bluuebunny/crossref_metadata_2025 huggingface dataset:
Scalable analysis of multi-modal biomedical data
Authors: Smith Jaclyn , Shi Yao , Benedikt Michael , Nikolic Milos
Published: September 2021

Background

Targeted diagnosis and treatment options are dependent on insights drawn from multi-modal analysis of large-scale biomedical datasets. Advances in genomics sequencing, image processing, and medical data management have supported data collection and management within medical institutions. These efforts have produced large-scale datasets and have enabled integrative analyses that provide a more thorough look of the impact of a disease on the underlying system. The integration of large-scale biomedical data commonly involves several complex data transformation steps, such as combining datasets to build feature vectors for learning analysis. Thus, scalable data integration solutions play a key role in the future of targeted medicine. Though large-scale data processing frameworks have shown promising performance for many domains, they fail to support scalable processing of complex datatypes.

Solution

To address these issues and achieve scalable processing of multi-modal biomedical data, we present TraNCE, a framework that automates the difficulties of designing distributed analyses with complex biomedical data types.

Performance

We outline research and clinical applications for the platform, including data integration support for building feature sets for classification. We show that the system is capable of outperforming the common alternative, based on “flattening” complex data structures, and runs efficiently when alternative approaches are unable to perform at all.
Successful pregnancy after ovulation induction with human chorionic gonadotropin in a woman with selective luteinising hormone deficiency
Authors: Sasaki Lizandra Moura Paravidine , de Carvalho Bruno Ramalho , Silva Adelino Amaral , Zaconeta Alberto Moreno , da Silva Wanderley Miriam , da Motta Luiz Augusto Casulari Roxo , Lofrano-Porto Adriana
Published: September 2021

Selective LH deficiency has been described in several men, but only in two women who presented normal pubertal development but secondary amenorrhoea due to anovulation. Despite its rarity, this condition represents a valuable model for studying the processes regulated by FSH or LH during late folliculogenesis and ovulation in humans. A woman previously diagnosed with selective LH deficiency due to a homozygous germline splice site mutation in LHB (IVS2 + 1G→C mutation) was submitted to an individualised ovarian induction protocol, first with recombinant LH and then with highly purified urinary hCG. Ovarian follicle growth and ovulation were achieved, and a healthy baby was born after an uneventful term pregnancy. The treatment described herein demonstrates that the clinical actions of exogenous LH or hCG in inducing late-stage follicular development in women with deficient LH production or performance might be interchangeable or inevitable, once FSH-dependent early follicular growth is assured.
Varieties of Populist Attitudes and Their Link to Islamophobia in Switzerland
Authors: Schmidt Franzisca , Eugster Beatrice , Arlt Dorothee
Published: September 2021

The aim of this article is to show whether distinct varieties of populist attitudes emerge within a society, and how they relate to citizens’ Islamophobic attitudes. The study is based on a representative survey conducted in Switzerland in 2019. We used latent class analysis and multinomial regression analyses to identify latent subgroups, yielding five classes of populist attitudes: direct democracy devotees, individuals with populist tendencies, moderate populists, radical anti-elite populists, and radical-universal populists. Compared with the direct democracy devotees class, members of the moderate and the radical-universal populists classes are significantly more likely to hold anti-Muslim and anti-immigrant attitudes and to be politically right-wing, while radical anti-elite populists are not associated with either anti-Muslim attitudes or a right-wing ideology.
The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity
Authors: Kovacevic Aleksandra , Eggo Rosalind M , Baguelin Marc , Domenech de Cellès Matthieu , Opatowski Lulla
Published: September 2021

Background

Circulation of seasonal non–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.

Methods

Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.

Results

We find that a non–SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.

Conclusions

This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.
Lysosomal amino acid transporters as key players in inflammatory diseases
Authors: Toyama-Sorimachi Noriko , Kobayashi Toshihiko
Published: September 2021

Controlling inflammation can alleviate immune-mediated, lifestyle-related and neurodegenerative diseases. The endolysosome system plays critical roles in inflammatory responses. Endolysosomes function as signal transduction hubs to convert various environmental danger signals into gene expression, enabling metabolic adaptation of immune cells and efficient orchestration of inflammation. Solute carrier family 15 member A3 (SLC15A3) and member A4 (SLC15A4) are endolysosome-resident amino acid transporters that are preferentially expressed in immune cells. These transporters play essential roles in signal transduction through endolysosomes, and the loss of either transporter can alleviate multiple inflammatory diseases because of perturbed endolysosome-dependent signaling events, including inflammatory and metabolic signaling. Here, we summarize the findings leading to a proof-of-concept for anti-inflammatory strategies based on targeting SLC15 transporters.
A critique of Chinese diplomatic modernization narratives: reinterpreting shifts in Qing foreign affairs institutions in the early 1860s from the Qing perspective
Authors: Hayamaru Kazumasa
Published: September 2021

