.14 ± 0.05 Bq l−1, mean annual effective dose due to ingestion for adult, child and infant was 1.03 ± 0.37μSv yr−1, 2.06 ± 0.74μSv yr−1, and 7.20 ± 0.74μSv yr−1respectively and the mean annual inhalation dose a mean of 0.46 ± 0.16 mSv yr−1for the dry season. In the rainy season, the mean indoor222Rn concentration in groundwater was 0.13 ± 0.04 Bq l−1, mean annual effective dose due to ingestion for adult, child and infant was 1.26 ± 0.31μSv yr−1, 1.89 ± 0.61μSv yr−1and 6.62 ± 2.15μSv yr−1respectively and the mean annual effective dose due to inhalation was mean of 0.41 ± 0.13 mSv yr−1. The mean annual effective doses of all the samples are lower than the reference level of 0.1 mSvyr−1for drinking water of WHO and EU Council. It has been concluded that drinking water of the study area is generally safe as far as radon related health hazards are concerned apart from a few isolated cases. It has been found that radon levels within the region have a positive correlation with depth of the water sources.
Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing
Authors: Han Renmin , Wang Sheng , Gao Xin 
Published: October 2019

Abstract

Motivation
Genome diagnostics have gradually become a prevailing routine for human healthcare. With the advances in understanding the causal genes for many human diseases, targeted sequencing provides a rapid, cost-efficient and focused option for clinical applications, such as single nucleotide polymorphism (SNP) detection and haplotype classification, in a specific genomic region. Although nanopore sequencing offers a perfect tool for targeted sequencing because of its mobility, PCR-freeness and long read properties, it poses a challenging computational problem of how to efficiently and accurately search and map genomic subsequences of interest in a pool of nanopore reads (or raw signals). Due to its relatively low sequencing accuracy, there is no reliable solution to this problem, especially at low sequencing coverage.

Results
Here, we propose a brand new signal-based subsequence inquiry pipeline as well as two novel algorithms to tackle this problem. The proposed algorithms follow the principle of subsequence dynamic time warping and directly operate on the electrical current signals, without loss of information in base-calling. Therefore, the proposed algorithms can serve as a tool for sequence inquiry in targeted sequencing. Two novel criteria are offered for the consequent signal quality analysis and data classification. Comprehensive experiments on real-world nanopore datasets show the efficiency and effectiveness of the proposed algorithms. We further demonstrate the potential applications of the proposed algorithms in two typical tasks in nanopore-based targeted sequencing: SNP detection under low sequencing coverage, and haplotype classification under low sequencing accuracy.

Availability and implementation
The project is accessible at https://github.com/icthrm/cwSDTWnano.git, and the presented bench data is available upon request.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian weighted Mendelian randomization for causal inference based on summary statistics
Authors: Zhao Jia , Ming Jingsi , Hu Xianghong , Chen Gang , Liu Jin , Yang Can 
Published: October 2019

Abstract

Motivation
The results from Genome-Wide Association Studies (GWAS) on thousands of phenotypes provide an unprecedented opportunity to infer the causal effect of one phenotype (exposure) on another (outcome). Mendelian randomization (MR), an instrumental variable (IV) method, has been introduced for causal inference using GWAS data. Due to the polygenic architecture of complex traits/diseases and the ubiquity of pleiotropy, however, MR has many unique challenges compared to conventional IV methods.

Results
We propose a Bayesian weighted Mendelian randomization (BWMR) for causal inference to address these challenges. In our BWMR model, the uncertainty of weak effects owing to polygenicity has been taken into account and the violation of IV assumption due to pleiotropy has been addressed through outlier detection by Bayesian weighting. To make the causal inference based on BWMR computationally stable and efficient, we developed a variational expectation-maximization (VEM) algorithm. Moreover, we have also derived an exact closed-form formula to correct the posterior covariance which is often underestimated in variational inference. Through comprehensive simulation studies, we evaluated the performance of BWMR, demonstrating the advantage of BWMR over its competitors. Then we applied BWMR to make causal inference between 130 metabolites and 93 complex human traits, uncovering novel causal relationship between exposure and outcome traits.

Availability and implementation
The BWMR software is available at https://github.com/jiazhao97/BWMR.

