bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic Implant Irrigation and Deep Infection: A Retrospective Study of 1508 Patients Undergoing Breast Reconstruction with Implants
Authors: Hemmingsen Mathilde N. , Bennedsen Anne K. , Kullab Randa B. , Weltz Tim K. , Larsen Andreas , Ørholt Mathias , Norlin Caroline Barskov , Kalstrup Julie , Bredgaard Rikke , Sørensen Søren J. , Bjarnsholt Thomas , Hölmich Lisbet R. , Damsgaard Tine E. , Vester-Glowinski Peter , Herly Mikkel 
Published: June 2023

Background:
Antibiotic implant irrigation is increasingly used to prevent deep infection after implant-based breast reconstruction. However, there is limited evidence of the clinical effect. In this study, the authors compare the risk of a deep infection in a Danish population of women who received antibiotic implant irrigation with either gentamicin or vancomycin, or no irrigation.

Methods:
The authors retrospectively reviewed consecutive patients undergoing all types of breast reconstruction with implants at Rigshospitalet and Herlev Hospital, Denmark, from 2010 to 2019. Logistic regression was used to compare the risk of deep infection between no irrigation and irrigation with gentamicin or vancomycin, and to account for the difference in risk between patient subgroups and risk factors.

Results:
The authors included 1508 patients who received antibiotic irrigation with gentamicin (500 patients), vancomycin (304 patients), or no irrigation (704 patients). The univariable risk analysis showed a significant decreased risk of deep infection using gentamicin irrigation compared with no irrigation (OR, 0.58; P < 0.05). However, when adjusting for risk factors for infection, there was no significant decrease in the risk of infection when using gentamicin (OR, 0.90; P = 0.71) or vancomycin (OR, 1.0; P = 0.99) compared with the control group.

Conclusions:
The authors found no significant effect of using antibiotic implant irrigation after isolating it from risk factors for deep infection. However, because of the limitations of the study, the authors cannot conclude that there is no effect of antibiotic implant irrigation. There is a need for a randomized, placebo-controlled trial to investigate the effect, and potential side-effects, of antibiotic implant irrigation.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Risk, II.
Pediatric emergency resuscitative thoracotomy: A Western Trauma Association, Pediatric Trauma Society, and Eastern Association for the Surgery of Trauma collaborative critical decisions algorithm
Authors: Martin Matthew J. , Brasel Karen J. , Brown Carlos V.R. , Hartwell Jennifer L. , de Moya Marc , Inaba Kenji , Ley Eric J. , Moore Ernest E. , Peck Kimberly A. , Rizzo Anne G. , Rosen Nelson G. , Weinberg Jordan A. , Coimbra Raul , Crandall Marie , Mukherjee Kaushik , Ignacio Romeo , Longshore Shannon , Flynn-O’Brien Katherine T. , Ng Grace , Selesner Leigh , Jafri Mubeen 
Published: June 2023

LEVEL OF EVIDENCE
Literature synthesis and expert opinion, Level V.
Mental health symptoms and engagement in a stepped-care mental health service among patients with a violent versus nonviolent injury
Authors: O'Connor Kelly E. , Shanholtz Caroline E. , Espeleta Hannah C. , Ridings Leigh E. , Gavrilova Yulia , Hink Ashley , Ruggiero Kenneth J. , Davidson Tatiana M. 
Published: June 2023

BACKGROUND
Few studies have examined mental health symptom trajectories and engagement in mental health follow-up in relation to mechanism of injury. This study examined differences in engagement between survivors of nonviolent and violent injury in the Trauma Resilience and Recovery Program (TRRP), a stepped-care, technology-enhanced model that provides evidence-based mental health screening and treatment to patients admitted to our Level I trauma service.

METHODS
This study analyzed data from 2,527 adults enrolled in TRRP at hospital bedside between 2018 and 2022, including 398 patients (16%) with a violent injury and 2,129 patients (84%) with a nonviolent injury. Bivariate and hierarchical logistic regression analyses examined relations between injury type (violent vs. nonviolent) engagement in TRRP and mental health symptoms at 30 day follow-up.

RESULTS
Engagement in services at bedside was similar across survivors of violent and nonviolent traumatic injury. Patients with violent injury had higher levels of posttraumatic stress disorder and depressive symptoms 30 days postinjury but were less likely to engage in mental health screening. Among patients who screened positive for posttraumatic stress disorder and depression, patients with violent injury were more likely to accept treatment referrals.

