bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithm design and the development of a discrete element method for simulating particulate flow and heat transfer
Authors: Liu Bing 
Published: April 2021

AbstractAn algorithm using the discrete element method (DEM) for simulating the particulate behaviour of flow and heat transfer is developed and described, the reasonable hypothesis and the ingenious design of which have been presented in detail. The organizational structure of the developed algorithm contains an efficient method for determining particle collisions, the status analysis for each particle and the particulate-kinematics analysis during the time step. The reasonability and correctness of the developed DEM algorithm are validated by laboratory experiments: the discharge process of glass beads from a silo; and heating of metal alloy particles in a calciner. Afterwards, a group of validated mechanics parameter values for coal and sand have been tested and verified in the article, preparing for the simulation of the pyrolysis process in a downer or screw reactor in subsequent research projects.
The Missing Link: Network Influences on Class Divides in Political Attitudes
Authors: Lindh Arvid , Andersson Anton B , Volker Beate 
Published: April 2021

AbstractPrevious research provides a detailed picture of class differences in political attitudes. Less is however known about the social structures that enforce this political divide across social classes. This article contributes towards filling this gap by considering how the class profile of personal social networks influences political attitudes. We propose a general framework for incorporating an individual’s social network into class analysis of political preferences. Using Sweden as a case, we empirically evaluate our approach using a population survey with information about the respondents’ own employment situation, egocentric networks, and political attitudes in terms of redistribution and welfare chauvinism. We find that there is considerable class segregation in social networks as individuals tend to have more ties within their own and neighbouring class positions. Concerning political preferences, results show that: (i) a substantive part of the class–attitude relationship is shaped by a person’s social network; (ii) the class profile of networks influences attitudes over and above one’s own class position; (iii) class segregation in networks fortifies class divides in political attitudes. We thus conclude that social networks constitute a (hitherto) ‘missing link’ in class analysis of political preferences that merits careful consideration in theoretical models of contemporary politics.
Correlation of Rhs elements with Escherichia coli population structure.
Authors: Hill C W , Feulner G , Brody M S , Zhao S , Sadosky A B , Sandt C H 
Published: April 2021

Abstract
The Rhs family of composite genetic elements was assessed for variation among independent Escherichia coli strains of the ECOR reference collection. The location and content of the RhsA-B-C-F subfamily correlates highly with the clonal structure of the ECOR collection. This correlation exists at several levels: the presence of Rhs core homology in the strain, the location of the Rhs elements present, and the identity of the Rhs core-extensions associated with each element. A provocative finding was that an identical 1518-bp segment, covering core-extension-b1 and its associated downstream open reading frame, is present in two distinct clonal groups, but in association with different Rhs elements. The sequence identity of this segment when contrasted with the divergence of other chromosomal segments suggests that shuffling of Rhs core extensions has been a relatively recent variation. Nevertheless the copies of core-extension-b1 were placed within the respective Rhs elements before the emergence of the clonal groups. In the course of this analysis, two new Rhs elements absent from E. coli K-12 were discovered: RhsF, a fourth member of the RhsA-B-C-F subfamily, and RhsG, the prototype of a third Rhs subfamily.
Isolation and Characterization of HRT1 Using a Genetic Screen for Mutants Unable to Degrade Gic2p in Saccharomyces cerevisiae
Authors: Blondel Marc , Galan Jean-Marc , Peter Matthias 
Published: April 2021

