bluuebunny/crossref_metadata_2025_split huggingface dataset:
PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform
Authors: Wang Yimin , Ling Yunchao , Gong Jiao , Zhao Xiaohan , Zhou Hanwen , Xie Bo , Lou Haiyi , Zhuang Xinhao , Jin Li ,   The Han100K Initiative, Fan Shaohua , Zhang Guoqing , Xu Shuhua 
Published: October 2022

Abstract
Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https://www.biosino.org/pggsv.
Catalytically inactive DNA ligase IV promotes DNA repair in living cells
Authors: Goff Noah J , Brenière Manon , Buehl Christopher J , de Melo Abinadabe J , Huskova Hana , Ochi Takashi , Blundell Tom L , Mao Weifeng , Yu Kefei , Modesti Mauro , Meek Katheryn 
Published: October 2022

Abstract
DNA double strand breaks (DSBs) are induced by external genotoxic agents (ionizing radiation or genotoxins) or by internal processes (recombination intermediates in lymphocytes or by replication errors). The DNA ends induced by these genotoxic processes are often not ligatable, requiring potentially mutagenic end-processing to render ends compatible for ligation by non-homologous end-joining (NHEJ). Using single molecule approaches, Loparo et al. propose that NHEJ fidelity can be maintained by restricting end-processing to a ligation competent short-range NHEJ complex that ‘maximizes the fidelity of DNA repair’. These in vitro studies show that although this short-range NHEJ complex requires DNA ligase IV (Lig4), its catalytic activity is dispensable. Here using cellular models, we show that inactive Lig4 robustly promotes DNA repair in living cells. Compared to repair products from wild-type cells, those isolated from cells with inactive Lig4 show a somewhat increased fraction that utilize micro-homology (MH) at the joining site consistent with alternative end-joining (a-EJ). But unlike a-EJ in the absence of NHEJ, a large percentage of joints isolated from cells with inactive Lig4 occur with no MH – thus, clearly distinct from a-EJ. Finally, biochemical assays demonstrate that the inactive Lig4 complex promotes the activity of DNA ligase III (Lig3).
Analysis of nested alternate open reading frames and their encoded proteins
Authors: Vasu Kommireddy , Khan Debjit , Ramachandiran Iyappan , Blankenberg Daniel , Fox Paul L 
Published: October 2022

Abstract
Transcriptional and post-transcriptional mechanisms diversify the proteome beyond gene number, while maintaining a sequence relationship between original and altered proteins. A new mechanism breaks this paradigm, generating novel proteins by translating alternative open reading frames (Alt-ORFs) within canonical host mRNAs. Uniquely, ‘alt-proteins’ lack sequence homology with host ORF-derived proteins. We show global amino acid frequencies, and consequent biochemical characteristics of Alt-ORFs nested within host ORFs (nAlt-ORFs), are genetically-driven, and predicted by summation of frequencies of hundreds of encompassing host codon-pairs. Analysis of 101 human nAlt-ORFs of length ≥150 codons confirms the theoretical predictions, revealing an extraordinarily high median isoelectric point (pI) of 11.68, due to anomalous charged amino acid levels. Also, nAlt-ORF proteins exhibit a &gt;2-fold preference for reading frame 2 versus 3, predicted mitochondrial and nuclear localization, and elevated codon adaptation index indicative of natural selection. Our results provide a theoretical and conceptual framework for exploration of these largely unannotated, but potentially significant, alternative ORFs and their encoded proteins.
Prevalence and Factors Associated With Antigen Test Positivity Following SARS-CoV-2 Infection Among Health Care Workers in Los Angeles
Authors: Adamson Paul C , Currier Judith S , Uslan Daniel Z , Garner Omai B 
Published: October 2022

Abstract
Surges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections among health care workers (HCWs) have led to critical staffing shortages. From January 4 to February 4, 2022, we implemented a return-to-work antigen testing program for HCWs, and 870 HCWs participated. Antigen test positivity was 60.5% for those ≤5 days from symptom onset or positive polymerase chain reaction (PCR), and 47.4% were positive at day 7. Antigen positivity was associated with receiving a booster vaccination and being ≤6 days from symptom onset or PCR test, but not age or a symptomatic infection. Rapid antigen testing can be a useful tool to guide return-to-work and isolation precautions for HCWs following infection.
Steady jet ejections from the innermost region of advection-dominated accretion flow around a black hole
Authors: Inoue Hajime 
Published: October 2022