CONCLUSION
Patients with a violent traumatic injury have higher levels of mental health needs yet face greater barriers to accessing mental health services following their injury relative to those with a nonviolent injury. Effective strategies are needed to ensure continuity of care and access to mental health care to promote resilience and emotional and functional recovery.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level IV.
Abnormal energy metabolism in ALS: a key player?
Authors: Burg Thibaut , Van Den Bosch Ludo 
Published: June 2023

Purpose of the review
Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease of the motor system due to the selective and progressive degeneration of both upper and lower motor neurons. Disturbances in energy homeostasis were repeatedly associated with the ALS pathogenesis and appear early during the disease process. In this review, we highlight recent work demonstrating the crucial role of energy metabolism in ALS and discuss its potential clinical relevance.

Recent findings
The alteration of various metabolic pathways contributes to the heterogeneity of the clinical phenotype of ALS. Recent work showed that different ALS mutations selectively impact these pathways and translate to the disease phenotypes in patients and disease models. Strikingly, a growing number of studies point towards an early, even presymptomatic, contribution of abnormal energy homeostasis to the ALS pathogenesis. Advances in metabolomics generated valuable tools to study altered metabolic pathways, to test their therapeutic potential, and to develop personalized medicine. Importantly, recent preclinical studies and clinical trials demonstrated that targeting energy metabolism is a promising therapeutic approach.

Summary
Abnormal energy metabolism is a key player in ALS pathogenesis, emerging as a source of potential disease biomarkers and therapeutic targets.
Evaluation and comparison of nine growth- and development-based measures of pubertal timing
Authors: Elhakeem Ahmed , Frysz Monika , Soares Ana G , Bell Joshua A , Cole Tim J , Heron Jon , Howe Laura D , Sebert Sylvain , Tilling Kate , Timpson Nicholas J , Lawlor Deborah A 
Published: June 2023

ABSTRACTPuberty timing is fundamentally part of life-course health. Yet, little is known about the value of different measures of pubertal timing, particularly in males. We used a population-based cohort to examine nine measures of pubertal age (n=8,500), identifying development of pubic hair in males (12.6y) and breasts in females (11.5y) as early indicators of puberty, and voice breaking (14.2y) and menarche (12.7y) as late indicators. All measures showed evidence of positive phenotypic intercorrelations (e.g., r=0.49: male genitalia and pubic hair ages), and positive genetic intercorrelations. A genetic risk score (GRS) for age at menarche associated positively with all other measures (e.g., difference in female peak height velocity age per SD higher GRS: 0.24y, 95%CI: 0.21 to 0.26), as did GRS for voice breaking age (e.g., difference in male axillary hair age: 0.11y, 0.07 to 0.15). We illustrate the value of different pubertal age measures and their use in life-course research.
Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity
Authors: Brunet-Ratnasingham Elsa , Morin Sacha , Randolph Haley E. , Labrecque Marjorie , Bélair Justin , Lima-Barbosa Raphaël , Pagliuzza Amélie , Marchitto Lorie , Hultström Michael , Niessl Julia , Cloutier Rose , Sreng Flores Alina M. , Brassard Nathalie , Benlarbi Mehdi , Prévost Jérémie , Ding Shilei , Anand Sai Priya , Sannier Gérémy , Bareke Eric , Zeberg Hugo , Lipcsey Miklos , Frithiof Robert , Larsson Anders , Zhou Sirui , Nakanishi Tomoko , Morrison David , Vezina Dani , Bourassa Catherine , Gendron-Lepage Gabrielle , Medjahed Halima , Point Floriane , Richard Jonathan , Larochelle Catherine , Prat Alexandre , Arbour Nathalie , Durand Madeleine , Brent Richards J , Moon Kevin , Chomont Nicolas , Finzi Andrés , Tétreault Martine , Barreiro Luis , Wolf Guy , Kaufmann Daniel E. 
Published: June 2023

