bluuebunny/crossref_metadata_2025 huggingface dataset:
Vision, vision-specific functioning and mobility, and their relationship with clinically assessed cognitive impairment
Authors: Fenwick Eva K , Gan Alfred T L , Man Ryan E K , Gupta Preeti , Sabanayagam Charumathi , Cheng Ching-Yu , Chen Christopher Li-Hsian , Cheung Carol Y , Wong Kah Hie , Venketasubramanian Narayanaswamy , Xu Xin , Hilal Saima , Chong Eddie J Y , Tham Yih-Chung , Wong Tien Y , Lamoureux Ecosse L
Published: December 2020

Background

The relationship between self-reported visual disability and cognitive impairment in older individuals is unclear.

Objective

To determine the relationship of vision-specific functioning (VSF), vision-specific mobility (VSM) and visual acuity (VA) with clinically assessed cognitive impairment in the Epidemiology of Dementia in Singapore study.

Design

Cross-sectional.

Setting

Population-based.

Subjects

Eight hundred and seventy-four adults aged ≥60 years at higher risk of possible cognitive impairment by the Abbreviated Mental Test and progressive forgetfulness question.

Methods

VSF and VSM were measured using Rasch-transformed continuous scores of two Impact of Vision Impairment questionnaire domains. Cognitive impairment was objectively determined using detailed neuropsychological testing and defined as no cognitive impairment (NCI), mild cognitive impairment-no dementia (CIND), moderate CIND only and moderate CIND or dementia. Associations were assessed using multinomial logistic regression models.

Results

Of the 874 participants (49.0% males, mean age (SD) 65.5 (7.0) years), 277, 281 and 316 had NCI, mild CIND and moderate CIND or dementia, respectively. Compared to NCI, the odds of moderate CIND, and moderate CIND or dementia increased for every SD worsening in VSF (OR: 1.44, 95% CI 1.14–1.82, and OR: 1.52, 95%CI 1.19–1.94, respectively) and VSM (OR: 1.42, 95%CI 1.11–1.81, and OR: 1.50, 95%CI 1.15–1.95). Similarly, the odds of mild CIND (OR: 1.62, 95%CI 1.19–2.22), moderate CIND (OR: 1.93, 95%CI 1.45–2.58), and moderate CIND or dementia (OR: 2.25, 95%CI 1.62–3.11) increased significantly with every SD worsening of VA.

Conclusions

Our results emphasise the importance of interventions to prevent vision loss and improve quality of life to reduce likelihood of age-related cognitive decline.
iCysMod: an integrative database for protein cysteine modifications in eukaryotes
Authors: Wang Panqin , Zhang Qingfeng , Li Shihua , Cheng Ben , Xue Han , Wei Zhen , Shao Tian , Liu Ze-Xian , Cheng Han , Wang Zhenlong
Published: December 2020

As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
Authors: Chiara Matteo , Zambelli Federico , Tangaro Marco Antonio , Mandreoli Pietro , Horner David S , Pesole Graziano
Published: December 2020

While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2.

Availabilityand implementation

Galaxy

 

http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat.

Supplementary information

Supplementary data are available at Bioinformatics online.
IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors
Authors: Shen Cong , Luo Jiawei , Ouyang Wenjue , Ding Pingjian , Chen Xiangtao
Published: December 2020

Motivation

Protein kinases have been the focus of drug discovery research for many years because they play a causal role in many human diseases. Understanding the binding profile of kinase inhibitors is a prerequisite for drug discovery, and traditional methods of predicting kinase inhibitors are time-consuming and inefficient. Calculation-based predictive methods provide a relatively low-cost and high-efficiency approach to the rapid development and effective understanding of the binding profile of kinase inhibitors. Particularly, the continuous improvement of network pharmacology methods provides unprecedented opportunities for drug discovery, network-based computational methods could be employed to aggregate the effective information from heterogeneous sources, which have become a new way for predicting the binding profile of kinase inhibitors.

Results

In this study, we proposed a network-based influence deep diffusion model, named IDDkin, for enhancing the prediction of kinase inhibitors. IDDkin uses deep graph convolutional networks, graph attention networks and adaptive weighting methods to diffuse the effective information of heterogeneous networks. The updated kinase and compound representations are used to predict potential compound-kinase pairs. The experimental results show that the performance of IDDkin is superior to the comparison methods, including the state-of-the-art kinase inhibitor prediction method and the classic model widely used in relationship prediction. In experiments conducted to verify its generalizability and in case studies, the IDDkin model also shows excellent performance. All of these results demonstrate the powerful predictive ability of the IDDkin model in the field of kinase inhibitors.

Availability and implementation

Source code and data can be downloaded from https://github.com/CS-BIO/IDDkin.

