bluuebunny/crossref_metadata_2025_split huggingface dataset:
Judges in the Lab: No Precedent Effects, No Common/Civil Law Differences
Authors: Spamann Holger , Klöhn Lars , Jamin Christophe , Khanna Vikramaditya , Liu John Zhuang , Mamidi Pavan , Morell Alexander , Reidel Ivan 
Published: October 2020

AbstractIn our lab, 299 real judges from seven major jurisdictions (Argentina, Brazil, China, France, Germany, India, and USA) spend up to fifty-five minutes to judge an international criminal appeals case and determine the appropriate prison sentence. The lab computer (i) logs their use of the documents (briefs, statement of facts, trial judgment, statute, precedent) and (ii) randomly assigns each judge (a) a horizontal precedent disfavoring, favoring, or strongly favoring defendant, (b) a sympathetic or an unsympathetic defendant, and (c) a short, medium, or long sentence anchor. Document use and written reasons differ between countries but not between common and civil law. Precedent effect is barely detectable and estimated to be less, and bounded to be not much greater than, that of legally irrelevant defendant attributes and sentence anchors.
3 per cent-accurate predictions for the clustering of dark matter, haloes, and subhaloes, over a wide range of cosmologies and scales
Authors: Contreras S , Angulo R E , Zennaro M , Aricò G , Pellejero-Ibañez M 
Published: October 2020

ABSTRACT
Predicting the spatial distribution of objects as a function of cosmology is an essential ingredient for the exploitation of future galaxy surveys. In this paper, we show that a specially designed suite of gravity-only simulations together with cosmology-rescaling algorithms can provide the clustering of dark matter, haloes, and subhaloes with high precision. Specifically, with only three N-body simulations, we obtain the power spectrum of dark matter at z = 0 and 1 to better than 3 per cent precision for essentially all currently viable values of eight cosmological parameters, including massive neutrinos and dynamical dark energy, and over the whole range of scales explored, 0.03 &lt; $k/{h}^{-1}\, {\rm Mpc}^{-1}$ &lt; 5. This precision holds at the same level for mass-selected haloes and for subhaloes selected according to their peak maximum circular velocity. As an initial application of these predictions, we successfully constrain Ωm, σ8, and the scatter in subhalo-abundance-matching employing the projected correlation function of mock SDSS galaxies.
Measuring the integrated Sachs–Wolfe effect from the low-density regions of the universe
Authors: Dong Fuyu , Yu Yu , Zhang Jun , Yang Xiaohu , Zhang Pengjie 
Published: October 2020

ABSTRACT
The integrated Sachs–Wolfe (ISW) effect is caused by the decay of cosmological gravitational potential and is therefore a unique probe of dark energy. However, its robust detection is still problematic. Various tensions between different data sets, different large-scale structure (LSS) tracers, and between data and the ΛCDM theory prediction exist. We propose a novel method of ISW measurement by cross-correlating cosmic microwave background (CMB) and the LSS traced by ‘low-density position’ (LDP). It isolates the ISW effect generated by low-density regions of the universe but insensitive to selection effects associated with voids. We apply it to the DR8 galaxy catalogue of the DESI Legacy imaging surveys and obtain the LDPs at z ≤ 0.6 over ∼20 000 deg2 sky coverage. We then cross-correlate with the Planck temperature map and detect the ISW effect at 3.2σ. We further compare the measurement with numerical simulations of the concordance ΛCDM cosmology and find the ISW amplitude parameter AISW = 1.14 ± 0.38 when we adopt an LDP definition radius $R_\mathrm{ s}=3^{^{\prime }}$, fully consistent with the prediction of the standard ΛCDM cosmology (AISW = 1). This agreement with ΛCDM cosmology holds for all the galaxy samples and Rs that we have investigated. Furthermore, the S/N is comparable to that of galaxy ISW measurement. These results demonstrate the LDP method as a competitive alternative to existing ISW measurement methods and provide independent checks to existing tensions.
Detection of millihertz quasi-periodic oscillations in the X-Ray binary 1RXS J180408.9−342058
Authors: Tse Kaho , Galloway Duncan K , Chou Yi , Heger Alexander , Hsieh Hung-En 
Published: October 2020

