bluuebunny/crossref_metadata_2025_split huggingface dataset:
Astrometric orbits of spectral binary brown dwarfs – I. Massive T dwarf companions to 2M1059−21 and 2M0805+48
Authors: Sahlmann J , Burgasser A J , Bardalez Gagliuffi D C , Lazorenko P F , Ségransan D , Zapatero Osorio M R , Blake C H , Gelino C R , Martín E L , Bouy H 
Published: May 2020

ABSTRACT
Near-infrared spectroscopic surveys have uncovered a population of short-period, blended-light spectral binaries composed of low-mass stars and brown dwarfs. These systems are amenable to orbit determination and individual mass measurements via astrometric monitoring. Here, we present first results of a multiyear campaign to obtain high-precision absolute astrometry for spectral binaries using the Gemini-South and Gemini-North GMOS imagers. We measure the complete astrometric orbits for two systems: 2M0805+48 and 2M1059−21. Our astrometric orbit of 2M0805+48 is consistent with its 2-yr radial velocity orbit determined previously and we find a mass of $66^{+5}_{-14} M_\mathrm{Jup}$ for its T5.5 companion. For 2M1059−21, we find a 1.9-yr orbital period and a mass of $67^{+4}_{-5} M_\mathrm{Jup}$ for its T3.5 companion. We demonstrate that sub-milliarcsecond absolute astrometry can be obtained with both GMOS imagers and that this is an efficient avenue for confirming and characterizing ultracool binary systems.
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq
Authors: Ma Anjun , Wang Cankun , Chang Yuzhou , Brennan Faith H , McDermaid Adam , Liu Bingqiang , Zhang Chi , Popovich Phillip G , Ma Qin 
Published: May 2020

AbstractA group of genes controlled as a unit, usually by the same repressor or activator gene, is known as a regulon. The ability to identify active regulons within a specific cell type, i.e., cell-type-specific regulons (CTSR), provides an extraordinary opportunity to pinpoint crucial regulators and target genes responsible for complex diseases. However, the identification of CTSRs from single-cell RNA-Seq (scRNA-Seq) data is computationally challenging. We introduce IRIS3, the first-of-its-kind web server for CTSR inference from scRNA-Seq data for human and mouse. IRIS3 is an easy-to-use server empowered by over 20 functionalities to support comprehensive interpretations and graphical visualizations of identified CTSRs. CTSR data can be used to reliably characterize and distinguish the corresponding cell type from others and can be combined with other computational or experimental analyses for biomedical studies. CTSRs can, therefore, aid in the discovery of major regulatory mechanisms and allow reliable constructions of global transcriptional regulation networks encoded in a specific cell type. The broader impact of IRIS3 includes, but is not limited to, investigation of complex diseases hierarchies and heterogeneity, causal gene regulatory network construction, and drug development. IRIS3 is freely accessible from https://bmbl.bmi.osumc.edu/iris3/ with no login requirement.
Novel insights into the disease transcriptome of human diabetic glomeruli and tubulointerstitium
Authors: Levin Anna , Reznichenko Anna , Witasp Anna , Liu Peidi , Greasley Peter J , Sorrentino Antonio , Blondal Thorarinn , Zambrano Sonia , Nordström Johan , Bruchfeld Annette , Barany Peter , Ebefors Kerstin , Erlandsson Fredrik , Patrakka Jaakko , Stenvinkel Peter , Nyström Jenny , Wernerson Annika 
Published: May 2020

Abstract

Background
Diabetic nephropathy (DN) is the most common cause of end-stage renal disease, affecting ∼30% of the rapidly growing diabetic population, and strongly associated with cardiovascular risk. Despite this, the molecular mechanisms of disease remain unknown.

Methods
RNA sequencing (RNAseq) was performed on paired, micro-dissected glomerular and tubulointerstitial tissue from patients diagnosed with DN [n = 19, 15 males, median (range) age: 61 (30–85) years, chronic kidney disease stages 1–4] and living kidney donors [n = 20, 12 males, median (range) age: 56 (30–70) years].