Supplementary information
Supplementary data are available at Bioinformatics online.
BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis
Authors: Tian Yu , Wu Ling , Yuan Le , Ding Shaozhen , Chen Fu , Zhang Tong , Ren Ailin , Zhang Dachuan , Tu Weizhong , Chen Junni , Hu Qian-Nan 
Published: October 2019

Abstract

Summary
The biosynthetic ability of living organisms has important applications in producing bulk chemicals, biofuels and natural products. Based on the most comprehensive biosynthesis knowledgebase, a computational system, BCSExplorer, is proposed to discover the unexplored chemical space using nature’s biosynthetic potential. BCSExplorer first integrates the most comprehensive biosynthetic reaction database with 280 000 biochemical reactions and 60 000 chemicals biosynthesized globally over the past 130 years. Second, in this study, a biosynthesis tree is computed for a starting chemical molecule based on a comprehensive biotransformation rule library covering almost all biosynthetic possibilities, in which redundant rules are removed using a new algorithm. Moreover, biosynthesis feasibility, drug-likeness and toxicity analysis of a new generation of compounds will be pursued in further studies to meet various needs. BCSExplorer represents a novel method to explore biosynthetically available chemical space.

Availability and implementation
BCSExplorer is available at: http://www.rxnfinder.org/bcsexplorer/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Functional Territories of Human Dentate Nucleus
Authors: Guell Xavier , D’Mello Anila M , Hubbard Nicholas A , Romeo Rachel R , Gabrieli John D E , Whitfield-Gabrieli Susan , Schmahmann Jeremy D , Anteraper Sheeba Arnold 
Published: October 2019

Abstract
Anatomical connections link the cerebellar cortex with multiple sensory, motor, association, and paralimbic cerebral areas. The majority of fibers that exit cerebellar cortex synapse in dentate nuclei (DN) before reaching extracerebellar structures such as cerebral cortex, but the functional neuroanatomy of human DN remains largely unmapped. Neuroimaging research has redefined broad categories of functional division in the human brain showing that primary processing, attentional (task positive) processing, and default-mode (task negative) processing are three central poles of neural macroscale functional organization. This broad spectrum of human neural processing categories is represented not only in the cerebral cortex, but also in the thalamus, striatum, and cerebellar cortex. Whether functional organization in DN obeys a similar set of macroscale divisions, and whether DN are yet another compartment of representation of a broad spectrum of human neural processing categories, remains unknown. Here, we show for the first time that human DN are optimally divided into three functional territories as indexed by high spatio-temporal resolution resting-state MRI in 77 healthy humans, and that these three distinct territories contribute uniquely to default-mode, salience-motor, and visual cerebral cortical networks. Our findings provide a systems neuroscience substrate for cerebellar output to influence multiple broad categories of neural control.
Analysing tropical elasmobranch blood samples in the field: blood stability during storage and validation of the HemoCue® haemoglobin analyser
Authors: Schwieterman Gail D , Bouyoucos Ian A , Potgieter Kristy , Simpfendorfer Colin A , Brill Richard W , Rummer Jodie L 
Published: October 2019

Lay summary
Elasmobranch blood haematological parameters remained stable over 3 hours of storage duration, indicating that they do not need to be measured immediately. The HemoCue haemoglobin analyser can be used to measure haemoglobin concentrations from elasmobranch blood samples with the use of a correction equation.
The Clinical Accuracy of the BÜHLMANN fCAL ELISA in the Differentiation of Inflammatory Bowel Disease From Irritable Bowel Syndrome: A Multicenter Prospective Case–Control Study
Authors: Berinstein Jeffrey A , Steiner Calen A , Bousvaros Athos , Tiongco Felix P , Greenberg Eugene , Hardi Robert , Lembo Anthony J , Friedenberg Keith , Sedghi Shahriar , Fint Alison , Florez David A , Kumar Ashutosh , Arsenescu Razvan , Park K T , Kupchak Peter , Grob Alanna , Leavitt James , Higgins Peter D R 
Published: October 2019

Abstract

Background
Fecal calprotectin (fCAL) is a noninvasive biomarker used to differentiate between inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS).

Methods
A multicenter prospective case–control study evaluating the BÜHLMANN fCAL enzyme-linked immunosorbent assay (ELISA) was conducted in 478 subjects. Sensitivity, specificity, predictive values, and area under the receiver operator characteristic (AuROC) curve are reported and compared to another device.

