bluuebunny/crossref_metadata_2025 huggingface dataset:
Delivering esophago-gastric cancer care during the COVID-19 pandemic in the United Kingdom: a surgical perspective
Authors: Wahed S , Chmelo J , Navidi M , Hayes N , Phillips A W , Immanuel A
Published: August 2020

Background

The COVID-19 pandemic continues to have a significant impact on the provision of medical care. Planning to ensure there is capability to treat those that become ill with the virus has led to an almost complete moratorium on elective work. This study evaluates the impact of COVID-19 on cancer, in particular surgical intervention, in patients with esophago-gastric cancer at a high-volume tertiary center.

Methods

All patients undergoing potential management for esophago-gastric cancer from 12 March to 22 May 2020 had their outcomes reviewed. Multi-disciplinary team (MDT) decisions, volume of cases, and outcomes following resection were evaluated.

Results

Overall 191 patients were discussed by the MDT, with a 12% fall from the same period in 2019, including a fall in new referrals from 120 to 83 (P = 0.0322). The majority of patients (80%) had no deviation from the pre-COVID-19 pathway. Sixteen patients had reduced staging investigations, 4 had potential changes to their treatment only, and 10 had a deviation from both investigation and potential treatment. Only one patient had palliation rather than potentially curative treatment. Overall 19 patients underwent surgical resection. Eight patients (41%) developed complications with two (11%) graded Clavien-Dindo 3 or greater. Two patients developed COVID-19 within a month of surgery, one spending 4 weeks in critical care due to respiratory complications; both recovered. Twelve patients underwent endoscopic resections with no complications.

Conclusion

Care must be taken not to compromise cancer treatment and outcomes during the COVID-19 pandemic. Excellent results can be achieved through meticulous logistical planning, good communication, and maintaining high-level clinical care.
A rare but serious complication of ticagrelor therapy: a case report
Authors: Arioti Manfredi , Sirianni Giovanni , Laudisa Maria Luisa , De Cesare Nicoletta Bianca
Published: August 2020

Background

Ticagrelor is a widely used P2Y12 inhibitor and represents a fundamental therapeutic agent in acute coronary syndrome treatment and selected post-percutaneous coronary intervention (PCI) cases. Dyspnoea and bradycardia are the most common side effects but the latter has been reported to be of trivial clinical significance

Case summary

A 51-year-old gentleman underwent PCI to left anterior descending and obtuse marginal for unstable angina receiving a loading dose of ticagrelor (180 mg). During hospital stay, whilst on telemetry monitoring, a 16 s long, symptomatic, asystolic ventricular standstill was recorded prompting ticagrelor interruption and a switch to prasugrel.

Discussion

Despite ventricular pauses have been reported in dedicated analyses of Phase III trials, no apparent clinical consequences were documented. However, several reports have shown that significant brady-arrhythmic events might be linked to ticagrelor administration presenting both as sino-atrial and atrio-ventricular conduction disturbances. We report a case of asystole occurring 36 h after the administration of a loading dose.
Long-term results after aortic valve replacement for bicuspid or tricuspid valve morphology in a Swedish population
Authors: Holmgren Anders , Enger Tone Bull , Näslund Ulf , Videm Vibeke , Valle Solveig , Evjemo Karen Julie Dybvad , Friberg Örjan , Wahba Alexander
Published: August 2020

OBJECTIVES

Our goal was to study long-term observed and relative survival after first-time aortic valve replacement surgery with or without concomitant coronary artery bypass surgery with reference to valve morphology (i.e. bicuspid vs tricuspid).

METHODS

Consecutive patients (n = 5086) from 3 Swedish hospitals, operated on between 1 January 2005 and 31 December 2016, were included. The 30-day mortality (n = 116, 2.3%) was excluded from the analysis of long-term observed and relative survival (n = 4970). Observed survival was analysed using Cox regression. Relative survival was calculated as the ratio between observed and expected survival based on data from the general Swedish population, matched for age, sex and calendar year. Risk factors for death were explored using multivariable analysis.

RESULTS

During the follow-up (median 4.7 years) period, 1157 (23%) patients died. Observed survival excluding 30-day mortality was 96.6%, 82.7% and 57.6% after 1, 5 and 10 years. Compared with the general Swedish population, the relative 1-, 5- and 10-year survival rates were 99.0%, 97.5% and 89.0%. Bicuspid morphology was independently associated with higher observed and relative long-term survival. Renal dysfunction, diabetes, chronic obstructive pulmonary disease, heart failure, smoking and atrial fibrillation were associated with higher long-term mortality. Combined surgery was not associated with higher observed or relative mortality.

