bluuebunny/crossref_metadata_2025_split huggingface dataset:
A self-attention model for inferring cooperativity between regulatory features
Authors: Ullah Fahad , Ben-Hur Asa 
Published: April 2021

AbstractDeep learning has demonstrated its predictive power in modeling complex biological phenomena such as gene expression. The value of these models hinges not only on their accuracy, but also on the ability to extract biologically relevant information from the trained models. While there has been much recent work on developing feature attribution methods that discover the most important features for a given sequence, inferring cooperativity between regulatory elements, which is the hallmark of phenomena such as gene expression, remains an open problem. We present SATORI, a Self-ATtentiOn based model to detect Regulatory element Interactions. Our approach combines convolutional layers with a self-attention mechanism that helps us capture a global view of the landscape of interactions between regulatory elements in a sequence. A comprehensive evaluation demonstrates the ability of SATORI to identify numerous statistically significant TF-TF interactions, many of which have been previously reported. Our method is able to detect higher numbers of experimentally verified TF-TF interactions than existing methods, and has the advantage of not requiring a computationally expensive post-processing step. Finally, SATORI can be used for detection of any type of feature interaction in models that use a similar attention mechanism, and is not limited to the detection of TF-TF interactions.
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules
Authors: Mersmann Sophia F , Strömich Léonie , Song Florian J , Wu Nan , Vianello Francesca , Barahona Mauricio , Yaliraki Sophia N 
Published: April 2021

AbstractThe investigation of allosteric effects in biomolecular structures is of great current interest in diverse areas, from fundamental biological enquiry to drug discovery. Here we present ProteinLens, a user-friendly and interactive web application for the investigation of allosteric signalling based on atomistic graph-theoretical methods. Starting from the PDB file of a biomolecule (or a biomolecular complex) ProteinLens obtains an atomistic, energy-weighted graph description of the structure of the biomolecule, and subsequently provides a systematic analysis of allosteric signalling and communication across the structure using two computationally efficient methods: Markov Transients and bond-to-bond propensities. ProteinLens scores and ranks every bond and residue according to the speed and magnitude of the propagation of fluctuations emanating from any site of choice (e.g. the active site). The results are presented through statistical quantile scores visualised with interactive plots and adjustable 3D structure viewers, which can also be downloaded. ProteinLens thus allows the investigation of signalling in biomolecular structures of interest to aid the detection of allosteric sites and pathways. ProteinLens is implemented in Python/SQL and freely available to use at: www.proteinlens.io.
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data
Authors: Molendijk Jeffrey , Seldin Marcus M , Parker Benjamin L 
Published: April 2021

AbstractThe integration of genomics, transcriptomics, proteomics and phenotypic traits across genetically diverse populations is a powerful approach to discover novel biological regulators. The increasing volume of complex data require new and easy-to-use tools accessible to a variety of scientists for the discovery and visualization of functionally relevant associations. To meet this requirement, we developed CoffeeProt, an open-source tool that analyses genetic variants associated to protein networks, other omics datatypes and phenotypic traits. CoffeeProt uses transcriptomics or proteomics data to perform correlation network analyses and annotates results with protein-protein interactions, subcellular localisations and drug associations. It then integrates genetic variants associated with gene expression (eQTLs) or protein abundance (pQTLs) and includes predictions of the potential consequences of variants on gene function. Finally, genetic variants are co-mapped to molecular or phenotypic traits either provided by the user or retrieved directly from publicly available GWAS results. We demonstrate its utility with the analysis of mouse and human population data enabling the rapid identification of genetic variants associated with druggable proteins and clinical traits. We expect that CoffeeProt will serve the systems genetics and basic science research communities, leading to the discovery of novel biologically relevant associations. CoffeeProt is available at www.coffeeprot.com.
Discovery of 17 conserved structural RNAs in fungi
Authors: Gao William , Jones Thomas A , Rivas Elena 
Published: April 2021