Supplementary information

Supplementary data are available at Bioinformatics online.
Not out of the woods yet: genetic insights related to the recovery of the pine marten (Martes martes) in Ireland
Authors: O’Reilly Catherine , Turner Peter , O’Mahony Declan T , Twining Joshua P , Tosh David G , Smal Christopher , McAney Kate , Powell Ciara , Power John , O’Meara Denise B
Published: December 2020

In this study, the history of the pine marten (Martes martes) in Ireland is reviewed, revealing that the population has undergone several retractions and expansions over the last few hundred years. Here, we consider the genetic legacy of this flux in fortunes and its likely impacts upon the conservation and future recovery of the species. Using nuclear DNA markers (microsatellites), we found that the genetic diversity present in Ireland today is like that of other Irish carnivores, but there is evidence of a genetic bottleneck and low effective population size that might result in further reductions of diversity in the future. There is a lack of genetic structure, showing that the population has not been fragmented genetically, despite the low percentage of woodland in Ireland. We also reviewed the mitochondrial DNA diversity present in the Irish population and showed that there is only one contemporary and one extinct haplotype present; a reduced diversity relative to other Irish carnivores. The Irish haplotypes, both extant and extinct, are shared or are genetically similar to haplotypes commonly present in southern Europe today. We discuss the possibility of reinforcing the Irish population with animals from these sources to help supplement and maintain genetic diversity for future generations.
Surrogate post-coital testing for contraceptive efficacy against human sperm activity in the ovine vaginal model†
Authors: Zhu Yong , Saada Jamal , Bhawana Shrestha , Lai Sam , Villarreal Paula , Pyles Richard , Motamedi Massoud , Vargas Gracie , Moench Tom , Vincent Kathleen L
Published: December 2020

High unintended pregnancy rates are partially due to lack of effective nonhormonal contraceptives; development of safe, effective topical vaginal methods will address this need. Preclinical product safety and efficacy assessment requires in vivo testing in appropriate models. The sheep is a good model for the evaluation of vaginally delivered products due to its close similarities to humans. The study objective was to develop an ovine model for efficacy testing of female nonhormonal contraceptives that target human sperm. Fresh human semen was pooled from male volunteers. Nonpregnant female Merino sheep were treated with control or vaginal contraceptive product (IgG antibody with action against sperm or nonoxynol-9 [N9]). Pooled semen was added to the sheep vagina and mixed with product and vaginal secretions. Microscopic assessment of samples was performed immediately and progressive motility (PM) of sperm was compared between treatments. Cytokines CXCL8 and IL1B were assessed in vaginal fluid after instillation of human semen. No adverse reactions or elevations in proinflammatory cytokines occurred in response to human semen. N9 produced signs of acute cellular toxicity while there were no cellular changes after IgG treatment. N9 and IgG had dose-related effects with the highest dose achieving complete sperm immobilization (no sperm with PM). Surrogate post-coital testing of vaginally administered contraceptives that target human semen was developed in an ovine model established for vaginal product preclinical testing. This expanded model can aid the development of much needed nonhormonal topical vaginal contraceptives, providing opportunities for rapid iterative drug development prior to costly, time-intensive human testing.
A New Approach for Researching Victims: The ‘Strength-Growth-Resilience’ Framework
Authors: Green Simon , Calverley Adam , O’Leary Nicola
Published: December 2020

This paper proposes a new framework for researching victims that blends appreciative inquiry methods used by prison researchers with narrative interview methods used by desistance researchers to investigate victim ‘strength-growth-resilience’. Alongside established victimological concerns with the extent, distribution and treatment of crime victims, this framework offers an alternative lens that focuses on victim agency, identity and transformation. Building on the emancipatory project of feminist victimology, narrative and cultural criminology and an emerging narrative victimology the framework aims to provide a new conceptual reference point for victimological research. The article’s objectives are to demonstrate that this framework delivers a theoretically, empirically and ethically robust approach for exploring the mechanisms by which victims become resilient, and can even flourish, in the aftermath of criminal harm.
SNAIL regulates gastric carcinogenesis through CCN3 and NEFL
Authors: Chen Ru , Masuo Kenji , Yogo Akitada , Yokoyama Shoko , Sugiyama Aiko , Seno Hiroshi , Yoshizawa Akihiko , Takaishi Shigeo
Published: December 2020

Among cancer cells, there are specific cell populations of whose activities are comparable to those of stem cells in normal tissues, and for whom the levels of cell dedifferentiation are reported to correlate with poor prognosis. Information concerning the mechanisms that modulate the stemness like traits of cancer cells is limited. Therefore, we examined five gastric cancer cell lines and isolated gastric oncospheres from three gastric cancer cell lines. The gastric cancer cells that expanded in the spheres expressed relatively elevated proportion of CD44, which is a marker of gastric cancer stem cells (CSCs), and displayed many properties of CSCs, for example: chemoresistance, tumorigenicity and epithelial–mesenchymal transition (EMT) acquisition. SNAIL, which is a key factor in EMT, was highly expressed in the gastric spheres. Microarray analysis in gastric cancer cell line HGC27 showed that CCN3 and NEFL displayed the greatest differential expression by knocking down of SNAIL; the former was upregulated and the latter downregulated, respectively. Downregulation of CCN3 and upregulation of NEFL gene expression impaired the SNAIL-dependent EMT activity: high tumorigenicity, and chemoresistance in gastric cancer cells. Thus, approach that disrupts SNAIL/CCN3/NEFL axis may be credible in inhibiting gastric cancer development.
Three-Year Reliability of MEG Visual and Somatosensory Responses
Authors: McCusker Marie C , Lew Brandon J , Wilson Tony W
Published: December 2020