Results
Principal component analysis showed a clear separation between glomeruli and tubulointerstitium transcriptomes. Differential expression analysis identified 1550 and 4530 differentially expressed genes, respectively (adjusted P &lt; 0.01). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses highlighted activation of inflammation and extracellular matrix (ECM) organization pathways in glomeruli, and immune and apoptosis pathways in tubulointerstitium of DN patients. Specific gene modules were associated with renal function in weighted gene co-expression network analysis. Increased messengerRNA (mRNA) expression of renal damage markers lipocalin 2 (LCN) and hepatitis A virus cellular receptor1 (HAVCR1) in the tubulointerstitial fraction was observed alongside higher urinary concentrations of the corresponding proteins neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1) in DN patients.

Conclusions
Here we present the first RNAseq experiment performed on paired glomerular and tubulointerstitial samples from DN patients. We show that prominent disease-specific changes occur in both compartments, including relevant cellular processes such as reorganization of ECM and inflammation (glomeruli) as well as apoptosis (tubulointerstitium). The results emphasize the potential of utilizing high-throughput transcriptomics to decipher disease pathways and treatment targets in this high-risk patient population.
Multiple Equilibria in Open Economies with Collateral Constraints
Authors: Schmitt-Grohé Stephanie , Uribe Martín 
Published: May 2020

Abstract
This article establishes the existence of multiple equilibria in infinite-horizon open economy models in which the value of tradable and non-tradable endowments serves as collateral. In this environment, the economy displays self-fulfilling financial crises in which pessimistic views about the value of collateral induce agents to deleverage. Under plausible calibrations, there exist equilibria with underborrowing. This result stands in contrast to the overborrowing result stressed in the related literature. Underborrowing emerges in the present context because in economies that are prone to self-fulfilling financial crises, individual agents engage in excessive precautionary savings as a way to self-insure.
South Dakota’s “Trust Task Force”
Authors: Goetzinger Patrick G , Simmons Thomas E 
Published: May 2020

Abstract
The State of South Dakota is known internationally as a premier trust situs jurisdiction. Its top ranking is due to a number of factors. Among those factors is a committed band of gubernatorial appointees—both lawyers and non-lawyers—who consider, debate and draft proposed legislation for the South Dakota Legislature each year. This “Trust Task Force” was created by the Governor of the State more than twenty years ago. This article traces the origin and evolution of the South Dakota Trust Task Force, its achievements and its inner workings. It compares the legislative process to enact trust laws in other leading American jurisdictions while commenting on additional important factors which underpin a top ranking among competitor trust jurisdictions.
7Film Theory
Authors: Bettinson Gary 
Published: May 2020

AbstractSix exemplary works of film theory, published in 2018–19, receive consideration in this chapter: Johannes Riis and Aaron Taylor’s anthology Screening Characters: Theories of Character in Film, Television, and Interactive Media; Murray Pomerance’s Virtuoso: Film Performance and the Actor’s Magic; Jonathan Kirshner and Jon Lewis’s edited collection When the Movies Mattered: The New Hollywood Revisited; Jeff Menne’s Post-Fordist Cinema: Hollywood Auteurs and the Corporate Counterculture; Wieland Schwanebeck and Douglas McFarland’s edited volume Patricia Highsmith on Screen; and Clara Bradbury-Rance’s Lesbian Cinema after Queer Theory. The chapter is organized into three sections: 1. Character Engagement and Performance; 2. Revisiting the New Hollywood; 3. A Highsmith Hinge.
An integrative approach distinguishes three new species of Abyssochrysoidea (Mollusca: Caenogastropoda) associated with organic falls of the deep south-west Atlantic
Authors: Souza Bruno H M , Passos Flávio D , Shimabukuro Maurício , Sumida Paulo Y G 
Published: May 2020

