bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Microsatellite Variability Screen for Positive Selection Associated With the “Out of Africa” Habitat Expansion ofDrosophila melanogaster
Authors: Kauer M O , Dieringer D , Schlötterer C 
Published: April 2021

AbstractWe report a “hitchhiking mapping” study in D. melanogaster, which searches for genomic regions with reduced variability. The study's aim was to identify selective sweeps associated with the “out of Africa” habitat expansion. We scanned 103 microsatellites on chromosome 3 and 102 microsatellites on the X chromosome for reduced variability in non-African populations. When the chromosomes were analyzed separately, the number of loci with a significant reduction in variability only slightly exceeded the expectation under neutrality—six loci on the third chromosome and four loci on the X chromosome. However, non-African populations also have a more pronounced average loss in variability on the X chromosomes as compared to the third chromosome, which suggests the action of selection. Therefore, comparing the X chromosome to the autosome yields a higher number of significantly reduced loci. However, a more pronounced loss of variability on the X chromosome may be caused by demographic events rather than by natural selection. We therefore explored a range of demographic scenarios and found that some of these captured most, but not all aspects of our data. More theoretical work is needed to evaluate how demographic events might differentially affect X chromosomes and autosomes and to estimate the most likely scenario associated with the out of Africa expansion of D. melanogaster.
Heterochromatic Self-Association, a Determinant of Nuclear Organization, Does Not Require Sequence Homology in Drosophila
Authors: Sage Brian T , Csink Amy K 
Published: April 2021

AbstractChromosomes of higher eukaryotes contain blocks of heterochromatin that can associate with each other in the interphase nucleus. A well-studied example of heterochromatic interaction is the brownDominant (bwD) chromosome of D. melanogaster, which contains an ∼1.6-Mbp insertion of AAGAG repeats near the distal tip of chromosome 2. This insertion causes association of the tip with the centric heterochromatin of chromosome 2 (2h), which contains megabases of AAGAG repeats. Here we describe an example, other than bwD, in which distally translocated heterochromatin associates with centric heterochromatin. Additionally, we show that when a translocation places bwD on a different chromosome, bwD tends to associate with the centric heterochromatin of this chromosome, even when the chromosome contains a small fraction of the sequence homology present elsewhere. To further test the importance of sequence homology in these interactions, we used interspecific mating to introgress the bwD allele from D. melanogaster into D. simulans, which lacks the AAGAG on the autosomes. We find that D. simulans bwD associates with 2h, which lacks the AAGAG sequence, while it does not associate with the AAGAG containing X chromosome heterochromatin. Our results show that intranuclear association of separate heterochromatic blocks does not require that they contain the same sequence.
Genetic and Phenotypic Analysis of Alleles of the Drosophila Chromosomal JIL-1 Kinase Reveals a Functional Requirement at Multiple Developmental Stages
Authors: Zhang Weiguo , Jin Ye , Ji Yun , Girton Jack , Johansen Jørgen , Johansen Kristen M 
Published: April 2021

AbstractIn this study we provide a cytological and genetic characterization of the JIL-1 locus in Drosophila. JIL-1 is an essential chromosomal tandem kinase and in JIL-1 null animals chromatin structure is severely perturbed. Using a range of JIL-1 hypomorphic mutations, we show that they form an allelic series. JIL-1 has a strong maternal effect and JIL-1 activity is required at all stages of development, including embryonic, larval, and pupal stages. Furthermore, we identified a new allele of JIL-1, JIL-1h9, that encodes a truncated protein missing COOH-terminal sequences. Remarkably, the truncated JIL-1 protein can partially restore viability without rescuing the defects in polytene chromosome organization. This suggests that sequences within this region of JIL-1 play an important role in establishing and/or maintaining normal chromatin structure. By analyzing the effects of JIL-1 mutations we provide evidence that JIL-1 function is necessary for the normal progression of several developmental processes at different developmental stages such as oogenesis and segment specification. We propose that JIL-1 may exert such effects by a general regulation of chromatin structure affecting gene expression.
Rank-Based Statistical Methodologies for Quantitative Trait Locus Mapping
Authors: Zou Fei , Yandell Brian S , Fine Jason P 
Published: April 2021