A major goal of many translational neuroimaging studies is the identification of biomarkers of disease. However, a prerequisite for any such biomarker is robust reliability, which for magnetoencephalography (MEG) and many other imaging modalities has not been established. In this study, we examined the reliability of visual (Experiment 1) and somatosensory gating (Experiment 2) responses in 19 healthy adults who repeated these experiments for three visits spaced 18 months apart. Visual oscillatory and somatosensory oscillatory and evoked responses were imaged, and intraclass correlation coefficients (ICC) were computed to examine the long-term reliability of these responses. In Experiment 1, ICCs showed good reliability for visual theta and alpha responses in occipital cortices, but poor reliability for gamma responses. In Experiment 2, the time series of somatosensory gamma and evoked responses in the contralateral somatosensory cortex showed good reliability. Finally, analyses of spontaneous baseline activity indicated excellent reliability for occipital alpha, moderate reliability for occipital theta, and poor reliability for visual/somatosensory gamma activity. Overall, MEG responses to visual and somatosensory stimuli show a high degree of reliability across 3 years and therefore may be stable indicators of sensory processing long term and thereby of potential interest as biomarkers of disease.
PET Imaging Estimates of Regional Acetylcholine Concentration Variation in Living Human Brain
Authors: Smart Kelly , Naganawa Mika , Baldassarri Stephen R , Nabulsi Nabeel , Ropchan Jim , Najafzadeh Soheila , Gao Hong , Navarro Antonio , Barth Vanessa , Esterlis Irina , Cosgrove Kelly P , Huang Yiyun , Carson Richard E , Hillmer Ansel T
Published: December 2020

Acetylcholine (ACh) has distinct functional roles in striatum compared with cortex, and imbalance between these systems may contribute to neuropsychiatric disease. Preclinical studies indicate markedly higher ACh concentrations in the striatum. The goal of this work was to leverage positron emission tomography (PET) imaging estimates of drug occupancy at cholinergic receptors to explore ACh variation across the human brain, because these measures can be influenced by competition with endogenous neurotransmitter. PET scans were analyzed from healthy human volunteers (n = 4) and nonhuman primates (n = 2) scanned with the M1-selective radiotracer [11C]LSN3172176 in the presence of muscarinic antagonist scopolamine, and human volunteers (n = 10) scanned with the α4β2* nicotinic ligand (−)-[18F]flubatine during nicotine challenge. In all cases, occupancy estimates within striatal regions were consistently lower (M1/scopolamine human scans, 31 ± 3.4% occupancy in striatum, 43 ± 2.9% in extrastriatal regions, p = 0.0094; nonhuman primate scans, 42 ± 26% vs. 69 ± 28%, p < 0.0001; α4β2*/nicotine scans, 67 ± 15% vs. 74 ± 16%, p = 0.0065), indicating higher striatal ACh concentration. Subject-level measures of these concentration differences were estimated, and whole-brain images of regional ACh concentration gradients were generated. These results constitute the first in vivo estimates of regional variation in ACh concentration in the living brain and offer a novel experimental method to assess potential ACh imbalances in clinical populations.
Simple and Rapid LC–MS/MS Methods for Quantifying Catabolites of Antibody-Drug Conjugates with SMCC Linker
Authors: Li Li , Wang Chanrui , Wu Yijue , Dong Lihou , Chen Fang , Dong Kelly , Song Haifeng
Published: December 2020

The stability and exposure of toxin-related catabolites in system circulation contributes to the evaluation of the stability, targeted delivery and off-target toxicity for antibody–drug conjugates (ADC) at different stages during drug development. In this study, simple and rapid liquid chromatography–tandem mass spectrometry (LC–MS/MS) methods for determination catabolites of Mertansine (DM1), MCC-DM1 and Lys-MCC-DM1 in cynomolgus serum have been developed. The serum samples are processed by protein precipitation. The LC–MS/MS methods are applied on a Phenomenex C8 column (50 × 2.0 mm, 5 μm) with gradient elution with water–formic acid 0.1% (A) and acetonitrile-formic acid 0.1% (B) at a flow rate of 0.5 mL/min. The analytical run time is only 4.0 min and the calibration ranges of the standard curve are 0.500–200 ng/mL for DM1, 1.00–500 ng/mL for MCC-DM1 and 2.00–1000 ng/mL for Lys-MCC-DM1. Intra- and inter-day precision of low, middle and high quality controls was <15%, and accuracy was 99.2–110.9%. The methods were successfully applied to evaluate three catabolites of novel ADCs with N-succinimidyl-4-(N-maleimidomethyl)-cyclohexane-1-carboxylate linker in vitro and in vivo studies.
Validation of VIRSTA and Predicting Risk of Endocarditis Using a Clinical Tool (PREDICT) Scores to Determine the Priority of Echocardiography in Patients With Staphylococcus aureus Bacteremia
Authors: Peinado-Acevedo Juan Sebastián , Hurtado-Guerra Juan José , Hincapié Carolina , Mesa-Abad Juanita , Uribe-Delgado José Roberto , Giraldo-Ramírez Santiago , Lengerke-Diaz Paula A , Jaimes Fabián
Published: December 2020

