bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the Readability of Online English and Spanish Language Patient Education Resources Provided by the American Society of Plastic Surgeons, American Society of Aesthetic Plastic Surgeons, and American Society of Reconstructive Microsurgeons
Authors: Sathyanarayanan Sairandri , Paidisetty Praneet , Wang Leonard Kuan-Pei , Gosman Amanda , Williams Steven , Chen Wendy
Published: February 2024

Introduction

The National Institutes of Health recommends that patient education materials (PEMs) be written at the sixth grade level. However, PEMs online are still generally difficult to read. The usefulness of online PEMs depends on their comprehensibility.

Objectives

This study assessed the readability of PEMs from national Plastic and Reconstructive Surgery (PRS) organization websites.

Methods

Patient education materials were collected from 3 prominent PRS organizations—the American Society of Plastic Surgeons (ASPS), American Society of Aesthetic Plastic Surgeons (ASAPS), and the American Society of Reconstructive Microsurgeons (ASRM). ASPS PEMs were organized into reconstructive and cosmetic groups, and then further subdivided into English and Spanish subgroups. ASAPS and ASRM PEMs provided cosmetic and reconstructive comparison groups to ASPS, respectively. Readability scores were generated using the Simple Measure of Gobbledygook (SMOG) and the Spanish SMOG scales.

Results

Overall, all PEMs failed to meet readability guidelines. Within ASPS, Spanish PEMs were easier to read than English PEMs (P < 0.001), and cosmetic PEMs were easier to read than reconstructive PEMs (P < 0.05). There was no significant difference between ASPS cosmetic and ASAPS PEMs (P = 0.36), nor between ASPS reconstructive and ASRM PEMs (P = 0.65). ASAPS and ASRM did not have any Spanish PEMs, and 92% of all ASPS PEMs were in English.

Conclusion

Although PRS societies strive to better educate the public on the scope of PRS, PRS ranks lowly in public understanding of its role in patient care. In addition, Spanish language PEMs from the 3 PRS organizations are severely lacking. Addressing these concerns will make online patient resources more equitable for various patient populations.
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

Introduction

Autologous 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.

Methods

Using 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.

Results

A 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).

Conclusions

As 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.
Endoscopic Approach With an Innovative Mini-Trocar for Forehead Osteoma Excision
Authors: Chen Shiju , Deng Yu , Xu Yangbin , Xu Shuqia , Huang Huixian , Zhang Yujing , Zhu Zhaowei , Liu Xiangxia
Published: February 2024

Traditionally forehead bony lesion is approached directly through the forehead skin or invasive coronal incision resulting prominent scar. An endoscopic approach through mini hairline incisions may provide a unique way to achieve the best esthetic results, but often time the authors encounter potential soft tissue injury from the high-speed burr. The authors present a case with multiple frontal bone osteoma lesions which were successfully removed through 2 small hairline incisions with the help of an otorhinolaryngological system and an innovative mini-trocar. Significant improvement in forehead shape with minimal scars was observed at an 18-month follow-up. This innovative and easily manipulating technique may help surgeons achieve better outcomes when treating frontal bone osteoma endoscopically.
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

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

Random 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

Personalized 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 Summary

Increasing 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

The 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.

Significance

The 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

Urinary 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

Orphan 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

Medulloblastoma (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.
Perceptions, attitudes, and challenges regarding continuing professional development among Ethiopian Medical Laboratory professionals: A mixed-method study
Authors: Negussie Adugna , Sisay Abay , Shibabaw Agumas , Kebede Edosa , Tesfaye Firehiwot , Kedida Gizachew , Deneke Nadew , Teklu Takele , Cheneke Waqtola
Published: February 2024

Background

Medical laboratory professionals play vital role in healthcare. The growing demand for quality laboratory services and emerging technologies underscore the crucial need for Continuing Professional Development (CPD). However, there is limited information on CPD programs in Ethiopia. Thus, this study aimed to assess medical laboratory professionals’ perceptions, attitudes, and challenges towards CPD and improve engagement to enhance diagnostic service quality.

Methods

this cross-sectional study enrolled 228 medical laboratory professionals in Ethiopia from July to October 2023. Using a mixed-methods approach that combined quantitative data from an online survey and qualitative data from interviews. SPSS version 28 was used for data analysis.

Results

the average age of the study participants was 32.6 ±6.4 (SD) years, the majority were men (88.6%), and 44.3% have worked for more than ten years. Of the participants, 51% never had CPD training. About three-fourth of the participants perceived CPD as essential to their professional career. About 45.2% of the study participants perceived that the purpose of CPD course is to renew their license and gain knowledge and skills that are not covered in basic training. While the majority of participants had good attitudes towards CPD, about 10% of them stated that it is not important in their career growth. The majority of the study participants were not in support of the decentralized CPD system. A notable problem with finance, insufficient manpower, unsupportive employers, a lack of awareness by regulatory bodies, inadequate access to training close to their working area, were identified as significant challenges of the CPD program.