ABSTRACT
Millihertz quasi-periodic oscillations (mHz QPOs) observed in neutron-star low-mass X-ray binaries (NS LMXBs) are generally explained as marginally stable thermonuclear burning on the neutron star surface. We report the discovery of mHz QPOs in an XMM–Newton observation of the transient 1RXS J180408.9−342058, during a regular bursting phase of its 2015 outburst. We found significant periodic signals in the March observation, with frequencies in the range 5–8 $\, \mathrm{mHz}$, superimposed on a strong ∼1/f power-law noise continuum. Neither the QPO signals nor the power-law noise were present during the April observation, which exhibited a 2.5 × higher luminosity and had correspondingly more frequent bursts. When present, the QPO signal power decreases during bursts and disappears afterwards, similar to the behaviour in other sources. 1RXS J180408.9−342058 is the eighth source known to date that exhibits such QPOs driven by thermonuclear burning. We examine the range of properties of the QPO signals in different sources. Whereas the observed oscillation profile is similar to that predicted by numerical models, the amplitudes are significantly higher, challenging their explanation as originating from marginally stable burning.
Constraining photoionization models with a reprojected optical diagnostic diagram
Authors: Ji Xihan , Yan Renbin 
Published: October 2020

ABSTRACT
Optical diagnostic diagrams are powerful tools to separate different ionizing sources in galaxies. However, the model-constraining power of the most widely used diagrams is very limited and challenging to visualize. In addition, there have always been classification inconsistencies between diagrams based on different line ratios, and ambiguities between regions purely ionized by active galactic nuclei (AGNs) and composite regions. We present a simple reprojection of the 3D line ratio space composed of [N ii]λ6583/H α, [S ii]λλ6716, 6731/H α, and [O iii]λ5007/H β, which reveals its model-constraining power and removes the ambiguity for the true composite objects. It highlights the discrepancy between many theoretical models and the data loci. With this reprojection, we can put strong constraints on the photoionization models and the secondary nitrogen abundance prescription. We find that a single nitrogen prescription cannot fit both the star-forming locus and AGN locus simultaneously, with the latter requiring higher N/O ratios. The true composite regions stand separately from both models. We can compute the fractional AGN contributions for the composite regions, and define demarcations with specific upper limits on contamination from AGN or star formation. When the discrepancy about nitrogen prescriptions gets resolved in the future, it would also be possible to make robust metallicity measurements for composite regions and AGNs.
COG database update: focus on microbial diversity, model organisms, and widespread pathogens
Authors: Galperin Michael Y , Wolf Yuri I , Makarova Kira S , Vera Alvarez Roberto , Landsman David , Koonin Eugene V 
Published: October 2020

AbstractThe Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI’s gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for &gt;200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness
Authors: Jung Wei-Hung , Chen Enze , Veneziano Remi , Gaitanaros Stavros , Chen Yun 
Published: October 2020

Abstract
The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.
Europe PMC in 2020
Authors: Ferguson Christine , Araújo Dayane , Faulk Lynne , Gou Yuci , Hamelers Audrey , Huang Zhan , Ide-Smith Michele , Levchenko Maria , Marinos Nikos , Nambiar Rakesh , Nassar Maaly , Parkin Michael , Pi Xingjun , Rahman Faisal , Rogers Frances , Roochun Yogmatee , Saha Shyamasree , Selim Mohamed , Shafique Zunaira , Sharma Shrey , Stephenson David , Talo' Francesco , Thouvenin Arthur , Tirunagari Santosh , Vartak Vid , Venkatesan Aravind , Yang Xiao , McEntyre Johanna 
Published: October 2020