Background

Infective endocarditis (IE) secondary to Staphylococcus aureus bacteremia (SAB) has high morbidity and mortality. The systematic use of echocardiography in SAB is controversial. We aimed to validate VIRSTA and Predicting Risk of Endocarditis Using a Clinical Tool (PREDICT) scores for predicting the risk of IE in Colombian patients with SAB and, consequently, to determine the need for echocardiography.

Methods

Cohort of patients hospitalized with SAB in 2 high complexity institutions in Medellin, Colombia, between 2012 and 2018. The diagnosis of IE was established based on the modified Duke criteria. The VIRSTA and PREDICT scores were calculated from the clinical records, and their operational performance was calculated.

Results

The final analysis included 922 patients, 62 (6.7%) of whom were diagnosed with IE. The frequency of IE in patients with a negative VIRSTA scale was 0.44% (2/454). The frequency of IE in patients with a negative PREDICT scale on day 5 was 4.8% (30/622). The sensitivity and negative predictive value (NPV) of the VIRSTA scale was 96.7% and 99.5%, respectively. For the PREDICT scale on day 5, the sensitivity and NPV were 51.6% and 95.1%, respectively. The discrimination, given by the area under the receiver operating characteristic curve, was 0.86 for VIRSTA and 0.64 for PREDICT.

Conclusions

In patients with negative VIRSTA, screening echocardiography may be unnecessary because of the low frequency of IE. In PREDICT-negative patients, despite the low frequency of IE, it is not safe to omit echocardiography.
Understanding Drivers of Coronavirus Disease 2019 (COVID-19) Racial Disparities: A Population-Level Analysis of COVID-19 Testing Among Black and White Populations
Authors: Mody Aaloke , Pfeifauf Kristin , Bradley Cory , Fox Branson , Hlatshwayo Matifadza G , Ross Will , Sanders-Thompson Vetta , Joynt Maddox Karen , Reidhead Mat , Schootman Mario , Powderly William G , Geng Elvin H
Published: December 2020

Background

Disparities in coronavirus disease 2019 (COVID-19) testing—the pandemic’s most critical but limited resource—may be an important but modifiable driver of COVID-19 inequities.

Methods

We analyzed data from the Missouri State Department of Health and Senior Services on all COVID-19 tests conducted in the St Louis and Kansas City regions. We adapted a well-established tool for measuring inequity—the Lorenz curve—to compare COVID-19 testing rates per diagnosed case among Black and White populations.

Results

Between 14/3/2020 and 15/9/2020, 606 725 and 328 204 COVID-19 tests were conducted in the St Louis and Kansas City regions, respectively. Over time, Black individuals consistently had approximately half the rate of testing per case than White individuals. In the early period (14/3/2020 to 15/6/2020), zip codes in the lowest quartile of testing rates accounted for only 12.1% and 8.8% of all tests in the St Louis and Kansas City regions, respectively, even though they accounted for 25% of all cases in each region. These zip codes had higher proportions of residents who were Black, without insurance, and with lower median incomes. These disparities were reduced but still persisted during later phases of the pandemic (16/6/2020 to 15/9/2020). Last, even within the same zip code, Black residents had lower rates of tests per case than White residents.

Conclusions

Black populations had consistently lower COVID-19 testing rates per diagnosed case than White populations in 2 Missouri regions. Public health strategies should proactively focus on addressing equity gaps in COVID-19 testing to improve equity of the overall response.
Stress in Parents of School-Age Children and Adolescents With Cochlear Implants
Authors: Wiseman Kathryn B , Warner-Czyz Andrea D , Nelson Jackie A
Published: December 2020