AbstractTwo new species of Rubyspira and one of Cordesia (Gastropoda: Abyssochrysoidea) are described morphologically and genetically, based on specimens collected from whale bones and wood parcels artificially implanted in the deep south-west Atlantic Ocean, at c. 1500 and 3300 m depths. Rubyspira pescaprae sp. nov. and R. elongata sp. nov. occur preferentially on whale bones. Cordesia atlantica sp. nov. is dominant on wood parcels. Distribution of Cordesia was hitherto only associated with hydrocarbon seeps off West Africa. Stable isotopes and gut content analyses were carried out to check possible trophic pathways. Both Rubyspira species are bone eaters, while Cordesia atlantica seems to rely on a wider range of food sources, including juveniles of wood-specialized xylophagid bivalves. Morphological and genetic evidence suggest that Rubyspira and Cordesia are more closely related to Abyssochrysos than to any other Abyssochrysoidea snails. In the present study, Cordesia is considered part of the family Abyssochrysidae based on molecular and morphological evidence, such as the presence of a penis and pallial tentacles arrangement.
“Was It Worth It?”
Authors: Rost Lee , Chen Yiyi , Fain Robert S. , Hartvigson Pehr E. , Park Byung , Thomas Charles R. , Rana Shushan 
Published: May 2020

Objectives:
Radiation therapy is a core oncologic treatment, but literature detailing patient satisfaction post-treatment is sparse. The authors conducted a pilot study to determine whether a simple survey would be feasible to administer and could elucidate factors predictive of satisfaction with radiotherapy.

Materials and Methods:
Patients with cancer receiving radiotherapy in an academic radiation oncology department from 2014 to 2015 received a 4-item radiotherapy-focused version of the “Was It Worth It?” questionnaire (r-WIWI) on the last day of treatment and at the first follow-up. Univariate analysis and logistic regression modeling were performed on collected patient and treatment characteristics to explore predictors of satisfaction.

Results:
Two hundred patients completed an r-WIWI questionnaire at treatment completion and 60 at the time of the first follow-up. Seventy-one percent and 90% of patients found radiotherapy worthwhile on the last day of treatment and at first follow-up, respectively. Patients treated during the morning and for a longer duration as measured in elapsed days were more likely to report treatment being worthwhile. Age, sex, race, marital status, employment status, treatment intent or modalities, daily radiation treatment delays, distance traveled, insurance type, site of treatment, and cancer stage were not predictive of patient satisfaction.

Conclusions:
The r-WIWI survey was feasible to administer and most patients reported treatment being worthwhile on the last day of treatment and at first follow-up. Morning treatment times and longer treatment duration as measured in elapsed days were predictive of higher satisfaction in this pilot study. A broader study of factors associated with patient satisfaction with radiotherapy using the r-WIWI is indicated.
Glaucomatous Progression After Lens Extraction in Primary Angle Closure Disease Spectrum
Authors: Song Min Kyung , Sung Kyung Rim , Shin Joong Won , Jo Youn Hye , Won Hun Jae 
Published: May 2020

Precis:
Substantial proportion of primary angle closure glaucoma (PACG) eyes showed glaucomatous worsening after successful lens extraction and intraocular pressure (IOP) control, which may suggest that an earlier intervention may be required to prevent PACG.

Purpose:
The purpose of this study was to investigate the longitudinal clinical course of the primary angle closure (PAC) disease spectrum, including PAC, primary angle closure suspect (PACS), and PACG patients, who underwent lens extraction.

Methods:
This retrospective observational study included 77 eyes from patients with PACS, PAC, and PACG who underwent lens extraction and were followed up for >2 years after surgery. The mean, peak, and fluctuation of IOP were analyzed before and after lens extraction among groups. Visual field (VF) mean deviation was compared immediately after lens extraction and the final follow-up. Postoperative glaucoma progression determined by 3 criteria (optic disc/retinal nerve fiber layer photographs, optical coherent tomography, and VF) was compared among the 3 groups.

