bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability
Authors: Zhou Yiyang , Routh Andrew L. 
Published: February 2024

ABSTRACT

Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach (“XL-ClickSeq”) to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.

IMPORTANCE
Flock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.
HIV-1 Gag, Pol, and Env diversified with limited adaptation since the 1980s
Authors: Lewitus Eric , Li Yifan , Bai Hongjun , Pham Phuc , Rolland Morgane 
Published: February 2024

ABSTRACT

Knowledge of HIV-1 global sequence diversity is critical for developing an effective prophylactic against HIV-1 infection. We developed the Hervé platform to analyze and visualize trends in HIV-1 diversification. Using Hervé, we analyzed 4,830 Env, 4,407 Gag, and 3,002 Pol publicly available independent sequences corresponding to subtypes A1, A6, B, C, D, F1, and G and circulating recombinant forms (CRFs) 01_AE, 02_AG, and 07_BC; sequences were sampled between 1980 and 2020 from 82 countries. HIV-1 diversified with a median of 1.82 amino acid substitutions per year in Env, 0.297 in Gag, and 0.779 in Pol. Yet, Env subtype B diversification plateaued post-2000. Pairwise diversity within subtypes and CRFs increased by 41.82% (range = 24.85%–54.41%) in Env, 56.93% (15.38%–89.16%) in Gag, and 46.12% (11.70%–70.57%) in Pol. Consensus sequences based on sequences sampled in each decade remained relatively stable over time. Similarly, at antibody epitope sites, only 0–8 residues that were minority variants became consensus over time in any subtype/CRF and only one known drug resistance mutation site differed from the reference (subtype G). The apparent contradiction between the fast diversification of HIV-1 and its limited adaptation illustrates that HIV-1 evolution is not directional and its consensus is at the intersection of millions of within-host selective processes occurring in a star-like manner. While a consensus sequence is a better representation of HIV-1 diversity than any individual sequence, consensus sequences have progressively become more distant from the circulating sequences they represent.

IMPORTANCE
Global surveillance of HIV-1 sequences is critical for designing relevant prophylactic and therapeutic interventions to infection. We designed an open-source platform, Hervé, for analyzing and visualizing the diversification dynamics of HIV-1 protein sequences. We characterized the evolution of over 12,000 HIV-1 Env, Gag, and Pol protein sequences from 1980–2020 and found that, despite a steady increase in intra-subtype and circulating recombinant form diversity, the most frequent residue at each site, i.e., the consensus, has varied only moderately.
Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert
Authors: Nguyen Thuy M. , Pombubpa Nuttapon , Huntemann Marcel , Clum Alicia , Foster Brian , Foster Bryce , Roux Simon , Palaniappan Krishnaveni , Varghese Neha , Mukherjee Supratim , Reddy T. B. K. , Daum Chris , Copeland Alex , Chen I-Min A. , Ivanova Natalia N. , Kyrpides Nikos C. , Harmon-Smith Miranda , Eloe-Fadrosh Emiley A. , Pietrasiak Nicole , Stajich Jason E. , Hom Erik F. Y. 
Published: February 2024

ABSTRACT

We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.
Lifetime non-fatal overdose experiences among at-risk adolescents and young adults in the emergency department with past-year opioid use in the USA
Authors: Seewald Laura , Bonar Erin , Bohnert Amy S B , Carter Patrick M , King Cheryl A , Losman Eve D , Bacon Linnea , Wheeler Tiffany , Walton Maureen 
Published: February 2024