Abstract
We study ejection mechanisms for two kinds of steady jets: one observed from black hole binaries in the low/hard state and the other from SS 433. The specific energy of the ejected gas is required to be positive for the jets to get to infinity, while that of the accreted gas is naively considered to be negative at the outermost boundary of the accretion flow. To reconcile the opposite sign of the specific energies, we propose a situation where two layers exist in the accretion flow and one layer receives energy from the other sufficiently for the specific energy to be positive. For the steady jets in the low/hard state, the accretion ring at the outermost end of the accretion flow is considered to yield two-layer flow in which a geometrically thick advection-dominated accretion flow (ADAF) sandwiches a geometrically thin accretion disk and the thin disk is supposed to change to another ADAF on the inner side. The energy transfer is expected to occur through turbulent mixing between the two layers and the upper layer is discussed as having a positive specific energy large enough for the terminal velocity to be ∼0.1 c. For the steady jets from SS 433, it is argued that a slim disk separates into two stratified layers due to the photon diffusion in the direction perpendicular to the equatorial plane under the advection-dominated situation. In this case, the specific energy of the upper layer is expected to be positive such that the terminal velocity exceeds 0.2c. The jet ejection process near the black hole is investigated commonly to both the two-layer cases and predicts that the jet opening angle becomes as small as 2°.
The Language of Incarceration and of Persons Subject to Incarceration
Authors: Reid Lynette 
Published: October 2022

Abstract
Reflecting on Smith (2021) in this issue, this commentary extends our consideration of issues in carceral health and questions the dehumanizing language we sometimes use—including in public health and public health ethics—to talk about persons held in incarceration. Even the language we use for the carceral system itself (such as ‘criminal justice system’) is fraught: it casts a laudatory light on the system and papers over its role in compounding racial health inequities and in sustaining colonialism. A host of issues call out for ethical analysis, using lenses that can encompass the tensions and contradictions experienced by people within the system who deliver healthcare and those within the system trying to access that care. Beyond access to health care (promotion, prevention, treatment and palliation), the societal commitment to dealing with social issues by depriving people of many key social determinants of health is at the heart of many of these tensions and contradictions.
Hurdles in responsive community engagement for the development of environmental biotechnologies
Authors: Normandin Avery M , Fitzgerald Lily M , Yip Julianne , Evans Sam Weiss 
Published: October 2022

Abstract
Recent calls for engaging communities in biotechnology development do not draw enough attention to the hurdles that must be overcome for engagement strategies to effectively feed back into research design and conduct. These hurdles call into question many standard ways of operating and assessing in traditional scientific disciplines. The first steps in addressing these hurdles can be the most difficult. In reflecting on our own experiences in the early-stage development of environmental biotechnologies, we provide a set of techniques to help scientists and their collaborators learn to become more responsive to the needs and attitudes of communities with which they are engaging.
Graphical Abstract
Spiking burstiness and working memory in the human medial temporal lobe
Authors: Cocina Francesco , Vitalis Andreas , Caflisch Amedeo 
Published: October 2022

Abstract
Persistent activity has commonly been considered to be a hallmark of working memory (WM). Recent evidence indicates that neuronal discharges in the medial temporal lobe (MTL) are compatible with WM neural patterns observed in cortical areas. However, the characterization of this activity rarely consists of measurements other than firing rates of single neurons. Moreover, a varied repertoire of firing dynamics has been reported in the MTL regions, which motivate the more detailed examination of the relationships between WM processes and discharge patterns undertaken here. Specifically, we investigate‚ at different resolution levels, firing irregularities in electrode recordings from the hippocampus, amygdala, and the entorhinal cortex of epileptic patients during a WM task. We show that some types of (ir)regularities predict response times of the patients depending on the trial periods under consideration. Prominent burst activity at the population level is observed in the amygdala and entorhinal cortex during memory retrieval. In general, regular and bursty neurons contribute to the decoding of the memory load, yet they display important differences across the three anatomical areas. Our results suggest that nonrandom (non-Poisson) patterns are relevant for WM, which calls for the development and use of statistics complementary to mere spike counts.
Value of whole-body MRI for the assessment of response to albendazole in disseminated neurocysticercosis: a prospective follow-up study
Authors: Wangda Kinzang , Kumar Neeraj , Garg Ravindra Kumar , Malhotra Hardeep Singh , Rizvi Imran , Uniyal Ravi , Pandey Shweta , Malhotra Kiran Preet , Verma Rajesh , Sharma Praveen Kumar , Parihar Anit , Jain Amita 
Published: October 2022

