bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Potential of Brood Recapping to Select Varroa destructor (Acari: Varroidae) Resistant Honey Bees (Hymenoptera: Apidae)
Authors: Guichard Matthieu , von Virag Adrien , Dainat Benjamin 
Published: December 2022

Abstract
Several resistance traits have been proposed to select honey bees (Apis mellifera L.) that can survive in the presence of parasitic mite Varroa destructor (Anderson and Trueman) and enable a more sustainable apiculture. The interest for uncapping-recapping has recently increased following its identification in several naturally surviving honey bee populations, yet the utility of this trait for human-mediated selection is poorly known. Here, we evaluated the repeatability of recapping and its correlations with mite infestation levels, and assessed the expression of the trait in the often neglected drone brood. We also calculated correlations between recapping, mite infertility, and mite fecundity, expressed either at the level of individual brood cells or of the whole colony. Recapping measured in worker brood showed moderate repeatability (ranging between 0.30 and 0.46). Depending on sample, recapping slightly correlated negatively with colony infestation values. Recapping was also measured in drone brood, with values often comparable to recapping in worker brood, but no significant correlations were obtained between castes. At cell level, recapped cells in drone brood (but not in workers) were significantly less infested than nonrecapped cells, whereas in workers (but not in drones), recapped cells hosted mites with significantly lower fecundity. At colony level, with a few exceptions, recapping did not significantly correlate with mite infertility and fecundity, caste, sample, or number of infested cells considered. These results indicate limited possibilities of impeding mite reproduction and possibly mite infestation of honey bee colonies by recapping, which would need to be confirmed on larger, different populations.
Using COVID-19 to Address Environmental Threats to Health and Leverage for Prison Reform in South Africa, Malawi and Zimbabwe
Authors: Van Hout Marie Claire 
Published: December 2022

AbstractHealth rights of prisoners has long been a neglected political issue in Africa, where over one million people are detained, and almost half of whom are in pre-trial detention. African prisons constitute high-risk environments for communicable disease transmission. During the COVID-19 pandemic, the public health literature on African prison responses focused on preparedness as it related to testing capacity, quarantine practices and personal protective measures to mitigate disease spread. This article combines the right to health as narrowly defined by a prisoner’s right to access non-discriminatory equivalent health care, with a broader focus on assessing normative standards of detention. A comparative legal realist assessment of prison operations in South Africa, Malawi and Zimbabwe during COVID-19 state disaster measures is presented, focusing on the environmental determinants of health (ventilation, minimum floor space, water, sanitation, hygiene and nutrition) in prisons. It reveals the inherent tensions in ensuring a balance between respecting the fundamental rights of people living and working in prisons, ensuring adequate environmental health standards and mitigating disease during public health emergencies. Despite insufficient government resourcing and inadequate coverage of COVID-19 responses, few severe outbreaks were reported. This could be due to lack of testing, reporting or other factors (asymptomatic infection, acquired immunity). Prison congestion and unrest however affected prisoners and staff fearful of hazardous living and occupational health conditions. COVID-19 as public health emergency amplifies the need to address systemic deficits in infrastructure, resourcing and efficiency of criminal justice systems. Policy level and pragmatic recommendations for enhanced human rights practice are outlined.
Prosecuting Aggression against Ukraine as an ‘Other Inhumane Act’ before the ICC
Authors: Pinzauti Giulia , Pizzuti Alessandro 
Published: December 2022

Abstract
This article revisits the possibility of prosecuting the underlying acts of aggression as crimes against humanity before the International Criminal Court, with specific reference to the February 2022 unlawful use of force against Ukraine by the Russian Federation. The authors argue that Russia’s unlawful use of force in breach of the right to self-determination of the Ukrainian people, which caused them great suffering or serious injury to mental/physical health, can be qualified as other inhumane acts under Article 7(1)(k) of the Rome Statute. While this approach has its challenges, it would allow the Court to prosecute the underlying acts of aggression as crimes against humanity avoiding the jurisdictional limitations that apply to the crime of aggression.
Parental self-medication and associated factors in children: a cross-sectional study in Turkey
Authors: Karatas Yusuf , Khan Zakir , Öz Emine Ekemen , Özagil Ezgi Sena Gören , Abussuutoğlu Ayşe Büşra , Erkişi Tansu , Pelit Aykut , Khan Faiz Ullah , Rahman Hazir 
Published: December 2022

