bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Performance of Thyroid Nodule Risk Stratification Systems
Authors: Yucel Serap , Balci Isa Gokturk , Tomak Leman 
Published: November 2023

Abstract
The purpose of this study was to compare the diagnostic performance of 4 different ultrasound-based risk scoring systems for thyroid nodules (TNs). This study consecutively included 256 patients (mean age: 43.98 ± 12.94 years, min–max: 18–89 years; 225 females, 31 males) with 266 TNs. Each nodule was evaluated and classified according to the American Thyroid Association (ATA), American College of Radiology (ACR), European Thyroid Association, and Korean Thyroid Imaging Reporting and Data System (ACR-TIRADS, EU-TIRADS, and K-TIRADS, respectively) before performing ultrasound-guided fine-needle aspiration biopsy. Pathological results were reported according to the Bethesda system. Outcomes of the 4 classification systems were compared with respect to Bethesda results. Twenty-eight (10.5%) nodules had malignant cytology results. Diagnostic performances of the scoring systems were comparable with similar area under the curve values according to the reference standards of category 5 of each scoring system. The sensitivity and specificity values of these guidelines were as follows: ACR-TIRADS, 60.7% and 95.4%; EU-TIRADS, 71.4% and 93.3%; ATA-2015, 71.4% and 93.3%; and K-TIRADS, 67.9% and 93.3%. The biopsy rate of malignant nodules was 57.1% for K-TIRADS and ATA, whereas this value was 46.4% for ACR and EU-TIRADS. ACR-TIRADS had the lowest unnecessary biopsy rate (141 of 238 benign nodules, 46%). The diagnostic performance of 4 risk stratification systems appears to be comparable, as shown by similar sensitivity, specificity, and area under the curve values. However, the ACR-TIRADS had slightly higher accuracy and necessitated fewer unnecessary biopsies for benign nodules.
The Right Ventricular Fetal Tricuspid Annular Plane Systolic Excursion Index Is a New Index for Evaluating Fetal Cardiac Function of Gestational Hypertension
Authors: He Shao-Zheng , Lai Fang-Ping , Zeng Piao-Yi , Zhang Shi-Jie , Lyu Guo-Rong 
Published: November 2023

Abstract
The right ventricular fetal tricuspid annular plane systolic excursion index (FTI) can be used to evaluate right ventricular systolic function. The purpose of this study was to establish the reference range of the FTI in normal fetuses and evaluate its diagnostic value in hypertensive disorders during pregnancy. In this prospective observational study, the right ventricular FTI was measured in 208 normal single-gestation fetuses between 20 and 40 weeks. With the increase in gestational age, the right ventricular FTI did not significantly fluctuate. With the increase in the severity of HDCP, the right ventricular FTI decreased gradually. Compared with the normal group, the low right ventricular FTI group had a higher incidence of premature delivery and emergency delivery due to continuous abnormal fetal heart monitoring, but there were no significant differences in low birth weight, new born Apgar score less than 7 in 5 minutes, or admission to the neonatal intensive care unit. The FTI of the right ventricle of normal fetuses is relatively constant at different gestational weeks. The right ventricular FTI can be used to evaluate fetal cardiac function changes in pregnant women with HDCP.
Association of High Body Mass Index With Postoperative Complications After Chest Masculinization Surgery
Authors: Hassan Bashar , Schuster Calvin R. , Ascha Mona , Del Corral Gabriel , Fischer Beverly , Liang Fan 
Published: November 2023

Purpose
Body mass index (BMI) requirements for transgender and nonbinary patients undergoing chest masculinization surgery (CMS) are not standardized and based on small sample sizes. This is the largest and first national retrospective study to determine the association between BMI and postoperative complications.

Methods
The National Surgical Quality Improvement Program 2012–2020 was queried for CMS patients. The primary outcome was incidence of at least one complication within 30 days. Secondary outcomes were incidence of major and minor complications. Body mass index (in kilograms per square meter) was categorized as category 0 (<30), 1 (30–34.9), 2 (35–39.9), 3 (40–44.9), 4 (45–49.9), and 5 (≥50). Logistic regression was used to evaluate the association between BMI and outcomes.