CONCLUSIONS

Patients with a bicuspid morphology had better prognosis, matching that of the general population. With increased age, long-term relative survival compared favourably with survival in the general Swedish population. Adding coronary artery bypass surgery to an aortic valve replacement procedure did not affect long-term outcome.
Diatom DNA barcodes for forensic discrimination of drowning incidents
Authors: Liu Mengyan , Zhao Yi , Sun Yuzhe , Wu Ping , Zhou Shiliang , Ren Liang
Published: August 2020

The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens.
The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences
Authors: Babarinde Isaac Adeyemi , Saitou Naruya
Published: August 2020

Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae–Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.
Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness
Authors: Sato Daiki X , Rafati Nima , Ring Henrik , Younis Shady , Feng Chungang , Blanco-Aguiar José A , Rubin Carl-Johan , Villafuerte Rafael , Hallböök Finn , Carneiro Miguel , Andersson Leif
Published: August 2020

Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.
Ask Again: Including Gender Identity in Longitudinal Studies of Aging
Authors: Hanes Douglas William , Clouston Sean A P
Published: August 2020

Information on transgender people’s health, and especially their experiences of aging, is lacking, including from major longitudinal studies of aging like the Health and Retirement Study and its sister studies in the Gateway to Global Aging Data project. This paper surveys the state of gender data collection among major longitudinal studies and finds that all but one fail to collect adequate information on participants’ gender to determine participants’ gender identities. It identifies the unique challenges that population-wide longitudinal data collection poses to current best practices for identifying transgender survey participants and proposes a modified “two-question model”: one question for sex assigned at birth and a second for gender identity, both of which offer 3 responses.
Genetic determinants of increased body mass index mediate the effect of smoking on increased risk for type 2 diabetes but not coronary artery disease
Authors: Thom Christopher S , Ding Zhuoran , Levin Michael G , Damrauer Scott M , Lee Kyung Min , Lynch Julie , Chang Kyong-Mi , Tsao Philip S , Cho Kelly , Wilson Peter W F , Assimes Themistocles L , Sun Yan V , O’Donnell Christopher J ,   VA Million Veteran Program, Vujkovic Marijana , Voight Benjamin F
Published: August 2020

Clinical observations have linked tobacco smoking with increased type 2 diabetes risk. Mendelian randomization analysis has recently suggested smoking may be a causal risk factor for type 2 diabetes. However, this association could be mediated by additional risk factors correlated with smoking behavior, which have not been investigated. We hypothesized that body mass index (BMI) could help to explain the association between smoking and diabetes risk. First, we confirmed that genetic determinants of smoking initiation increased risk for type 2 diabetes (OR 1.21, 95% CI: 1.15–1.27, P = 1 × 10−12) and coronary artery disease (CAD; OR 1.21, 95% CI: 1.16–1.26, P = 2 × 10−20). Additionally, 2-fold increased smoking risk was positively associated with increased BMI (~0.8 kg/m2, 95% CI: 0.54–0.98 kg/m2, P = 1.8 × 10−11). Multivariable Mendelian randomization analyses showed that BMI accounted for nearly all the risk smoking exerted on type 2 diabetes (OR 1.06, 95% CI: 1.01–1.11, P = 0.03). In contrast, the independent effect of smoking on increased CAD risk persisted (OR 1.12, 95% CI: 1.08–1.17, P = 3 × 10−8). Causal mediation analyses agreed with these estimates. Furthermore, analysis using individual-level data from the Million Veteran Program independently replicated the association of smoking behavior with CAD (OR 1.24, 95% CI: 1.12–1.37, P = 2 × 10−5), but not type 2 diabetes (OR 0.98, 95% CI: 0.89–1.08, P = 0.69), after controlling for BMI. Our findings support a model whereby genetic determinants of smoking increase type 2 diabetes risk indirectly through their relationship with obesity. Smokers should be advised to stop smoking to limit type 2 diabetes and CAD risk. Therapeutic efforts should consider pathophysiology relating smoking and obesity.
Transapical approach versus transcervical approach for transcatheter aortic valve replacement: a retrospective monocentric study
Authors: Lu Henri , Fournier Stephane , Namasivayam Jegaruban , Roguelov Christian , Ferrari Enrico , Eeckhout Eric , Monney Pierre , Tozzi Piergiorgio , Marcucci Carlo , Muller Olivier , Kirsch Matthias
Published: August 2020

OBJECTIVES

Transfemoral approach is the standard access-route for transcatheter aortic valve replacement (TAVR). However, alternative approaches are needed in a number of patients and accesses such as transapical (TA) TAVR or transcervical (TC) are used. We aimed to compare clinical and echocardiographic outcomes after TA-TAVR or TC-TAVR.

