bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the shape of air–liquid interfaces with surface tension that bound rigidly rotating liquids in partially filled containers
Authors: Ramé Enrique , Weinstein Steven J , Barlow Nathaniel S 
Published: August 2021

Abstract
The interface shape of a fluid in rigid body rotation about its axis and partially filling the container is often the subject of a homework problem in the first graduate fluids class. In that problem, surface tension is neglected, the interface shape is parabolic and the contact angle boundary condition is not satisfied in general. When surface tension is accounted for, the shapes exhibit much richer dependencies as a function of rotation velocity. We analyze steady interface shapes in rotating right-circular cylindrical containers under rigid body rotation in zero gravity. We pay special attention to shapes near criticality, in which the interface, or part thereof, becomes straight and parallel to the axis of rotation at certain specific rotational speeds. We examine geometries where the container is axially infinite and derive properties of their solutions. We then examine in detail two special cases of menisci in a cylindrical container: a meniscus spanning the cross-section and a meniscus forming a bubble. In each case, we develop exact solutions for the respective axial lengths as infinite series in powers of appropriate rotation parameters, and we find the respective asymptotic behaviors as the shapes approach their critical configuration. Finally, we apply the method of asymptotic approximants to yield analytical expressions for the axial lengths of the menisci over the whole range of rotation speeds. In this application, the analytical solution is employed to examine errors introduced by the assumption that the interface is a right circular cylinder; this assumption is key to the spinning bubble method used to measure surface tension.
The Smallest Singular Value of Dense Random Regular Digraphs
Authors: Jain Vishesh , Sah Ashwin , Sawhney Mehtaab 
Published: August 2021

Abstract
Let $A$ be the adjacency matrix of a uniformly random $d$-regular digraph on $n$ vertices, and suppose that $\min (d,n-d)\ge \lambda n$. We show that for any $\kappa \geq 0$, $$\begin{align*} &\mathbb{P}[s_n(A)\le\kappa]\le C_\lambda\kappa\sqrt{n}+2e^{-c_\lambda n}.\end{align*}$$Up to the constants $C_\lambda , c_\lambda&gt; 0$, our bound matches optimal bounds for $n\times n$ random matrices, each of whose entries is an i.i.d $\operatorname{Ber}(d/n)$ random variable. The special case $\kappa = 0$ of our result confirms a conjecture of Cook regarding the probability of singularity of dense random regular digraphs.
Chiral de Rham Complex on the Upper Half Plane and Modular Forms
Authors: Dai Xuanzhong 
Published: August 2021

Abstract
For any congruence subgroup $\Gamma $, we study the vertex operator algebra $\Omega ^{ch}(\mathbb H,\Gamma )$ constructed from the $\Gamma $-invariant global sections of the chiral de Rham complex on the upper half plane, which are holomorphic at all the cusps. We construct a basis of $\Omega ^{ch}(\mathbb H,\Gamma )$ in terms of modular forms of $\Gamma $ and compute its character. We show that the vertex operations on $\Omega ^{ch}(\mathbb H,\Gamma )$ are determined by a modification of the Rankin–Cohen brackets of modular forms.
Factors Compromising Glucuronidase Performance in Urine Drug Testing Potentially Resulting in False Negatives
Authors: Lee L Andrew , McGee Amanda C , Sitasuwan Pongkwan , Tomashek John J , Riley Chris , Muñoz-Muñoz Ana Celia , Andrade Lawrence 
Published: August 2021

Abstract
Next generation β-glucuronidases can effectively cleave glucuronides in urine at room temperature. However, during the discovery studies, additional challenges were identified for urine drug testing across biologically relevant pH extremes and patient urine specimens. Different enzymes were evaluated across clinical urine specimens and commercially available urine control matrices. Each enzyme shows distinct substrate preferences, pH optima, and variability across clinical specimens. These results demonstrate how reliance on a single glucuronidated substrate as the internal hydrolysis control cannot ensure performance across a broader panel of analytes. Moreover, sample specific urine properties compromise β-glucuronidases to varying levels, more pronounced for some enzymes, and thereby lower the recovery of some drug analytes in an enzyme-specific manner. A minimum of 3-fold dilution of urine with buffer yields measurable improvements in achieving target pH and reducing the impact of endogenous compounds on enzyme performance. After subjecting the enzymes to pH extremes and compromising chemicals, one particular β-glucuronidase was identified that addressed many of these challenges and greatly lower the risk of failed hydrolyses. In summary, we present strategies to evaluate glucuronidases that aid in higher accuracy urine drug tests with lower potential for false negatives.
Metabolic engineering of microorganisms for L-alanine production
Authors: Liu Pingping , Xu Hongtao , Zhang Xueli 
Published: August 2021