Results
Of 2317 patients, median BMI was 27.4 kg/m2 (interquartile range, 23.4–32.2 kg/m2). Body mass index range was 15.6 to 64.9 kg/m2. While increasing BMI was significantly associated with greater odds of at least one complication, no patients experienced severe morbidity, regardless of BMI. Patients with BMI ≥50 kg/m2 had an adjusted odds ratio [aOR, 95% confidence interval (CI)] of 3.63 (1.02–12.85) and 36.62 (2.96–>100) greater odds of at least one complication and urinary tract infection compared with nonobese patients, respectively. Patients with BMI ≥35 kg/m2 had an adjusted odds ratio (95% CI) of 5.06 (1.5–17.04) and 5.13 (1.89–13.95) greater odds of readmission and surgical site infection compared with nonobese patients, respectively.

Conclusions
Chest masculinization surgery in higher BMI patients is associated with greater odds of unplanned readmission. Given the low risk for severe complications in higher BMI individuals, we recommend re-evaluation of BMI cutoffs for CMS patients.
Evolving Trends in Kidney Transplant Outcomes Among Older Adults: A Comparative Analysis Before and During the COVID-19 Pandemic
Authors: Li Yiting , Menon Gayathri , Wu Wenbo , Musunuru Amrusha , Chen Yusi , Quint Evelien E. , Clark-Cutaia Maya N. , Zeiser Laura B. , Segev Dorry L. , McAdams-DeMarco Mara A. 
Published: November 2023

Background.
Advancements in medical technology, healthcare delivery, and organ allocation resulted in improved patient/graft survival for older (age ≥65) kidney transplant (KT) recipients. However, the recent trends in these post-KT outcomes are uncertain in light of the mounting burden of cardiovascular disease, changing kidney allocation policies, heterogeneity in candidates’ risk profile, and the coronavirus disease 2019 pandemic. Thus, we examined secular trends in post-KT outcomes among older and younger KT recipients over the last 3 decades.

Methods.
We identified 73 078 older and 378 800 younger adult (aged 18–64) recipients using Scientific Registry of Transplant Recipients (1990–2022). KTs were grouped into 6 prepandemic eras and 1 postpandemic-onset era. Kaplan-Meier and Cox proportional hazards models were used to examine temporal trends in post-KT mortality and death-censored graft failure.

Results.
From 1990 to 2022, a 19-fold increase in the proportion of older KT recipients was observed compared to a 2-fold increase in younger adults despite a slight decline in the absolute number of older recipients in 2020. The mortality risk for older recipients between 2015 and March 14, 2020, was 39% (adjusted hazard ratio [aHR] = 0.61, 95% confidence interval [CI], 0.50-0.75) lower compared to 1990–1994, whereas that for younger adults was 47% lower (aHR = 0.53, 95% CI, 0.48-0.59). However, mortality risk during the pandemic was 25% lower (aHR = 0.75, 95% CI, 0.61-0.93) in older adults and 37% lower in younger adults (aHR = 0.63, 95% CI, 0.56-0.70) relative to 1990–1994. For both populations, the risk of graft failure declined over time and was unaffected during the pandemic relative to the preceding period.

Conclusions.
The steady improvements in 5-y mortality and graft survival were disrupted during the pandemic, particularly among older adults. Specifically, mortality among older adults reflected rates seen 20 y prior.
Functional expression of a Mo-dependent formate dehydrogenase inEscherichia coliunder aerobic conditions
Authors: Schulz Marion , Berger Anne , Dubois Ivan , Delmas Valérie , Cadillon Mélodie , Bouzon Madeleine , Döring Volker 
Published: November 2023