METHODS

All patients who underwent TA- and TC-TAVR for severe aortic stenosis in our institution between 2008 and 2020 were retrospectively included. End points included 30-day all-cause mortality, procedural complications (according to the Valve Academic Research Consortium-2 criteria), procedure duration, intensive care unit (ICU) length of stay (LOS) and overall hospital LOS. For 30-day all-cause mortality, we furthermore used a Cox proportional-hazards model to adjust for significant between-group differences in baseline characteristics as well as difference in year of intervention.

RESULTS

TAVR was performed in 176 patients, using a TA approach (n = 127) or a TC approach (n = 49). Baseline clinical and echocardiographic characteristics were comparable between the 2 groups, except age and peripheral artery disease. All-cause 30-day mortality rates were not significantly different (8.5% in the TA group vs 2.3% in the TC group, P = 0.124). TC approach was associated with significantly shorter procedure duration {71.0 [interquartile range (IQR) 52.5–101.0] vs 93 [IQR 80.0–120.0] min, P < 0.001}, shorter ICU LOS [0.0 (IQR 0.0–0.0) vs 1.0 (IQR 1.0–3.0) days, P < 0.001] and shorter hospital LOS [7.0 (IQR 5.0–9.5) vs 14.0 (IQR 10.0–22.0) days, P < 0.001].

CONCLUSIONS

The TC approach may be a good first-choice alternative in case of contraindications to transfemoral-TAVR.
Accumulation of childhood adversities and type 1 diabetes risk: a register-based cohort study of all children born in Denmark between 1980 and 2015
Authors: Bengtsson Jessica , Byberg Stine , Carstensen Bendix , De Stavola Bianca L , Svensson Jannet , Jørgensen Marit E , Rod Naja H
Published: August 2020

Background

Previous studies have indicated an association between childhood adversities and type 1 diabetes but have been underpowered and limited by selection. We aim to quantify the effect of accumulation of childhood adversities on type 1 diabetes risk, and to assess whether the effect differs between males and females in a large and unselected population sample.

Methods

We used register-based data covering all children born in Denmark between 1980 and 2015, totalling >2 million children. We specified a multi-state model to quantify the effect of accumulation of childhood adversities on type 1 diabetes risk. The effects of specific childhood adversities on type 1 diabetes were estimated using proportional hazards models.

Results

Accumulation of childhood adversities had a quantitatively small effect on type 1 diabetes risk among females [adjusted hazard ratio (HR) per adversity increase: 1.07; 95% confidence interval (CI): 1.02–1.11], but not among males (adjusted HR per adversity increase: 0.99; 95% CI: 0.97–1.03). Females exposed to extreme numbers (7+) of adversities had two times higher risk of type 1 diabetes compared with unexposed females (adjusted HR: 2.06; 95% CI: 1.10–3.86).

Conclusions

In an unselected total population sample, we generally find no or negligible effects of childhood adversities on type 1 diabetes risk, which may be reassuring to persons with type 1 diabetes who are concerned that personal trauma contributed to their disease. There is a very small group of females exposed to a high degree of adversity who may have a higher risk of type 1 diabetes and this group needs further attention.
Stirling numbers and Gregory coefficients for the factorization of Hermite subdivision operators
Authors: Moosmüller Caroline , Hüning Svenja , Conti Costanza
Published: August 2020

In this paper we present a factorization framework for Hermite subdivision schemes refining function values and first derivatives, which satisfy a spectral condition of high order. In particular we show that spectral order $d$ allows for $d$ factorizations of the subdivision operator with respect to the Gregory operators: a new sequence of operators we define using Stirling numbers and Gregory coefficients. We further prove that the $d$th factorization provides a ‘convergence from contractivity’ method for showing $C^d$-convergence of the associated Hermite subdivision scheme. Gregory operators are derived by explicitly solving a recursion based on the Taylor operator and iterated vector scheme factorizations. The explicit expression of these operators allows one to compute the $d$th factorization directly from the mask of the Hermite scheme. In particular, it is not necessary to compute intermediate factorizations, which simplifies the procedures used up to now.
Range-relaxed criteria for choosing the Lagrange multipliers in the Levenberg–Marquardt method
Authors: Leitão A , Margotti F , Svaiter B F
Published: August 2020