SUMMARYPlasma RNAemia, delayed antibody responses and inflammation predict COVID-19 outcomes, but the mechanisms underlying these immunovirological patterns are poorly understood. We profile 782 longitudinal plasma samples from 318 hospitalized COVID-19 patients. Integrated analysis using k-means reveal four patient clusters in a discovery cohort: mechanically ventilated critically-ill cases are subdivided into good prognosis and high-fatality clusters (reproduced in a validation cohort), while non-critical survivors are delineated by high and low antibody responses. Only the high-fatality cluster is enriched for transcriptomic signatures associated with COVID-19 severity, and each cluster has distinct RBD-specific antibody elicitation kinetics. Both critical and non-critical clusters with delayed antibody responses exhibit sustained IFN signatures, which negatively correlate with contemporaneous RBD-specific IgG levels and absolute SARS-CoV-2-specific B and CD4+T cell frequencies. These data suggest that the “Interferon paradox” previously described in murine LCMV models is operative in COVID-19, with excessive IFN signaling delaying development of adaptive virus-specific immunity.
BharatSim: An agent-based modelling framework for India
Authors: Cherian Philip , Kshirsagar Jayanta , Neekhra Bhavesh , Deshkar Gaurav , Hayatnagarkar Harshal , Kapoor Kshitij , Kaski Chandrakant , Kathar Ganesh , Khandekar Swapnil , Mookherjee Saurabh , Ninawe Praveen , Noronha Riz Fernando , Ranka Pranjal , Sinha Vaibhhav , Vinod Tina , Yadav Chhaya , Gupta Debayan , Menon Gautam I. 
Published: June 2023

AbstractBharatSim is an open-source agent-based modelling framework for the Indian population. It can simulate populations at multiple scales, from small communities to states. BharatSim uses a synthetic population created by applying statistical methods and machine learning algorithms to survey data from multiple sources, including the Census of India, the India Human Development Survey, the National Sample Survey, and the Gridded Population of the World. This synthetic population defines individual agents with multiple attributes, among them age, gender, home and work locations, pre-existing health conditions, and socio-economic and employment status. BharatSim’s domain-specific language provides a framework for the simulation of diverse models. Its computational core, coded inScala, supports simulations of a large number of individual agents, up to 50 million. Here, we describe the design and implementation of BharatSim, using it to address three questions motivated by the COVID-19 pandemic in India: (i) When can schools be safely reopened given specified levels of hybrid immunity?, (ii) How do new variants alter disease dynamics in the background of prior infections and vaccinations? and (iii) How can the effects of varied non-pharmaceutical interventions (NPIs) be quantified for a model Indian city? Through its India-specific synthetic population, BharatSim allows disease modellers to address questions unique to this country. It should also find use in the computational social sciences, potentially providing new insights into emergent patterns in social behaviour.Author summaryAgent-based simulations provide granular ways of describing the dynamics of each individual in a population. Such models are especially useful in describing the spread of an infectious disease, since they can be used to incorporate individual-level heterogeneity in behaviour and susceptibilities, as well as spatio-temporal information. BharatSim is such an agent-based modelling framework for India. It can simulate populations at multiple scales, from a few hundreds to several millions. It creates and uses a predefined synthetic population for India, assimilating it into a simulation framework. The synthetic population defines individuals with multiple attributes, among them age, sex, home, and work locations. We demonstrate the use of BharatSim in three contexts related to the COVID-19 pandemic in India.
The role of BST4 in the pyrenoid ofChlamydomonas reinhardtii
Authors: Adler Liat , Lau Chun Sing , Shaikh Kashif M. , Maldegem Kim A. van , Payne-Dwyer Alex L. , Lefoulon Cecile , Girr Philipp , Atkinson Nicky , Barrett James , Emrich-Mills Tom Z. , Dukic Emilija , Blatt Michael R. , Leake Mark C. , Peltier Gilles , Spetea Cornelia , Burlacot Adrien , McCormick Alistair J. , Mackinder Luke C. M. , Walker Charlotte E. 
Published: June 2023

ABSTRACTIn many eukaryotic algae, CO2 fixation by Rubisco is enhanced by a CO2- concentrating mechanism, which utilizes a Rubisco-rich organelle called the pyrenoid. The pyrenoid is traversed by a network of thylakoid-membranes called pyrenoid tubules, proposed to deliver CO2. In the model algaChlamydomonas reinhardtii(Chlamydomonas), the pyrenoid tubules have been proposed to be tethered to the Rubisco matrix by a bestrophin-like transmembrane protein, BST4. Here, we show that BST4 forms a complex that localizes to the pyrenoid tubules. A Chlamydomonas mutant impaired in the accumulation of BST4 (bst4) formed normal pyrenoid tubules and heterologous expression of BST4 inArabidopsis thalianadid not lead to the incorporation of thylakoids into a reconstituted Rubisco condensate. Chlamydomonasbst4mutant did not show impaired growth at air level CO2. By quantifying the non-photochemical quenching (NPQ) of chlorophyll fluorescence, we show thatbst4displays a transiently lower thylakoid lumenal pH during dark to light transition compared to control strains. When acclimated to high light,bst4had sustained higher NPQ and elevated levels of light-induced H2O2 production. We conclude that BST4 is not a tethering protein, but rather is an ion channel involved in lumenal pH regulation possibly by mediating bicarbonate transport across the pyrenoid tubules.One-sentence summaryIn Chlamydomonas, the pyrenoid-localized bestrophin-like protein BST4 is a putative ion channel involved in pH regulation of the thylakoid lumen, possibly by mediating bicarbonate transport.
Specific long-term changes in anti-SARS-CoV-2 IgG modifications and antibody functions in mRNA, adenovector, and protein subunit vaccines
Authors: Reinig Sebastian , Kuo Chin , Wu Chia-Chun , Huang Sheng-Yu , Yu Jau-Song , Shih Shin-Ru 
Published: June 2023

