bluuebunny/crossref_metadata_2025_split huggingface dataset:
Updated Trends and Outcomes in Autologous Breast Reconstruction in the United States, 2016–2019
Authors: Shah Jennifer K. , Amakiri Uchechukwu O. , Cevallos Priscila , Yesantharao Pooja , Ayyala Haripriya , Sheckter Clifford C. , Nazerali Rahim 
Published: February 2024

IntroductionAutologous breast reconstruction (ABR) has increased in recent decades, although concerns for access remain. As such, our goal is to trend national demographics and operative characteristics of ABR in the United States.MethodsUsing the National Inpatient Sample, 2016–2019, theInternational Classification of Disease,Tenth Editioncodes identified adult female encounters undergoing ABR. Demographics and procedure-related characteristics were recorded. Discharge weights generated national estimates. Statistical analysis included univariate testing and multivariate regression modeling.ResultsA total of 52,910 weighted encounters met the criteria (mean age, 51.5 ± 10.0 years). Autologous breast reconstruction utilization increased (Δ = +5%), 2016–2019, primarily driven by a rise in deep inferior epigastric perforator (DIEP) reconstructions (Δ = +28%; incidence rate ratio [IRR], 1.070;P< 0.001), which were predominant throughout the study period (69%). More recent surgery year, bilateral reconstruction, higher income levels, commercial insurance, and care in the South US region increased the odds of DIEP-based ABR (P≤ 0.036). Transverse rectus abdominis myocutaneous flaps, bilateral reconstructions, higher comorbidity levels, and experiencing complications increased the length of stay (P≤ 0.038). Most ABRs (75%) were privately insured. The rates of immediate reconstructions increased over the study period (from 26% to 46%; IRR, 1.223;P< 0.001), as did the rates of bilateral reconstructions (from 54% to 57%; IRR, 1.026;P= 0.030). The rates of ABRs performed at teaching hospitals remained high (90% to 93%;P= 0.242).ConclusionsAs of 2019, ABR has become more prevalent, with the DIEP flap constituting the most common modality. With the increasing ABR popularity, efforts should be made to ensure geographic and financial accessibility.
Pectoralis Major Muscle Flap Utilization in Salvage Esophagectomy Including Great Vessel Resection Reconstructed by Prosthetic Grafts
Authors: Furuse Kiichi , Nara Masayuki , Kageyama Daisuke , Arikawa Masaki , Akazawa Satoshi , Daiko Hiroyuki , Higashino Takuya 
Published: February 2024

Background
Salvage surgery is a therapeutic option for recurrent or residual esophageal cancer after definitive chemoradiation therapy. This report aimed to describe the procedure of reconstruction after salvage esophagectomy involving great vessel resection using prosthetic grafts, a pectoralis major muscle (PM) flap, and free jejunal transfer, if required. To the best of our knowledge, no previous report has described the reconstruction of the defect after combined esophageal and great vessel resection.

Patients and Methods
From January 2017 to December 2022, 4 patients underwent salvage esophagectomy with excision of the great vessels and reconstruction with prosthetic grafts, as well as a PM flap placement in a single center. We retrospectively investigated the patients' clinical data. The patients were all men, with a median age of 70 (range, 67–77) years. Regarding neoadjuvant therapy, 2 patients received chemoradiation therapy, 1 patient received radiotherapy only due to drug-induced pneumonia, and 1 patient received chemotherapy with adjuvant radiotherapy.

Results
Alimentary tract reconstruction was performed by free jejunal transfer in 2 cases, direct suture in 1 case, and stomach roll in 1 case. In all cases, a vascular bypass was established before tumor resection. We created mediastinal tracheostoma in 2 cases. A PM flap was inserted to cover the prosthetic grafts and approximate the tracheal mucosa. With regard to major complications, leakage from the jejunal esophageal anastomotic site was observed in 2 cases. The leakage improved with conservative treatment without graft removal or replacement in both cases.

Conclusions
In cases of locally recurrent or residual tumors after definitive chemoradiation therapy, salvage esophagectomy along with great vessel resection, followed by reconstruction using prosthetic grafts, PM flaps, and free jejunal transfer, if necessary, is a useful option.
Outcomes After Implant-Based Breast Reconstruction Following the National Institution of a Ban on Bacitracin Irrigation
Authors: Roy Nikita , Oleru Olachi , Amakiri Uchechukwu , Stratis Catherine , Kwon Daniel , Wang Anya , Akhavan Arya , Henderson Peter W. 
Published: February 2024

Background
The use of irrigation with bacitracin-containing solution is common among surgeons, as it was widely thought to have antibacterial properties and prevent postoperative infection. Current literature, however, suggests that antibiotic-containing irrigation confers little added benefit. On January 31, 2020, the Food and Drug Administration instituted a ban on bacitracin-containing irrigation for operative use. This study aimed to determine whether bacitracin has a beneficial effect on postoperative infection rates by analyzing infection rates before and after the Food and Drug Administration ban on bacitracin irrigation.