In this article we propose a novel strategy for choosing the Lagrange multipliers in the Levenberg–Marquardt method for solving ill-posed problems modeled by nonlinear operators acting between Hilbert spaces. Convergence analysis results are established for the proposed method, including monotonicity of iteration error, geometrical decay of the residual, convergence for exact data, stability and semi-convergence for noisy data. Numerical experiments are presented for an elliptic parameter identification two-dimensional electrical impedance tomography problem. The performance of our strategy is compared with standard implementations of the Levenberg–Marquardt method (using a priori choice of the multipliers).
The First Integral Cohomology of Pure Mapping Class Groups
Authors: Aramayona Javier , Patel Priyam , Vlamis Nicholas G
Published: August 2020

It is a classical result that pure mapping class groups of connected, orientable surfaces of finite type and genus at least 3 are perfect. In stark contrast, we construct nontrivial homomorphisms from infinite-genus mapping class groups to the integers. Moreover, we compute the first integral cohomology group associated to the pure mapping class group of any connected orientable surface of genus at least 2 in terms of the surface’s simplicial homology. In order to do this, we show that pure mapping class groups of infinite-genus surfaces split as a semi-direct product.
Modular Forms of Degree 2 and Curves of Genus 2 in Characteristic 2
Authors: Cléry Fabien , van der Geer Gerard
Published: August 2020

We describe the ring of modular forms of degree $2$ in characteristic $2$ using its relation with curves of genus $2$.
Triumph of Pneumococcal Conjugate Vaccines: Overcoming a Common Foe
Authors: Rodgers Gail L , Whitney Cynthia G , Klugman Keith P
Published: August 2020

Pneumococcal conjugate vaccine (PCV) has reduced the burden of pneumococcal disease by the near elimination of vaccine serotypes from countries giving a booster dose at >9 months of life. Herd protection, induced by interruption of pneumococcal vaccine type transmission has protected children too young to be immunized, children and adults with underlying risk conditions for invasive pneumococcal disease, and the elderly. PCV has rolled out in most poor countries, but millions of children remain un-immunized especially in middle income countries because of cost constraints. These are being met by considering fewer doses to maintain herd protection, and support for more affordable vaccine from developing country manufacturers. While 3rd generation PCV’s with potential inclusion of 20+ serotypes are close to market in adults, it will be their introduction into childhood immunization and herd protection that is most likely to maximize the public health benefits of these vaccines.
Nephrotoxicity of concomitant piperacillin/tazobactam and teicoplanin compared with monotherapy
Authors: Workum J D , Kramers C , Kolwijck E , Schouten J A , de Wildt S N , Brüggemann R J
Published: August 2020

Objectives

Piperacillin/tazobactam combined with vancomycin has been associated with a decline in renal function when compared with monotherapy. Teicoplanin is a glycopeptide similar to vancomycin. We investigated whether piperacillin/tazobactam combined with teicoplanin is associated with a decline in renal function as well.

Methods

We conducted a single-centre retrospective cohort study with data from our electronic health records from 9 August 2013 to 15 November 2019, including all adult patients that received either piperacillin/tazobactam, teicoplanin or piperacillin/tazobactam + teicoplanin. The incidence of acute kidney injury (AKI) at 48–72 h served as the primary outcome, whereas change in serum creatinine served as a secondary outcome.

Results

Of the 4202 included patients, 3188 (75.9%) received piperacillin/tazobactam, 791 (18.8%) received teicoplanin and 223 (5.3%) received piperacillin/tazobactam + teicoplanin. The incidence of AKI at 48–72 h after commencement of antibiotic therapy was 5.4% for piperacillin/tazobactam, 3.4% for teicoplanin and 11.7% for piperacillin/tazobactam + teicoplanin (P < 0.001). However, mean serum creatinine at 48–72 h was slightly higher in the piperacillin/tazobactam + teicoplanin group therapy compared with baseline [+1.61% (95% CI –2.25 to 5.70)], indicating a slight decrease in renal function, and decreased for piperacillin/tazobactam [–1.98% (95% CI –2.73 to –1.22)] and teicoplanin [–8.01% (95% CI –9.54 to –6.45)]. After correcting for significant confounders in a multivariate linear regression analysis, these patterns remained.

Conclusions

Our study suggests that piperacillin/tazobactam + teicoplanin is associated with a higher prevalence of AKI compared with monotherapy. However, as the overall decline in renal function with piperacillin/tazobactam + teicoplanin is very small, its clinical relevance is likely limited. Therefore, piperacillin/tazobactam + teicoplanin can probably be safely combined.
Better synonyms for enriching biomedical search
Authors: Yeganova Lana , Kim Sun , Chen Qingyu , Balasanov Grigory , Wilbur W John , Lu Zhiyong
Published: August 2020

Objective

In a biomedical literature search, the link between a query and a document is often not established, because they use different terms to refer to the same concept. Distributional word embeddings are frequently used for detecting related words by computing the cosine similarity between them. However, previous research has not established either the best embedding methods for detecting synonyms among related word pairs or how effective such methods may be.