Results
In differentiating IBD from IBS, the BÜHLMANN fCAL ELISA is very sensitive (93.3%) at a cutoff &lt;80 μg/g and balanced sensitivity (84.4%) and specificity (85.4%) at a cutoff &gt;160 μg/g (AuROC 0.933).

Conclusions
The BÜHLMANN fCAL ELISA demonstrates excellent discriminating between IBD and IBS.
Improvement in adherence to antibiotic duration of therapy recommendations for uncomplicated cystitis: a quasi-experimental study
Authors: Giancola Stephanie E , Higginbotham John M , Sutter Deena E , Spencer Steven E , Aden James K , Barsoumian Alice E 
Published: October 2019

Abstract

Background
Acute uncomplicated cystitis is one of the most common diagnoses for which antibiotic treatment is prescribed in the outpatient setting. Despite the availability of national guidelines, there remains a wide pattern in prescriber choices for therapy. Recent data portray a picture of consistently longer durations than recommended prescribed in outpatient settings.

Objective
The objective was to evaluate the effect of a system-based intervention on adherence to guideline-recommended durations of therapy for uncomplicated cystitis in the outpatient setting.

Methods
This quasi-experimental study included women aged 18–64 years who were seen at five family medicine clinics at an academic medical centre and were prescribed targeted antibiotics for uncomplicated cystitis (nitrofurantoin monohydrate/macrocrystals 100 mg, trimethoprim-sulfamethoxazole 160/800 mg or ciprofloxacin 250 mg). The intervention involved revising or adding pre-filled, but modifiable, default prescribing instructions in the electronic health record (EHR) for the targeted antibiotics. We evaluated adherence to guideline-recommended duration of therapy as well as days of therapy (DOT) before and after the intervention.

Results
A total of 787 pre-intervention and 862 post-intervention cases were included. Adherence to recommended duration of therapy increased from 29.4% to 76.3% (P < 0.01). The average DOT decreased by 23% from 6.6 to 5.1 (P < 0.01).

Conclusion
A stewardship intervention consisting of revising/adding default prescribing instructions to targeted antimicrobials in an EHR was associated with increased adherence to recommended durations of therapy for uncomplicated cystitis and reduction of unnecessary antibiotic exposure. More studies are needed to confirm effectiveness across multiple medical record platforms.
Association of polymorphisms in C1orf106, IL1RN, and IL10 with post-induction infliximab trough level in Crohn’s disease patients
Authors: Tang Jian , Zhang Cai-Bin , Lyu Kun-Sheng , Jin Zhong-Ming , Guan Shao-Xing , You Na , Huang Min , Wang Xue-Ding , Gao Xiang 
Published: October 2019

Abstract

Background
Trough levels of the post-induction serum infliximab (IFX) are associated with short-term and long-term responses of Crohn’s disease patients to IFX, but the inter-individual differences are large. We aimed to elucidate whether single gene polymorphisms (SNPs) within FCGR3A, ATG16L1, C1orf106, OSM, OSMR, NF-κB1, IL1RN, and IL10 partially account for these differences and employed a multivariate regression model to predict patients’ post-induction IFX levels.

Methods
The retrospective study included 189 Crohn’s disease patients undergoing IFX therapy. Post-induction IFX levels were measured and 41 tag SNPs within eight genes were genotyped. Associations between SNPs and IFX levels were analysed. Then, a multivariate logistic-regression model was developed to predict whether the patients’ IFX levels achieved the threshold of therapy (3 μg/mL).

Results
Six SNPs (rs7587051, rs143063741, rs442905, rs59457695, rs3213448, and rs3021094) were significantly associated with the post-induction IFX trough level (P = 0.015, P &lt; 0.001, P = 0.046, P = 0.022, P = 0.011, P = 0.013, respectively). A multivariate prediction model of the IFX level was established by baseline albumin (P = 0.002), rs442905 (P = 0.025), rs59457695 (P = 0.049), rs3213448 (P = 0.056), and rs3021094 (P = 0.047). The area under the receiver operating characteristic curve (AUROC) of this prediction model in a representative training dataset was 0.758. This result was verified in a representative testing dataset, with an AUROC of 0.733.