BackgroundAdolescents and young adults with risk factors for opioid misuse and opioid use disorder are at elevated risk for overdose. We examined prior non-fatal overdose experiences among at-risk adolescents/young adults to inform prevention efforts.MethodsAdolescents/young adults (ages 16–30) in two US emergency departments self-reporting past year opioid misuse or opioid use plus a misuse risk factor completed a baseline survey as part of an ongoing randomised controlled trial. We describe baseline factors associated with (a) overall non-fatal overdose experiences and (b) groups based on substance(s) used during the worst overdose experience.ResultsAmong 771 participants (27.9% male), 40.7% reported a non-fatal overdose experience. Compared with those without a prior overdose experience, those with prior overdose experience(s) were less likely to be heterosexual, and more likely to report a prior suicide attempt and greater peer substance misuse. Regarding the worst overdose experience, substance(s) included: 36.6% alcohol only, 28.0% alcohol and cannabis, 22.6% alcohol with other substance(s) and 12.7% other substance(s) only (eg, opioids). Compared with the alcohol only group, the alcohol and cannabis group were younger and less likely to be heterosexual; the alcohol with other substance(s) group were older and had greater peer substance misuse; and the other substance(s) only group were more likely to be male, receive public assistance, screen positive for anxiety and less likely to be heterosexual.ConclusionsAmong at-risk adolescents/young adults, findings support the need for tailored overdose prevention efforts based on substance(s) used, with consideration of sexuality, mental health and peer substance use.Trial registration numberNCT04550715.
How socio-political change is associated with the number of individually reported negative life events: a population-based study using the German reunification 1989/1990 as an example
Authors: Hahm Stefanie , Altweck Laura , Schmidt Silke , Fleischer Toni , Helmert Claudia , Ulke Christine , Speerforck Sven , Schomerus Georg , Klinger-König Johanna , Grabe Hans J , Schmidt Carsten Oliver , Beutel Manfred E , Brähler Elmar , Muehlan Holger 
Published: February 2024

BackgroundSocio-political change often leads to disruptions in employment and social networks, which can exacerbate health issues and increase mortality rates. These consequences are likely observed as an increase in negative life events (NLEs), serving as indicators of the broader social and health impacts. Using the German reunification in 1989/1990 as an example, this study investigates changes in reported numbers of NLEs and differences regarding sociodemographic characteristics.MethodsWe used data from the population-based Study of Health in Pomerania (SHIP-START-0, SHIP-Life-Events and Gene-Environment Interaction in Depression; N=1932). Numbers of NLEs in different categories (work/financial, social/interpersonal, illness (own) and illness/death (others)) were measured retrospectively in 5-year intervals (1980–2004) using a semistructured interview. Pre-reunification and post-reunification changes were modelled using piecewise mixed-effects Poisson regressions with the 1990–1994 interval (reunification) as change point. Interactions with age, sex and education were examined.ResultsThe number of most NLE categories, except social/interpersonal NLEs, increased at reunification. Whereas work/financial NLEs slightly decreased post-reunification, illness-related NLEs continued to increase. Higher numbers of social/interpersonal NLEs were found with younger age. More illness-related NLEs were reported with older age, lower education (illness (own)) and by women (illness/death (others)). However, the majority reported no NLEs at reunification (68.2%–80.7%, varying by category).ConclusionOur findings suggest that although some individuals experience a marked increase in NLEs due to socio-political changes, many remain unaffected, emphasising the need for a differentiated understanding of these effects. This increase in NLEs may partly account for ongoing health and well-being disparities among countries with differing transformation histories.
Association of same-sex criminalisation laws and national HIV policies with HIV testing in African MSM: an ecological single-level and multilevel cross-sectional study of sub-Saharan African countries
Authors: Kalu Ngozi , Ross Michael W , Taegtmeyer Miriam , Lamontagne Erik , Howell Sean , Neuman Melissa 
Published: February 2024