AbstractVarious vaccine platforms were developed and deployed against the COVID-19 disease. The Fc-mediated functions of IgG antibodies are essential in the adaptive immune response elicited by vaccines. However, the long-term changes of protein subunit vaccines and their combinations with mRNA vaccines are unknown. A total of 272 serum and plasma samples were collected from individuals who received first to third doses of the protein subunit Medigen, the mRNA (BNT), or the adenovector AstraZeneca vaccines. The IgG subclass level was measured using enzyme-linked immunosorbent assay, and Fc-N glycosylation was measured using LC-MS/MS. Antibody-dependent phagocytosis (ADCP) and complement deposition (ADCD) of anti-spike (S) IgG antibodies were measured. IgG1 and 3 reached the highest anti-S IgG subclass level. IgG1, 2, and 4 subclass levels significantly increased in mRNA- and Medigen-vaccinated individuals. Fc-glycosylation was stable, except in female BNT vaccinees, who showed increased bisection and decreased galactosylation. Female BNT vaccinees had a higher anti-S IgG titer than that of males. ADCP declined in all groups. ADCD increased in Medigen-vaccinated individuals after the third dose. Each vaccine produced specific long-term changes in Fc structure and function. This finding is critical when selecting a vaccine platform or combination to achieve the desired immune response.
The roles of GpsB and DivIVA inStaphylococcus aureusgrowth and division
Authors: Sutton Joshua A. F. , Cooke Mark , Tinajero-Trejo Mariana , Wacnik Katarzyna , Salamaga Bartłomiej , Portman-Ross Callum , Lund Victoria A. , Hobbs Jamie K. , Foster Simon J. 
Published: June 2023

AbstractThe spheroid bacteriumS. aureusis often used as a model of morphogenesis due to its apparent simple cell cycle.S. aureushas many cell division proteins that are conserved across bacteria alluding to common functions. However, despite intensive study we still do not know the roles of many of these components. Here we have examined the functions of the paralogues DivIVA and GpsB in theS. aureuscell cycle. Cells lackinggpsBdisplay a more spherical phenotype than wild type, associated with a decrease in peripheral cell wall peptidoglycan synthesis. This correlates with an increased localisation of penicillin binding proteins at the developing septum, notably PBPs 2 and 3. Our results highlight the role of GpsB as an apparent regulator of cell morphogenesis inS.aureus.
A supermatrix phylogeny of the world’s bees (Hymenoptera: Anthophila)
Authors: Henríquez-Piskulich Patricia , Hugall Andrew F. , Stuart-Fox Devi 
Published: June 2023

AbstractThe increasing availability of large phylogenies has provided new opportunities to study the evolution of species traits, their origins and diversification, and biogeography; yet, with the exception of butterflies, taxonomically well-curated phylogenies are currently lacking for major insect groups. Bees (Hymenoptera: Anthophila) are a large group of insect pollinators that have a worldwide distribution, and a wide variation in ecology, morphology, and life-history traits, including sociality. For these reasons, as well as their major economic importance as pollinators, numerous molecular phylogenetic studies of relationships between and/or within families or genera for this group have been published. We used publicly available sequence data, a family-level phylogenomic backbone, and ultra-conserved element (UCE) data, reconciled to a taxonomic database, to produce a dated phylogeny for bees. The phylogeny comprises 4651 bee species, representing 23% of species and 86% of genera. At family, subfamily, and tribe levels, the data were robust, but between and within some genera relationships remain uncertain. In addition, most of the species with available sequence data are geographically distributed in North America and Europe, highlighting gaps that should be considered in future research to improve our understanding of bee evolution and phylogeography. We provide a summary of the current state of molecular data available and its gaps, and discuss the advantages and limitations of this bee supermatrix phylogeny (available online atbeetreeoflife.org), which may enable new insights into long standing questions about evolutionary drivers in bees, and potentially insects.HighlightsBee supermatrix phylogeny constructed with public and published sequence data.Includes 23% of currently recognised species and covers 86% of genera.Provides a summary of remaining gaps in bee phylogenetics.Available online at beetreeoflife.org, with subsetting tool to facilitate comparative analyses.
High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children with and without SARS-CoV-2
Authors: Watkins Timothy A. , Cheemarla Nagarjuna R. , Hänsel Katrin , Green Alex B. , Amat Julien A.R. , Lozano Richard , Dudgeon Sarah N. , Landry Marie L. , Schulz Wade L. , Foxman Ellen F. 
Published: June 2023