Parents of children with cochlear implants (CIs) face unique challenges in caring for their child, potentially fostering parental stress. Most studies of stress in parents of CI users do not examine stress specific to having a deaf and hard-of-hearing (DHH) child. This study compares general and condition-specific stress (via the Family Stress Scale) in 31 parents of CI users (8–16 years) to previously published samples of DHH children, and it examines child- and CI-related factors associated with parental stress. Parents of modern-day CI users reported significantly lower stress than parents of children using older-generation CI technology and similar levels of overall stress to parents of young children preimplantation. However, significant item-level differences emerged (e.g., communication, device management) pre- versus postimplant. Child temperament significantly predicted parental stress after controlling for other variables. Intervention strategies for children with CIs should engage a family systems approach to reduce parental stress and better support the child.
Food Additive Emulsifiers and Their Impact on Gut Microbiome, Permeability, and Inflammation: Mechanistic Insights in Inflammatory Bowel Disease
Authors: Bancil Aaron S , Sandall Alicia M , Rossi Megan , Chassaing Benoit , Lindsay James O , Whelan Kevin
Published: December 2020

The global burden of inflammatory bowel disease [IBD] has increased over the 21st century. Despite multiple studies investigating the pathogenesis of IBD, the causative mechanisms pertaining to its increased prevalence remain unclear. There is growing evidence that aspects of a ‘Western diet’ increase the risk of developing IBD. More recently, evidence implicating dietary emulsifiers has accumulated, with ecological studies showing a positive correlation between inflammatory bowel disease and emulsifier consumption. Further to these, cell and animal studies have demonstrated plausible mechanisms by which dietary emulsifiers may contribute to IBD pathogenesis through mechanisms including: promotion of pro-inflammatory intestinal microbiota; disruption of mucus architecture; increased intestinal permeability; activation of inflammatory pathways; and disruption of the cell cycle. This review critically analyses the current evidence for these mechanisms that may be of pathological relevance to IBD, evaluates recent dietary trials, acknowledges the challenges of dietary intervention studies, and gives an overview of ongoing and future clinical trials in this important area.
Probe-based Confocal Laser Endomicroscopy for In Vivo Assessment of Histological Healing in Ulcerative Colitis: Development and Validation of the ENHANCE Index
Authors: Rahmi Gabriel , Coron Emmanuel , Perrod Guillaume , Levy Michael , Moreau Jacques , Moussata Driffa , Perez-Cuadrado-Robles Enrique , Chupin Antoine , Quénéhervé Lucille , Bourreille Arnaud , Marchal Aude , Cellier Christophe , Peyrin-Biroulet Laurent
Published: December 2020

Background and Aims

Histological healing may represent the ultimate therapeutic goal in ulcerative colitis [UC], but it requires biopsies. Our aim was to develop a non-invasive index able to assess histological disease activity in ulcerative colitis, using probe-based confocal laser endomicroscopy [pCLE].

Methods

One hundred patients with quiescent UC were prospectively included in five French centres. After fluorescein intravenous injection, during colonoscopy, the colorectal mucosa was analysed by white light imaging and pCLE, and then biopsied in different locations. Five endoscopists performed central reading of pCLE images blinded to clinical, endoscopic, and histological data. One expert pathologist performed a central histological reading [Nancy index: gold standard]. Univariate and multivariate analyses were performed to identify the endomicroscopic items associated with the presence of histologically active disease.

Results

Over 1000 pCLE videos sequences performed in 100 UC patients in endoscopic remission [Mayo 0 and 1] were evaluated. We observed that vessel diameter >20 µm, dilated crypt lumen, fluorescein leakage, and irregular crypt architecture were statistically associated with histologically proven inflammation according to the Nancy index. Hence, we built a pCLE index of mucosal inflammation with overall accuracy of 79.6% and overall sensitivity and specificity of, respectively, 57.8% and 82.8%. Negative predictive value, especially when a pCLE index ≤1 was observed, was high [93.1%].

Conclusions

Using a robust methodology, large vessel diameter, dilated crypt lumen, fluorescein leakage,and irregular crypt architecture are reliable endomicroscopic items defining the ENHANCE index for real-time assessment of histological disease activity in UC.
Luminal Narrowing Alone Allows an Accurate Diagnosis of Crohn’s Disease Small Bowel Strictures at Cross-Sectional Imaging
Authors: Stocker Daniel , King Michael J , El Homsi Maria , Carbonell Guillermo , Bane Octavia , Cuevas Jordan , Liu Qingqing , Cho Judy , Doucette John T , Greenstein Alexander J , Colombel Jean-Frederic , Harpaz Noam , Taouli Bachir
Published: December 2020

Background and Aims

Current consensus recommendations define small bowel strictures [SBS] in Crohn’s disease [CD] on imaging as luminal narrowing with unequivocal upstream bowel dilation. The aim of this study was to [1] evaluate the performance of cross-sectional imaging for SBS diagnosis in CD using luminal narrowing with upstream SB dilation and luminal narrowing with or without upstream dilation, and [2] compare the diagnostic performance of computed tomography [CT] and magnetic resonance enterography [MRE] for SBS diagnosis.