BackgroundHIV incidence among men who have sex with men (MSM) in sub-Saharan Africa (SSA) remains high compared with the general population. Many countries in the region still criminalise consensual homosexual relationships, and some are yet to adopt WHO-recommended interventions for MSM into national HIV policies. This study examines how HIV testing of adult MSM in SSA varies according to the legal climate and presence of targeted HIV policy using data from the cross-sectional 2019 Global LGBTI Internet Survey study.MethodsUsing data from 3191 MSM in 44 SSA countries, we assessed associations of legal climate and HIV policy with ever and recent HIV testing using linear ecological and logistic multilevel analyses. From the single-level analysis, we can compare our findings to previously reported data, then, extending to a two-level multilevel analysis, we account for the hierarchical structure of the population and simultaneously adjust for differences in context and composition in each country. We then test the sensitivity of our analyses to excluding countries from the model.ResultsWe find evidence that legalised same-sex relationships were associated with increased odds of ever testing (OR=2.00, 95% CI 1.04, 3.82) in multilevel analyses. We also find evidence of an association of targeted HIV policies with increased odds of ever testing (OR=2.49, 95% CI 1.12, 5.52). We did not find evidence of an association of the legal climate (OR=1.01, 95% CI 0.69, 1.46) and targeted HIV policies (OR=1.26, 95% CI 0.78, 2.04) with recent testing.ConclusionsThis study suggests elimination of discriminatory laws and policies might be important for increasing HIV status awareness of MSM, an important first step in epidemic control. Additionally, we highlight heterogeneity between South Africa and other SSA countries, which has implications for studying SSA countries as a homogeneous group.
Investigating the link between frailty and outcomes in geriatric patients with isolated rib fractures
Authors: Mohseni Shahin , Forssten Maximilian Peter , Mohammad Ismail Ahmad , Cao Yang , Hildebrand Frank , Sarani Babak , Ribeiro Marcelo AF 
Published: February 2024

BackgroundStudies have shown an increased risk of morbidity in elderly patients suffering rib fractures from blunt trauma. The association between frailty and rib fractures on adverse outcomes is still ill-defined. In the current investigation, we sought to delineate the association between frailty, measured using the Orthopedic Frailty Score (OFS), and outcomes in geriatric patients with isolated rib fractures.MethodsAll geriatric (aged 65 years or older) patients registered in the 2013–2019 Trauma Quality Improvement database with a conservatively managed isolated rib fracture were considered for inclusion. An isolated rib fracture was defined as the presence of ≥1 rib fracture, a thorax Abbreviated Injury Scale (AIS) between 1 and 5, an AIS ≤1 in all other regions, as well as the absence of pneumothorax, hemothorax, or pulmonary contusion. Based on patients’ OFS, patients were classified as non-frail (OFS 0), pre-frail (OFS 1), or frail (OFS ≥2). The prevalence ratio (PR) of composite complications, in-hospital mortality, failure-to-rescue (FTR), and intensive care unit (ICU) admission between the OFS groups was determined using Poisson regression models to adjust for potential confounding.ResultsA total of 65 375 patients met the study’s inclusion criteria of whom 60% were non-frail, 29% were pre-frail, and 11% were frail. There was a stepwise increased risk of complications, in-hospital mortality, and FTR from non-frail to pre-frail and frail. Compared with non-frail patients, frail patients exhibited a 87% increased risk of in-hospital mortality [adjusted PR (95% CI): 1.87 (1.52-2.31), p<0.001], a 44% increased risk of complications [adjusted PR (95% CI): 1.44 (1.23-1.67), p<0.001], a doubling in the risk of FTR [adjusted PR (95% CI): 2.08 (1.45-2.98), p<0.001], and a 17% increased risk of ICU admission [adjusted PR (95% CI): 1.17 (1.11-1.23), p<0.001].ConclusionThere is a strong association between frailty, measured using the OFS, and adverse outcomes in geriatric patients managed conservatively for rib fractures.
Failure after operative repair is higher for ballistic femoral neck fractures than for closed, blunt-injury fractures: a multicenter retrospective cohort study
Authors: Shu Henry Tout , Ghanem Diane , Rogers Davis L. , Covarrubias Oscar , Izard Paul , Hacquebord Jacques , Lim Philip , Gupta Ranjan , Osgood Greg M. , Shafiq Babar 
Published: February 2024