Conclusions
Polymorphisms in C1orf106, IL1RN, and IL10 play an important role in the variability of IFX post-induction levels, as indicated in this multivariate prediction model of IFX levels with fair performance.
Community structured production of zooplankton in the eastern boundary upwelling system off central/southern Chile (2003–2012)
Authors: Medellín-Mora Johanna , Atkinson Angus , Escribano Rubén 
Published: October 2019

AbstractEastern boundary upwelling systems (EBUS) are highly productive and climatically sensitive ecosystems of the ocean. A critical component sustaining EBUS is the zooplankton secondary production (ZSP) which links primary production (PP) and the higher trophic levels. However, estimating ZSP is a complex task and many questions remain regarding its controlling factors. Here, we used automated analysis to assess taxonomic-structured biomass of zooplankton from a time series (2003–2012) at a fixed station off central-southern Chile. Zooplankton biomasses combined with empirically estimated growth rates, as a function of temperature, Chorophyll-a concentration, and body size, were used to estimate seasonal and interannual changes in ZSP. The annual integrated ZSP yielded a mean of 8.0 g C m−2 y−1, with a minimum in 2009 of 5.7 g C m−2 y−1 and a maximum in 2011 of 13 g C m−2 y−1, and an average annual P/B ratio of 35. The transfer efficiency from PP to ZSP was only 0.8%, indicating a surplus of PP to the system and/or the importance of intermediate microzooplankton levels. Seasonal variation in biomass, ZSP and the P/B ratio were explained mostly by changes in taxonomic structure while interannual variation reflected large-scale climatic changes, such as the Pacific decadal oscillation.
Seasonality of spatial patterns of abundance, biomass, and biodiversity in a demersal community of the NW Mediterranean Sea
Authors: Vilas Daniel , Pennino Maria Grazia , Bellido Jose Maria , Navarro Joan , Palomera Isabel , Coll Marta 
Published: October 2019

AbstractInformation on the spatial patterns and habitat preferences of marine species is key to understand the functioning of marine ecosystem and to manage and protect marine resources efficiently. However, the study of spatial patterns of marine ecosystems is challenging because they are dynamic environments that can vary seasonally. We modelled the spatial patterns of abundance, biomass, and biodiversity in a demersal community of the northwestern Mediterranean Sea by season using hierarchical Bayesian spatial models and environmental, physical, and anthropogenic factors. Overall, our findings revealed the importance of seasonality in the spatial patterns of the demersal community, which were mainly driven by sea surface temperature. Results also underlined important patterns of movements of demersal organisms: fishes, cephalopods, and crustaceans showed high densities in the area surrounding the Ebro Delta River in winter mainly driven by species-specific behaviour. Our results are relevant to inform future management measures in the study area, such as seasonal fishing restrictions, or to adapt local marine protected areas to seasonal processes. This study provides evidence of the need to expand current monitoring schemes to capture the seasonality of marine demersal communities for a more comprehensive marine spatial planning framework.
Study on propagation characteristics of the secondary explosion of coal dust
Authors: Song Baichao , Li Yucheng 
Published: October 2019

Abstract
In the era when renewable energy resources are advocated, traditional fuels still account for a dominant proportion. During coal exploitation, coal dust explosion has been one of the most common and serious disasters. Nevertheless, the generated dust can suspend in the air, further leading to a secondary explosion. However, there are limited studies focusing on the propagation characteristics of secondary explosion induced by coal dust. Therefore, this paper aims to detect coal dust explosion in a pipe network and investigate the secondary explosion caused by the first explosion. In specific, this paper numerically analyzed the propagation characteristics of first and secondary explosion of coal dust in aspects of flame temperature, airflow rate and CO mass concentration. The results indicate that the maximum flame temperature of the secondary explosion of coal dust could reach up to 4500 K, which was more intense than the first explosion. After the secondary explosion, the air velocity witnessed a significant increase, compared with the first explosion, but the air velocity at the linear section of the pipe network witnessed the highest because of the air supplement at two sides. Different from the highest CO concentration at the ignition area in the first explosion, the CO concentration in the secondary explosion source area decreased rapidly and the maximum CO concentration appeared in the flame front. Moreover, because of enough oxygen supplement, the explosion reaction was much more sufficient, so that the maximum CO concentration was less than that in the first explosion.