AbstractMany non-coding RNAs with known functions are structurally conserved: their intramolecular secondary and tertiary interactions are maintained across evolutionary time. Consequently, the presence of conserved structure in multiple sequence alignments can be used to identify candidate functional non-coding RNAs. Here, we present a bioinformatics method that couples iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. We used this method to examine all unannotated regions of five well-studied fungal genomes (Saccharomyces cerevisiae, Candida albicans, Neurospora crassa, Aspergillus fumigatus, and Schizosaccharomyces pombe). We identified 17 novel structurally conserved non-coding RNA candidates, which include four H/ACA box small nucleolar RNAs, four intergenic RNAs and nine RNA structures located within the introns and untranslated regions (UTRs) of mRNAs. For the two structures in the 3′ UTRs of the metabolic genes GLY1 and MET13, we performed experiments that provide evidence against them being eukaryotic riboswitches.
Smoking and the Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection
Authors: Lee Sang Chul , Son Kang Ju , Kim Dong Wook , Han Chang Hoon , Choi Yoon Jung , Kim Seong Woo , Park Seon Cheol 
Published: April 2021

Abstract

Introduction
It is unclear whether smokers are more vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This study aimed to evaluate the association between smoking and the risk of SARS-CoV-2 infection.

Methods
A matched case–control study was conducted using a large nationwide database. The case group included patients with SARS-CoV-2 infection confirmed by the Korea Centers for Disease Control and Prevention, and the control group was randomly sampled from the general Korean population in the National Health Insurance Service database by matching sex, age, and region of residence. Conditional logistic regression models were used to investigate whether the risk of infection with SARS-CoV-2 was affected by smoking status.

Results
A total of 4167 patients with SARS-CoV-2 infection and 20 937 matched controls were enrolled. The proportion of ex-smokers and current smokers was 26.6% of the total participants. In multivariate analysis, smoking was not associated with an increased risk of SARS-CoV-2 infection (odds ratio [OR] = 0.56, confidence interval [CI] = 0.50–0.62). When ex-smokers and current smokers were analyzed separately, similar results were obtained (current smoker OR = 0.33, CI = 0.28–0.38; ex-smoker OR = 0.81, CI = 0.72–0.91).

Conclusions
This study showed that smoking may not be associated with an increased risk of SARS-CoV-2 infection. Smoking tends to lower the risk of SARS-CoV-2 infection; however, these findings should be interpreted with caution.

Implications
It is unclear whether smokers are more vulnerable to coronavirus disease 2019. In this large nationwide study in South Korea, smoking tended to lower the risk of infection with severe acute respiratory syndrome coronavirus 2. However, these findings should be interpreted with caution, and further confirmatory studies are required.
Nicotine Induces Maternal and Fetal Inflammatory Responses Which Predispose Intrauterine Infection Risk in a Rat Model
Authors: von Chamier Maria , Reyes Leticia , Hayward Linda F , Brown Mary B 
Published: April 2021

Abstract

Introduction
Both smoking and infection adversely impact pregnancy. Previously, our group identified in a rodent model that 6 mg/kg/d nicotine increased the risk of fetal infection at gestation day (GD) 18. Here, we investigate lower nicotine doses.

Methods
Pregnant Sprague-Dawley rats received nicotine infusion at 0, 1, or 3 mg/kg/d (no, low-, and mid-dose nicotine, respectively) from GD 6, with intravenous inoculation with Mycoplasma pulmonis (MP) at 107 CFU (N = 20) or sterile broth (sham) (N = 11) on GD 14. Uterus and fetuses were retrieved on GD 18 for MP culture and histopathologic evaluation of maternal and fetal inflammatory responses (MIR and FIR).

Results
At 1 mg/kg/d nicotine, MP colonization rates were decreased, from 100% (9 of 9) to 40% (2 of 5) of MP-inoculated dams (p = .03), and 59% (66 of 111) to 39% (24 of 62) of fetuses (p = .01), versus no nicotine. Low-dose nicotine resulted in increased MIR and FIR in the sham-inoculated group; in the MP-inoculated group, this resulted in reduced relative risk (RR) for placental colonization (RR, 95% CI with high MIR = 0.14, 0.02 to 0.65; FIR = 0.38, 0.12 to 0.93). In contrast, 3 mg/kg/d nicotine treatment did not alter colonization rates; furthermore, FIR was completely suppressed, even in the face of placental or amniotic fluid colonization.