IntroductionThe purpose of this study was to describe the outcomes after operative repair of ballistic femoral neck fractures. To better highlight the devastating nature of these injuries, we compared a cohort of ballistic femoral neck fractures to a cohort of young, closed, blunt-injury femoral neck fractures treated with open reduction and internal fixation (ORIF).MethodsRetrospective chart review identified all patients presenting with ballistic femoral neck fractures treated at three academic trauma centers between January 2016 and December 2021, as well as patients aged ≤50 with closed, blunt-injury femoral neck fractures who received ORIF. The primary outcome was failure of ORIF, which includes the diagnosis of non-union, avascular necrosis, conversion to total hip arthroplasty, and conversion to Girdlestone procedure. Additional outcomes included deep infection, postoperative osteoarthritis, and ambulatory status at last follow-up.ResultsFourteen ballistic femoral neck fractures and 29 closed blunt injury fractures were identified. Of the ballistic fractures, 7 (50%) patients had a minimum of 1-year follow-up or met the failure criteria. Of the closed fractures, 16 (55%) patients had a minimum of 1-year follow-up or met the failure criteria. Median follow-up was 21 months. 58% of patients with ballistic fractures were active tobacco users. Five of 7 (71%) ballistic fractures failed, all of which involved non-union, whereas 8 of 16 (50%) closed fractures failed (p=0.340). No outcomes were significantly different between cohorts.ConclusionOur results demonstrate that ballistic femoral neck fractures are associated with high rates of non-union. Large-scale multicenter studies are necessary to better determine optimal treatment techniques for these fractures.Level of evidenceLevel III. Retrospective cohort study.
Timing and volume of transfusion for adult major trauma patients with hemorrhagic shock: a registry-based cohort study
Authors: Mitra Biswadev , Singh Bivekjeet , Mathew Joseph , Stewart Cara , Koolstra Christine , Hendel Simon , Fitzgerald Mark 
Published: February 2024

IntroductionTransfusion of blood components is vital for the resuscitation of injured patients in hemorrhagic shock. Delays in initiating transfusion have been associated with harm, as has excess transfusion. The aim of this study was to evaluate variables associated with hospital mortality, with a focus on the two modifiable risk factors— time to initiate transfusion and volume of blood components—with hospital mortality.MethodsThis was a registry-based cohort study, including all consecutive adult patients presenting with hemorrhagic shock (systolic blood pressure (SBP) ≤90 mm Hg and transfusion of blood components) to a level 1 adult trauma center during a 5-year period (January 1, 2017–December 31, 2021). Associations with hospital mortality were assessed using multivariable logistic regression analysis, with final models developed using backward elimination.ResultsThere were 195 patients included and there were 49 (25.1%) in-hospital deaths. The median time to first transfusion was 10 (IQR 6–16) minutes. Age (adjusted OR (aOR) 1.06; 95% CI: 1.03 to 1.08), initial SBP (aOR 0.96; 95% CI: 0.3 to 0.98), intracranial bleeding or diffuse axonal injury (aOR 2.63; 95% CI: 1.11 to 6.23), and the volume of blood components in the first 4 hours (aOR 1.08; 95% CI: 1.03 to 1.13) were associated with mortality. Time to transfusion was not associated with in-hospital mortality (aOR 0.99; 95% CI: 0.95 to 1.03). Among the 90 patients who underwent urgent transfer to the operating room or angiography suite, the median time to transfer was 2.38 hours (IQR 1.5–3.7). In this subgroup, age (aOR 1.11; 95% CI: 1.05 to 1.18) and volume of blood components (aOR 1.20; 95% CI: 1.08 to 1.34) were associated with mortality.DiscussionIn this setting where times to transfusion are short, further reductions in the time to transfusion are unlikely to improve outcome. In our population, for every unit of blood component transfused, the adjusted odds of death increased by 8%. These findings suggest investigation into strategies to achieve earlier control of hemorrhage.Level of evidenceIII.
Numerical computations for Darcy–Forchheimer-based dual convection reactive flow considering Casson nanomaterial by convected permeable surface
Authors: Kausar M. S. , Waqas M. , Shehzad S. A. , Hosseinzadeh Kh. , Hejazi Hala A. , Mtaouaa Wafa 
Published: February 2024