Abstract
L-alanine is extensively used in chemical, food, and medicine industries. Industrial production of L-alanine has been mainly based on the enzymatic process using petroleum-based L-aspartic acid as the substrate. L-alanine production from renewable biomass using microbial fermentation process is an alternative route. Many microorganisms can naturally produce L-alanine using aminotransferase or L-alanine dehydrogenase. However, production of L-alanine using the native strains has been limited due to their low yields and productivities. In this review, metabolic engineering of microorganisms for L-alanine production was summarized. Among them, the Escherichia coli strains developed by Dr. Lonnie Ingram's group which can produce L-alanine with anaerobic fermentation process had several advantages, especially having high L-alanine yield, and it was the first one that realized commercialization. L-alanine is also the first amino acid that could be industrially produced by anaerobic fermentation.
Gamma-ray emission from young radio galaxies and quasars
Authors: Principe G , Di Venere L , Orienti M , Migliori G , D’Ammando F , Mazziotta M N , Giroletti M 
Published: August 2021

ABSTRACT
According to radiative models, radio galaxies and quasars are predicted to produce gamma rays from the earliest stages of their evolution. Exploring their high-energy emission is crucial for providing information on the most energetic processes, the origin and the structure of the newly born radio jets. Taking advantage of more than 11 yr of Fermi-LAT data, we investigate the gamma-ray emission of 162 young radio sources (103 galaxies and 59 quasars), the largest sample of young radio sources used so far for such a gamma-ray study. We separately analyse each source and perform the first stacking analysis of this class of sources to investigate the gamma-ray emission of the undetected sources. We detect significant gamma-ray emission from 11 young radio sources, 4 galaxies, and 7 quasars, including the discovery of significant gamma-ray emission from the compact radio galaxy PKS 1007+142 (z = 0.213). The cumulative signal of below-threshold young radio sources is not significantly detected. However, it is about one order of magnitude lower than those derived from the individual sources, providing stringent upper limits on the gamma-ray emission from young radio galaxies (Fγ &lt; 4.6 × 10−11 ph cm−2 s−1) and quasars (Fγ &lt; 10.1 × 10−11 ph cm−2 s−1), and enabling a comparison with the models proposed. With this analysis of more than a decade of Fermi-LAT observations, we can conclude that while individual young radio sources can be bright gamma-ray emitters, the collective gamma-ray emission of this class of sources is not bright enough to be detected by Fermi-LAT.
The impact of intrinsic magnetic field on the absorption signatures of elements probing the upper atmosphere of HD209458b
Authors: Khodachenko M L , Shaikhislamov I F , Lammer H , Miroshnichenko I B , Rumenskikh M S , Berezutsky A G , Fossati L 
Published: August 2021