Scholars have long read the shifts in late Qing China’s institutional framework for diplomatic interactions through a lens derived from the Western European diplomatic paradigm. However, such a methodology fails to accommodate the autochthonous perspective of the Qing bureaucrats who initiated these shifts in the first place. Drawing upon two case studies from the 1860s, the Zongli Yamen and the proposed Superintendent of Trade for the Yangzi, this article attempts to understand the motivations and priorities of the Qing in establishing new frameworks for diplomatic interactions in this period. The article argues that, for the Qing, it was not the establishment and the efficacy of these new institutions that was important. What mattered to them in this period was how these new institutions could eventually be abolished and an older, idealized form of practice reinstated in their place.
Characterization of the novel plasmid-encoded MBL gene blaAFM-1, integrated into a blaIMP-45-bearing transposon Tn6485e in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate
Authors: Zhang Xuefei , Wang Leilei , Li Dan , Wang Chen , Guo Qinglan , Wang Minggui
Published: September 2021

Objectives

To characterize the novel subclass B1 MBL AFM-1, encoded by a blaIMP-45-bearing megaplasmid from a carbapenem-resistant Pseudomonas aeruginosa (CRPA) clinical isolate.

Methods

CRPA HS17-127 and its transconjugant were discovered to carry blaAFM-1 in our previous study. blaAFM-1 and blaNDM-1 were cloned and expressed in Escherichia coli TOP10 and P. aeruginosa PAO1, respectively, to test the resistance phenotype. Kinetic studies were performed to elucidate the biochemical characteristics of the AFM-1 enzyme. Comparative genomic analysis was applied to investigate the genetic context of blaAFM-1.

Results

PAO1 transconjugant TcHS17-127 exhibited carbapenem resistance with an imipenem MIC of 64 mg/L. E. coli transformants with cloned blaAFM-1 or blaNDM-1 had increased MICs of all β-lactams tested (except aztreonam) and imipenem MICs of 4–8 mg/L. Kinetic studies showed that AFM-1 had greater catalytic efficiency against cephalosporins than carbapenems. blaAFM-1 was located on a 486 963 bp IncP-2 plasmid, pHS17-127, containing a 57.3 kb MDR Tn1403-derivative transposon, Tn6485e, which is genetically closest to the blaIMP-45-bearing Tn6485 transposon but has acquired an extra ISCR27n3-blaAFM-1 module. Multicentre surveillance of 605 P. aeruginosa clinical isolates identified three blaAFM carriers from different STs. Two of them co-carried blaAFM-1 and blaIMP-45. A BLAST search against the NCBI database showed six blaAFM carriers on various plasmids and the chromosomes of different Gram-negative species.

Conclusions

The blaAFM-1 gene confers carbapenem resistance and has been captured in distinct species of non-fermenters. Co-carriage of blaAFM-1 and blaIMP-45 in an MDR transposon on a conjugative plasmid can be expected to promote further dissemination of blaMBLs.
Noninvasive Prenatal Test for β-Thalassemia and Sickle Cell Disease Using Probe Capture Enrichment and Next-Generation Sequencing of DNA in Maternal Plasma
Authors: Erlich Henry A , López-Peña Christian , Carlberg Katie T , Shih Shelly , Bali Gunmeet , Yamaguchi Ken D , Salamon Hugh , Das Reena , Lal Ashutosh , Calloway Cassandra D
Published: September 2021

Background

Noninvasive prenatal testing (NIPT) of chromosomal aneuploidies based on next-generation sequencing (NGS) analysis of fetal DNA in maternal plasma is well established, but testing for autosomal recessive disorders remains challenging. NGS libraries prepared by probe capture facilitate the analysis of the short DNA fragments plasma. This system has been applied to the β-hemoglobinopathies to reduce the risk to the fetus.

Method

Our probe panel captures >4 kb of the HBB region and 435 single-nucleotide polymorphisms (SNPs) used to estimate fetal fraction. Contrived mixtures of DNA samples, plasma, and whole blood samples from 7 pregnant women with β-thalassemia or sickle cell anemia mutations and samples from the father, sibling, and baby or chorionic villus were analyzed. The fetal genotypes, including point mutations and deletions, were inferred by comparing the observed and expected plasma sequence read ratios, based on fetal fraction, at the mutation site and linked SNPs. Accuracy was increased by removing PCR duplicates and by in silico size selection of plasma sequence reads. A probability was assigned to each of the potential fetal genotypes using a statistical model for the experimental variation, and thresholds were established for assigning clinical status.