Methods

In total, 111 CD patients [81 with pathologically confirmed SBS, 30 controls] who underwent CT and/or MRE were assessed. Two radiologists [R1, R2] blinded to pathology findings independently assessed the presence of luminal narrowing and upstream SB dilation. Statistical analysis was performed for [1] luminal narrowing with or without SB upstream dilation [‘possible SBS’], and [2] luminal narrowing with upstream SB dilation ≥3 cm [‘definite SBS’].

Results

Sensitivity for detecting SBS was significantly higher using ‘possible SBS’ [R1, 82.1%; R2, 77.9%] compared to ‘definite SBS’ [R1, 62.1%; R2, 65.3%; p < 0.0001] with equivalent specificity [R1, 96.7%; R2, 93.3%; p > 0.9]. Using the criterion ‘possible SBS’, sensitivity/specificity were equivalent between CT [R1, 87.3%/93.3%; R2, 83.6%/86.7%] and MRE [R1, 75.0%/100%; R2: 70.0%/100%]. Using the criterion ‘definite SBS’, CT showed significantly higher sensitivity [78.2%] compared to MRE [40.0%] for R1 but not R2 with similar specificities [CT, 86.7–93.3%; MRE, 100%].

Conclusion

SBS can be diagnosed using luminal narrowing alone without the need for upstream dilation. CT and MRE show similar diagnostic performance for SBS diagnosis using luminal narrowing with or without upstream dilation.
Mortality Dynamics and Life Tables ofMegachile rotundata(Hymenoptera: Megachilidae), a Pollinator Managed for Alfalfa Seed Production
Authors: Donahoo Claire K , O’Neill Kevin M , Delphia Casey M , Peterson Robert K D
Published: December 2020

The alfalfa leafcutting bee, Megachile rotundata (F.), contributes to the pollination of more than two-thirds of alfalfa used in seed production in North America. However, losses in managed populations of more than 50% are common in the United States. Thus, understanding the causes of mortality of M. rotundata is critical to find ways to maintain and increase bee populations. Over 2 yr, we identified and quantified six mortality classes of M. rotundata, as well as estimated mortality risk using the demographic life-table model, M-DEC. Research was conducted on an alfalfa field in Toston, Montana and offspring mortality was assessed in the fall of each year. Nest shelters were manipulated for a main temperature treatment (low vs high), and nest boxes inside the shelters were manipulated for a parasitism sub-treatment (parasitism-resistant vs parasitism-enabled). Total mortality was approximately 15% for both years, but the proportion for each mortality class differed substantially. Mortality increased with increasing internal nest-tunnel temperature, and nest boxes with parasitism-enabled entry had nearly double the mortality than those with parasitism-resistant entry. Based on demographic multiple decrement life table analyses, mortality from each class was highly irreplaceable. Identifying and quantifying irreplaceable mortality classes and strategies to mitigate those causes may help producers decrease total population loss of M. rotundata before the adult stage.
Isolated right ventricular myocardial infarction: a case report
Authors: Olusan Adeogo Akinwale , Brennan Paul Francis , Johnston Paul Weir
Published: December 2020

Background

Isolated right ventricular myocardial infarction (RVMI) due to a recessive right coronary artery (RCA) occlusion is a rare presentation. It is typically caused by right ventricle (RV) branch occlusion complicating percutaneous coronary intervention. We report a case of an isolated RVMI due to flush RCA occlusion presenting via our primary percutaneous coronary intervention ST-elevation myocardial infarction pathway.

Case summary

A 61-year-old female smoker with a history of hypercholesterolaemia presented via the primary percutaneous coronary intervention pathway with sudden onset of shortness of breath, dizziness, and chest pain while walking. Transradial coronary angiography revealed a normal left main coronary artery, large left anterior descending artery that wrapped around the apex and dominant left circumflex artery with the non-obstructive disease. The RCA was not selectively entered despite multiple attempts. The left ventriculogram showed normal left ventricle (LV) systolic function. She was in cardiogenic shock with a persistent ectopic atrial rhythm with retrograde p-waves and stabilized with intravenous dobutamine thus avoiding the need for a transcutaneous venous pacing system. A computed tomography pulmonary angiogram demonstrated no evidence of pulmonary embolism while an urgent cardiac gated computed tomography revealed a recessive RCA with ostial occlusive lesion. A cardiac magnetic resonance imaging confirmed RV free wall infarction. She was managed conservatively and discharged to her local district general hospital after 5th day of hospitalization at the tertiary centre.