AbstractBackgroundOxygen tolerant complex metal-dependent formate dehydrogenases hold potential for biotechnological applications.Principle FindingsIn this work, we report the functional expression of the complex, molybdenum-dependent soluble formate dehydrogenase encoded by thefdsGBACDoperon fromCupriavidus necator(CnFDH) inEscherichia coli.Expression of the operon from plasmids or from a copy integrated in the chromosome enabled growth of an energy-auxotrophic selection strain on formate as sole energy source under aerobic conditions. Growth could be accelerated in turbidostat, leading to a drop of the generation time of 1 hour. While no mutation was found in the operon of evolved isolates, genome sequencing revealed non-synonymous point mutations in the genefocAcoding for a bidirectional formate transporter carried in all isolates sequenced. Reverting the mutations led to a drop in the growth rate demonstrating thefocAmutation as principle target of continuous culture adaptation.SignificanceA member of the oxygen-tolerant subclass of complex FDH showed stable formate oxidation activity when expressed in the heterologous hostE. coli, a model organism of biotechnology. The integration of the operon in the chromosome offers the possibility of structure/function studies and activity enhancements throughin vivomutagenesis, which can also be applied to CO2reduction in appropriate selection hosts.
A polydiolcitrate-MoS2composite for 3D printing Radio-opaque, Bioresorbable Vascular Scaffolds
Authors: Szydlowska Beata M. , Ding Yonghui , Moore Connor , Cai Zizhen , Torres-Castanedo Carlos G. , Jones Evan , Hersam Mark C. , Sun Cheng , Ameer Guillermo A. 
Published: November 2023

ABSTRACTImplantable polymeric biodegradable devices, such as biodegradable vascular stents or scaffolds, cannot be fully visualized using standard X-ray-based techniques, compromising their performance due to malposition after deployment. To address this challenge, we describe composites of methacrylated poly(1,12 dodecamethylene citrate) (mPDC) and MoS2 nanosheets to fabricate novel X-ray visible radiopaque and photocurable liquid polymer-ceramic composite (mPDC-MoS2). The composite was used as an ink with micro continuous liquid interface production (μCLIP) to fabricate bioresorbable vascular scaffolds (BVS). Prints exhibited excellent crimping and expansion mechanics without strut failures and, importantly, required X-ray visibility in air and muscle tissue. Notably, MoS2nanosheets displayed physical degradation over time in a PBS environment, indicating the potential for producing bioresorbable devices. mPDC-MoS2is a promising bioresorbable X-ray-visible composite material suitable for 3D printing medical devices, particularly vascular scaffolds or stents, that require non-invasive X-ray-based monitoring techniques for implantation and evaluation. This innovative composite system holds significant promise for the development of biocompatible and highly visible medical implants, potentially enhancing patient outcomes and reducing medical complications.TOC
What is Known, Unknown, and Needed to be Known about Damage Caused by Wild Pigs
Authors: VerCauteren Kurt C. , Pepin Kim M. , Cook Seth M. , McKee Sophie , Pagels Abigail , Kohen Keely J. , Messer Ingrid A. , Glow Michael P. , Snow Nathan P. 
Published: November 2023

AbstractDamage assessments provide evidence for initiating and evaluating management programs that protect natural resources and human livelihoods against invasive species. Wild pigs (Sus scrofa) cause extensive damage in their native and non-native ranges, but the extent of current damage and efficacy of management of the damage (i.e., population control of wild pigs, exclusion fencing, etc.) remains poorly described. We conducted a systematic review of physical damage caused by wild pigs to summarize what is known and identify knowledge gaps for damage assessment. Wild pig damage assessments have been overwhelmingly qualitative (84% of studies) and measured differently across studies, which prevents the determination of typical damage amounts to a particular resource and comparison across studies. Key priorities going forward are to standardize damage assessments quantitatively and measure population density (or index of such) of wild pigs concurrently with damage assessments to determine the relationship between damage and population levels. We provide a framework for inferring damage in new areas and assessing the benefits of management – to evaluate and optimize landscape-scale management programs. Overall, we recommend future studies strive for: 1) report the amount of damages in a standardized fashion (e.g., area damaged/area surveyed), 2) evaluate and report the amount of damage relative to the density of wild pigs, and 3) when reporting economic costs of damages incurred and management actions, describe the economic valuation method used along with the year of reference for the valuation. Capturing these elements are necessary steps to predict the benefits of management for an area with particular profile of resources and wild pig density, even in areas where damage assessments are not available. Meeting these criteria with allow for more generalizable results that can inform managers across the nearly global distribution of wild pigs
Simplifying bioinformatics data analysis through conversation
Authors: Dong Zhengyuan , Zhou Han , Jiang Yifan , Zhong Victor , Lu Yang Young 
Published: November 2023