Abstract
This article addresses the identification of genetic loci (QTL and elsewhere) that influence nonnormal quantitative traits with focus on experimental crosses. QTL mapping is typically based on the assumption that the traits follow normal distributions, which may not be true in practice. Model-free tests have been proposed. However, nonparametric estimation of genetic effects has not been studied. We propose an estimation procedure based on the linear rank test statistics. The properties of the new procedure are compared with those of traditional likelihood-based interval mapping and regression interval mapping via simulations and a real data example. The results indicate that the nonparametric method is a competitive alternative to the existing parametric methodologies.
Chromosome Condensation Defects in barren RNA-Interfered Drosophila Cells
Authors: Somma Maria Patrizia , Fasulo Barbara , Siriaco Giorgia , Cenci Giovanni 
Published: April 2021

Abstract
Barren, the Drosophila homolog of XCAP-H, is one of three non-SMC subunits of condensin, a conserved 13S multiprotein complex required for chromosome condensation. Mutations in barren (barr) were originally shown to affect sister-chromatid separation during mitosis 16 of the Drosophila embryo, whereas condensation defects were not detected. In contrast, mutations in yeast homologs of barren result in defective mitotic chromosome condensation as well as irregular chromatid separation. We have used double-stranded RNA-mediated interference (RNAi) to deplete Barren in Drosophila S2 cells. Our analyses indicate that inactivation of barr leads to extensive chromosome condensation and disrupts chromatid segregation.
Genomic Rearrangements at rrn Operons in Salmonella
Authors: Helm R Allen , Lee Alison G , Christman Harry D , Maloy Stanley 
Published: April 2021

Abstract
Most Salmonella serovars are general pathogens that infect a variety of hosts. These “generalist” serovars cause disease in many animals from reptiles to mammals. In contrast, a few serovars cause disease only in a specific host. Host-specific serovars can cause a systemic, often fatal disease in one species yet remain avirulent in other species. Host-specific Salmonella frequently have large genomic rearrangements due to recombination at the ribosomal RNA (rrn) operons while the generalists consistently have a conserved chromosomal arrangement. To determine whether this is the result of an intrinsic difference in recombination frequency or a consequence of lifestyle difference between generalist and host-specific Salmonella, we determined the frequency of rearrangements in vitro. Using lacZ genes as portable regions of homology for inversion analysis, we found that both generalist and host-specific serovars of Salmonella have similar tolerances to chromosomal rearrangements in vitro. Using PCR and genetic selection, we found that generalist and host-specific serovars also undergo rearrangements at rrn operons at similar frequencies in vitro. These observations indicate that the observed difference in genomic stability between generalist and host-specific serovars is a consequence of their distinct lifestyles, not intrinsic differences in recombination frequencies.
Epipelagic zooplankton diversity in the deep water region of the Gulf of Mexico: a metabarcoding survey
Authors: Martinez Miguel A , Hereu Clara María , Arteaga María Clara , Jiménez-Rosenberg Sylvia P A , Herzka Sharon Z , Saavedra-Flores Anaid , Robles-Flores Javier , Gomez-Reyes Ricardo , Batta-Lona Paola Gabriela , Gasca-Pineda Jaime , Galindo-Sánchez Clara E 
Published: April 2021