Abstract
Europe PMC (https://europepmc.org) is a database of research articles, including peer reviewed full text articles and abstracts, and preprints - all freely available for use via website, APIs and bulk download. This article outlines new developments since 2017 where work has focussed on three key areas: (i) Europe PMC has added to its core content to include life science preprint abstracts and a special collection of full text of COVID-19-related preprints. Europe PMC is unique as an aggregator of biomedical preprints alongside peer-reviewed articles, with over 180 000 preprints available to search. (ii) Europe PMC has significantly expanded its links to content related to the publications, such as links to Unpaywall, providing wider access to full text, preprint peer-review platforms, all major curated data resources in the life sciences, and experimental protocols. The redesigned Europe PMC website features the PubMed abstract and corresponding PMC full text merged into one article page; there is more evident and user-friendly navigation within articles and to related content, plus a figure browse feature. (iii) The expanded annotations platform offers ∼1.3 billion text mined biological terms and concepts sourced from 10 providers and over 40 global data resources.
Exposure to intimate partner violence and children’s dynamic skill accumulation: evidence from a UK longitudinal study
Authors: Anderberg Dan , Moroni Gloria 
Published: October 2020

AbstractChildren are increasingly recognized as secondary victims of intimate partner violence. This paper uses a unique UK longitudinal child development survey to study the relationship between verbal and physical abuse experienced by mothers and children’s development up to the age of seven. Estimating production functions for cognitive, social, and socio-emotional skills, we find that exposure during pre-school years has a quantitatively important negative effect on socio-emotional skills among toddlers and negatively affects cognitive and social skills after the age of three. The estimated impact on cognitive development is consistent with measures of cognitive skills based on school-based tests.
In Planta Monitoring of Cold-Responsive Promoter Activity Reveals a Distinctive Photoperiodic Response in Cold Acclimation
Authors: Tominaga Yoko , Suzuki Kensaku , Uemura Matsuo , Kawamura Yukio 
Published: October 2020

Abstract
Plant cold acclimation involves complicated pathways that integrate signals from temperature changes and light conditions. To understand plant responses to environmental signals in detail, molecular events that are regulated by temperature and light must be investigated at the whole-plant level in a nondestructive way. Using the promoter of COR15A connected to the luciferase reporter gene as a cold-responsive indicator, we developed an in planta monitoring system for gene expression under controlled temperature and photoperiod conditions. COR15A promoter activity was intensified by day–night cycles at 2�C, while its induction was abruptly suppressed in the dark at 8�C or higher, indicating a difference in responsiveness to photocycle between these two acclimation conditions. Freeze–thawing tests of whole plants proved that lower acclimation temperature resulted in higher tolerance to freezing, consistent with the temperature-dependent induction of COR15A. Inhibition of photosynthetic electron transport by 3-(3,4-dichlorophenyl)-1,1-dimethylurea eliminated the responsiveness to the day–night cycles at 2�C, indicating a possibility that the photosynthetic redox and/or the accumulation of photosynthates modulate COR15A responsiveness to photoperiod during cold acclimation, in addition to the well-known regulation by CBF (C-repeat binding factor) genes. These findings indicate that the cold-responsive promoter is regulated by distinctive mechanisms dependent on temperature and simultaneously affected by photocycle and photosynthesis.
Early Physical Therapist Interventions for Patients With COVID-19 in the Acute Care Hospital: A Case Report Series
Authors: Eggmann Sabrina , Kindler Angela , Perren Andrea , Ott Natalie , Johannes Frauke , Vollenweider Rahel , Balma Théophile , Bennett Claire , Silva Ivo Neto , Jakob Stephan M 
Published: October 2020

Abstract

Objective
The aim of this case series was to describe the experience of Swiss physical therapists in the treatment of patients with COVID-19 during their acute care hospital stay and to discuss challenges and potential strategies in the clinical management of these patients.