Results

Using in silico size selection of plasma sequence files, the predicted clinical fetal genotype assignments were correct in 9 of 10 plasma libraries with maternal point mutations, with 1 inconclusive result. For 2 additional plasmas with deletions, the most probable fetal genotype was correct. The β-globin haplotype determined from linked SNPs, when available, was used to infer the fetal genotype at the mutation site.

Conclusion

This probe capture NGS assay demonstrates the potential of NIPT for β-hemoglobinopathies.
Alert burden in pediatric hospitals: a cross-sectional analysis of six academic pediatric health systems using novel metrics
Authors: Orenstein Evan W , Kandaswamy Swaminathan , Muthu Naveen , Chaparro Juan D , Hagedorn Philip A , Dziorny Adam C , Moses Adam , Hernandez Sean , Khan Amina , Huth Hannah B , Beus Jonathan M , Kirkendall Eric S
Published: September 2021

Background

Excessive electronic health record (EHR) alerts reduce the salience of actionable alerts. Little is known about the frequency of interruptive alerts across health systems and how the choice of metric affects which users appear to have the highest alert burden.

Objective

(1) Analyze alert burden by alert type, care setting, provider type, and individual provider across 6 pediatric health systems. (2) Compare alert burden using different metrics.

Materials and Methods

We analyzed interruptive alert firings logged in EHR databases at 6 pediatric health systems from 2016–2019 using 4 metrics: (1) alerts per patient encounter, (2) alerts per inpatient-day, (3) alerts per 100 orders, and (4) alerts per unique clinician days (calendar days with at least 1 EHR log in the system). We assessed intra- and interinstitutional variation and how alert burden rankings differed based on the chosen metric.

Results

Alert burden varied widely across institutions, ranging from 0.06 to 0.76 firings per encounter, 0.22 to 1.06 firings per inpatient-day, 0.98 to 17.42 per 100 orders, and 0.08 to 3.34 firings per clinician day logged in the EHR. Custom alerts accounted for the greatest burden at all 6 sites. The rank order of institutions by alert burden was similar regardless of which alert burden metric was chosen. Within institutions, the alert burden metric choice substantially affected which provider types and care settings appeared to experience the highest alert burden.

Conclusion

Estimates of the clinical areas with highest alert burden varied substantially by institution and based on the metric used.
Socially situated risk: challenges and strategies for implementing algorithmic risk scoring for care management
Authors: Nong Paige , Adler-Milstein Julia
Published: September 2021

Objective

To characterize challenges and strategies related to algorithmic risk scoring for care management eligibility determinations.

Materials and Methods

Interviews with 19 administrators from 13 physician organizations representing over 2200 physician offices and 8800 physicians in Michigan. Post-implementation interviews were coded using thematic analysis.

Results

Utility of algorithmic risk scores was limited due to outdated claims or incomplete information about patients’ socially situated risks (eg, caregiver turnover, social isolation). Resulting challenges included lack of physician engagement and inefficient use of staff time reviewing eligibility determinations. To address these challenges, risk scores were supplemented with physician knowledge and clinical data.

Discussion and Conclusion

Current approaches to risk scoring based on claims data for payer-led programs struggle to gain physician acceptance and support because of data limitations. To respond to these limitations, physician input regarding socially situated risk and utilization of more timely data may improve eligibility determinations.
Development and Interlaboratory Evaluation of an LC–MS/MS Method for the Quantification of Lysozyme in Wine Across Independent Instrument Platforms
Authors: Downs Melanie L , McClure Beth Anne , Jayasena Shyamali , Ramachandran Bini , Krawitzky Michael , Ribeiro Tony , Wallace Julie , Tallman Steve , Mortola Bill
Published: September 2021

Background

Various processing aids and fining agents are used in winemaking to help improve sensory characteristics. Some of these materials may contain or be derived from allergenic foods, such as eggs. In order to ensure food safety and that products meet regulatory compliance, it is essential to have robust and effective analytical methods to verify the removal of allergenic proteins following their use. Current methods include ELISA and MS methods, which can target either whole foods or individual proteins, and provide either quantitative data or qualitative confirmation of proteins. MS methods offer the potential to test for multiple proteins within a single assay to improve cost and efficiency, whereas ELISA methods typically analyze for a single protein per assay.