AbstractZooplankton is a key component in marine ecosystem health assessment. Here, we present a taxonomically comprehensive description of the zooplankton community (0–200 m) based on metabarcoding of the V9 hypervariable region of the 18S rRNA gene of 47 samples collected in the Gulf of Mexico (GoM) during summer 2015. Fourteen phyla were identified Arthropoda were dominant, with Calanidae, Metridinidae, and Euphausiidae as the most conspicuous families. Other abundant phyla were Cnidaria (Hydrozoa), Chordata (Tunicata), and Chaetognatha. The V9-18S sequence data were clustered into 1888 Operational Taxonomic Units (OTUs), of which 39 were cosmopolitan and belonging to various phyla, suggesting the presence of a core community with high local diversity throughout the GoM. Evaluation of metabarcoding sequences abundance showed overall positive correlations with morphologically quantified abundances except for specific groups. Cluster analysis of OTU distributions indicated two primary biographically distinctive groups of stations: one restricted to the Bay of Campeche, while the other occurred in the Central-West GoM, similar to previous descriptions of regional variation of the GoM based on environmental variables. Together these results provide a foundation for broad-scale zooplankton molecular biodiversity assessments in the southern GoM allowing evaluation of the effects of environmental changes on zooplankton communities.
Rebel Fragmentation and the Recruitment of Child Soldiers
Authors: Faulkner Christopher M , Doctor Austin C 
Published: April 2021

AbstractThe recruitment and use of children in armed conflict remains a prevalent feature of modern civil war. But which conflict actors are more likely to recruit children? We argue that the process by which rebel groups form shapes their recruitment strategies. Specifically, we contend that rebels that form as splinter factions from the ranks of pre-existing rebel organizations are more likely to recruit child soldiers than other rebel groups. Splinter groups face unique constraints as they materialize in the midst of an active conflict environment, necessitating that they mobilize a sufficient force to contend with existing competitors. As a result, rebel factions are more likely to pursue recruitment strategies that are low cost vis-à-vis alternatives, focusing on their immediate survival. Under such conditions, children become especially attractive recruits. Leveraging the Foundations of Rebel Group Emergence Dataset, our cross-national investigation of 237 rebel groups active between 1989 and 2011 provides robust support for our hypothesis that splinter factions are strongly associated with the recruitment of children.
Contrast-enhanced Mammography: A Guide to Setting Up a New Clinical Program
Authors: Kim Geunwon , Patel Bhavika , Mehta Tejas S , Du Linda , Mehta Rashmi J , Phillips Jordana 
Published: April 2021

Abstract
Contrast-enhanced mammography (CEM) is gaining rapid traction following the U.S. Food and Drug Administration approval for diagnostic indications. Contrast-enhanced mammography is an alternative form of mammography that uses a dual-energy technique for image acquisition after the intravenous administration of iodinated contrast material. The resulting exam includes a dual set of images, one that appears similar to a routine 2D mammogram and one that highlights areas of contrast uptake. Studies have shown improved sensitivity compared to mammography and similar performance to contrast-enhanced breast MRI. As radiology groups incorporate CEM into clinical practice they must first select the indications for which CEM will be used. Many practices initially use CEM as an MRI alternative or in cases recommended for biopsy. Practices should then define the CEM clinical workflow and patient selection to include ordering, scheduling, contrast safety screening, and managing imaging on the day of the exam. The main equipment requirements for performing CEM include CEM-capable mammography equipment, a power injector for contrast administration, and imaging-viewing capability. The main staffing requirements include personnel to place the intravenous line, perform the CEM exam, and interpret the CEM. To safely and appropriately perform CEM, staff must be trained in their respective roles and to manage potential contrast-related events. Lastly, informing referring colleagues and patients of CEM through marketing campaigns is helpful for successful implementation.
Prognostic role of interstitial pneumonia with or without emphysema in patients with clinical stage I lung cancer
Authors: Tsutani Yasuhiro , Kagimoto Atsushi , Handa Yoshinori , Mimae Takahiro , Miyata Yoshihiro , Okada Morihito 
Published: April 2021

Abstract

Objectives
The prognostic role of interstitial pneumonia with emphysema in lung cancer is not fully understood. This study aimed to examine the prognostic role of the presence of emphysema in patients with clinical stage I lung cancer and interstitial pneumonia.

Methods
The presence of interstitial pneumonia and emphysema was evaluated on preoperative high-resolution computed tomography. In total, 836 consecutive patients with clinical stage I lung cancer who underwent complete resection between April 2007 and March 2016 were retrospectively analyzed using the log-rank test and Cox proportional hazard model to examine survival differences.