Conclusion
The 1 mg/kg/d nicotine dose decreased risk of intrauterine infection, with increased MIR and FIR. The 3 mg/kg/d nicotine dose inhibited FIR, and increased risk for intrauterine infection. Nicotine alterations of the intrauterine environment were markedly dose-dependent.

Implications
Nicotine exposure alters intrauterine infection and inflammation in a dose-dependent manner, potentially impacting fetal development and programming. Previous work in a rodent model showed that high-dose nicotine (6 mg/kg/d) exposure exacerbated intrauterine infection during pregnancy. The current study found that low-dose nicotine (1 mg/kg/d) exposure reduced colonization of placenta and amniotic fluid; this decrease was associated with increased intrauterine inflammation. Exposure to mid-dose nicotine (3 mg/kg/d) suppressed fetal inflammation. Elucidation of underlying mechanisms of these phenomena will inform public health and clinical care decisions, particularly in the context of risk assessment of nicotine replacement therapy during pregnancy for smoking cessation.
Experience With Ventriculoperitoneal and Lumboperitoneal Shunting for the Treatment of Idiopathic Intracranial Hypertension: A Single Institution Series
Authors: Sweid Ahmad , Daou Badih J , Weinberg Joshua H , Starke Robert M , Sergott Robert C , Schaefer Joseph , Hauge Julie , Elizabeth Caroline , Chalouhi Nohra , Gooch Reid , Herial Nabeel , Zarzour Hekmat , Jabbour Pascal , Rosenwasser Robert H , Tjoumakaris Stavropoula 
Published: April 2021

Abstract

BACKGROUND
CSF shunting is among the most widely utilized interventions in patients with idiopathic intracranial hypertension (IIH). Ventriculoperitoneal shunting (VPS) and lumboperitoneal shunting (LPS) are 2 possible treatment modalities.

OBJECTIVE
To evaluate and compare complications, malfunction, infection, and revision rates associated with VPS compared to LPS.

METHODS
Electronic medical records were reviewed to identify baseline and treatment characteristics for patients diagnosed with IIH treated with VPS or LPS.

RESULTS
A total of 163 patients treated with either VPS (74.2%) or LPS (25.8%) were identified. The mean follow-up was 35 mo. Shunt revision was required in 40.9% of patients. There was a nonsignificant higher rate of revision with LPS (52.4%) than VPS (36.4%, P = .07). In multivariate analysis, increasing patient age was associated with higher odds of shunt revision (P = .04). LPS had higher odds of shunt revision, yet this association was not significant (P = .06). Shunt malfunction was the main indication for revision occurring in 32.7%, with a significantly higher rate with LPS than VPS (P = .03). In total, 15 patients had shunt infection (9.4% VPS vs 12.2% LPS P = .50). The only significant predictor of procedural infection was the increasing number of revisions (P = .02).

CONCLUSION
The incidence of shunt revision was 40.9%, with increasing patient age as the sole predictor of shunt revision. The incidence of shunt malfunction was significantly higher in patients undergoing LPS, while there was no significant difference in the incidence of shunt infection between the 2 modalities.
Combined Endovascular and Microsurgical Management of Unruptured, Partially Thrombosed, Giant, Internal Carotid Artery Aneurysm: 2-Dimensional Operative Video
Authors: Bortolotti Carlo , Bertolini Giacomo , Sorenson Thomas J , Acciarri Nicola , Cirillo Luigi , Lanzino Giuseppe , Sturiale Carmelo 
Published: April 2021