AbstractObjectiveThis study was conducted to evaluate the parental self-medication (SM) practices in children and associated factors in Adana, Turkey.MethodsA web-based cross-sectional survey was carried out among the parents between December 2020 and April 2021. This study was conducted according to the ‘Checklist for Reporting Results of Internet E-Surveys (CHERRIES)’ guidelines. A one-page survey included details about sociodemographic characteristics (gender, age, profession, education of parents and others) sources of information, questions related to parental SM practices for their children (SM practices, common illnesses, drugs used as SM practices and drug-related information) and the reasons behind SM practices were disseminated via social media networks (Instagram, WhatsApp and Facebook) to eligible participants. Online sample size calculator was used, and snow-ball sampling was employed during the study. The final automatic responses from Google Forms were retrieved as ‘Excel datasheet’ and then cleaned, coded and imported into the SPSS statistical tool (v.25.0).Key findingsThis study included a total of 370 participants (response rate of 95.4%). Parental SM practices were revealed to be more (n = 234; 63.5%) prevalent. The most frequent problems for parents who follow SM practices were fever (39.5%; n = 146) and abdominal pain (23.8%; n = 88). The most commonly used class of drugs was antipyretics followed by analgesics and antibiotics. The main reasons for SM practices were personal experience in treating children (n = 186; 50.3%) and high consultation charges (n = 72; 19.5%). Mother working status and parental educational level were two main factors found to be statistically associated with SM practices (P &lt; 0.05).ConclusionsThe prevalence of parental SM practices was high. There is an urgent need for the parental educational program, the development of national policies about rational medicine usage and durable actions to discourage SM practices.
Combat Injury Profile in Urban Warfare
Authors: Satanovsky Alexandra , Gilor Yuval , Benov Avi , Chen Jacob , Shlaifer Amir , Talmy Tomer , Radomislensky Irina , Siman-Tov Maya , Peleg Kobi , Weil Yoram A , Eisenkraft Arik 
Published: December 2022

ABSTRACT

Introduction
Combat ground maneuvers consist of various platforms and have several environmental characteristics, influenced by the terrain, the operational mission, and the force’s capabilities. This study assesses data on injuries sustained during urban warfare, aiming to evaluate the relationship between injury characteristics, maneuver platform, and personal protective gear on the battlefield.

Materials and Methods
IDF soldiers injured infantry soldiers from the “Cast Lead” and the “Protective Edge” operations in the Gaza Strip (2008-2009 and 2014, respectively) were divided into four groups according to the maneuver platform and the environment: mounted infantry (armored and unarmored vehicle) and dismounted infantry (urban and open area). The primary outcome was the severity of the injury, and the secondary outcome was the injured body part.

Results
Overall, 588 casualties were included in the final analysis, of whom 507 were dismounted infantry soldiers (265 in open terrain and 242 in urban area) and 81 were mounted infantry soldiers (20 in unarmored and 61 were injured in armored vehicles). The Injury Severity Score was similar in all subgroups. Open terrain subgroups were found to have fewer head injuries and higher levels of lower extremity injuries, similar to the unarmored vehicle group. More facial injuries were documented in the urban area group.

Conclusions
The Injury Severity Score was not influenced by environmental protection. Although we found differences in the injured body parts, further studies on the exact mechanism of injury are needed to elucidate further the relationship and differences between the various platforms used and injuries seen in urban warfare, aiming for tailor-made protection.
Segmental aneuploid hotspots identified across the genome concordant on reanalysis
Authors: McCarty Keelee J , Haywood Mary E , Lee Rachel , Henry Lauren , Arnold Alison , McReynolds Susanna , McCallie Blair , Schoolcraft Bill , Katz-Jaffe Mandy 
Published: December 2022