Results
There was a significant difference in 5-year overall survival between patients with interstitial pneumonia and emphysema (n = 65) and those without (n = 771) (62.6% vs. 86.5%; P &lt; 0.001). However, in patients with interstitial pneumonia on high-resolution computed tomography, there was no significant difference in 5-year overall survival between patients with emphysema (n = 65) and those without emphysema (n = 50) (62.6% vs. 59.4%, P = 0.84). Multivariable backward stepwise Cox proportional hazard analysis in patients with interstitial pneumonia showed that histology, %diffusing capacity of the lungs for carbon monoxide, radiologic interstitial pneumonia pattern and surgical procedure were independent prognostic factors for overall survival, but the presence of emphysema was not.

Conclusions
The presence of emphysema was not an independent prognostic factor for overall survival in patients with clinical stage I lung cancer with interstitial pneumonia. Poor survival of patients with IP and emphysema may be due to the presence of interstitial pneumonia.
The Semantics of Emotive Markers and Other Illocutionary Content
Authors: Rett Jessica 
Published: April 2021

AbstractI identify a class of expressions called ‘emotive markers,’ exemplified by fortunately and alas, which encode not-at-issue information about the speaker’s emotive attitude towards the content of the utterances they occur in. I argue that there are important differences emotive markers and other encoders of not-at-issue content, in particular utterance modifiers like frankly or evidential adverbs like apparently. In contrast to these, emotive markers can result in Moore’s Paradox and always range over their local argument. I conclude that the contribution of emotive markers should be treated as ‘illocutionary content’, on par with the speaker’s other Discourse Commitments (Gunlogson, 2001), and I model this analysis in the dynamic sub-sentential update framework in Farkas & Bruce (2010).
COVID-19 Contact Tracing in an Overseas U.S. Military Population
Authors: Sikorski Cynthia S , Scheel Misty D , Harris Stephanie M , Nefczyk Julia A 
Published: April 2021

ABSTRACT
The purpose of this study was to describe the early epidemiology and contact tracing challenges for Covid-19 infection in an overseas military and DoD population.
From February 28, 2020 to April 27, 2020, patients who were diagnosed with Covid-19 infection completed a Centers for Disease Control Persons Under Investigation (PUI) form during their encounter with a medical provider. Positive results were forwarded to the Public Health Department. The results of the contact tracing and PUI form were entered into a database and analyzed.
Eight Covid-19 cases were diagnosed in this overseas population. Based on beneficiary population, the cumulative incidence was ∼80/100,000 persons. The age distribution ranged from 25 to 60 years, median 36 years. Most patients were male (75%). More infection occurred in those living off base in the community (87.5%). With the capability of on-site testing at the hospital, the median duration from symptom onset to diagnosis improved from 5 days to 1 day.
Disease contact tracing for DoD populations presents unique considerations in an overseas location. Public Health guidelines for the USA may have varying relevance in an overseas location. Rapid case identification with on-site testing is critical to disrupt disease transmission. Preventive measures for Covid-19 infection have decreased incidence of influenza-like illness.
Learning Fundamentals of Laparoscopic Surgery Manual Skills: An Institutional Experience With Remote Coaching and Assessment
Authors: Miles Shana , Donnellan Nicole 
Published: April 2021

ABSTRACT

Introduction
COVID-19 has altered the landscape of traditional surgical education. This is a pilot study of remote coaching and assessment of Fundamentals of Laparoscopic Surgery (FLS) manual skills in obstetrics and gynecology residents.

Materials and Methods
PGY-3 obstetrics and gynecology residents participated in remote assessment of FLS manual skills using a live streaming platform. Learners who showed deficiencies in proficiency participated in live-streamed coaching sessions. The coaching sessions continued until the learner and coach mutually agreed that the learner was prepared for the skills portion of the FLS certification exam. The primary outcome was learner performance on skills assessment with external validation through the FLS manual skills exam pass rate.