Results:
Seventeen PACS, 24 PAC, and 36 PACG eyes were included. The mean and peak IOP, and IOP fluctuation IOP were significantly reduced postoperatively in all groups. Postoperative VF mean deviation was significantly aggravated only in the PACG group (from −7.26 to −8.82 dB, P<0.001). The prevalence of postoperative glaucoma progression by at least 1 criterion was significantly higher in PACG, and none of the eyes with PACS and PAC showed VF conversion (PACS, PAC, PACG; 11.8%, 12.5% vs. 61.1% in disc/retinal nerve fiber layer, 11.8%, 8.3% vs. 63.9% in optical coherent tomography, 0%, 0% vs. 33.3% in VF, all P<0.001).

Conclusions:
In the PAC spectrum, lens extraction achieved significant IOP reduction. However, despite IOP control, a substantial proportion of PACG eyes showed glaucomatous progression. This result may suggest that lens extraction should be performed early to prevent PACG.
Cohort Profile: A national prospective cohort study of SARS-CoV-2 pandemic outcomes in the U.S. - The CHASING COVID Cohort Study
Authors: Robertson McKaylee M. , Kulkarni Sarah Gorrell , Berry Amanda , Mirzayi Chloe , Rane Madhura , Chang Mindy , Kochhar Shivani , You William , Maroko Andrew , Zimba Rebecca , Westmoreland Drew , Grov Christian , Parcesepe Angela , Waldron Levi , Nash Denis ,   for the CHASING COVID Cohort Study
Published: May 2020

ABSTRACTPurposeThe CHASING COVID Cohort study is a U.S.-based prospective cohort study launched during the upswing of the U.S. COVID-19 epidemic. The objectives are to: 1) estimate and evaluate determinants of the cumulative incidence of SARS-CoV-2 infection, disease, and deaths; 2) assess the impact of the pandemic on psychosocial and economic outcomes; and 3) assess the uptake of pandemic mitigation strategies.ParticipantsWe began enrolling participants March 28, 2020 using internet-based strategies. Adults ≥18 years residing anywhere in the U.S. or U.S. territories were eligible. 6,753 people are enrolled in the cohort, including participants from all 50 U.S. states, the District of Columbia, Puerto Rico, and Guam. Participants are contacted regularly to complete study assessments, including interviews and specimen collection.Findings to dateOf 4,247 participants who provided a specimen for baseline serologic testing, 135 were seropositive by screening antibody testing (3.2%, 95% CI 2.7%-3.5%) and 90 were seropositive by confirmatory antibody testing (2.1%, 95% CI 1.7%-2.6%). Cohort data have been used to assess the role of household crowding and the presence of children in the household as potential risk factors for severe COVID-19 early in the U.S. pandemic; to describe the prevalence of anxiety symptoms and its relationship to COVID-19 outcomes and other potential stressors; and to identify preferences for SARS-CoV-2 diagnostic testing when community transmission is on the rise via a discrete choice experiment.Future plansThe CHASING COVID Cohort Study has outlined a research agenda that involves ongoing monitoring of the cumulative incidence and determinants of SARS-CoV-2 outcomes, mental health outcomes and economic outcomes. Additional priorities include COVID-19 vaccine hesitancy, uptake and effectiveness; incidence, prevalence and correlates of long-haul COVID-19; and the extent and duration of the protective effect of SARS-CoV-2 antibodies.
COVID-19 Pandemic Response Simulation: Impact of Non-pharmaceutical Interventions on Ending Lockdowns
Authors: Lee Serin , Zabinsky Zelda B. , Kofsky Stephen , Liu Shan 
Published: May 2020

AbstractAs many federal and state governments are starting to ease restrictions on non-pharmaceutical interventions (NPIs) used to flatten the curve, we developed an agent-based simulation to model the incidence of COVID-19 in King County, WA under several scenarios. While NPIs were effective in flattening the curve, any relaxation of social distancing strategies yielded a second wave. Even if daily confirmed cases dropped to one digit, daily incidence can peak again to 874 cases without import cases. Therefore, policy makers should be very cautious in reopening society.
Development and validation of direct RT-LAMP for SARS-CoV-2
Authors: Mohon Abu Naser , Hundt Jana , van Marle Guido , Pabbaraju Kanti , Berenger Byron , Griener Thomas , Lisboa Luiz , Church Deirdre , Czub Markus , Greninger Alexander , Jerome Keith , Doolan Cody , Pillai Dylan R. 
Published: May 2020