Discussion

This case describes a relatively rare myocardial infarction presentation that can present with many disease mimics which can require as in this case, a multi-modality imaging approach to establish the diagnosis.
Addressing LGBTQ erasure through literature in the ELT classroom
Authors: Gray John
Published: December 2020

This article argues the case for the use of well-chosen literary texts as a means of addressing ongoing LGBTQ (lesbian, gay, bisexual, transgender, and queer or questioning) erasure in the ELT classroom. In this way LGBTQ students are offered much-needed recognition and those students who are not LGBTQ are given the opportunity to come to an understanding of those who are. Given the very different circumstances and constraints in which teachers work globally a distinction is made between explicitly queer texts and implicitly queer texts as suitable for different settings. Suggested titles and practical recommendations are included to enable teachers to plan lessons using literary texts in emotionally engaging ways.
Postpartum depression and mother–offspring conflict over maternal investment
Authors: Gunst Annika , Sundén My , Korja Riikka , Boddy Amy M , Kotler Jennifer , Paavonen E Juulia , Uusitupa Henna-Maria , Karlsson Linnea , Karlsson Hasse , Antfolk Jan
Published: December 2020

Background and objectives

As the mother–offspring relationship is central to human reproduction, postpartum depression symptoms are difficult to explain in evolutionary terms. We proposed that postpartum depression might arise as a result of evolutionary mother–offspring conflict over maternal investment, and investigated the association between postpartum depression symptoms, infant night waking, maternal sleep disturbance and breastfeeding frequency.

Methodology

We conducted a cross-sectional analysis using survey responses at 6 months postpartum from 1598 Finnish mothers. We hypothesized that infant night waking at 6 months postpartum would be associated with postpartum depression symptoms, and that this association would be mediated by maternal sleep disturbance and a higher breastfeeding frequency.

Results

Infant night waking was moderately associated with postpartum depression symptoms, and this association was mediated by maternal sleep disturbance (R2=0.09). Contrary to our prediction, we found that increased breastfeeding was associated with less postpartum depression symptoms.

Conclusions and implications

We conclude that postpartum depression symptoms might partly be the result of increased maternal fatigue stemming from high offspring demands on maternal investment, but that this is not due to the metabolic strain from increased breastfeeding. Studying postpartum depression from the mother–offspring conflict perspective can potentially improve our understanding of the involved behavioral processes of both mother and offspring, and allow interventions designed to benefit the well-being of both parties.

Lay Summary: We proposed that postpartum depression is due to an evolutionary conflict between mother and infant, where the infant tires the mother to delay the arrival of a sibling. We found a link between infant night waking and postpartum depression, mediated by the mother’s sleep, but not by breastfeeding frequency.
Brugada syndrome and reduced right ventricular outflow tract conduction reserve: a final common pathway?
Authors: Behr Elijah R , Ben-Haim Yael , Ackerman Michael J , Krahn Andrew D , Wilde Arthur A M
Published: December 2020

Brugada syndrome (BrS) was first described as a primary electrical disorder predisposing to the risk of sudden cardiac death and characterized by right precordial lead ST elevation. Early description of right ventricular structural abnormalities and of right ventricular outflow tract (RVOT) conduction delay in BrS patients set the stage for the current controversy over the pathophysiology underlying the syndrome: channelopathy or cardiomyopathy; repolarization or depolarization. This review examines the current understanding of the BrS substrate, its genetic and non-genetic basis, theories of pathophysiology, and the clinical implications thereof. We propose that the final common pathway for BrS could be viewed as a disease of ‘reduced RVOT conduction reserve’.
The pico-sized Mamiellophyceae and a novelBathycoccusclade from the summer plankton of Russian Arctic Seas and adjacent waters
Authors: Belevich Tatiana A , Milyutina Irina A , Abyzova Galina A , Troitsky Aleksey V
Published: December 2020

Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To gain more knowledge about Mamiellophyceae distribution and diversity special studies were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July–September 2017 in the Barents, Kara and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A—uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with Micromonas polaris dominating north of 72°N. The presence of Ostreococcus tauri, Ostreococcus lucimarinus and Ostreococcus mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.
Polygenic Selection within a Single Generation Leads to Subtle Divergence among Ecological Niches
Authors: Ehrlich Moritz A , Wagner Dominique N , Oleksiak Marjorie F , Crawford Douglas L
Published: December 2020

Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus that inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time points within a single generation, we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the “number” of moderate changes exceeds the neutral expectation by 10–100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches.
Chromosome-level draft genome of a diploid plum (Prunus salicina)
Authors: Liu Chaoyang , Feng Chao , Peng Weizhuo , Hao Jingjing , Wang Juntao , Pan Jianjun , He Yehua
Published: December 2020

Background

Plums are one of the most economically important Rosaceae fruit crops and comprise dozens of species distributed across the world. Until now, only limited genomic information has been available for the genetic studies and breeding programs of plums. Prunus salicina, an important diploid plum species, plays a predominant role in modern commercial plum production. Here we selected P. salicina for whole-genome sequencing and present a chromosome-level genome assembly through the combination of Pacific Biosciences sequencing, Illumina sequencing, and Hi-C technology.