Conclusion

the study highlights the perception that CPD is crucial for enhanced laboratory practices and career advancement. The study highlights the need for targeted strategies to address the identified problems and increase the engagement of medical laboratory professionals in the CPD program.
Variability in drought gene expression datasets highlight the need for community standardization
Authors: VanBuren Robert , Nguyen Annie , Marks Rose A. , Mercado Catherine , Pardo Anna , Pardo Jeremy , Schuster Jenny , Aubin Brian St. , Wilson Mckena Lipham , Rhee Seung Y.
Published: February 2024

Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.
Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts
Authors: Sadiq Sabrina , Holmes Edward C. , Mahar Jackie E.
Published: February 2024

The RNA virus familyPicobirnaviridaehas traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing picobirnavirus genera that we tentatively nameAlpha-, Beta-, Gamma-, Delta-, Epsilon-, Zeta-,andEtapicobirnavirus. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in picobirnavirus genomes than in the two groups of established RNA bacteriophage – theLeviviricetesandCystoviridae. Overall, our findings support the hypothesis that thePicobirnaviridaehave bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.
Human-AI Collaboration in Large Language Model-Assisted Brain MRI Differential Diagnosis: A Usability Study
Authors: Kim Su Hwan , Schramm Severin , Berberich Cornelius , Rosenkranz Enrike , Schmitzer Lena , Serguen Kerem , Klenk Christopher , Lenhart Nicolas , Zimmer Claus , Wiestler Benedikt , Hedderich Dennis M.
Published: February 2024

Background

Prior studies have shown the potential of large language models (LLMs) to support in differential diagnosis in radiology. However, the interaction of human users with LLMs in this context has not been evaluated.

Purpose

To investigate the impact of human-LLM collaboration on accuracy and efficiency of brain MRI differential diagnosis.

Methods

In this retrospective study, twenty brain MRI cases with a challenging but definitive diagnosis were selected and randomized into two groups. Six inexperienced radiology residents were instructed to determine the three most likely differential diagnoses for each of these cases via conventional internet search or utilizing an LLM-based search engine (© Perplexity AI, powered by GPT-4). Accuracy of suggested differential diagnoses was analyzed using the chi-square test and Mann-Whitney U test. Interpretation times were analyzed using the student’s t-test. Benefits and challenges in human-LLM interaction were derived from observations and participant feedback.

Results

LLM-assisted brain MRI differential diagnosis yielded superior accuracy (38/59 [LLM-assisted] vs 25/59 [conventional] correct diagnoses, p = 0.03). No difference in interpretation time (8.12 +/- 3.22 min [LLM-assisted] vs 7.96 +/- 2.65 min [conventional], p = 0.76) or level of confidence (median of 2.5 [LLM-assisted] vs 3.0 [conventional], p = 0.96) was observed. Several challenges related to human errors and technical limitations were identified.

Conclusion

Human-LLM collaboration has the potential to improve brain MRI differential diagnosis. Yet, several challenges must be addressed to ensure effective adoption and user acceptance.
Clinical evaluation of the Roche distributed SD Biosensor SARS-CoV-2 & Flu A/B Rapid Antigen Test amongst mild symptomatic people during the 2022/2023 winter season
Authors: Iglὁi Zsὁfia , Velzing Jans , Koopmans Marion , Molenkamp Richard
Published: February 2024

Both influenza and SARS-CoV-2 are seasonal respiratory illnesses with similar symptoms, however distinguishing one from the other can have benefits for the patient and have different implications in various settings.

In this study we have evaluated the clinical performance of the Roche distributed SD Biosensor SARS-CoV-2 & Flu A/B Rapid Antigen Test during the 2022/2023 winter season, in a non-hospitalized, mild symptomatic population, comparing results with reverse transcription quantitative polymerase chain reaction (RT-qPCR). Participants also filled in a short questionnaire about their symptom onset, symptoms, vaccination status for both influenza and SARS-CoV-2.