Abstract
Giant intracranial aneurysms still represent a serious threat because of high mortality and morbidity and an absence of a widely accepted treatment. Herein, we illustrate the case of a 54-yr-old woman with progressive neurological decline who was found to have an unruptured, giant, partially thrombosed aneurysm of the left supraclinoid portion of internal carotid artery (ICA) with brainstem compression. In this video, we demonstrate the successful stepwise treatment of this lesion with endovascular embolization of the patent portion of the aneurysm, followed by microsurgical debulking and clipping. At 3-yr follow-up, the patient experienced a neurological improvement and performed all normal activity. For patients in which single-modality therapy does not assure a safe treatment option, multimodal management with endovascular and open techniques should be considered as a therapeutic option for complex giant intracranial aneurysms.
Consent was given by the patient prior to the surgical procedure. Consent and approval for this operative video, in light of the retrospective nature and use of anonymized material, were waived.
Oil and gas development does not reduce duck pair abundance in the Prairie Pothole Region
Authors: Loesch Charles R , Kemink Kaylan M , Cressey-Smith Ryann , Gue C Tanner , Sieges Mason , Szymanski Mike L 
Published: April 2021

AbstractConservation partners are concerned that oil and gas development in the Prairie Pothole Region may reduce the abundance of breeding duck pairs using associated wetland habitat. We conducted wetland-based surveys for breeding pairs of 5 species of dabbling ducks in the Bakken oil field during 2015–2017 across a gradient of oil and gas development intensity to test the hypothesis that the abundance of breeding duck pairs on survey wetlands would decrease as the development of oil and gas resources increased. We included covariates traditionally used to predict breeding duck pairs (i.e. wetland size and class) and a spatiotemporal index of disturbance when developing zero-inflated Poisson models relating pair abundance to environmental predictors. Similar to past analyses, pair abundance was strongly associated with wetland size. Our results were mixed and suggested that the abundance of early and late nesting species was positively and negatively related, respectively, to an index of disturbance that was largely driven by oil and gas development. Regardless of the direction of the relationship, effect sizes were small and not considered biologically significant. Our findings indicate that in our study area, strategies to conserve wetland resources for breeding duck pairs should not deviate from previous prioritization metrics within the range of oil and gas development we observed. We believe that our findings may have implications to similar landscapes within the Bakken.
Greater Sage-Grouse survival varies with breeding season events in West Nile virus non-outbreak years
Authors: Parsons Lindsey A , Runia Travis J , Vincent Geoffrey P , Gregory Andrew J , Jenks Jonathan A 
Published: April 2021

Abstract
Greater Sage-Grouse (Centrocercus urophasianus) is a species of conservation concern and is highly susceptible to mortality from West Nile virus (WNV). Culex tarsalis, a mosquito species, is the suspected primary vector for transmitting WNV to sage-grouse. We captured, radio-tagged, and monitored female sage-grouse to estimate breeding season (April 15 to September 15) survival, 2016–2017. Deceased sage-grouse were tested for active WNV; live-captured and hunter-harvested sage-grouse were tested for WNV antibody titers. Additionally, we trapped mosquitoes with CO2-baited traps 4 nights per week (542 trap nights) to estimate WNV minimum infection rate (MIR). Eight sage-grouse mortalities occurred during the WNV seasons of 2016 and 2017, 5 had recoverable tissue, and 1 of 5 tested positive for WNV infection. Survival varied temporally with sage-grouse biological seasons, not WNV seasonality. Survival was 0.68 (95% CI: 0.56–0.78; n = 74) during the reproductive season (April 1 to September 15). Mammalian predators were the leading suspected cause of mortality (40%), followed by unknown cause (25%), avian predation (15%), unknown predation (15%), and WNV (5%). These results indicate WNV was not a significant driver of adult sage-grouse survival during this study. Three sage-grouse (1.9%; 95% CI: 0.5–5.9%) contained WNV antibodies. We captured 12,472 mosquitoes of which 3,933 (32%) were C. tarsalis. The estimated WNV MIR of C. tarsalis during 2016 and 2017 was 3.3 and 1.6, respectively. Our results suggest sage-grouse in South Dakota have limited exposure to WNV, and WNV was not a significant source of sage-grouse mortality in South Dakota during 2016 and 2017. Based on our finding that a majority of sage-grouse in South Dakota are susceptible to WNV infection, WNV could potentially have an impact on the population during an epizootic event; however, when WNV is at or near-endemic levels, it appears to have little impact on sage-grouse survival.
The Post Office Window, 1880–92
Authors: Blevins Cameron 
Published: April 2021