Abstract
Skp1p-cullin-F-box (SCF) protein complexes are ubiquitin ligases required for degradation of many regulatory proteins involved in cell cycle progression, morphogenesis, and signal transduction. Using a genetic screen, we have isolated a novel allele of the HRT1/RBX1 gene in budding yeast (hrt1-C81Y). hrt1-C81Y mutant cells exhibited an aberrant morphology but were viable at all temperatures. The cells displayed multiple genetic interactions with mutations in known SCF components and were defective for the degradation of several SCF targets including Gic2p, Far1p, Sic1p, and Cln2p. In addition, they also failed to degrade the F-box proteins Grr1p, Cdc4p, and Met30p. Wild-type Hrt1p but not Hrt1p-C81Y was able to bind multiple F-box proteins in an F-box-dependent manner. Hrt1p-C81Y harbors a single mutation in its ring-finger domain, which is conserved in subunits of distinct E3 ligases. Finally, Hrt1p was localized in both nucleus and cytoplasm and despite a short half-life was expressed constitutively throughout the cell cycle. Taken together, these results suggest that Hrt1p is a core subunit of multiple SCF complexes.
Abnormal Turning Behavior in Drosophila Larvae: Identification and Molecular Analysis ofscribbler(sbb)
Authors: Yang Ping , Shaver Susan A , Hilliker Arthur J , Sokolowski Marla B 
Published: April 2021

AbstractOur genetic dissection of behavior has isolated scribbler (sbb), a vital gene that encodes a novel protein expressed in the embryonic and larval nervous systems and in the imaginal discs. Larvae with mutations in sbb exhibit abnormally high amounts of turning behavior in the absence of food. sbb is a large gene spanning &gt;50 kb of genomic DNA with four major developmentally regulated transcripts. Transgenic rescue of scribbler behavior was demonstrated by targeting expression of a normal sbb transgene (sbb+) expressing one of the major transcripts to the nervous system. The vital function of sbb was restored by ubiquitous expression of this transgene throughout development.
A Physical Map of the Polytenized Region (101EF–102F) of Chromosome 4 in Drosophila melanogaster
Authors: Locke John , Podemski Lynn , Aippersbach Nicole , Kemp Hilary , Hodgetts Ross 
Published: April 2021

Abstract
Chromosome 4, the smallest autosome (~5 Mb in length) in Drosophila melanogaster contains two major regions. The centromeric domain (~4 Mb) is heterochromatic and consists primarily of short, satellite repeats. The remaining ~1.2 Mb, which constitutes the banded region (101E–102F) on salivary gland polytene chromosomes and contains the identified genes, is the region mapped in this study. Chromosome walking was hindered by the abundance of moderately repeated sequences dispersed along the chromosome, so we used many entry points to recover overlapping cosmid and BAC clones. In situ hybridization of probes from the two ends of the map to polytene chromosomes confirmed that the cloned region had spanned the 101E–102F interval. Our BAC clones comprised three contigs; one gap was positioned distally in 102EF and the other was located proximally at 102B. Twenty-three genes, representing about half of our revised estimate of the total number of genes on chromosome 4, were positioned on the BAC contigs. A minimal tiling set of the clones we have mapped will facilitate both the assembly of the DNA sequence of the chromosome and a functional analysis of its genes.
Patterns of Variation in the Intergenic Spacers of Ribosomal DNA inDrosophila melanogasterSupport a Model for Genetic Exchanges DuringX-YPairing
Authors: Polanco Carlos , González Ana I , Dover Gabriel A 
Published: April 2021

AbstractDetailed analysis of variation in intergenic spacer (IGS) and internal transcribed spacer (ITS) regions of rDNA drawn from natural populations of Drosophila melanogaster has revealed contrasting patterns of homogenization although both spacers are located in the same rDNA unit. On the basis of the role of IGS regions in X-Y chromosome pairing, we proposed a mechanism of single-strand exchanges at the IGS regions, which can explain the different evolutionary trajectories followed by the IGS and the ITS regions. Here, we provide data from the chromosomal distribution of selected IGS length variants, as well as the detailed internal structure of a large number of IGS regions obtained from specific X and Y chromosomes. The variability found in the different internal subrepeat regions of IGS regions isolated from X and Y chromosomes supports the proposed mechanism of genetic exchanges and suggests that only the “240” subrepeats are involved. The presence of a putative site for topoisomerase I at the 5′ end of the 18S rRNA gene would allow for the exchange between X and Y chromosomes of some 240 subrepeats, the promoter, and the ETS region, leaving the rest of the rDNA unit to evolve along separate chromosomal lineages. The phenomenon of localized units (modules) of homogenization has implications for multigene family evolution in general.
Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation
Authors: Kim Yuseob , Stephan Wolfgang 
Published: April 2021