We could include 290 people with complete records with female majority (72%, 209/290). Age ranged from 18 years old (minimum age for inclusion) to 71 years (mean age was 40.4 years). From the 290 inclusions 93 tested positive with SARS-CoV-2 PCR, 12 by influenza A and 6 by influenza B PCR. For SARS-CoV-2 overall sensitivity was 72.0% (confidence interval, CI 61.8-80.9%) and specificity 99.5% (CI 97.2-99.9%). SARS-CoV-2 RDT performed best up to and including PCR ct value of 25 (sensitivity 96% CI 85.8-99.5%), but could also detect samples less or equal to PCR ct 33, however with lower sensitivity (sensitivity 80.0% CI 69.6-88.1%). For influenza limited amount of samples were available; the RDT detected influenza A with 58.3% sensitivity (CI 27.7-84.8) and 100% specificity (CI 98.6-100.0%). In case of influenza B the inclusions were too low to calculate sensitivity reliably (2/6, 33.3% CI 4.3-77.7%); specificity was 98.2% (5/274, CI 95.8-99.4%). No cross reaction between SARS-CoV-2 and Flu A/B was experienced.

As was shown before, SARS-CoV-2 could be determined with high sensitivity in recent onset and lower than ct 25 samples. In spite of performing the study throughout the influenza season, we had sub optimal inclusions for determining RDT clinical performance; further studies are needed.
Predictors of breast cancer screening among women of reproductive age in Tanzania: Evidence from DHS 2022
Authors: Tibenderana Jovin R. , Kessy Sanun Ally , Mlaponi Dosanto Felix , Mwaitete Ndinagwe Lloyd , Mtenga John Elyas
Published: February 2024

Background

Breast cancer is a global concern, registering 2.3 million new cases and 685,000 deaths in 2020, with projections reaching 4.4 million cases by 2070. In Tanzania, it’s the second leading cause of cancer-related deaths among women, often diagnosed at advanced stages, leading to poor outcomes. Only 5% of women in the country report undergoing breast cancer screening, the aim study is to determine factors associated with breast cancer screening in Tanzania.

Methods

A cross-sectional study among women of reproductive age in Tanzania, utilizing data from the Demographic and Health Surveys (DHS). We used available data on breast cancer screening the DHS. The outcome of the study was breast cancer screening. To find independent variables associated with breast cancer screening, logistic regression was used.

Results

After controlling for other factors, the following factors remained significantly associated with breast cancer screening among women of reproductive age; age(AOR=5.33, 95% CI 3.72, 7.63), being wealthy (AOR=2.34, 95% CI 1.61, 3.38), residing in rural(AOR= 0.59, 95% CI 0.46, 0.763), being educated(AOR=2.43, 95% CI 1.60, 3.68), being insured(AOR= 2.40, 95% CI 1.89, 3.06), healthcare facility visits in the past 12 months(AOR=1.43, 95% CI 1.14, 1.78) and living in Northern zone(AOR= 2.43, 95% CI 1.42, 4.15) compared to western zone

Conclusion

Breast cancer screening is still under-utilized and have shown to be marginalized in women of reproductive age. Policies to address disparities, comprehensive health education and awareness campaigns are instrumental to increase utilization and reduction of burden of breast cancers in Tanzania
The timing of surgical interventions following the implantation of coronary drug-eluting stents in patients undergoing gastrointestinal cancer surgery: A multicenter retrospective cohort study
Authors: Xu Ziyao , Hao Xinyu , Tian Jingyang , Song Qiying , Li Tian , Gao Lei , Wang Xinxin
Published: February 2024

Background

The guidelines recommending a minimum deferral of six months for non-cardiac surgeries following drug-eluting stent percutaneous coronary intervention (DES-PCI) do not adequately address the requirements for individuals undergoing gastrointestinal cancer surgery (GCS). We aim to investigate the optimal timing for surgical interventions to maximize patient benefit.

Methods

The study encompassed 2,501 patients treated from January 2017 to December 2021, all of whom underwent GCS within one year after DES-PCI. We conducted an analysis by comparing the occurrence of Major Adverse Cardiovascular Events (MACEs) within 30 days post-surgery at different time points.

Results

This study enrolled a total of 2501 participants with meticulously recorded data who underwent DES-PCI and subsequently underwent GCS within one year post-implantation. The incidence rate of MACEs is 14.2%, including MI(5.1%), HF(5.8%), IS(3.2%), Cardiac death(0.2%) across all patients in this study. The threshold probability was determined using the Youden Index, resulting in a value of 0.320, corresponding to a “Time of surgery value” of 87. Significant statistical differences were observed in the occurrence rates of MACEs for adjacent time intervals at 30 days (p < 0.001), 90 days (p < 0.009), and 180 days (p < 0.001).