Abstract
The aim of this study was to characterize a large set of full segmental aneuploidies identified in trophectoderm (TE) biopsies and evaluate concordance in human blastocysts. Full segmental aneuploid errors were identified in TE biopsies (n = 2766) from preimplantation genetic testing for aneuploid (PGT-A) cycles. Full segmental deletions (n = 1872; 66.1%) presented twice as many times as duplications (n = 939; 33.9%), mapped more often to the q-arm (n = 1696; 61.3%) than the p-arm (n = 847; 31.0%) or both arms (n = 223; 8.1%; P &lt; 0.05), and were eight times more likely to include the distal end of a chromosome than not (P &lt; 0.05). Additionally, 37 recurring coordinates (each ≥ 10 events) were discovered across 17 different chromosomes, which were also significantly enriched for distal regions (P = 4.1 × 10−56). Blinded concordance analysis of 162 dissected blastocysts validated the original TE PGT-A full segmental result for a concordance of 96.3% (n = 156); remaining dissected blastocysts were identified as mosaic (n = 6; 3.7%). Origin of aneuploid analysis revealed full segmental aneuploid errors were mostly paternally derived (67%) in contrast to whole chromosome aneuploid errors (5.8% paternally derived). Errors from both parental gametes were observed in 6.5% of aneuploid embryos when multiple whole chromosomes were affected. The average number of recombination events was significantly less in paternally derived (1.81) compared to maternally derived (3.81) segmental aneuploidies (P &lt; 0.0001). In summary, full segmental aneuploidies were identified at hotspots across the genome and were highly concordant upon blinded analysis. Nevertheless, future studies assessing the reproductive potential of full (non-mosaic) segmental aneuploid embryos are critical to rule out potential harmful reproductive risks.
Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection
Authors: Amrane Samir , Jaubert Chloé , Bedrat Amina , Rundstadler Tiffany , Recordon-Pinson Patricia , Aknin Cindy , Guédin Aurore , De Rache Aurore , Bartolucci Laura , Diene Ibra , Lemoine Frédéric , Gascuel Olivier , Pratviel Geneviève , Mergny Jean-Louis , Andreola Marie-Line 
Published: December 2022

Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Authors: Krepl Miroslav , Pokorná Pavlína , Mlýnský Vojtěch , Stadlbauer Petr , Šponer Jiří 
Published: December 2022

AbstractRecognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein–RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein–RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA–RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA–RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein–RNA complexes, and future perspectives of such research are discussed.
DDX17 helicase promotes resolution of R-loop-mediated transcription–replication conflicts in human cells
Authors: Boleslavska Barbora , Oravetzova Anna , Shukla Kaustubh , Nascakova Zuzana , Ibini Oluwakemi Ngozi , Hasanova Zdenka , Andrs Martin , Kanagaraj Radhakrishnan , Dobrovolna Jana , Janscak Pavel 
Published: December 2022

Abstract
R-loops are three-stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced DNA strand. These structures can halt DNA replication when formed co-transcriptionally in the opposite orientation to replication fork progression. A recent study has shown that replication forks stalled by co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage by MUS81 endonuclease, followed by ELL-dependent reactivation of transcription, and fork religation by the DNA ligase IV (LIG4)/XRCC4 complex. However, how R-loops are eliminated to allow the sequential restart of transcription and replication in this pathway remains elusive. Here, we identified the human DDX17 helicase as a factor that associates with R-loops and counteracts R-loop-mediated replication stress to preserve genome stability. We show that DDX17 unwinds R-loops in vitro and promotes MUS81-dependent restart of R-loop-stalled forks in human cells in a manner dependent on its helicase activity. Loss of DDX17 helicase induces accumulation of R-loops and the formation of R-loop-dependent anaphase bridges and micronuclei. These findings establish DDX17 as a component of the MUS81–LIG4–ELL pathway for resolution of R-loop-mediated transcription–replication conflicts, which may be involved in R-loop unwinding.
The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes
Authors: Gómez-Liñán Claudia , Gómez-Díaz Elena , Ceballos-Pérez Gloria , Fernández-Moya Sandra M , Estévez Antonio M 
Published: December 2022

AbstractIn-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.
PBSIM3: a simulator for all types of PacBio and ONT long reads
Authors: Ono Yukiteru , Hamada Michiaki , Asai Kiyoshi 
Published: December 2022