Methods
A single-institution retrospective chart review was conducted. Eligible patients underwent implant-based breast reconstruction after mastectomy from October 1, 2016, to July 31, 2022. Procedure date, reconstruction type, patient comorbidities, use of bacitracin irrigation, postoperative infection, and secondary outcomes were collected. Univariate and multivariable logistic regression analyses were performed.

Results
A total of 188 female patients were included in the study. Bacitracin use did not protect against infection in univariate or multivariable analysis. Age greater than 50 years was associated with an increased risk of postoperative infection (P = 0.0366). The presence of comorbidities, smoker status, neoadjuvant therapy treatment before surgery, implant placement, and laterality were all not significantly associated with postoperative infection development.

Conclusions
The results of this study demonstrate a lack of association between bacitracin use and postoperative infection. Additional research into the optimal antibiotic for perioperative irrigation is needed, as bacitracin is not encouraged for use.
Xeroform Stick-Down Dressing
Authors: Grauberger Jennifer N. , Joshi Nikita , Joo Alex , Phelan Alannah L. , Lalikos Janice F. 
Published: February 2024

Background
Burns traditionally require frequent, painful dressing changes to minimize infection risk and promote wound healing. To improve care for our pediatric population, our institution adapted a skin graft donor site dressing into a “stick-down” burn dressing consisting of a one-time application of bacitracin and 3% bismuth tribromophenate/vaseline impregnated gauze (Xeroform) that adheres to the burn and peels off as new epithelialized skin forms. The goal of which is to minimize dressing change frequency and patient discomfort in a cost-effective, widely available manner. This study aimed to compare clinical outcomes of the stick-down versus traditional topical dressings.

Methods
A retrospective cohort study of pediatric patients (age <18 year) with partial-thickness burns treated at a level I pediatric trauma center for 4 years was conducted. One hundred eleven patients were included: 74 patients treated with daily silver sulfadiazene (Silvadene) dressings matched to 37 patients treated with the Xeroform stick-down dressing using 2:1 propensity score matching. Univariate analyses used Wilcoxon rank sum and Fisher exact tests.

Results
The cohorts had similar demographics and burn characteristics. Both groups had similar hospitalization rates (31.1% Silvadene, 32.4% Xeroform), most commonly for pain control (54.5% Silvadene, 58.3% Xeroform), with similar average daily narcotic usage (7.7 ± 12.1 morphine milliequivalents Silvadene, 5.1 ± 9.5 Xeroform; P = 0.91). The Xeroform cohort had a shorter but statistically similar hospital stay (median, 1 vs 2 days). In addition, the Xeroform cohort required significantly less dressing changes with a median of 0.5 changes compared with 12 for the Silvadene cohort (P < 0.0001). There was no difference in time to burn reepithelialization (median, 13.0 days for Silvadene and 12.0 days for Xeroform; P = 0.20) or wound healing complications (12.5% Silvadene, 2.7% Xeroform; P = 0.15).

Conclusions
The Xeroform stick-down dressing has equivalent clinical outcomes to that of standard Silvadene dressings for the treatment of pediatric partial-thickness burns with the major advantages of decreasing dressing change frequency, minimizing patient distress and pain, and streamlining clinical care.
25% Human Serum Albumin Improves Hemodynamics and Prevents the Need for Nearly All Pre-Hospital Resuscitation in a Rat (Rattus Norvegicus) Model of Trauma and Hemorrhage
Authors: Penn Alexander H. , Falabella Michael , Sanchez Antonio , Hernandez Orlando , McFadden Kassandra , Hutcheson Jack 
Published: February 2024

Abstract
Combat casualty care can be complicated by transport times exceeding the “golden hour,” with intervention and resuscitation limited to what the medic can carry. Pharmaceutical albumin comes highly saturated with non-esterified fatty acids (NEFAs). We recently showed that treatment with 25% bovine serum albumin (BSA) loaded with oleic acid (OA), but not NEFA-free BSA, improved survival for hours after severe hemorrhage and often eliminated the need for resuscitation in rats. However, it was unknown if pharmaceutical albumin, derived from human sources and loaded with caprylic acid (CA), would have the same benefits. We compared adjunct treatment with OA-saturated BSA, CA-saturated BSA, pharmaceutical human serum albumin (HSA), or a no-albumin control in a similar rat hemorrhagic shock model to determine if the three NEFA-albumin groups provided the same benefits relative to control. We found almost no significant differences among the NEFA-albumin groups in any measure. Mortality in controls was too low to allow for detection of improvement in survival, but NEFA-albumin groups had significantly improved hemodynamics, lactate clearance, and greatly reduced fluid requirements compared to controls. Contrary to expectations of “dehydration”, 25% albumins shifted little additional fluid into the vasculature. Rather, they restored protein to the auto-transfusion fluid. NEFA-albumin did not worsen lung permeability, but we observed a loss of circulating protein suggesting it may have increased overall vascular permeability. Our findings suggest that, though imperfect, 25% HSA could be a solution for resuscitation in austere conditions requiring prolonged field care.
Wasted efforts impair random search efficiency and reduce choosiness in mate-pairing termites
Authors: Mizumoto Nobuaki , Nagaya Naohisa , Fujisawa Ryusuke 
Published: February 2024