SummaryRecent work indicates that heightened nasal innate immunity in children may impact SARS-CoV-2 pathogenesis. Here, we identified drivers of nasal innate immune activation in children using cytokine profiling and multiplex pathogen detection in 291 pediatric nasopharyngeal samples from the 2022 Omicron surge. Nasal viruses and bacterial pathobionts were highly prevalent, especially in younger children (81% of symptomatic and 37% asymptomatic children overall; 91% and 62% in subjects <5 yrs). For SARS-CoV-2, viral load was highest in young children, and viral load in single infections or combined viral loads in coinfections best predicted nasal CXCL10, a biomarker of the mucosal interferon response. Bacterial pathobionts correlated with high nasal IL-1β and TNF, but not CXCL10, and viral-bacterial coinfections showed a combined immunophenotype. These findings reveal virus and bacteria as drivers of heightened nasal innate immunity in children and suggest that frequent host-pathogen interactions shape responses to respiratory viruses in this age group.
Effective vaccination strategies to control COVID-19 outbreak: A modeling study
Authors: Ko Youngsuk , Peck Kyong Ran , Kim Yae-Jean , Kim Dong-Hyun , Jung Eunok 
Published: June 2023

AbstractOBJECTIVESThree years following the start of the COVID-19 pandemic, the World Health Organization (WHO) declared COVID-19 a global health emergency of international concern. As immunity levels in the population acquired through past infections and vaccinations have been decreasing, booster vaccinations have become necessary to control new outbreaks. This study aimed to determine the most suitable vaccination strategy to control the COVID-19 surge.METHODSA mathematical model was developed to simultaneously consider the immunity levels induced by vaccines and infections, and employed to analyze the possibility of future resurgence and control using vaccines and antivirals.RESULTSAs of May 11, 2023, a peak in resurgence is predicted to occur around mid-October of the same year if the current epidemic trend continues without additional vaccinations. In the best scenario, the peak number of severely hospitalized patients can be reduced by 43% (480) compared to the scenario without vaccine intervention (849). Depending on the outbreak trends and vaccination strategies, the best timing for vaccination in terms of minimizing the said peak varies from May to August 2023.CONCLUSIONSOur results indicate that if the epidemic continues, the best timing for vaccinations must be earlier than specified by the current plan in Korea. Further monitoring of outbreak trends is crucial for determining the optimal timing of vaccinations to manage future surges.
Sequence features of transcriptional activation domains are consistent with the surfactant mechanism of gene activation
Authors: Broyles Bradley K. , Erkina Tamara Y. , Maris Theodore P. , Gutierrez Andrew T. , Coil Daniel A. , Wagner Thomas M. , Class Caleb A. , Erkine Alexandre M. 
Published: June 2023

SummaryTranscriptional activation domains (ADs) of gene activators remain enigmatic for decades as they are short, extremely variable in sequence, structurally disordered, and interact fuzzily to a spectrum of targets. We showed that the single required characteristic of the most common acidic ADs is an amphiphilic aromatic–acidic surfactant-like property which is the key for the local gene-promoter chromatin phase transition and the formation of “transcription factory” condensates. We demonstrate that the presence of tryptophan and aspartic acid residues in the AD sequence is sufficient for in vivo functionality, even when present only as a single pair of residues within a 20-amino-acid sequence containing only 18 additional glycine residues. We demonstrate that breaking the amphipathic α-helix in AD by prolines increases AD functionality. The proposed mechanism is paradigm-shifting for gene activation area and generally for biochemistry as it relies on near-stochastic allosteric interactions critical for the key biological function.