Materials and Methods

In this study, we first create the BioSearchSyn set, a manually annotated set of synonyms, to assess and compare 3 widely used word-embedding methods (word2vec, fastText, and GloVe) in their ability to detect synonyms among related pairs of words. We demonstrate the shortcomings of the cosine similarity score between word embeddings for this task: the same scores have very different meanings for the different methods. To address the problem, we propose utilizing pool adjacent violators (PAV), an isotonic regression algorithm, to transform a cosine similarity into a probability of 2 words being synonyms.

Results

Experimental results using the BioSearchSyn set as a gold standard reveal which embedding methods have the best performance in identifying synonym pairs. The BioSearchSyn set also allows converting cosine similarity scores into probabilities, which provides a uniform interpretation of the synonymy score over different methods.

Conclusions

We introduced the BioSearchSyn corpus of 1000 term pairs, which allowed us to identify the best embedding method for detecting synonymy for biomedical search. Using the proposed method, we created PubTermVariants2.0: a large, automatically extracted set of synonym pairs that have augmented PubMed searches since the spring of 2019.
Innovative use of health informatics to augment contact tracing during the COVID-19 pandemic in an acute hospital
Authors: Venkataraman Narayan , Poon Beng Hoong , Siau Chuin
Published: August 2020

This case report describes the innovative design and build of an algorithm that integrates available data from separate hospital-based informatics systems, which perform different daily functions to augment the contact-tracing process of COVID-19 patients by identifying exposed neighboring patients and healthcare workers and assessing their risk. Prior to the establishment of the algorithm, contact-tracing teams comprising 6 members would spend up to 10 hours each to complete contact tracing for 5 new COVID-19 patients. With the augmentation by the algorithm, we observed ≥ 60% savings in overall man-hours needed for contact tracing when there were 5 or more daily new cases through a time–motion study and Monte Carlo simulation.

This improvement to the hospital’s contact-tracing process supported more expeditious and comprehensive downstream contact-tracing activities as well as improved manpower utilization in contact tracing.
Real-time clinical note monitoring to detect conditions for rapid follow-up: A case study of clinical trial enrollment in drug-induced torsades de pointes and Stevens-Johnson syndrome
Authors: DeLozier Sarah , Speltz Peter , Brito Jason , Tang Leigh Anne , Wang Janey , Smith Joshua C , Giuse Dario , Phillips Elizabeth , Williams Kristina , Strickland Teresa , Davogustto Giovanni , Roden Dan , Denny Joshua C
Published: August 2020

Identifying acute events as they occur is challenging in large hospital systems. Here, we describe an automated method to detect 2 rare adverse drug events (ADEs), drug-induced torsades de pointes and Stevens-Johnson syndrome and toxic epidermal necrolysis, in near real time for participant recruitment into prospective clinical studies. A text processing system searched clinical notes from the electronic health record (EHR) for relevant keywords and alerted study personnel via email of potential patients for chart review or in-person evaluation. Between 2016 and 2018, the automated recruitment system resulted in capture of 138 true cases of drug-induced rare events, improving recall from 43% to 93%. Our focused electronic alert system maintained 2-year enrollment, including across an EHR migration from a bespoke system to Epic. Real-time monitoring of EHR notes may accelerate research for certain conditions less amenable to conventional study recruitment paradigms.
Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries)
Authors: Ross Elizabeth M , Hayes Ben J , Tucker David , Bond Jude , Denman Stuart E , Oddy Victor Hutton
Published: August 2020

Methane production from rumen methanogenesis contributes approximately 71% of greenhouse gas emissions from the agricultural sector. This study has performed genomic predictions for methane production from 99 sheep across 3 yr using a residual methane phenotype that is log methane yield corrected for live weight, rumen volume, and feed intake. Using genomic relationships, the prediction accuracies (as determined by the correlation between predicted and observed residual methane production) ranged from 0.058 to 0.220 depending on the time point being predicted. The best linear unbiased prediction algorithm was then applied to relationships between animals that were built on the rumen metabolome and microbiome. Prediction accuracies for the metabolome-based relationships for the two available time points were 0.254 and 0.132; the prediction accuracy for the first microbiome time point was 0.142. The second microbiome time point could not successfully predict residual methane production. When the metabolomic relationships were added to the genomic relationships, the accuracy of predictions increased to 0.274 (from 0.201 when only the genomic relationship was used) and 0.158 (from 0.081 when only the genomic relationship was used) for the two time points, respectively. When the microbiome relationships from the first time point were added to the genomic relationships, the maximum prediction accuracy increased to 0.247 (from 0.216 when only the genomic relationship was used), which was achieved by giving the genomic relationships 10 times more weighting than the microbiome relationships. These accuracies were higher than the genomic, metabolomic, and microbiome relationship matrixes achieved alone when identical sets of animals were used.
Novel and Nonroutine Benzodiazepines and Suvorexant by LC–MS-MS
Authors: Garcia Luke , Tiscione Nicholas B , Yeatman Dustin Tate , Richards-Waugh Lauren
Published: August 2020