AbstractBackgroundDisseminated neurocysticercosis is defined as simultaneous involvement of the brain (≥3 cysts) and at least one additional body site/organ. We aimed to identify disseminated cystic lesions in other body parts and investigate the effect of albendazole.MethodsWe enrolled patients with multiple (≥3) neurocysticercosis brain lesions. Whole-body MRI (short tau inversion recovery coronal sequences) was performed to assess the number of lesions in the brain and other body parts at baseline and 3 months after albendazole therapy.ResultsWe screened 35 patients with multiple brain neurocysticercosis. In 13 patients, whole-body MRI demonstrated disseminated neurocysticercosis lesions. Ten patients were treated with albendazole. We excluded three patients. Brain MRI showed a mean lesion count of 163.6±193.8. Whole-body MRI (excluding the brain) showed a mean lesion count of 629.9±486.1. After albendazole therapy, the lesion load of the brain reduced significantly (163.6±193.8 to 99±178.3; p=0.008). Similarly, whole-body MRI showed a significant reduction in extracerebral neurocysticercosis lesion load (629.9±486.1 to 183.4±301.9; p=0.005). Three patients had complete resolution, five patients showed ≥50% reduction and two patients had &lt;50% reduction in extracerebral lesion load.ConclusionWhole-body MRI should routinely be performed in multiple neurocysticercosis lesions of the brain. Albendazole treatment leads to a remarkable reduction in neurocysticercosis lesions throughout the body.
Current Management of Late Posttraumatic Enophthalmos
Authors: DeSerres Joshua J. , Budning Andrew , Antonyshyn Oleh M. 
Published: October 2022

Learning Objectives:
After studying this article, the participant should be able to: 1. Describe the orbital anatomy and completely understand the important components relevant to surgical correction of enophthalmos, including oculo-orbito relations. 2. Understand the pathophysiology and predictive factors for posttraumatic enophthalmos and identify the challenges associated with correction of enophthalmos in the late setting. 3. Develop a surgical plan for late enophthalmos repair and understand the value and utility of osteotomies, intraoperative navigation, and patient-specific implants. 4. Discuss the expected outcomes, possible complications, and adjunctive surgery as related to late enophthalmos repair.

Summary:
This article addresses the current management of late posttraumatic enophthalmos. In this article, the authors describe surgically relevant orbital anatomy and oculo-orbital relations, the pathophysiology of enophthalmos, clinical and radiologic findings, decision-making in management, and surgical treatment. The authors attempt to cover some of the main challenges and recent advances in the management of late posttraumatic enophthalmos, including intraoperative navigation and patient-specific implants.
KmerAperture: Retainingk-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes
Authors: Moore Matthew P. , Laager Mirjam , Ribeca Paolo , Didelot Xavier 
Published: October 2022

ABSTRACTBy decomposing genome sequences intok-mers, it is possible to estimate genome differences without alignment. Techniques such ask-mer minimisers (MinHash), have been developed and are often accurate approximations of distances based on fullk-mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment or mapping. However, thesek-mer set comparisons are not entirely accurate within-species and can be completely inaccurate within-lineage. This is due, in part, to their inability to distinguish core polymorphism from accessory differences. Here we present a new approach,KmerAperture, which uses information on thek-mer relative genomic positions to determine the type of polymorphism causing differences ink-mer presence and absence between pairs of genomes. Single SNPs are expected to result in contiguous series of relative uniquek-mers of lengthL=k. On the other hand, series of lengthL>kmay be caused by accessory differences of lengthL-k+1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs withinkbp from each other andKmerAperturecan determine whether that is the case. To demonstrate use casesKmerAperturewas benchmarked using datasets including a very low diversity simulated population with accessory content independent from the number of SNPs, a simulated population were SNPs are spatially dense, a moderately diverse real cluster of genomes (Escherichia coliST1193) with a large accessory genome and a low diversity real genome cluster (SalmonellaTyphimurium ST34). We show thatKmerAperturecan accurately distinguish both core and accessory sequence diversity without alignment, outperforming otherk-mer based tools.
A spatio-temporal framework for modelling wastewater concentration during the COVID-19 pandemic
Authors: Li Guangquan , Denise Hubert , Diggle Peter , Grimsley Jasmine , Holmes Chris , James Daniel , Jersakova Radka , Mole Callum , Nicholson George , Smith Camila Rangel , Richardson Sylvia , Rowe William , Rowlingson Barry , Torabi Fatemeh , Wade Matthew J. , Blangiardo Marta 
Published: October 2022