Abstract
Chapter 5 focuses on the role of post offices and postmasters in western towns during the 1880s. Small-town post offices exemplified the US Post’s localized agency model at work, offering a much different perspective on the history of the American state than a traditional bureaucratic framework. Post offices defined the spatial practices of local communities. Whoever housed the post office on their premises enjoyed a regular stream of potential customers into their place of business. This made postmaster appointments highly sought-after positions that provided the main source of political patronage for whichever party controlled the presidency. There was no clear division between public and private space in local post offices, as postmasters simultaneously ran stores, sold magazine subscriptions, and acted as agents for telegraph and express companies. Finally, the agency model meant that post offices operated with little administrative oversight and routinely frustrated attempts at centralized reform.
Brokering Sales
Authors: Korver-Glenn Elizabeth 
Published: April 2021

Abstract
This chapter examines how real estate brokerage routines pressured agents to use the racist market rubric in their work and how brokerages’ silence about unofficial yet potentially discriminatory routines served as a form of approval for agents adopting these routines. When agents interpreted established brokerage routines through the racist market rubric, they cultivated relationships with White individuals and excluded Asian, Black, and Latinx individuals. At times, brokerage routines—such as the automated use of the local real estate board’s market area map—required agents to advertise homes according to a racial–spatial hierarchy. In addition, brokerages remained silent when White agents pursued alternate routines outside the bounds of brokerage organizations, such as when they took on pocket listings—that is, homes not advertised on the Multiple Listing Service. Given the racial patterns of real estate networking in Houston, White home buyers had disproportionate access to pocket listings, yet White agents faced no verbal, professional, or legal sanctions for adopting this behavior.
Network agency and network dynamics
Authors: Elfring Tom , Klyver Kim , van Burg Elco 
Published: April 2021

Abstract
The literature often has assumed, explicitly or implicitly, that entrepreneurs use networks to develop opportunity, access resources, and gain legitimacy in order to perform and achieve success. Entrepreneurs’ networks have become a powerful explanation of success and performance in academia, in the business world, and in the popular press. However, research so far predominantly has relied on static pictures of entrepreneurs’ networks, which potentially provide incomplete and inadequate understanding of what actually occurs. Rather than relying on such static pictures of networks, research should rely on and build on a more social-interactive and dynamic understanding of networks. This chapter develops a social-interactive network dynamics framework that outlines various theories, perspectives, and empirical results related to network agency and network dynamics. Thus, this network dynamics framework becomes the core of the authors’ entrepreneurship-as-networking perspective. The chapter ends with discussions of potential avenues for future research.
Conclusion
Authors: Elfring Tom , Klyver Kim , van Burg Elco 
Published: April 2021

Abstract
Throughout this book, based on several literatures, the authors have developed the entrepreneurship-as-networking perspective. That is, networking among entrepreneurs—in their attempts to develop opportunity, mobilize resource, and obtain legitimacy—is the key and primary component of entrepreneurial action. Entrepreneurship always involves networking, and therefore networking is entrepreneurial action. This conceptual model answers two guiding questions. First, what kind of network helps entrepreneurs become successful? Second, how do networking activities of entrepreneurs affect their networks and entrepreneurial endeavors? Whereas the first question primarily focuses on structural issues and related networking mechanisms, the second question primarily relates to network agency of entrepreneurs.
The Paradoxes of Postwar Domesticity
Authors: Heinz Annelise 
Published: April 2021

Abstract
At the height of the postwar domestic revival, a subset of women who fully participated in the culture of domesticity nonetheless claimed a unique space for leisure with their peers in the form of a weekly evening mahjong game. Although the culture of mahjong could reinforce their domestic roles as much as undermine them, the weekly mahjong ritual explicitly came at the expense of both household labor and their family members’ comfort. Despite their claims on autonomous domestic leisure, mahjong-playing middle-class women became emblematic of the trappings of stereotypical postwar domesticity. As Jewish mahjong players established their strong cultural norms in the 1950s and 1960s, they became embedded in the evolving stereotype of the domineering Jewish mother. This association signaled the waning of both postwar domestic norms and the patterns of leisured domesticity that thrived within them, as economic changes and generational shifts transformed middle-class home life.