Benzodiazepines are a commonly prescribed class of drugs that have the potential for abuse. The Palm Beach County Sheriff’s Office received drug seizure submissions that included novel and/or nonroutine benzodiazepines of increasing prevalence from 2017 to 2019. This prompted the development of a method of analysis for these compounds in biological specimens. The method tests for 16 novel and nonroutine benzodiazepines and suvorexant in whole blood by liquid chromatography–tandem mass spectrometry (LC–MS-MS). The target analytes included bromazepam, clobazam, clonazolam, clotiazepam, diclazepam, estazolam, etizolam, flualprazolam, flubromazepam, flubromazolam, loprazolam, lormetazepam, phenazepam, prazepam, suvorexant, tetrazepam and triazolam. The method uses 200 µL of sample, protein precipitation and an instrument run-time of 8 min. The limit of detection was either 1 or 5 ng/mL and the limit of quantitation was either 5 or 25 ng/mL depending on the analyte. The method was validated for quantitative analysis for 15 out of the 17 analytes. Flubromazepam and prazepam were validated for qualitative identification only. A quadratic calibration model (r2 > 0.990) with 1/x weighting was used for all analytes for quantitative analysis. The calibration range was either 5–100 or 25–500 ng/mL depending on the analyte. The coefficient of variation of replicate analyses was within 14% and bias was within ±14%. The method provides a sensitive, efficient and robust procedure for the quantitation and/or qualitative identification of select novel and nonroutine benzodiazepines and suvorexant using LC–MS-MS and a sample volume of 200 µL.
Eutylone Intoxications—An Emerging Synthetic Stimulant in Forensic Investigations
Authors: Krotulski Alex J , Papsun Donna M , Chronister Chris W , Homan Joseph , Crosby Michele M , Hoyer Jennifer , Goldberger Bruce A , Logan Barry K
Published: August 2020

Synthetic stimulants are the largest class of novel psychoactive substances identified each year by forensic laboratories internationally. While hundreds of these drugs appear in drug powders, only a few proliferate in use among forensically relevant populations and eventually emerge in postmortem and clinical investigations. Beta-keto-methylenedioxyamphetamines (i.e., novel psychoactive substances with names ending in “ylone”) are currently the most popular subclass of synthetic stimulants. Leading up to its federal scheduling in 2018, N-ethyl pentylone was the most encountered synthetic stimulant. The popularity of N-ethyl pentylone declined once it was scheduled, but it was quickly replaced by eutylone (bk-EBDB), a structurally related analog from the same family. In cases encountered between January 2019 and April 2020, eutylone was quantitatively confirmed in 83 forensic investigations, including postmortem cases and driving under the influence of drugs cases. Matrix types included blood, urine and tissue. Eutylone was identified in cases submitted from 13 states, demonstrating proliferation around the United States; Florida accounted for 60% of the positive cases. The mean concentration of eutylone in postmortem blood was 1,020 ng/mL (standard deviation = ±2,242 ng/mL; median = 110 ng/mL, range = 1.2–11,000 ng/mL, n = 67). The mean concentration of eutylone in blood from driving under the influence of drugs cases was 942 ng/mL (standard deviation = ±1,407 ng/mL; median = 140 ng/mL, range = 17–3,600 ng/mL, n = 7). This report includes cause and manner of death data for 22 postmortem cases. Further analysis of authentic human specimens revealed the presence of three eutylone metabolites, including one unique biomarker and one metabolite in common with butylone. Laboratories should be aware that eutylone may be present in cases of suspected Ecstasy, “Molly” and/or methylenedioxymethamphetamine use, causing or contributing to impairment or death.
The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest
Authors: Ferreira Anthony S , Lima Albertina P , Jehle Robert , Ferrão Miquéias , Stow Adam
Published: August 2020

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.
Extraction procedure of a stingray spine
Authors: Cappa Giovanni , Barcella Bruno , Pettenazza Pietro
Published: August 2020

Stingrays stings are becoming an increasingly common marine injury. Stingray spine extraction is a complicated maneuver without a precise method: we present here a novel approach to safely remove a penetrating stingray sting. This procedure is easy and does not require specialized medical devices.
Probing the nuclear and circumnuclear properties of NGC 6300 using X-ray observations
Authors: Jana Arghajit , Chatterjee Arka , Kumari Neeraj , Nandi Prantik , Naik Sachindra , Patra Dusmanta
Published: August 2020