Methods
We report 11 cases of patients with COVID-19 from 5 Swiss hospitals that illustrate the various indications for physical therapy, clinical challenges, potential treatment methods, and short-term response to treatment.

Results
Physical therapists actively treated patients with COVID-19 on wards and in the intensive care unit. Interventions ranged from patient education, to prone positioning, to early mobilization and respiratory therapy. Patients were often unstable with quick exacerbation of symptoms and a slow and fluctuant recovery. Additionally, many patients who were critically ill developed severe weakness, postextubation dysphagia, weaning failure, or presented with anxiety or delirium. In this setting, physical therapy was challenging and required specialized and individualized therapeutic strategies. Most patients adopted the proposed treatment strategies, and lung function and physical strength improved over time.

Conclusion
Physical therapists clearly have a role in the COVID-19 pandemic. Based on our experience in Switzerland, we recommend that physical therapists routinely screen and assess patients for respiratory symptoms and exercise tolerance on acute wards. Treatment of patients who are critically ill should start as soon as possible to limit further sequelae. More research is needed for awake prone positioning and early breathing exercises as well as post-COVID rehabilitation.

Impact
To date, there are few data on the physical therapist management of patients with COVID-19. This article is among the first to describe the role of physical therapists in the complex pandemic environment and to describe the potential treatment strategies for countering the various challenges in the treatment of these patients.
A neutrophil signature is strongly associated with increased cardiovascular risk in gout
Authors: Vedder Daisy , Gerritsen Martijn , Nurmohamed Michael T , van Vollenhoven Ronald F , Lood Christian 
Published: October 2020

AbstractObjectiveTo investigate the association between neutrophil activation and cardiovascular risk in gout patients. We hypothesize that neutrophil activation mediates inflammation and therefore takes part in atherogenesis in gout patients.MethodPatient data were collected from 75 consecutive gout patients participating in the Reade gout cohort Amsterdam. Levels of neutrophil extracellular traps (NETs) and neutrophil activation (calprotectin and peroxidase activity) were analysed by ELISA and fluorimetry in plasma and compared with healthy controls. Markers of neutrophil activation were related to clinical markers of cardiovascular risk, including BMI, smoking, blood pressure, lipid profile and 10 year risk of cardiovascular mortality (EU-SCORE).ResultsIncreased levels of NETs were found in gout patients, although increased levels were not associated with cardiovascular risk. However, markers of neutrophil activation, including peroxidase activity correlated with waist:hip ratio (β = 0.33, P &lt; 0.001), cholesterol ratio (β = 0.46, P &lt; 0.005) and triglycerides (β = 0.60, P &lt; 0.001) as well as the 10 year risk of cardiovascular mortality (β = 0.44, P = 0.001). Calprotectin levels were elevated in hypertension (P = 0.005) and diabetes (P = 0.02). Finally, gout patients with high levels of both peroxidase and calprotectin (‘neutrophil activation signature’) had a markedly elevated cardiovascular risk score (P = 0.001), with 68% of the patients having high cardiovascular risk (odds ratio 2.9, P = 0.03).ConclusionWe demonstrated elevated levels of neutrophil activation markers, MPO and calprotectin in gout patients as compared with healthy controls. Of note, neutrophil activation markers were associated with several risk factors for cardiovascular disease, including hyperlipidaemia, hypertension and diabetes. Finally, the presence of a neutrophil activation signature was strongly associated with an increased 10 year risk of cardiovascular mortality. Further studies are needed to determine whether gout-specific factors and/or cardiovascular risk factors contribute to the elevated neutrophil activation observed in these patients.
EXPOSURE TO EXTREMELY LOW-FREQUENCY MAGNETIC FIELDS IN LOW- AND MIDDLE-INCOME COUNTRIES: AN OVERVIEW
Authors: Baaken Dan , Wollschläger Daniel , Samaras Theodoros , Schüz Joachim , Deltour Isabelle 
Published: October 2020