ABSTRACT
The signs of an expanding atmosphere of HD209458b have been observed with far-ultraviolet transmission spectroscopy and in the measurements of transit absorption by metastable He i. These observations are interpreted using the hydrodynamic and Monte Carlo numerical simulations of various degree of complexity and consistency. At the same time, no attempt has been made to model atmospheric escape of a magnetized HD209458b, to see how the planetary magnetic field might affect the measured transit absorption lines. This paper presents the global 3D MHD self-consistent simulations of the expanding upper atmosphere of HD209458b interacting with the stellar wind, and models the observed H i (Ly α), O i (1306 Å), C ii (1337 Å), and He i (10 830 Å) transit absorption features. We find that the planetary dipole magnetic field with the equatorial surface value of Bp = 1 G profoundly changes the character of atmospheric material outflow and the related absorption. We also investigate the formation of planetary magnetosphere in the stellar wind and show that its size is more determined by the escaping atmosphere flow rather than by the strength of magnetic field. Fitting of the simulation results to observations enables constraining the stellar XUV flux and He abundance at FXUV ∼ 10 erg cm2 s–1 (at 1 au) and He/H ≈ 0.02, respectively, as well as setting an upper limit for the dipole magnetic field of Bp &lt; 0.1 G on the planetary surface at the equator. This implies that the magnetic dipole moment µP of HD209458b should be less than 6 per cent of the Jovian value.
A sparse regression approach to modelling the relation between galaxy stellar masses and their host haloes
Authors: Icaza-Lizaola M , Bower Richard G , Norberg Peder , Cole Shaun , Schaller Matthieu , Egan Stefan 
Published: August 2021

ABSTRACT
Sparse regression algorithms have been proposed as the appropriate framework to model the governing equations of a system from data, without needing prior knowledge of the underlying physics. In this work, we use sparse regression to build an accurate and explainable model of the stellar mass of central galaxies given properties of their host dark matter (DM) halo. Our data set comprises 9521 central galaxies from the EAGLE hydrodynamic simulation. By matching the host haloes to a DM-only simulation, we collect the halo mass and specific angular momentum at present time and for their main progenitors in 10 redshift bins from z = 0 to z = 4. The principal component of our governing equation is a third-order polynomial of the host halo mass, which models the stellar-mass–halo-mass relation. The scatter about this relation is driven by the halo mass evolution and is captured by second- and third-order correlations of the halo mass evolution with the present halo mass. An advantage of sparse regression approaches is that unnecessary terms are removed. Although we include information on halo specific angular momentum, these parameters are discarded by our methodology. This suggests that halo angular momentum has little connection to galaxy formation efficiency. Our model has a root mean square error (RMSE) of 0.167log10(M*/M⊙), and accurately reproduces both the stellar mass function and central galaxy correlation function of EAGLE. The methodology appears to be an encouraging approach for populating the haloes of DM-only simulations with galaxies, and we discuss the next steps that are required.
Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes
Authors: Baum Chloé , Lin Yu-Cheng , Fomenkov Alexey , Anton Brian P , Chen Lixin , Yan Bo , Evans Thomas C , Roberts Richard J , Tolonen Andrew C , Ettwiller Laurence 
Published: August 2021

Abstract
DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and single molecule, real-time (SMRT) sequencing usually misses m5C. Here, we present a new method called RIMS-seq (rapid identification of methylase specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.
Clinical and Microbiological Characteristics of Hospital-Acquired Methicillin-ResistantStaphylococcus aureusBacteremia Caused by a Community-Associated PVL-Negative Strain
Authors: Lee Yun Woo , Bae Seongman , Yang Eunmi , Chung Hyemin , Kim Eunsil , Jung Jiwon , Kim Min Jae , Chong Yong Pil , Kim Sung-Han , Choi Sang-Ho , Lee Sang-Oh , Kim Yang Soo 
Published: August 2021

AbstractBackgroundST72-SCCmecIV, a community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain in Korea, originated in the community and has been spreading in health care settings. Herein, we describe the clinical and microbiological characteristics of patients with hospital-acquired MRSA bacteremia (MRSAB) caused by community-associated strains.MethodsWe analyzed hospital-acquired MRSAB cases caused by ST72-SCCmecIV using a prospective cohort of patients with SAB in a tertiary hospital in Korea from July 2008 to December 2018. We compared the clinical and microbiological characteristics of ST72-SCCmecIV with ST5-SCCmecII, a representative hospital-associated genotype strain.ResultsOf the 1782 S. aureus bacteremia (SAB) cases, 628 (35.2%) were hospital-acquired MRSAB. Of the 628 isolates, 431 (68.6%) were ST5-SCCmecII and 152 (24.2%) were ST72-SCCmecIV. Patients with ST72-SCCmecIV were younger than those with ST5-SCCmecII and less likely to have a history of recent surgery, antibiotic treatment, nasal MRSA colonization, and central venous catheter placement. Compared with ST5-SCCmecII, ST72-SCCmecIV isolates were more likely to have vancomycin MICs ≤1.0 mg/L (P &lt; .001). Osteoarticular infection as the site of infection (7.2% [11/152] vs 1.4% [6/431]) was more common in patients with ST72-SCCmecIV. There were no significant differences in the rate of recurrence (≤90 days), persistent bacteremia (≥7 days), or 30- and 90-day mortality rates between the 2 groups.ConclusionsOsteoarticular infections were more prevalent in ST72-SCCmecIV MRSAB. Mortality rates between the ST72-SCCmecIV and ST5-SCCmecII groups were not significantly different.
Learning faces as concepts improves face recognition by engaging the social brain network
Authors: Shoham Adva , Kliger Libi , Yovel Galit 
Published: August 2021