Objective

This study focuses on the development of a LC–tandem MS (MS/MS) quantitative method for lysozyme in white wine and compares performance across two laboratories utilizing two different instrument platforms.

Methods

Lysozyme target peptides were selected by conducting bottom-up discovery proteomics. Candidate targets were evaluated using parallel reaction monitoring (PRM) or selected reaction monitoring (SRM) LC–MS/MS, depending on the instrument in each laboratory. Quantification of lysozyme was conducted using internal, stable isotope-labeled synthetic peptide standards.

Results

Three of eight candidate target peptides showed performance suitable for the final quantitative method. White wine spiked with 0.1 and 0.5 ppm lysozyme demonstrated quantitative recovery of 70–120%. While the PRM method delivered better repeatability, the SRM method gave higher quantitative recovery values.

Conclusion

A targeted LC–MS/MS method for quantification of lysozyme in white wine has been developed and deployed on two different MS instrument platforms in two laboratories.

Highlights

Both SRM and PRM targeted LC–MS/MS methodologies can be used for quantification of lysozyme in white wine. This study is among the first to evaluate an MS method for food allergen quantification in multiple laboratories.
Linear temporal justification logics with past and future time modalities
Authors: Ghari Meghdad
Published: September 2021

Temporal justification logic is a new family of temporal logics of knowledge in which the knowledge of agents is modelled using a justification logic. In this paper, we present various temporal justification logics involving both past and future time modalities. We combine Artemov’s logic of proofs with linear temporal logic with past, and we also investigate several principles describing the interaction of justification and time. We present two kinds of semantics for our temporal justification logics, one based on interpreted systems and Fitting models and the other based on Mkrtychev models, and further, we establish soundness and completeness. We show that the internalization property holds in some of the temporal justification logics. We further investigate the two well-known epistemic-temporal notions of no forgetting and no learning in the framework of justification logics. Finally, we present temporal justification logics that avoid the logical omniscience problem.
Bringing the Forest Home: Lessons Learned during the COVID-19 Pandemic about E-Planning in Community Forestry Contexts
Authors: Beck Samantha , Coleman Kimberly , Tapper J Ethan
Published: September 2021

This paper examines “e-planning,” or the use of computer-based systems to conduct planning and decision-making, in the context of community forest management. E-planning is growing in the field of environmental planning, as it promises greater equity in terms of public participation. However, a lack of scholarly work exists on the applicability for forest planning. During the COVID-19 pandemic, county foresters and other natural resource professionals in Vermont turned to e-planning when safety restrictions limited their ability to engage in face-to-face efforts. This provided an opportunity to collect empirical data about the potential for e-planning to support the public engagement process in the context of forest planning. We provide an overview of e-planning theory and examine data from Vermont to explore the promise of e-planning for forest management. We make recommendations about the applicability of e-planning in the context of forest planning, and highlight areas for future research to investigate.
How Will COVID-19 Change Forestry Education? A Study of US Forest Operations Instructors
Authors: Dodson Elizabeth M , Blinn Charles R
Published: September 2021

The COVID-19 (COVID) pandemic affected nearly every aspect of higher education. It has been particularly disruptive to forest operations courses that rely heavily on field experiences. Dodson and Blinn (2021) surveyed US forest operations instructors at four-year institutions granting SAF-accredited forestry degrees to understand how they rapidly modified courses during spring 2020 to accommodate a move to fully remote instruction. Through an online survey and interviews, a follow-up study was conducted to understand how courses were modified when instructors had time to prepare and what, if any, of those modifications are likely to be retained upon a return to in-person instruction. Two main themes emerged from the survey and interviews: instructors will expand the range of tools and methods used to convey course content, and they have a renewed respect for the importance of field experience and personal interactions.
Coloration and phenology manifest nutrient variability in senesced leaves of 46 temperate deciduous woody species
Authors: Wang Xingchang , Wang Qi , Chen Yue , Zhao Rui , Zhang Jiahui , Quan Xiankui , Liu Fan , Wang Chuankuan
Published: September 2021