Abstract
To compare extremely low-frequency magnetic field (ELF-MF) exposure in the general population in low- and middle-income countries (LMICs) with high-income countries (HIC), we carried out a systematic literature search resulting in 1483 potentially eligible articles; however, only 25 studies could be included in the qualitative synthesis. Studies showed large heterogeneity in design, exposure environment and exposure assessment. Exposure assessed by outdoor spot measurements ranged from 0.03 to 4μT. Average exposure by indoor spot measurements in homes ranged from 0.02 to 0.4μT. Proportions of homes exposed to a threshold of ≥0.3μT were many times higher in LMICs compared to HIC. Based on the limited data available, exposure to ELF-MF in LMICs appeared higher than in HIC, but a direct comparison is hampered by a lack of representative and systematic monitoring studies. Representative measurement studies on residential exposure to ELF-MF are needed in LMICs together with better standardisation in the reporting.
Pancreatic Ductal Adenocarcinoma Tumor Suppressors Rgs8–16
Authors: Choudhuri Shreoshi Pal , Wilkie Thomas Martin 
Published: October 2020

IntroductionG protein‐coupled receptors (GPCRs) are the largest family of targets for approved drugs, but rarely exploited in cancer treatment. Kras oncogenic mutations (e.g. KrasG12D) are found in over 90% of human pancreatic ductal adenocarcinoma (PDA) and can be activated by protein kinases and GPCR signaling. Regulator of G protein signaling (Rgs) proteins modulate GPCR signaling by accelerating the GTPase activity of Gq‐ and Gi‐class alpha subunits. Rgs genes are often upregulated in primary cancers. We showed that Rgs8::GFP and Rgs16::GFP reporter genes are highly expressed in an oncogenic Kras (KrasG12D)‐dependent PDA model at initiation and throughout progression. Furthermore, activating alleles of Gq that are resistant to Rgs inhibition are found in benign precursors of PDA in humans. By contrast, Rgs16 down‐regulation is associated with increased lymph node metastasis in PDA. Here we test our hypothesis that Rgs8–16 deletion will accelerate PDA initiation, progression, and metastasis.MethodsWe made the Rgs8–16 double knockout (dKO) and crossed it into pancreas‐specific KrasG12D (KC) mutant mice (termed KCR8–16). Caerulein (analog of the Gq‐coupled GPCR agonist CCK) induced acute and chronic pancreatitis, PDA initiation and progression. Response to caerulein was compared in KC and KCR8–16 mice using physiologic, histologic and immunologic assays.ResultsCaerulein induced Rgs16 expression in acute pancreatitis within 2 days in Rgs16::GFP transgenic mice, and they recovered normally within 7days. Although deletion of Rgs8–16 did not cause PDA initiation, Rgs8–16 dKO mice took longer to recover from caerulein‐induced pancreatitis than normal mice. PDA initiation and progression was greatly accelerated in KCR8–16 compared to KC mice. Caerulein treatment caused the entire pancreas to transform to aggressive PDA within 7 days in KCR8–16 mice, whereas KC pancreata showed milder acinar‐to‐ducal metaplasia and differentiated, early stage PDA. Cell proliferation and epithelial‐to‐mesenchymal transmission (EMT) was amplified in KCR8–16 mice, with increased Ki67 and EMT marker expression, suggesting a greater potential for metastasis.DiscussionWe find Rgs8 and Rgs16 are tumor suppressors in PDA initiation and progression. Little is known about GPCR expression and function in PDA. Few GPCR‐targeted therapeutics exist for PDA. The KCR8–16 and Rgs16::GFP mice we developed provide excellent models for screening ligands to identify GPCRs involved in PDA initiation and progression. KCR8–16 hypersensitivity to Gq‐coupled ligands provides a model for rapid in vivo validation of PDA therapeutics.Support or Funding InformationThis work supported by NCI CA161624 and UT Southwestern Cancer Center Pilot Project Award to RAB and TMWThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.