Abstract
Face recognition benefits from associating social information to faces during learning. This has been demonstrated by better recognition for faces that underwent social than perceptual evaluations. Two hypotheses were proposed to account for this effect. According to the feature-elaboration hypothesis, social evaluations encourage elaborated processing of perceptual information from faces. According to a social representation hypothesis, social evaluations convert faces from a perceptual representation to a socially meaningful representation of a person. To decide between these two hypotheses, we ran a functional magnetic resonance imaging (fMRI) study in which we functionally localized the posterior face-selective brain areas and social processing brain areas. Participants watched video-clips of young adults and were asked to study them for a recognition test, while making either perceptual evaluations or social evaluations about them. During the fMRI scan, participants performed an old/new recognition test. Behavioural findings replicated better recognition for faces that underwent social then perceptual evaluations. fMRI results showed higher response during the recognition phase for the faces that were learned socially than perceptually, in the social-brain network but not in posterior face-selective network. These results support the social-representation hypothesis and highlight the important role that social processing mechanisms, rather than purely perceptual processes, play in face recognition.
Plasma Levels of the Cytokines B Cell-Activating Factor (BAFF) and A Proliferation-Inducing Ligand (APRIL) in Schizophrenia, Bipolar, and Major Depressive Disorder: A Cross Sectional, Multisite Study
Authors: Engh John Abel , Ueland Thor , Agartz Ingrid , Andreou Dimitrios , Aukrust Pål , Boye Birgitte , Bøen Erlend , Drange Ole Kristian , Elvsåshagen Torbjørn , Hope Sigrun , Høegh Margrethe Collier , Joa Inge , Johnsen Erik , Kroken Rune Andreas , Lagerberg Trine Vik , Lekva Tove , Malt Ulrik Fredrik , Melle Ingrid , Morken Gunnar , Nærland Terje , Steen Vidar Martin , Wedervang-Resell Kirsten , Weibell Melissa Auten , Westlye Lars Tjelta , Djurovic Srdjan , Steen Nils Eiel , Andreassen Ole Andreas 
Published: August 2021