Senesced-leaf nutrient concentrations vary significantly among coexisting plant species reflecting different leaf nutrient use strategies. However, interspecific variation in senesced-leaf nutrients and its driving factors are not well understood. Here, we aimed to determine interspecific variation and its driving factors in senesced-leaf nutrients. We explored interspecific variation in carbon (C), nitrogen (N) and phosphorus (P) concentrations in newly fallen leaves of 46 coexisting temperate deciduous woody species across the Maoershan Forest Ecosystem Research Station, Northeast China. The relative importance of 10 biotic factors (i.e. mycorrhiza type, N-fixing type, growth form, shade tolerance, laminar texture, coloring degree, coloring type, peak leaf-coloration date, peak leaf-fall date and end leaf-fall date) was quantified with the random forest model. N and P concentrations varied 4- and 9-fold among species, respectively. The high mean N (15.38 mg g−1) and P (1.24 mg g−1) concentrations suggested a weak N and P limitation in the studied forest. Functional groups had only significant effects on specific nutrients and their ratios. P concentration and N:P were negatively correlated with peak and end leaf-fall dates for the ectomycorrhiza species group. Brighter-colored leaves (red > brown > yellow > yellow-green > green) tended to have lower N and P concentrations and higher C:N and C:P than darker-colored leaves. The random forest model showed that autumn coloration and leaf-fall phenology contributed 80% to the total explanation of nutrient variability among species. The results increase our understanding of the variability in senesced-leaf nutrients as a strategy of woody plant nutrition in temperate forests.
Radiotherapy inhibits neointimal hyperplasia after artificial vascular replacement through Skp2/P27kip1
Authors: Qiu Jian , Shu Chang , Li Shuang , Xiong Qinggen , Wang Lunchang , Liu Zhongtao , Li Xin , Zhang Weichang
Published: September 2021

We aimed to establish an animal model of abdominal aortic vascular replacement in mongrel dogs to investigate the effect of extracorporeal radiotherapy on the intima. Twenty healthy mongrel dogs were randomly divided into four groups: 5-week control group, 5-week radiotherapy group, 10-week control group and 10-week radiotherapy group. We first performed an artificial vascular replacement of the abdominal aortic segment. The radiotherapy group received external radiotherapy with a dose of 7 Gy for 4 days. The thickness of neointimal hyperplasia, immunoreactivity and expression of proliferation-related factors were detected by hematoxylin and eosin (HE) staining, immunohistochemistry, quantitative real-time polymerase chain reaction (qRT-PCR )and western blotting at 5 and 10 weeks after the reconstruction. The results showed that the intimal thickness of the artificial blood vessel in the 5- and 10-week radiotherapy groups was thinner than that in the control groups by HE staining. The immunoreactivity and expression levels of Skp2, c-Myc and CyclinE1 were significantly decreased in the radiotherapy groups than those in control groups by immunohistochemistry, qRT-PCR and western blotting. On the contrary, immunoreactivity and expression levels of P27kip1 were increased. In conclusion, we discovered that postoperative external radiotherapy significantly decreases the intimal hyperplasia of artificial blood vessels by regulating c-Myc-Skp2-P27-CyclinE1 network.
WAKsing plant immunity, waning diseases
Authors: Stephens Christopher , Hammond-Kosack Kim E , Kanyuka Kostya
Published: September 2021

With the requirement to breed more productive crop plants in order to feed a growing global population, compounded by increasingly widespread resistance to pesticides exhibited by pathogens, plant immunity is becoming an increasingly important area of research. Of the genes that contribute to disease resistance, the wall-associated receptor-like kinases (WAKs) are increasingly shown to play a major role, in addition to their contribution to plant growth and development or tolerance to abiotic stresses. Being transmembrane proteins, WAKs form a central pillar of a plant cell’s ability to monitor and interact with the extracellular environment. Found in both dicots and monocots, WAKs have been implicated in defence against pathogens with diverse lifestyles and contribute to plant immunity in a variety of ways. Whilst some act as cell surface-localized immune receptors recognizing either pathogen- or plant-derived invasion molecules (e.g. effectors or damage-associated molecular patterns, respectively), others promote innate immunity through cell wall modification and strengthening, thus limiting pathogen intrusion. The ability of some WAKs to provide both durable resistance against pathogens and other agronomic benefits makes this gene family important targets in the development of future crop ideotypes and important to a greater understanding of the complexity and robustness of plant immunity.
‘A Word of Song’: Reverberations of the Psalms in Christina Rossetti’s Roundels
Authors: Johnson Stephanie L
Published: September 2021

Christina Rossetti’s Verses (1893) collects poetry published originally in her devotional prose works, and 57 of its 331 lyric poems are roundels. Structured helically, the roundels use refrains to accrue meaning through repetition with a difference. While Rossetti follows Swinburne’s 11-line form, she uses the songs of the Word—the liturgical and wisdom psalms in particular—as the inspiration for her words of song. By recognising the antiphonal dialogue of the roundels modelled on the Psalms, we see more clearly how Rossetti’s lyric poetry emphasises not introspection or a Romantic solipsism but rather an interchange with others that turns its participants toward God. The reverberations of the Psalms in her roundels make audible her commitment to a communal, lyric form that unites its dialogic participants in worship and in an inclusive eschatology; that overlays the temporal with the eternal; and that conveys the priestly act of proclaiming the Kingdom of God in the present.
On the influence of halo mass accretion history on galaxy properties and assembly bias
Authors: Montero-Dorta Antonio D , Chaves-Montero Jonás , Artale M Celeste , Favole Ginevra
Published: September 2021