Abstract
Due to relatively high rates of strongly selected deleterious mutations, directional selection on favorable alleles (causing hitchhiking effects on linked neutral polymorphisms) is expected to occur while a deleterious mutation-selection balance is present in a population. We analyze this interaction of directional selection and background selection and study their combined effects on neutral variation, using a three-locus model in which each locus is subjected to either deleterious, favorable, or neutral mutations. Average heterozygosity is measured by simulations (1) at the stationary state under the assumption of recurrent hitchhiking events and (2) as a transient level after a single hitchhiking event. The simulation results are compared to theoretical predictions. It is shown that known analytical solutions describing the hitchhiking effect without background selection can be modified such that they accurately predict the joint effects of hitchhiking and background on linked, neutral variation. Generalization of these results to a more appropriate multilocus model (such that background selection can occur at multiple sites) suggests that, in regions of very low recombination rates, stationary levels of nucleotide diversity are primarily determined by hitchhiking, whereas in regions of high recombination, background selection is the dominant force. The implications of these results on the identification and estimation of the relevant parameters of the model are discussed.
An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies
Authors: Pybus Oliver G , Rambaut Andrew , Harvey Paul H 
Published: April 2021

AbstractWe describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.
Codominant Analysis of Banding Data From a Dominant Marker System by Normal Mixtures
Authors: Piepho Hans-Peter , Koch Georg 
Published: April 2021

AbstractAmplified fragment length polymorphisms (AFLPs) currently are among the most widely used marker systems. In many studies, AFLPs are analyzed on the basis of the presence or absence of a band on an electrophoretic gel. As a result, dominant homozygous individuals are not distinguished from heterozygous individuals, resulting in a considerable loss of information. This article shows how codominant information can be obtained if the amount of PCR products is quantified. Due to measurement variation, genotyping on the basis of such information is not error-free. We propose use of normal mixture distributions to determine the most likely genotype, given the data. The method is exemplified using AFLP data from sugar beet.
Visual Impairment and Objectively Measured Physical Activity in Middle-Aged and Older Adults
Authors: Cai Yurun , Schrack Jennifer A , Wang Hang , E Jian-Yu , Wanigatunga Amal A , Agrawal Yuri , Urbanek Jacek K , Simonsick Eleanor M , Ferrucci Luigi , Swenor Bonnielin K 
Published: April 2021

AbstractBackgroundVision loss is associated with increased risk of falls and restricted physical activity, yet the relationship between multiple vision measures and objectively measured physical activity, especially activity patterns, in mid-to-late life is not well understood.MethodThis study included 603 participants aged 50 years and older (mean age = 73.5) in the Baltimore Longitudinal Study of Aging who had the following assessments: presenting and best-corrected visual acuity, contrast sensitivity, visual fields, stereo acuity, and free-living physical activity using a wrist-worn ActiGraph accelerometer for 7 days. Linear regression models were used to examine the association between vision measures and daily activity counts, active minutes, and activity fragmentation (defined as an active-to-sedentary transition probability), adjusting for potential confounders. Mixed-effects models estimated differences in activity by time of day comparing those with and without each visual impairment.ResultsIn the fully adjusted model, worse presenting visual acuity, contrast sensitivity, and visual fields were associated with fewer activity counts, less active time, and more fragmented activity patterns (p &lt; .05 for all). Participants with presenting or best-corrected visual acuity impairment had 19.2 and 29.3 fewer active minutes (p = .05 and p = .03, respectively) per day. Visual field impairment was associated with 268 636 fewer activity counts (p = .02), 46.2 fewer active minutes (p = .02) per day, and 3% greater activity fragmentation (p = .009). Differences in activity levels tended to be greatest from 6 am to 6 pm (p &lt; .05).ConclusionsOlder adults with visual impairment have restricted and more fragmented patterns of daily activity. Longitudinal studies to quantify the long-term impacts of visual impairments on activity decline are warranted.
Multicentre experience with an iliac fenestrated device
Authors: Taher Fadi , Langer Stephan , Falkensammer Juergen , Plimon Markus , Kliewer Miriam , Walter Corinna , Assadian Afshin , Stehr Alexander 
Published: April 2021

Abstract

OBJECTIVES
The aim of this study was to present a multicentre experience of technical results and mid-term follow-up using a custom-made iliac fenestrated device (Terumo Aortic, Inchinnan, Renfrewshire, UK) for the treatment of iliac aneurysms and endoleaks.