AbstractThe potential utility of wastewater-based epidemiology as an early warning tool has been explored widely across the globe during the current COVID-19 pandemic. Methods to detect the presence of SARS-CoV-2 RNA in wastewater were developed early in the pandemic, and extensive work has been conducted to evaluate the relationship between viral concentration and COVID-19 case numbers at the catchment areas of sewage treatment works (STWs) over time. However, no attempt has been made to develop a model that predicts wastewater concentration at fine spatio-temporal resolutions covering an entire country, a necessary step towards using wastewater monitoring for the early detection of local outbreaks.We consider weekly averages of flow-normalised viral concentration, reported as the number of SARS-CoV-2 N1 gene copies per litre (gc/L) of wastewater available at 303 STWs over the period between 1 June 2021 and 30 March 2022. We specify a spatially continuous statistical model that quantifies the relationship between weekly viral concentration and a collection of covariates covering socio-demographics, land cover and virus-associated genomic characteristics at STW catchment areas while accounting for spatial and temporal correlation.We evaluate the model’s predictive performance at the catchment level through 10-fold cross-validation. We predict the weekly viral concentration at the population-weighted centroid of the 32,844 lower super output areas (LSOAs) in England, then aggregate these LSOA predictions to the Lower Tier Local Authority level (LTLA), a geography that is more relevant to public health policy-making. We also use the model outputs to quantify the probability of local changes of direction (increases or decreases) in viral concentration over short periods (e.g. two consecutive weeks).The proposed statistical framework is able to predict SARS-CoV-2 viral concentration in wastewater at high spatio-temporal resolution across England. Additionally, the probabilistic quantification of local changes can be used as an early warning tool for public health surveillance.
Long-read genome sequencing accelerated the cloning ofPm69by resolving the complexity of a rapidly evolving resistance gene cluster in wheat
Authors: Li Yinghui , Wei Zhen-Zhen , Sela Hanan , Govta Liubov , Klymiuk Valentyna , Roychowdhury Rajib , Chawla Harmeet Singh , Ens Jennifer , Wiebe Krystalee , Bocharova Valeria , Ben-David Roi , Pawar Prerna B. , Jaiwar Samidha , Molnár István , Doležel Jaroslav , Pozniak Curtis J. , Fahima Tzion 
Published: October 2022

AbstractGene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene)Pm69derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach encountered suppressed recombination due to structural variations, while chromosome sorting yielded an insufficient purity level. APm69physical map, constructed by assembling ONT long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster. A single candidate NLR was identified within this cluster by anchoring RNASeq reads of susceptible mutants to ONT contigs and was validated by the virus-induced gene silencing (VIGS) approach.Pm69, comprising Rx_N with RanGAP interaction sites, NB-ARC, and LRR domains, is probably a newly evolved NLR discovered only in one location across the WEW distribution range in the Fertile Crescent.Pm69was successfully introgressed into durum and bread wheat, and a diagnostic molecular marker could be used to accelerate its deployment and pyramiding with other resistance genes.
Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis
Authors: Hildebrand Erica M. , Polovnikov Kirill , Dekker Bastiaan , Liu Yu , Lafontaine Denis L. , Fox A. Nicole , Li Ying , Venev Sergey V. , Mirny Leonid , Dekker Job 
Published: October 2022

SUMMARYThe topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired.
The Symmetry and Asymmetry Behind Histone Folding Across Eukarya and Archaea
Authors: Zhao Haiqing , Wu Hao , Guseman Alex , Abeykoon Dulith , Camara Christina M. , Dalal Yamini , Fushman David , Papoian Garegin A. 
Published: October 2022

AbstractHistones are the dominant proteins to compact and store DNA in both Eukarya and Archaea. For a long time, histones are observed to exist in the unit of dimers but diverge into different formats such as heterodimers in Eukarya or homodimers in Archaea. Here, by studying 11 types of histone proteins, both monomers and their dimeric complexes, using multiscale molecular dynamics (MD) simulations combined with NMR and circular dichroism experiments, we confirm the widely applied “folding upon binding” mechanism of histone structures. A histone dimer appears to form the longestα2 helices followed by other shorter helices and inter-molecular tertiary structures. We report an alternative conformation, namely, the inverted non-native dimer, which has a minimum free energy state. Protein sequence analysis indicates that the inverted conformation can be attributed to a hidden head-tail sequence symmetry underlying all histone proteins. This finding strongly support previously proposed histone evolution hypotheses. Finally, we separately used the MD-based AWSEM and AI-based AlphaFold-Multimer model to predict eukaryotic histone homodimer structures and performed extensive allatom MD simulations to examine their structural stabilities. Our results suggest that eukaryotic histones can also form stable homodimers, whereas their disordered tails— the structurally asymmetrical region—may tip the balance towards the formation of heterotypic dimers.