AbstractBackgroundImmune dysfunction has been implicated in the pathogenesis of schizophrenia and other nonaffective psychosis (SCZ), bipolar spectrum disorder (BIP) and major depressive disorder (MDD). The cytokines B cell-activating factor (BAFF) and A proliferation-inducing ligand (APRIL) belong to the tumor necrosis factor (TNF) super family and are essential in orchestrating immune responses. Abnormal levels of BAFF and APRIL have been found in autoimmune diseases with CNS affection.MethodsWe investigated if plasma levels of BAFF and APRIL differed between patients with SCZ, BIP, and MDD with psychotic symptoms (n = 2009) and healthy control subjects (HC, n = 1212), and tested for associations with psychotic symptom load, controlling for sociodemographic status, antipsychotic and other psychotropic medication, smoking, body-mass-index, and high sensitivity CRP.ResultsPlasma APRIL level was significantly lower across all patient groups compared to HC (P &lt; .001; Cohen’s d = 0.33), and in SCZ compared to HC (P &lt; .001; d = 0.28) and in BIP compared to HC (P &lt; .001; d = 0.37). Lower plasma APRIL was associated with higher psychotic symptom load with nominal significance (P = .017), but not with any other clinical characteristics. Plasma BAFF was not significantly different across patient groups vs HC, but significantly higher in BIP compared to HC (P = .040; d = 0.12) and SCZ (P = .027; d = 0.10).ConclusionsThese results show aberrant levels of BAFF and APRIL and association with psychotic symptoms in patients with SCZ and BIP. This suggest that dysregulation of the TNF system, mediated by BAFF and APRIL, is involved in the pathophysiology of psychotic disorders.
Prediction of Early Symptom Remission in Two Independent Samples of First-Episode Psychosis Patients Using Machine Learning
Authors: Soldatos Rigas F , Cearns Micah , Nielsen Mette Ø , Kollias Costas , Xenaki Lida-Alkisti , Stefanatou Pentagiotissa , Ralli Irene , Dimitrakopoulos Stefanos , Hatzimanolis Alex , Kosteletos Ioannis , Vlachos Ilias I , Selakovic Mirjana , Foteli Stefania , Nianiakas Nikolaos , Mantonakis Leonidas , Triantafyllou Theoni F , Ntigridaki Aggeliki , Ermiliou Vanessa , Voulgaraki Marina , Psarra Evaggelia , Sørensen Mikkel E , Bojesen Kirsten B , Tangmose Karen , Sigvard Anne M , Ambrosen Karen S , Meritt Toni , Syeda Warda , Glenthøj Birte Y , Koutsouleris Nikolaos , Pantelis Christos , Ebdrup Bjørn H , Stefanis Nikos 
Published: August 2021

Abstract

Background
Validated clinical prediction models of short-term remission in psychosis are lacking. Our aim was to develop a clinical prediction model aimed at predicting 4−6-week remission following a first episode of psychosis.

Method
Baseline clinical data from the Athens First Episode Research Study was used to develop a Support Vector Machine prediction model of 4-week symptom remission in first-episode psychosis patients using repeated nested cross-validation. This model was further tested to predict 6-week remission in a sample of two independent, consecutive Danish first-episode cohorts.

Results
Of the 179 participants in Athens, 120 were male with an average age of 25.8 years and average duration of untreated psychosis of 32.8 weeks. 62.9% were antipsychotic-naïve. Fifty-seven percent attained remission after 4 weeks. In the Danish cohort, 31% attained remission. Eleven clinical scale items were selected in the Athens 4-week remission cohort. These included the Duration of Untreated Psychosis, Personal and Social Performance Scale, Global Assessment of Functioning and eight items from the Positive and Negative Syndrome Scale. This model significantly predicted 4-week remission status (area under the receiver operator characteristic curve (ROC-AUC) = 71.45, P &lt; .0001). It also predicted 6-week remission status in the Danish cohort (ROC-AUC = 67.74, P &lt; .0001), demonstrating reliability.

Conclusions
Using items from common and validated clinical scales, our model significantly predicted early remission in patients with first-episode psychosis. Although replicated in an independent cohort, forward testing between machine learning models and clinicians’ assessment should be undertaken to evaluate the possible utility as a routine clinical tool.
Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley
Authors: Issaka Souley , Traoré Oumar , Longué Régis Dimitri Skopé , Pinel-Galzi Agnès , Gill Mandev S , Dellicour Simon , Bastide Paul , Guindon Stéphane , Hébrard Eugénie , Dugué Marie-Jo , Séré Yacouba , Semballa Silla , Aké Séverin , Lemey Philippe , Fargette Denis 
Published: August 2021

Abstract
To investigate the spread of Rice yellow mottle virus (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework applied previously to reconstruct its dispersal history in West Africa, East Africa, and Madagascar. The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus. We benefited from the results of early field surveys of the disease for the validation of the phylogeographic reconstruction and from the well-documented history of rice cultivation changes along the Niger River for their interpretation. As a prerequisite, the temporal signal of the RYMV data sets was revisited in the light of recent methodological advances. The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from areas to the southwest of the country where rice was increasingly grown. Viral spread was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed for a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometres, and led to the development of severe epidemics. There was no evidence of long-distance dissemination of the virus through natural water. Floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV along the Niger River is an insightful example of how agricultural intensification favours pathogen emergence and spread.