AbstractWe have developed a reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2. The LAMP assay achieves comparable limit of detection as commonly used RT-PCR protocols based on artificial targets, recombinant Sindbis virus, and clinical samples. Clinical validation of single-target (S gene) LAMP (N=120) showed a positive percent agreement (PPA) of 41/42 (97.62%) and negative percent agreement (NPA) of 77/78 (98.72%) compared to reference RT-PCR. Dual-target RT-LAMP (S and RdRP gene) achieved a PPA of 44/48 (91.97%) and NPA 72/72 (100%) when including discrepant samples. The assay can be performed without a formal extraction procedure, with lyophilized reagents which do need cold chain, and is amenable to point-of-care application with visual detection.
Dropout in Neural Networks Simulates the Paradoxical Effects of Deep Brain Stimulation on Memory
Authors: Tan Shawn Zheng Kai , Du Richard , Perucho Jose Angelo Udal , Chopra Shauhrat S. , Vardhanabhuti Varut , Lim Lee Wei 
Published: May 2020

AbstractNeuromodulation techniques such as Deep Brain Stimulation (DBS) are a promising treatment for memory-related disorders including anxiety, addiction, and dementia. However, the outcome of these treatments appears to be paradoxical, as the use of these techniques can both disrupt and enhance memory even when applied to the same brain target. In this paper, we hypothesize that disruption and enhancement of memory through neuromodulation can be explained by the dropout of engram nodes. We used a convolutional neural network to classify handwritten digits and letters, applying dropout at different stages to simulate DBS effects on engrams. We showed that dropout applied during training improves the accuracy of prediction, whereas dropout applied during testing dramatically decreases accuracy of prediction, which mimics enhancement and disruption of memory, respectively. We further showed that transfer learning of neural networks with dropout had increased accuracy and rate of learning. Dropout during training provided a more robust “skeleton” network where transfer learning can be applied, mimicking the effects of chronic DBS on memory. Overall, we show that dropout of nodes can be a potential mechanism by which neuromodulation techniques such as DBS can both disrupt and enhance memory and provides a unique perspective on this paradox.
The electrophysiological underpinnings of variation in verbal working memory capacity
Authors: Pavlov Yuri G. , Kotchoubey Boris 
Published: May 2020

AbstractWorking memory (WM) consists of short-term storage and executive components. We studied cortical oscillatory correlates of these two components in a large sample of 156 participants to assess separately the contribution of them to individual differences in WM. The participants were presented with WM tasks of above-average complexity. Some of the tasks required only storage in WM, others required storage and mental manipulations. Our data indicate a close relationship between frontal midline theta, central beta activity and the executive components of WM. The oscillatory counterparts of the executive components were associated with individual differences in verbal WM performance. In contrast, alpha activity was not related to the individual differences. The results demonstrate that executive components of WM, rather than short-term storage capacity, play the decisive role in individual WM capacity limits.
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Authors: Lee Alexandra J. , Park YoSon , Doing Georgia , Hogan Deborah A. , Greene Casey S. 
Published: May 2020

AbstractMotivationIn the last two decades, scientists working in different labs have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, sometimes referred to as batch effects, may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to interpret and extract true underlying biological patterns. As more multi-experiment, integrative analysis methods are developed and available data collections increase in size, it is crucial to determine how technical variability affect our ability to detect desired patterns when many experiments are combinedObjectiveWe sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprised of data aggregated across multiple experiments.MethodWe developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability.ResultsWe found that the signal from a baseline compendium was obscured when the number of added sources of variability was small. Perhaps as expected, applying statistical correction methods rescued the underlying signal in these cases. As the number of sources of variability increased, surprisingly, we observed that detecting the original signal became increasingly easier even without correction. In fact, applying statistical correction methods reduced our power to detect the underlying signal.ConclusionWhen combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces one’s ability to extract underlying patterns.