Halo assembly bias is the secondary dependence of the clustering of dark matter haloes on their assembly histories at fixed halo mass. This established dependence is expected to manifest itself on galaxy clustering, a potential effect commonly known as galaxy assembly bias. Using the IllustrisTNG300 magnetohydrodynamical simulation, we analyse the dependence of the properties and clustering of galaxies on the specific mass accretion history of their hosting haloes (sMAH). We first show that several halo and galaxy properties strongly correlate with the slope of the sMAH (β) at fixed halo mass. Haloes with increasingly steeper β increment their masses faster early on, and their hosted galaxies present larger stellar-to-halo mass ratios, lose their gas faster, reach the peak of their star formation histories at higher redshift, and become quenched earlier. We also demonstrate that β provides a more stable link to these key galaxy formation properties than other broadly employed halo proxies, such as formation time. Finally, we measure the secondary dependence of galaxy clustering on β at fixed halo mass. By tracing back the evolution of individual haloes, we show that the amplitude of the galaxy assembly bias signal for the progenitors of z = 0 galaxies increases with redshift, reaching a factor of 2 at z = 1 for haloes of Mhalo = 1011.5–1012 h−1 M⊙. The measurement of the evolution of assembly bias along the merger tree provides a new theoretical perspective to the study of secondary bias. Our findings have also important implications for the generation of mock catalogues for upcoming cosmological surveys.
Probing the physical properties of the intergalactic medium using blazars
Authors: Dalton Tony , Morris Simon L , Fumagalli Michele , Gatuzz Efrain
Published: September 2021

We use Swift blazar spectra to estimate the key intergalactic medium (IGM) properties of hydrogen column density ($\mathit {N}\small {\rm HXIGM}$), metallicity, and temperature over a redshift range of 0.03 ≤ z ≤ 4.7, using a collisional ionization equilibrium model for the ionized plasma. We adopted a conservative approach to the blazar continuum model given its intrinsic variability and use a range of power-law models. We subjected our results to a number of tests and found that the $\mathit {N}\small {\rm HXIGM}$ parameter was robust with respect to individual exposure data and co-added spectra for each source, and between Swift and XMM–Newton source data. We also found no relation between $\mathit {N}\small {\rm HXIGM}$ and variations in source flux or intrinsic power laws. Though some objects may have a bulk Comptonization component that could mimic absorption, it did not alter our overall results. The $\mathit {N}\small {\rm HXIGM}$ from the combined blazar sample scales as (1 + z)1.8 ± 0.2. The mean hydrogen density at z = 0 is n0 = (3.2 ± 0.5) × 10−7 cm−3. The mean IGM temperature over the full redshift range is log(T/K) =6.1 ± 0.1, and the mean metallicity is [X/H] = −1.62 ± 0.04(Z ∼ 0.02). When combining with the results with a gamma-ray burst (GRB) sample, we find the results are consistent over an extended redshift range of 0.03 ≤ z ≤ 6.3. Using our model for blazars and GRBs, we conclude that the IGM contributes substantially to the total absorption seen in both blazar and GRB spectra.
Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross
Authors: Bredemeyer Kevin R , Seabury Christopher M , Stickney Mark J , McCarrey John R , vonHoldt Bridgett M , Murphy William J
Published: September 2021

The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
Predict long-range enhancer regulation based on protein–protein interactions between transcription factors
Authors: Wang Hao , Huang Binbin , Wang Jianrong
Published: September 2021