Results
One learner demonstrated proficiency at baseline and the remaining nine underwent remote coaching sessions. Learners received a mean of two coaching sessions to reach mutually agreed readiness for the FLS exam as per learner and coach. All residents performed significantly better at the conclusion of the remote coaching series (11.3 ± 0.82) as compared to their baseline scores (8.8 ± 2.82) (P &lt; .03; 95% CI, 0.31-4.69). Proficiency was externally validated through the FLS exam taken by each resident 1-2 weeks following their final assessment, with all learners passing the manual portion. The average satisfaction of learners with remote coaching was 77/100 (range 50-100). 100% of learners felt prepared for their FLS certification exam and 100% would recommend this remote training program to a colleague.

Conclusion
Remote coaching and assessment of FLS skills yields similar results to traditional face-to-face instruction.
Vulture Genomes Reveal Molecular Adaptations Underlying Obligate Scavenging and Low Levels of Genetic Diversity
Authors: Zou Dahu , Tian Shilin , Zhang Tongzuo , Zhuoma Nima , Wu Guosheng , Wang Muyang , Dong Lu , Rossiter Stephen J , Zhao Huabin 
Published: April 2021

Abstract
Obligate scavenging on the dead and decaying animal matter is a rare dietary specialization that in extant vertebrates is restricted to vultures. These birds perform essential ecological services, yet many vulture species have undergone recent steep population declines and are now endangered. To test for molecular adaptations underlying obligate scavenging in vultures, and to assess whether genomic features might have contributed to their population declines, we generated high-quality genomes of the Himalayan and bearded vultures, representing both independent origins of scavenging within the Accipitridae, alongside a sister taxon, the upland buzzard. By comparing our data to published sequences from other birds, we show that the evolution of obligate scavenging in vultures has been accompanied by widespread positive selection acting on genes underlying gastric acid production, and immunity. Moreover, we find evidence of parallel molecular evolution, with amino acid replacements shared among divergent lineages of these scavengers. Our genome-wide screens also reveal that both the Himalayan and bearded vultures exhibit low levels of genetic diversity, equating to around a half of the mean genetic diversity of other bird genomes examined. However, demographic reconstructions indicate that population declines began at around the Last Glacial Maximum, predating the well-documented dramatic declines of the past three decades. Taken together, our genomic analyses imply that vultures harbor unique adaptations for processing carrion, but that modern populations are genetically depauperate and thus especially vulnerable to further genetic erosion through anthropogenic activities.
The DNA binding domain of theVibrio vulnificusSmcR transcription factor is flexible and binds diverse DNA sequences
Authors: Newman Jane D , Russell Meghan M , Fan Lixin , Wang Yun-Xing , Gonzalez-Gutierrez Giovanni , van Kessel Julia C 
Published: April 2021

AbstractQuorum sensing gene expression in vibrios is regulated by the LuxR/HapR family of transcriptional factors, which includes Vibrio vulnificus SmcR. The consensus binding site of Vibrio LuxR/HapR/SmcR proteins is palindromic but highly degenerate with sequence variations at each promoter. To examine the mechanism by which SmcR recognizes diverse DNA sites, we generated SmcR separation-of-function mutants that either repress or activate transcription but not both. SmcR N55I is restricted in recognition of single base-pair variations in DNA binding site sequences and thus is defective at transcription activation but retains interaction with RNA polymerase (RNAP) alpha. SmcR S76A, L139R and N142D substitutions disrupt the interaction with RNAP alpha but retain functional DNA binding activity. X-ray crystallography and small angle X-ray scattering data show that the SmcR DNA binding domain exists in two conformations (wide and narrow), and the protein complex forms a mixture of dimers and tetramers in solution. The three RNAP interaction-deficient variants also have two DNA binding domain conformations, whereas SmcR N55I exhibits only the wide conformation. These data support a model in which two mechanisms drive SmcR transcriptional activation: interaction with RNAP and a multi-conformational DNA binding domain that permits recognition of variable DNA sites.