Conclusions

The timing of surgical intervention following DES-PCI significantly influences the occurrence of MACEs at 1 month, 3 months, and 6 months. GCS may be appropriately advanced within the 6-month timeframe, but with the exception of emergency, efforts should be made to defer them beyond the initial month.
The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming
Authors: Paiardi Giulia , Ferraz Matheus , Rusnati Marco , Wade Rebecca C.
Published: February 2024

Although it is well established that the SARS-CoV-2 spike glycoprotein binds to the host cell ACE2 receptor to initiate infection, far less is known about the tissue tropism and host cell susceptibility to the virus. Differential expression across different cell types of heparan sulfate (HS) proteoglycans, with variably sulfated glycosaminoglycans (GAGs), and their synergistic interactions with host and viral N-glycans may contribute to tissue tropism and host cell susceptibility. Nevertheless, their contribution remains unclear since HS and N-glycans evade experimental characterization. We, therefore, carried out microsecond-long all-atom molecular dynamics simulations, followed by random acceleration molecular dynamics simulations, of the fully glycosylated spike:ACE2 complex with and without highly sulfated GAG chains bound. By considering the model GAGs as surrogates for the highly sulfated HS expressed in lung cells, we identified key novel cell entry mechanisms of spike SARS-CoV-2. We find that HS promotes structural and energetic stabilization of the active conformation of the spike receptor binding domain (RBD) and reorientation of ACE2 toward the N-terminal domain in the same spike subunit as the RBD. Spike and ACE2 N-glycans exert synergistic effects, promoting better packing, strengthening the protein:protein interaction, and prolonging the residence time of the complex. ACE2 and HS binding trigger rearrangement of the S2’ functional protease cleavage site through allosteric interdomain communication. These results thus show that HS has a multifaceted role in facilitating SARS-CoV-2 infection and they provide a mechanistic basis for the development of novel GAG derivatives with anti-SARS-CoV-2 potential.

Significance Statement

A key to blocking SARS-CoV-2 infection is to understand why it infects some cell types more than others. Heparan sulfate (HS) proteoglycans are differentially expressed on the surface of host cells and, with ACE2 receptors, provide an entry route for SARS-CoV-2. Here, we used computer simulations to investigate how highly sulfated glycosaminoglycans, a model for HS expressed in lungs, impact the interaction between virus spike and host ACE2. The simulations indicate that HS, together with host and spike N-glycans, stabilizes the spike:ACE2 complex and triggers structural changes, including host protease cleavage, contributing to the SARS-CoV-2 infection mechanism. This study lays the basis for a better understanding of the cell-specificity of SARS-CoV-2 infection and for developing strategies for inhibiting SARS-CoV-2 infection.
Feature and space-based interference with functionally active and passive items in working memory
Authors: Wilhelm Sophia A. , Weng Yuanyuan , Borst Jelmer P. , Havekes Robbert , Akyürek Elkan G.
Published: February 2024

Functionally active and passive states in working memory have been related to different neural mechanisms. Memoranda in active states might be maintained by persistent neural firing, whereas memoranda in passive states might be maintained through short-term synaptic plasticity. We reasoned that this might make these items differentially susceptible to interference during maintenance, in particular that passively maintained items might be more robust. To test this hypothesis, we gave our participants a working memory task in which one item was prioritised (active) by always probing it first, while the other item was deprioritised (passive) by always probing it second. In two experiments, on half the trials, we presented an interfering task during memory maintenance, in which the stimuli matched either the feature dimension of the memory items (colour or orientation), or their spatial location. Whether the interfering task appeared on a given trial was unpredictable. Finally, we conducted a third experiment where participants were given prior knowledge of the interference condition. We found that both active and passive memory items were affected by interference to a similar extent, with overall performance being closely matched in all experiments. We further investigated precision and probability of target response parameters from the standard mixture model, which also showed no differences between states. We conclude that active and passive items, although potentially stored in different neuronal states, do not show differential susceptibility to interference.

Public significance statement

The ability to briefly remember information is critical to human cognition. Our so-called working memory is nevertheless rather limited, able to hold only a few items at any one time, and prone to forgetting when we are briefly distracted. Yet, there is reason to believe that not all information in working memory is equally vulnerable. Items that are more passively stored, because they will only be required after some time, might be more resilient to interference. Items that are stored actively, for more immediate recall, might be more easily disrupted. Here, we investigated the effect of an interference task on the retention of both active and passive items in working memory. Our results showed that active and passive items are equally affected by interference, suggesting that resilience in working memory does not depend on the functional state of the items therein.
Single-cell and spatial transcriptomics of the avian embryo tailbud
Authors: Mok GF , Turner S , Smith E , Mincarelli L , Lister A , Lipscombe J , Uzun V , Haerty W , Macaulay IC , Münsterberg A
Published: February 2024

Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord - forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Here we use single-cell RNA sequencing and RNA tomography to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, high-throughput RNA-seq of sequential tissue sections provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single-cell and spatial datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.