Long-range regulation by distal enhancers plays critical roles in cell-type specific transcriptional programs. Computational predictions of genome-wide enhancer–promoter interactions are still challenging due to limited accuracy and the lack of knowledge on the molecular mechanisms. Based on recent biological investigations, the protein–protein interactions (PPIs) between transcription factors (TFs) have been found to participate in the regulation of chromatin loops. Therefore, we developed a novel predictive model for cell-type specific enhancer–promoter interactions by leveraging the information of TF PPI signatures. Evaluated by a series of rigorous performance comparisons, the new model achieves superior performance over other methods. The model also identifies specific TF PPIs that may mediate long-range regulatory interactions, revealing new mechanistic understandings of enhancer regulation. The prioritized TF PPIs are associated with genes in distinct biological pathways, and the predicted enhancer–promoter interactions are strongly enriched with cis-eQTLs. Most interestingly, the model discovers enhancer-mediated trans-regulatory links between TFs and genes, which are significantly enriched with trans-eQTLs. The new predictive model, along with the genome-wide analyses, provides a platform to systematically delineate the complex interplay among TFs, enhancers and genes in long-range regulation. The novel predictions also lead to mechanistic interpretations of eQTLs to decode the genetic associations with gene expression.
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale
Authors: Zhang Wenliang , Zhang Yan , Min Zhuochao , Mo Jing , Ju Zhen , Guan Wen , Zeng Binghui , Liu Yang , Chen Jianliang , Zhang Qianshen , Li Hanguang , Zeng Chunxia , Wei Yanjie , Chan Godfrey Chi-Fung
Published: September 2021

Many open access transcriptomic data of coronavirus disease 2019 (COVID-19) were generated, they have great heterogeneity and are difficult to analyze. To utilize these invaluable data for better understanding of COVID-19, additional software should be developed. Especially for researchers without bioinformatic skills, a user-friendly platform is mandatory. We developed the COVID19db platform (http://hpcc.siat.ac.cn/covid19db & http://www.biomedical-web.com/covid19db) that provides 39 930 drug–target–pathway interactions and 95 COVID-19 related datasets, which include transcriptomes of 4127 human samples across 13 body sites associated with the exposure of 33 microbes and 33 drugs/agents. To facilitate data application, each dataset was standardized and annotated with rich clinical information. The platform further provides 14 different analytical applications to analyze various mechanisms underlying COVID-19. Moreover, the 14 applications enable researchers to customize grouping and setting for different analyses and allow them to perform analyses using their own data. Furthermore, a Drug Discovery tool is designed to identify potential drugs and targets at whole transcriptomic scale. For proof of concept, we used COVID19db and identified multiple potential drugs and targets for COVID-19. In summary, COVID19db provides user-friendly web interfaces to freely analyze, download data, and submit new data for further integration, it can accelerate the identification of effective strategies against COVID-19.
Tobacco Tracker: A New Tool to Support College Smoke and Tobacco Free Policies
Authors: Pulvers Kim , Rice Myra , Stewart Susan LeRoy , Tong Elisa
Published: September 2021

Introduction

University community members are critical to the success of their smoke and tobacco free (STF) policies. The present study evaluates changes in social enforcement-related attitudes and behaviors following introduction of a new online Tobacco Tracker tool in two university settings.

Methods

Campus wide surveys were administered to current students, faculty, and staff at two California public universities with 100% STF policies before (November 2018; N = 5078) and after (December 2019–January 2020; N = 4853) introduction of Tobacco Tracker in February 2019. Prospective surveillance reports over 12 months from Tobacco Tracker, a GIS tool for the campus community to report tobacco use and related litter that displays crowdsourced maps of hotspots, were analyzed. Outcomes included awareness and self-reported use of a tobacco reporting tool, readiness for policy social enforcement, an Intellectual Social Affective (ISA) Engagement scale, and environmental surveillance reports from Tobacco Tracker.

Results

In campus surveys, awareness of a tobacco reporting tool doubled (8.0%–16.9%, p < .0001), use of an online reporting tool tripled (1.1%–3.2%, p < .0001), and readiness to enforce the policy increased (p = .0008). ISA engagement did not change (p = .72). In Tobacco Tracker campus reports (N = 1163), active tobacco use was reported more frequently than tobacco-related litter.

Conclusions

Tobacco Tracker is a promising tool for college communities to support STF policy. Introduction of Tobacco Tracker was associated with an increase in campus awareness and utilization of a reporting tool, readiness to enforce policy, and campus tobacco surveillance. Future research should determine how Tobacco Tracker may improve policy compliance.