AbstractRandom search theories predict that animals employ movement patterns that optimize encounter rates with target resources. However, animals are not always able to achieve the best search strategy. Energy depletion, for example, limits searchers’ movement activities, forcing them to adjust their behaviors before and after encounters. Here, we quantified the cost of mate search in a termite,Reticulitermes speratus, and revealed that the searching cost reduces the selectivity of mating partners. After a dispersal flight, termites search for a mating partner with limited reserved energy. We found that their movement activity and diffusiveness progressively declined over extended mate search. Our data-based simulations qualitatively confirmed that the reduced movement diffusiveness decreased the searching efficiency. Also, prolonged search periods reduced colony foundation success and the number of offspring. Thus, mate search imposes doubled costs on termites. Finally, we found that termites with an extended mate search reduced the selectivity of mating partners, where males immediately paired with any encountering females. Thus, termites dramatically changed their mate search behavior depending on their physiological conditions. Our finding highlights that accounting for the searchers’ internal states is essential to fill the gap between random search theories and empirical behavioral observations.
Allele age estimators designed for whole genome datasets show only a modest decrease in accuracy when applied to whole exome datasets
Authors: Pivirotto Alyssa , Peles Noah , Hey Jody 
Published: February 2024

AbstractPersonalized genomics in the healthcare system is becoming increasingly accessible as the costs of sequencing decreases. With the increase in number of genomes, larger numbers of rare variants are being discovered and much work is being done to identify their functional impacts in relation to disease phenotypes. One way to characterize these variants is to estimate the time the mutation entered the population. However, allele age estimators such as Relate, Genealogical Estimator of Variant Age, and time of coalescence, were developed based on the assumption that datasets include the entire genome. We examined the performance of each of these estimators on simulated exome data under a neutral constant population size model and found that each provides usable estimates of allele age from whole-exome datasets. To test the robustness of these methods, analyses were undertaken to simulate data under a population expansion model and background selection. Relate performs the best amongst all three estimators with Pearson coefficients of 0.64 and 0.68 (neutral constant and expansion population model) with a 17 percent and 15 percent drop in accuracy between whole genome and whole exome estimations.Of the three estimators, Relate is best able to parallelize to yield quick results with little resources, however even Relate is only able to scale to thousands of samples making it unable to match the hundreds of thousands of samples being currently released. While more work is needed to expand the capabilities of current methods of estimating allele age, these methods estimate the age of mutations with a modest decrease in performance.Article SummaryIncreasing availability of whole exome sequencing yields large numbers of rare variants that have direct impact on disease phenotypes. Many methods of identifying the functional impact of mutations exist including the estimation of the time a mutation entered a population. Popular methods of estimating this time assume whole genome data in the estimate of the allele age based on haplotypes. We simulated genome and exome data under a constant and expansion population demography model and found that there is a decrease in accuracy in all three methods for exome data of 15-30% depending on the method. Testing the robustness of the best performing method, Relate, further simulations introducing background selection and varying the sample size were also undertaken with similar results.
Chromosome-scale genome assembly of the rough periwinkleLittorina saxatilis
Authors: De Jode Aurélien , Faria Rui , Formenti Giulio , Sims Ying , Smith Timothy P. , Tracey Alan , Wood Jonathan M. D. , Zagrodzka Zuzanna B. , Johannesson Kerstin , Butlin Roger K. , Leder Erica H 
Published: February 2024

AbstractThe intertidal gastropodLittorina saxatilisis a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makesL. saxatilisparticularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome ofL. saxatilisis 1.35Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44kb) and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1 % of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.SignificanceThe rough periwinkle,L. saxatilishas become a model to study adaptation, evolutionary innovation and speciation, including the role of chromosomal inversions in these processes. Chromosomal inversions have also been identified in other species ofLittorinaproviding a valuable opportunity for investigating their origin and evolution. Here, we present a new chromosome-scale reference genome ofL. saxatilisgenerated from long reads and HiC chromatin proximity mapping replacing an earlier highly fragmented genome. This will enable detailed investigations of how inversions contribute to adaptation and reproductive isolation inL. saxatilisand related taxa, including studies of the effects of individual loci within and outside inversions.
Tamm-Horsfall protein augments neutrophil NETosis during urinary tract infection
Authors: Mercado-Evans Vicki , Chew Claude , Serchejian Camille , Saltzman Alexander , Mejia Marlyd E. , Zulk Jacob J. , Cornax Ingrid , Nizet Victor , Patras Kathryn A. 
Published: February 2024