METHODS
A multicentre retrospective evaluation of 22 patients (3–12 per institution) with either an iliac artery aneurysm or endoleak treated with an iliac fenestrated device was performed. Data were gathered from 3 departments of vascular and endovascular surgery at 3 European institutions.

RESULTS
Ten of the included patients (45.5%) were treated for an endoleak and 12 had aorto-iliac aneurysms (54.5%). Two patients underwent bilateral fenestrated device implantation for a total of 24 devices included in this analysis. Primary technical success was 91.7% (22 of 24 implanted devices). One of the 24 internal iliac arteries could not be cannulated and was covered (primary assisted technical success rate 95.8%) and 1 patient required a relining of the stent graft due to a mid-grade stenosis opposite the internal iliac artery fenestration. Survival at the last available follow-up (mean 15.2 ± 12.0 months, range 0.5–36.6 months) was 90.9%.

CONCLUSIONS
The present investigation adds to a growing body of literature on custom-made endografts and their usefulness in achieving endovascular repair without compromising blood flow via important arterial branch vessels, such as the internal iliac artery. It presents encouraging technical and mid-term follow-up data from consecutive patients treated for iliac aneurysms or endoleaks using this custom-made device. The technique may help avoid adverse sequelae associated to a coil-and-cover approach when iliac branch devices are not feasible.
Predicting Influenza and Rhinovirus Infections in Airway Cells Utilizing Volatile Emissions
Authors: McCartney Mitchell M , Linderholm Angela L , Yamaguchi Mei S , Falcon Alexandria K , Harper Richart W , Thompson George R , Ebeler Susan E , Kenyon Nicholas J , Davis Cristina E , Schivo Michael 
Published: April 2021

Abstract

Background
Respiratory viral infections are common and potentially devastating to patients with underlying lung disease. Diagnosing viral infections often requires invasive sampling, and interpretation often requires specialized laboratory equipment. Here, we test the hypothesis that a breath test could diagnose influenza and rhinovirus infections using an in vitro model of the human airway.

Methods
Cultured primary human tracheobronchial epithelial cells were infected with either influenza A H1N1 or rhinovirus 1B and compared with healthy control cells. Headspace volatile metabolite measurements of cell cultures were made at 12-hour time points postinfection using a thermal desorption-gas chromatography-mass spectrometry method.

Results
Based on 54 compounds, statistical models distinguished volatile organic compound profiles of influenza- and rhinovirus-infected cells from healthy counterparts. Area under the curve values were 0.94 for influenza, 0.90 for rhinovirus, and 0.75 for controls. Regression analysis predicted how many hours prior cells became infected with a root mean square error of 6.35 hours for influenza- and 3.32 hours for rhinovirus-infected cells.

Conclusions
Volatile biomarkers released by bronchial epithelial cells could not only be used to diagnose whether cells were infected, but also the timing of infection. Our model supports the hypothesis that a breath test could serve to diagnose viral infections.
Outpatient continuous-infusion benzylpenicillin combined with either gentamicin or ceftriaxone for enterococcal endocarditis
Authors: Briggs Simon , Broom Matthew , Duffy Eamon , Everts Richard , Everts Gabrielle , Lowe Boris , McBride Stephen , Bhally Hasan 
Published: April 2021

Abstract

Background
Treatment regimens requiring multiple daily dosing for enterococcal endocarditis are challenging to deliver in the outpatient setting. Continuous-infusion benzylpenicillin via a 24 h elastomeric infusor, combined with either once-daily gentamicin or ceftriaxone, requires only one nursing encounter daily and is commonly used in New Zealand.