We present the results obtained from a detailed X-ray timing and spectral analysis of the Seyfert 2 galaxy NGC 6300 by using observations from the Suzaku observatory, theChandra X-ray Observatory and the Nuclear Spectroscopic Telescope Array(NuSTAR) mission between 2007 and 2016. We calculate the variance and the rms fractional variability of the source in different energy bands and we find variabilities in various energy bands. Spectral properties of the source are studied by using various phenomenological and physical models. The properties of the Compton clouds, reflection, Fe Kα line emission and soft X-ray excess are studied in detail. Several physical parameters of the source are extracted and investigated to establish the presence/absence of any correlation between them. We also investigate the nature of the circumnuclear ‘torus’ and we find that the torus is not uniform, but clumpy. The observed changes in the line-of-sight column density can be explained in terms of transiting clouds. The iron line-emitting region is found to be different in the different epochs of observations. We also observe that the torus and the nucleus independently evolve over the years.
A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra–Tcrd locus
Authors: Zhao Hao , Li Zhaoqiang , Zhu Yongchang , Bian Shasha , Zhang Yan , Qin Litao , Naik Abani Kanta , He Jiangtu , Zhang Zhenhai , Krangel Michael S , Hao Bingtao
Published: August 2020

The regulation of T cell receptor Tcra gene rearrangement has been extensively studied. The enhancer Eα plays an essential role in Tcra rearrangement by establishing a recombination centre in the Jα array and a chromatin hub for interactions between Vα and Jα genes. But the mechanism of the Eα and its downstream CTCF binding site (here named EACBE) in dynamic chromatin regulation is unknown. The Hi-C data showed that the EACBE is located at the sub-TAD boundary which separates the Tcra–Tcrd locus and the downstream region including the Dad1 gene. The EACBE is required for long-distance regulation of the Eα on the proximal Vα genes, and its deletion impaired the Tcra rearrangement. We also noticed that the EACBE and Eα regulate the genes in the downstream sub-TAD via asymmetric chromatin extrusion. This study provides a new insight into the role of CTCF binding sites at TAD boundaries in gene regulation.
International Affairs
Authors: Barash David P.
Published: August 2020

This chapter explores how the use of military threats—that is, deterrence—has operated between and among nations. It begins with a brief history of conventional deterrence aimed at preventing wars by threatening either that an initial attack will fail to gain its objective (deterrence by denial) or that an attacker will be sufficiently punished so as to regret the initial action and thus prevent such an attack in the first place (deterrence by punishment). This leads to the self-serving phenomenon of bureaucratic “threat inflation” and then to the most consequential uses and abuses of threats: nuclear deterrence. The chapter then discusses how nuclear deterrence is supposed to work and whether it has in fact worked. It also provides a critical analysis of the strengths and weaknesses of nuclear deterrence.
Affirmative Religion
Authors: Smith Bradley C.
Published: August 2020

Evangelical Christians are typically known for what they oppose, often taking hard-line stances against certain behaviors. Yet trends in the character of both American business and American religion enable evangelical executives to affirm the spiritual value of business and the choices required of business leaders. Evangelicalism is an individualistic religious tradition, encouraging spiritual improvisation, including personally interpreting the Bible. The Bible, in turn, is sufficiently diverse and ambiguous as to support all manner of priorities and perspectives. Paralleling this diversity, the panoply of stakeholder interests urged on companies by proponents of corporate social responsibility presents an array of possible contributions on which to base the spiritual worth of business. While evangelicalism, like religion more broadly, is often understood to be self-consistent, characterized by proscriptions and prohibitions, and rigidly dogmatic, in fact it is flexible, adaptable, often incoherent, and abundantly capable of affirming institutions and activities, including business.
Success to Significance
Authors: Smith Bradley C.
Published: August 2020

While scholars generally posit upward mobility as a secularizing force, for evangelical executives, success in business catalyzes a deeper commitment to faithful living. Fame and fortune do not quench evangelical business leaders’ appetite for spiritual things, but rather activate or intensify such longings. Evangelical executives are deeply committed to exercising positive influence at their companies and beyond. But the executives who do so are those—and only those—who have acquired sufficient discretion and resources to exercise influence without compromising their professional standing or altering their lifestyle. While the deferral of significance is not unique to evangelical executives, their explicit endorsement of the transition from success to significance is important inasmuch as the ability to point to activities of significance that are facilitated by success in business strengthens the case that business is a worthy spiritual calling and legitimates lofty career aspirations, along with the accompanying sacrifices and eventual perquisites.
Into the Headwind
Authors: Smith Bradley C.
Published: August 2020