ABSTRACTUrinary neutrophils are a hallmark of urinary tract infection (UTI), yet the mechanisms governing their activation, function, and efficacy in controlling infection remain incompletely understood. Tamm-Horsfall glycoprotein (THP), the most abundant protein in urine, uses terminal sialic acids to bind an inhibitory receptor and dampen neutrophil inflammatory responses. We hypothesized that neutrophil modulation is an integral part of THP-mediated host protection. In a UTI model, THP-deficient mice showed elevated urinary tract bacterial burdens, increased neutrophil recruitment, and more severe tissue histopathological changes compared to WT mice. Furthermore, THP-deficient mice displayed impaired urinary NETosis during UTI. To investigate the impact of THP on NETosis, we coupledin vitrofluorescence-based NET assays, proteomic analyses, and standard and imaging flow cytometry with peripheral human neutrophils. We found that THP increases proteins involved in respiratory chain, neutrophil granules, and chromatin remodeling pathways, enhances NETosis in an ROS-dependent manner, and drives NET-associated morphologic features including nuclear decondensation. These effects were observed only in the presence of a NETosis stimulus and could not be solely replicated with equivalent levels of sialic acid alone. We conclude that THP is a critical regulator of NETosis in the urinary tract, playing a key role in host defense against UTI.
The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family
Authors: Cheng Lin , Hao Yanlin , Han Qunwei , Qiao Zhen , Li Mengge , Liu Daliang , Yin Hao , Li Tao , Long Wen , Luo Shanshan , Gao Ya , Zhang Zhihan , Yu Houlin , Sun Xinhao , Zhao Yiyong 
Published: February 2024

AbstractOrphan genes and transcription factor genes (TFs) are pervasive across genomes, play pivotal roles as regulators in a myriad of biological processes. Despite their ubiquity, the evolutionary trajectories and functional divergence of these genes remain largely unexplored. Theaceae family, encompassing the economically and culturally significant tea plant, presents a unique opportunity to study these dynamics. Here, we decoded a nearly complete, chromosome-scale reference genome ofStewartia gemmataspanning 2.95 Gb. This study is enhanced by integrating the genome ofS. gemmata, an early-diverging species within Theaceae, crucial for phylogenomic analyses and understanding the functional dynamics of orphan genes in this family. Our analysis confirmed the absence of a recent specific whole-genome duplication (WGD) event, with tandem duplications emerging as the predominant mechanism for gene duplication at ancestral nodes within Theaceae. By conducting an extensive comparative genomics analysis across 13 Theaceae and comparing these with a wide array of eukaryotic and prokaryotic proteins, we identified 37,618 orphan genes and 25,884 TFs in Theaceae. Interestingly, some orphan genes appear to have ancient origins in tea plant ancestors, suggesting relatively early origins with frequent gains and losses, conversely, many others seem more specific and recent. Notably, the orphan genes are characterized by shorter lengths, fewer exons and functional domains than TFs, implying relatively simpler functional roles. These orphan genes demonstrate diverse cellular localization and functions as predicted by GO/KEGG analysis, and are implicated in environmental response and flavor formation in tea plants. This study not only sheds light on the distinct evolutionary histories and functional divergences between orphan genes and TFs in Theaceae, but also contributes to our understanding of the genetic complexity and adaptability of this economically and culturally valuable plant family.Short summary:The nearly complete genome of an early-diverging speciesStewartia gemmataand phylogenomic studies provide insights into new gene evolution in Theaceae.
A Simple and Scalable Zebrafish Model of Sonic Hedgehog Medulloblastoma
Authors: Casey Mattie J. , Chan Priya P. , Li Qing , Jette Cicely A. , Kohler Missia , Myers Benjamin R. , Stewart Rodney A. 
Published: February 2024

SummaryMedulloblastoma (MB) is the most common malignant brain tumor in children and is stratified into three major subgroups. The Sonic hedgehog (SHH) subgroup represents ∼30% of all MB cases and has significant survival disparity depending upon TP53 status. Here, we describe the first zebrafish model of SHH MB using CRISPR to mutateptch1, the primary genetic driver in human SHH MB. These tumors rapidly arise adjacent to the valvula cerebelli and resemble human SHH MB by histology and comparative genomics. In addition,ptch1-deficient MB tumors with loss oftp53have aggressive tumor histology and significantly worse survival outcomes, comparable to human patients. The simplicity and scalability of theptch1MB model makes it highly amenable to CRISPR-based genome editing screens to identify genes required for SHH MB tumor formationin vivo, and here we identify thegrk3kinase as one such target.