Abstract
Long-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencers, have improved their read length and accuracy, thereby opening up unprecedented research. Many tools and algorithms have been developed to analyze long reads, and rapid progress in PacBio and ONT has further accelerated their development. Together with the development of high-throughput sequencing technologies and their analysis tools, many read simulators have been developed and effectively utilized. PBSIM is one of the popular long-read simulators. In this study, we developed PBSIM3 with three new functions: error models for long reads, multi-pass sequencing for high-fidelity read simulation and transcriptome sequencing simulation. Therefore, PBSIM3 is now able to meet a wide range of long-read simulation requirements.
Molecular mimicry among human proteinase 3 and bacterial antigens: implications for development of c-ANCA associated vasculitis
Authors: Chavez Y , Garces J , Díaz R , Escobar M , Sanchez A , Buendía E , Múnera M 
Published: December 2022

Abstract
Wegener’s granulomatosis is an autoimmune disease where autoantibodies target human autoantigen PR3, a serine protease locates on the neutrophil membrane. This disease affects blood small vessels and could be deadly. The origin of these autoantibodies is unknown, but infections have been implicated with autoimmune disease. In this study, we explored potential molecular mimicry between human PR3 and homologous pathogens through in silico analysis. Thirteen serine proteases from human pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Salmonella sp., Streptococcus suis, Vibrio parahaemolyticus, Bacteroides fragilis, Enterobacter ludwigii, Vibrio alginolyticus, Staphylococcus haemolyticus, Enterobacter cloacae, Escherichia coli and Pseudomonas aeruginosa) shared structural homology and amino acid sequence identity with human PR3. Epitope prediction found an only conserved epitope IVGG, located between residues 59–74. However, multiple alignments showed conserved regions that could be involved in cross-reactivity between human and pathogens serine proteases (90–98, 101–108, 162–169, 267 and 262 residues positions). In conclusion, this is the first report providing in silico evidence about the existence of molecular mimicry between human and pathogens serine proteases, that could explain the origins of autoantibodies found in patients suffering from Wegener’s granulomatosis.
XMM-Newton view of the shock heating in an early merging cluster, CIZA J1358.9−4750
Authors: Omiya Yuki , Nakazawa Kazuhiro , Matsushita Kyoko , Kobayashi Shogo B , Okabe Nobuhiro , Sato Kosuke , Tamura Takayuki , Fujita Yutaka , Gu Liyi , Kitayama Tetsu , Akahori Takuya , Kurahara Kohei , Yamaguchi Tomohiro 
Published: December 2022

AbstractCIZA J1358.9−4750 is a nearby galaxy cluster in the early phase of a major merger. The two-dimensional temperature map using XMM-Newton EPIC-PN observation confirms the existence of a high-temperature region, which we call the “hot region,” in the “bridge region” connecting the two clusters. The ∼500 kpc wide region between the south-east and north-west boundaries also has higher pseudo-pressure compared to the unshocked regions, suggesting the existence of two shocks. The southern shock front is clearly visible in the X-ray surface brightness image and has already been reported by Kato et al. (2015, PASJ, 67, 71). The northern one, on the other hand, is newly discovered. To evaluate their Mach number, we constructed a three-dimensional toy merger model with overlapping shocked and unshocked components in the line of sight. The unshocked and pre-shock intracluster medium (ICM) conditions are estimated based on those outside the interacting bridge region, assuming point symmetry. The hot-region spectra are modeled with two-temperature thermal components, assuming that the shocked condition follows the Rankin–Hugoniot relation with the pre-shock condition. As a result, the shocked region is estimated to have a line-of-sight depth of ∼1 Mpc with a Mach number of ∼1.3 in the south-east shock and ∼1.7 in the north-west shock. The age of the shock waves is estimated to be ∼260 Myr. This three-dimensional merger model is consistent with the Sunyaev–Zel’dovich signal obtained using the Planck observation within the cosmic microwave background fluctuations. The total flow of the kinetic energy of the ICM through the south-east shock was estimated to be ∼2.2 × 1042 erg s−1. Assuming that $10\%$ of this energy is converted into ICM turbulence, the line–of–sight velocity dispersion is calculated to be ∼200 km s−1, which is basically resolvable via upcoming high spectral resolution observations.