Findings

The assembly had a total size of 284.2 Mb, with contig N50 of 1.78 Mb and scaffold N50 of 32.32 Mb. A total of 96.56% of the assembled sequences were anchored onto 8 pseudochromosomes, and 24,448 protein-coding genes were identified. Phylogenetic analysis showed that P. salicina had a close relationship with Prunus mume and Prunus armeniaca, with P. salicina diverging from their common ancestor ∼9.05 million years ago. During P. salicina evolution 146 gene families were expanded, and some cell wall–related GO terms were significantly enriched. It was noteworthy that members of the DUF579 family, a new class involved in xylan biosynthesis, were significantly expanded in P. salicina, which provided new insight into the xylan metabolism in plums.

Conclusions

We constructed the first high-quality chromosome-level plum genome using Pacific Biosciences, Illumina, and Hi-C technologies. This work provides a valuable resource for facilitating plum breeding programs and studying the genetic diversity mechanisms of plums and Prunus species.
Local coupling and conversion of surface waves due to Earth’s rotation. Part 1: theory
Authors: Snieder Roel , Sens-Schönfelder Christoph
Published: December 2020

Earth’s rotation affects wave propagation to first order in the rotation through the Coriolis force. The imprint of rotation on wave motion has been accounted for in normal mode theory. By extending the theory to propagating surface waves we account for the imprint of rotation as a function of propagation distance. We describe the change in phase velocity and polarization, and the mode conversion of surface waves by Earth’s rotation by extending the formalism of Kennett for surface wave mode conversion due to lateral heterogeneity to include the Coriolis force. The wavenumber of Rayleigh waves is changed by Earth’s rotation and Rayleigh waves acquire a transverse component. The wavenumber of Love waves in not affected by Earth’s rotation, but Love waves acquire a small additional Rayleigh wave polarization. In contrast to different Rayleigh wave modes, different Love wave modes are not coupled by Earth’s rotation. We show that the backscattering of surface waves by Earth’s rotation is weak. The coupling between Rayleigh waves and Love waves is strong when the phase velocities of these modes are close. In that regime of resonant coupling, Earth’s rotation causes the difference between the Rayleigh wave and Love wave phase velocities that are coupled to increase through the process of level-repulsion.
An active source seismo-acoustic experiment using tethered balloons to validate instrument concepts and modelling tools for atmospheric seismology
Authors: Garcia R F , Martire L , Chaigneau Y , Cadu A , Mimoun D , Bassas Portus M , Sournac A , Sylvander M , Pauchet H , Benahmed S , Martin R
Published: December 2020

The measurements of acoustic waves created by a quake are of great interest for planets with hot and dense atmospheres, like Venus, because surface deployments of seismometers will last only a few hours, whereas freeflying balloons could fly many days. Infrasound sensors can also be used to constrain subsurface properties during active seismic experiments. This study presents a controlled source seismo-acoustic experiment using infrasonic sensors and accelerometers mounted on a tethered helium balloon. Both the acoustic waves generated below the balloon by seismic surface waves, and the ones generated by strong ground motions above the seismic source are clearly observed and separated on the records of the various instruments. This data set allows various validations and investigations. First, it validates the ground to air coupling theory and our numerical modelling tools. Then, it allows us to demonstrate that antenna processing of infrasound sensors deployed below the balloon can estimate the arrival incidence angle of the acoustic waves within 10°. Finally, a polarization analysis of the accelerometers taped on the balloon envelope is presented. It demonstrates that accelerometer records are strongly dependent on their location on the balloon due to its deformations and rotations. However, the different acoustic signals can be distinguished through their polarization, and a best sensor location is estimated at the bottom of the balloon envelope. These results are a first step towards detecting and locating seismic activity using airborne acoustic sensors on Venus and elsewhere. However, some observations of earthquake signals in a more realistic geometry are still missing.
Clinical and Mechanistic Characteristics of Current JAK Inhibitors in IBD
Authors: Pippis Elleni J , Yacyshyn Bruce R
Published: December 2020

Crohn’s disease (CD) and ulcerative colitis (UC) are chronic, immune-mediated diseases of the gastrointestinal (GI) tract. Their etiology is complex and involves immune (eg, cytokines) and nonimmune (eg, environment) mediated contributions, causing inflammatory damage to the GI tract. Though cytokines contribute a major role in the inflammatory process of both CD and UC, there are some key differences in which cytokines are involved in the pathobiology of CD and UC. Over the past several years, new biologic-directed therapies have focused on controlling specific aspects of inflammation associated with both conditions. Although these treatments have benefited patients overall, approximately 30% of patients still do not respond to induction (initial) therapy, and up to 50% of patients lose response to treatment over a year. Many of these therapies are administered parenterally and have been associated with adverse events such as serious infections or malignancy. Therefore, there is a significant unmet medical need for these patients to minimize symptoms and promote GI healing. There are several therapeutic agents in the pipeline, including oral, small molecules, which hold much promise. One group of small molecules known as Janus kinase (JAK) inhibitors offers an additional option for treatment of chronic inflammatory conditions, based on currently available data. The article will focus on the potential benefits of JAK inhibitors as oral, small molecules, such as the potential role of selectivity, and potential risks.