Objectives
To assess the therapeutic success and adverse antibiotic effects of these regimens.

Methods
A retrospective observational case series from multiple hospitals of patients aged 15 years or over with enterococcal endocarditis diagnosed between July 2013 and June 2019 who received at least 14 days of outpatient continuous-infusion benzylpenicillin combined with either gentamicin or ceftriaxone for synergy.

Results
Forty-three episodes of enterococcal endocarditis in 41 patients met inclusion criteria. The primary synergy antibiotic was gentamicin in 20 episodes and ceftriaxone in 23 episodes. For the 41 initial treatment courses, 31 (76%) patients were cured, 3 (7%) patients developed relapsed endocarditis during or following antibiotic treatment and 7 (17%) patients continued with long-term suppressive oral amoxicillin following IV antibiotic treatment. There was no difference in the relapse rate between the two groups (P = 0.59). Seven (35%) adverse antibiotic effects were documented in the gentamicin group and none in the ceftriaxone group (P &lt; 0.01). Two deaths (5%) occurred within the 6 month follow-up period.

Conclusions
Outpatient treatment of enterococcal endocarditis with continuous-infusion benzylpenicillin combined with either once-daily gentamicin or ceftriaxone following a period of inpatient treatment is usually effective. A significantly higher rate of adverse effects was seen with gentamicin, favouring ceftriaxone as the initial synergy antibiotic.
Development of biparatopic bispecific antibody possessing tetravalent scFv-Fc capable of binding to ROBO1 expressed in hepatocellular carcinoma cells
Authors: Watanabe Yuji , Tanabe Aki , Hamakubo Takao , Nagatoishi Satoru , Tsumoto Kouhei 
Published: April 2021

Abstract
There is no standard structural format of the biparatopic bispecific antibody (bbsAb) which is used against the target molecule because of the diversity of biophysical features of bispecific antibodies (bsAbs). It is therefore essential that the interaction between the antibody and antigen is quantitatively analyzed to design antibodies that possess the desired properties. Here, we generated bsAbs, namely, a tandem scFv-Fc, a diabody-Fc, and an immunofusion–scFv-Fc–scFv, that possessed four scFv arms at different positions and were capable of recognizing the extracellular domains of ROBO1. We examined the interactions between these bsAbs and ROBO1 at the biophysical and cellular levels. Of these, immunofusion–B2212A scFv-Fc–B5209B scFv was stably expressed with the highest relative yield. The kinetic and thermodynamic features of the interactions of each bsAb with soluble ROBO1 (sROBO1) were validated using surface plasmon resonance and isothermal titration calorimetry. In all bsAbs, the immunofusion–scFv-Fc–scFv format showed homogeneous interaction with the antigen with higher affinity compared with that of monospecific antibodies. In conclusion, our study presents constructive information to design druggable bbsAbs in drug applications.
Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures
Authors: Cao Jingyi , Xue Yi 
Published: April 2021

Abstract
RNA structures play a fundamental role in nearly every aspect of cellular physiology and pathology. Gaining insights into the functions of RNA molecules requires accurate predictions of RNA secondary structures. However, the existing thermodynamic folding models remain less accurate than desired, even when chemical probing data, such as selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities, are used as restraints. Unlike most SHAPE-directed algorithms that only consider SHAPE restraints for base pairing, we extract two-dimensional structural features encoded in SHAPE data and establish robust relationships between characteristic SHAPE patterns and loop motifs of various types (hairpin, internal, and bulge) and lengths (2–11 nucleotides). Such characteristic SHAPE patterns are closely related to the sugar pucker conformations of loop residues. Based on these patterns, we propose a computational method, SHAPELoop, which refines the predicted results of the existing methods, thereby further improving their prediction accuracy. In addition, SHAPELoop can provide information about local or global structural rearrangements (including pseudoknots) and help researchers to easily test their hypothesized secondary structures.