Implications

Tobacco Tracker is a promising tool for college communities to support smoke and tobacco free (STF) policy through active surveillance of smoking, vaping, and related litter on campus. Introduction of Tobacco Tracker was associated with changes in social enforcement-related attitudes and behaviors critical to realizing the preventive potential of STF policies. A crowdsourcing-based tool for monitoring tobacco use on college campuses can address a major barrier to social enforcement: discomfort confronting tobacco users. Further, it provides an alternative to punitive enforcement approaches and promises a sustainable solution to an infrastructure issue faced by many universities lacking resources to collect data on campus tobacco use and related litter.
A rich and bountiful harvest: Key discoveries in plant cell biology
Authors: Cheung Alice Y , Cosgrove Daniel J , Hara-Nishimura Ikuko , Jürgens Gerd , Lloyd Clive , Robinson David G , Staehelin L Andrew , Weijers Dolf
Published: September 2021

The field of plant cell biology has a rich history of discovery, going back to Robert Hooke’s discovery of cells themselves. The development of microscopes and preparation techniques has allowed for the visualization of subcellular structures, and the use of protein biochemistry, genetics, and molecular biology has enabled the identification of proteins and mechanisms that regulate key cellular processes. In this review, seven senior plant cell biologists reflect on the development of this research field in the past decades, including the foundational contributions that their teams have made to our rich, current insights into cell biology. Topics covered include signaling and cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology. In addition, these scientists illustrate the pathways to discovery in this exciting research field.
A Theory of Monetary Union and Financial Integration
Authors: Fornaro Luca
Published: September 2021

Since the creation of the euro, capital flows among member countries have been large and volatile. Motivated by this fact, I provide a theory connecting the exchange rate regime to financial integration. The key feature of the model is that monetary policy affects the value of collateral that creditors seize upon default. Under flexible exchange rates, national governments can expropriate foreign creditors by depreciating the exchange rate, which induces investors to impose tight constraints on international borrowing. Creating a monetary union, by eliminating this source of currency risk, increases financial integration among member countries. This process, however, does not necessarily lead to higher welfare. The reason is that a high degree of capital mobility can generate multiple equilibria, with bad equilibria characterized by inefficient capital flights. Capital controls or fiscal transfers can eliminate bad equilibria, but their implementation requires international cooperation.
Harnessing of real-world data and real-world evidence using digital tools: utility and potential models in rheumatology practice
Authors: Kataria Suchitra , Ravindran Vinod
Published: September 2021

The diversity of diseases in rheumatology and variability in disease prevalence necessitates greater data parity in disease presentation, treatment responses including adverse events to drugs and various comorbidities. Randomized controlled trials are the gold standard for drug development and performance evaluation. However, when the drug is applied outside the controlled environment, the outcomes may differ in patient populations. In this context, the need to understand the macro and micro changes involved in disease evolution and progression becomes important and so is the need for harvesting and harnessing the real-world data from various resources to use them in generating real-world evidence. Digital tools with potential relevance to rheumatology can potentially be leveraged to obtain greater patient insights, greater information on disease progression and disease micro processes and even in the early diagnosis of diseases. Since the patients spend only a minuscule portion of their time in hospital or in a clinic, using modern digital tools to generate realistic, bias-proof, real-world data in a non-invasive patient-friendly manner becomes critical. In this review we have appraised different digital mediums and mechanisms for collecting real-world data and proposed digital care models for generating real-world evidence in rheumatology.
“It’s Like Giving Birth to This Girl Again”: Social Repair and Motherhood After Conflict-Related Sexual Violence
Authors: Oliveira Camile , Baines Erin
Published: September 2021

In the strain of remaking the social world after a violent conflict, women who conceive children as the result of sexual violence must often raise them amongst resentful victim communities. Abducted and forced into marriage by the Lord’s Resistance Army in northern Uganda, Acholi women are perceived to have returned with the children of the enemy and are subsequently told they do not belong. Based on ten years of collaborative research with war-affected mothers in northern Uganda, we consider the ways women repair webs of kin relations to secure a future no longer dictated by the circumstances of their children’s birth.
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks
Authors: Yang Bing , Zhang Zhenxin , Yang Cai-Qing , Wang Ying , Orr Michael C , Wang Hongbin , Zhang Ai-Bing
Published: September 2021

Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.]
A review of electrical signal-based train transmission machinery diagnosis technology
Authors: Dai Jisheng , Ding Rongjun , Guan Zhaoyi , Xu Shaolong
Published: September 2021

Transmission machinery is widely used in railway vehicles and is an important component in driving the operation of trains. Such transmission components are prone to faults under long exposure to harsh environments and complex working conditions. This affects normal operation and order, and thus it is important to ensure their safe and reliable operation. Electrical signal-based diagnosis technology has advantages of easy signal acquisition, with no need to install additional sensors, nor embedded monitoring of the object components. It has gradually become a research hotspot in the field of rail transportation diagnosis. This paper describes the fault modes of transmission machinery, takes the electrical signal-based diagnosis method as the entry point, collates and compares the existing diagnosis methods and research results in this field. It analyses their advantages and disadvantages, and finally puts forward problems for current and future research and development.