The use of nanoparticles in heat transmission is an interesting research subject and many scholars have shown an interest in this topic. In accordance with the motivating relevance of nanomaterials, the current research advocates for an evaluation of Casson nanofluid using porous medium thermal analysis in conjunction with vibrant implementations of mixed convection through a chemical reaction. Additionally, a nonlinear suction/injection phenomenon is taken into consideration. A consistent flow pattern is created by the stretched porous structure. The extended Casson nanofluid model is used to identify the heat production of non-Newtonian fluids. The essential incentives for choosing the Casson nanofluid model are validated as it simultaneously achieves Casson fluid, nanofluid and porous medium outcomes. The convective transport of nanofluid has been addressed using convective temperature boundary conditions and convective flow. A dimensionless form with similarity variables is used to simplify the fundamental equations for the provided flow model. The fourth-order Runge–Kutta (RK) strategy is deployed to arrive at a numerical solution for simulated flow. The physical conveyance of flow variables is accessed visually. It is calculated from engineering quantities (i.e., skin friction, Nusselt number and Sherwood number) to generate the numerical values. The velocity declines with increasing porosity and material factors while opposite outcomes are witnessed for buoyancy factors (mixed convection and buoyancy ratio) and injection factor.
3D Printing of Conversion Cathodes for Enhanced Custom-Form Lithium Batteries
Authors: Cardenas Jorge Antonio , Bullivant John Paul , Wygant Bryan R , Merrill Laura C , Kolesnichenko Igor V. , Lapp Aliya S. , Lambert Timothy N. , Whetten Shaun R. , Allcorn Eric , Talin Albert Alec , Cook Adam , Harrison Katharine L 
Published: February 2024

Additive manufacturing techniques can enable the fabrication of batteries in nonconventional form factors, enabling higher practical energy densities due to improved power source packing efficiency. Furthermore, energy density can be improved by transitioning from conventional Li-ion materials to lithium metal anodes and conversion cathodes. Iron disulfide (FeS2) and iron trifluoride (FeF3) are two promising conversion cathodes of commercial and academic interest, but the 3D printing of inks made from these materials for custom-form battery applications has yet to be demonstrated. In this work, the deposition of FeS2 and FeF3 inks are investigated and optimized using direct-ink-write (DIW) 3D printing, in addition to the development of printable separators and packages to produce custom-form batteries. Two distinct custom form-factors, one on wave-shaped current collectors and the other on cylindrical rod current collectors, are demonstrated and shown to exhibit performance similar to coin cells when conventional Celgard separators are used. Additionally, FeF3 cells were integrated with a DIW printed separator consisting of an electrolyte exchanged PVDF-HFP based ionogel [1]. In the case of FeS2, it was found that cathodes with a ridged surface, produced from the filamentary extrusion of highly concentrated inks (60-70% solids w/w%) exhibited optimal power, uniformity, and stability [2]. Finally, progress toward fully-printing custom-form batteries using metal powder bed printed cases and stereolithographically printed gaskets is demonstrated. Overall, the additive manufacturing of conversion electrodes, separators, and battery packaging is shown to be a viable path toward the making of custom-form cells. More broadly, electrode ridging is found to optimize rate capability, a finding that may have broad impact beyond FeS2, FeF3 and additive manufacturing.
[1] A.S. Lapp, L.C. Merrill, B.R. Wygant, D.S. Ashby, A.S. Bhandarkar, A. Zhang, E.J. Fuller, K.L. Harrison, T.N. Lambert, and A.A. Talin. Room Temperature Pseudo-Solid State Iron Fluoride Conversion Battery with High Ionic Conductivity. ACS Applied Materials & Interfaces 15, 893-902, 2022.
[2] J.A. Cardenas, J.P. Bullivant, I.V. Kolesnichenko, D.J. Roach, M.A. Gallegos, E.N. Coker, T.N. Lambert, E. Allcorn, A.A. Talin, A.W. Cook, and K.L. Harrison. 3D Printing of Ridged FeS2 Cathodes for Improved Rate Capability and Custom-Form Lithium Batteries. ACS Applied Materials & Interfaces 14, 45342-45351. 2022.