For aspiring evangelical women, already subject to the metaphorical glass ceiling, evangelical perspectives on gender roles represent an exacerbating headwind. Ironically, though, when female evangelical executives advance arguments from distinction in advocating for greater representation among the business elite, they may actually reinforce the complementarian theological perspectives that undermine the legitimacy of evangelical women in leadership roles in the first place. Female evangelical executives are indeed more likely than their male counterparts to articulate concern for people relative to profits, embrace broader corporate social responsibilities, and cite feelings and intuition in support of career and business decisions. But women also disproportionately occupy the types of contexts that prompted evangelical executives more broadly—whether women or men—to articulate these particular orientations. Thus, the perspectives of women suggest that professional context and associated expectations supersede gender norms when ordering faith expressions in business.
Conclusion
Authors: Smith Bradley C.
Published: August 2020

For most evangelical executives, being an evangelical Christian in a corner office is not so much confusing or tension-filled as lonely. While the faith at work movement encourages evangelical business leaders to integrate their faith and their work, evangelical executives do not lack ways to implement their faith. Rather, they thirst for companionship and legitimation—for reassurance that their vocational choices have been sound and their time and energy well spent. Such is the primary effect of the faith at work movement for evangelical executives, the gist of whose rhetoric is to baptize business, or provide symbolic justification of business as a sacred enterprise. Eager indeed to integrate faith and work, for them, integration works in reverse. Evangelical business leaders are as likely to export business concepts into other contexts as to import religious concepts into the corporate domain, prompting reconsideration of the direction of influence between religious and economic life.
Empirical Methods for Studying Decision-Making in Child Welfare and Protection
Authors: Gautschi Joel , Benbenishty Rami
Published: August 2020

Studying the complex nature of decision-making in child welfare and protection is challenging. Researcher in this field uses various empirical methods, each with its advantages and limitation. This chapter describes the current state of the art of the most prominent empirical methods used to study this subject and to identify empirical methods from other fields, with the potential to advance decision-making research in child protection. The authors briefly describe methods for decision-making research, give examples of how these methods were used, and critically assess their strengths and limitations. “Black-box” input-output analysis is reviewed, and the authors describe the use of case files and administrative data, agency surveys, and experimental designs with simulated cases. The chapter then describes methods to trace decision processes based on verbalization (think-aloud), behavior (tracing information acquisition), and people’s sense-making in everyday contexts (ethnographic observations). The review ends with recommendations of future directions for research on decision-making in child protection.
The Decision-Making Ecology of Placing a Child into Foster Care
Authors: Graham J. Christopher , Dettlaff Alan J. , Baumann Donald J. , Fluke John D.
Published: August 2020

The Decision-Making Ecology provided a framework for empirically testing the impact of case, caseworker, and organizational factors on the decision to place children in out-of-home care. The structural equation model developed fit the data extremely well, indicating a complex relationship between the variables. The main findings indicate that case factors, even as aggregated to the worker level, were of most importance: Percent removed was increased in part by greater average risk being assessed and more families on a worker’s caseload being low income. Furthermore, removal rates were increased by lower proportions of Hispanic families on the caseload, as well as by lower organizational support and a perception of manageable workload and sufficient resources. Individual factors (i.e., variables characterizing the caseworkers themselves) were not found to directly influence the placement decision, including workers’ own race/ethnicity, although various orders of mediated effects were indicated, and these are detailed. Interrelationships between variables that affect case, caseworker, and organizational factors are discussed along with implications for practice.
The Decision to Substantiate Allegations of Child Maltreatment
Authors: Font Sarah A. , Maguire-Jack Kathryn , Dillard Rebecca
Published: August 2020

In the United States, the Child Protective Services system is responsible for investigating and responding to allegations of child abuse and neglect. At the conclusion of an investigation, caseworkers are expected to decide whether allegations are “substantiated” (demonstrated to be true) or not. How that decision is made—and whether it reflects an objective assessment of the evidence available—is widely debated. This chapter first presents an overview of the decision-making process and the implications of decision-making for vulnerable children and families. Next, it describes how rates of substantiation vary across and within states. The authors then present data from a nationally representative study of child protective services investigations on the factors associated with the decision to substantiate child maltreatment. They find that agency characteristics are predictive of substantiation, net of child and family characteristics. Overall, the authors conclude that substantiation is unlikely to be a valid indicator of the incidence of child maltreatment, and they discuss possible strategies for improving the consistency and utility of the substantiation decision.