AbstractThe rapid advancements in high-throughput sequencing technologies have produced a wealth of omics data, facilitating significant biological insights but presenting immense computational challenges. Traditional bioinformatics tools require substantial programming expertise, limiting accessibility for experimental researchers. Despite efforts to develop user-friendly platforms, the complexity of these tools continues to hinder efficient biological data analysis. In this paper, we introduce BioMANIA– an AI-driven, natural language-oriented bioinformatics pipeline that addresses these challenges by enabling the automatic and codeless execution of biological analyses. BioMANIA leverages large language models (LLMs) to interpret user instructions and execute sophisticated bioinformatics work-flows, integrating API knowledge from existing Python tools. By streamlining the analysis process, BioMANIA simplifies complex omics data exploration and accelerates bioinformatics research. Compared to relying on general-purpose LLMs to conduct analysis from scratch, BioMANIA, informed by domain-specific biological tools, helps mitigate hallucinations and significantly reduces the likelihood of confusion and errors. Through comprehensive benchmarking and application to diverse biological data, ranging from single-cell omics to electronic health records, we demonstrate BioMANIA’s ability to lower technical barriers, enabling more accurate and comprehensive biological discoveries.
dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets
Authors: Hannon William W. , Bloom Jesse D. 
Published: November 2023

Summary and PurposeUnderstanding how mutations impact a protein’s functions is valuable for many types of biological questions. High-throughput techniques such as deep-mutational scanning (DMS) have greatly expanded the number of mutation-function datasets. For instance, DMS has been used to determine how mutations to viral proteins affect antibody escape (Dadonaite et al. 2023), receptor affinity (Starr et al. 2020), and essential functions such as viral genome transcription and replication (Li et al. 2023). With the growth of sequence databases, in some cases the effects of mutations can also be inferred from phylogenies of natural sequences (Bloom and Neher 2023) (Figure 1).The mutation-based data generated by these approaches is often best understood in the context of a protein’s 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a protein’s structure are often cumbersome and require multiple steps and softwares. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool,dms-viz. Withdms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format. Seehttps://dms-viz.github.io/to usedms-viz.
Proteomic evidence of depression-associated astrocytic dysfunction in the human male olfactory bulb
Authors: Rahimian Reza , Perlman Kelly , Fakhfouri Gohar , Mpai Refilwe , Richard Vincent R. , Hercher Christa , Penney Lucy , Davoli Maria Antonietta , Nagy Corina , Zahedi René P. , Borchers Christoph H. , Giros Bruno , Turecki Gustavo , Mechawar Naguib 
Published: November 2023

AbstractThe olfactory bulb (OB), a major structure of the limbic system, has been understudied in human investigations of psychopathologies such as depression. To explore more directly the molecular features of the OB in depression, a global comparative proteome analysis was carried out with human post-mortem OB samples from 11 males having suffered from depression and 12 healthy controls. We identified 188 differentially abundant proteins (with adjusted p<0.05) between depressed cases and controls. Gene ontology and gene enrichment analyses suggested that these proteins are involved in biological processes including the complement and coagulation cascades. Cell type enrichment analysis displayed a significant reduction in several canonical astrocytic proteins in OBs from depressed patients. Furthermore, using RNA-fluorescencein-situhybridization, we observed a decrease in the percentage of ALDH1L1+cells expressing canonical astrocytic markers includingALDOC,NFIA,GJA1 (connexin 43)andSLC1A3 (EAAT1). These results are consistent with previous reports of downregulated astrocytic marker expression in other brain regions in depressed patients. We also conducted a comparative phosphoproteomic analysis of OB samples and found a dysregulation of proteins involved in neuronal and astrocytic functions. To determine whether OB astrocytic abnormalities is specific to humans, we also performed proteomics on the OB of socially defeated male mice, a commonly used model of depression. Cell-type specific analysis revealed that in socially defeated animals, the most striking OB protein alterations were associated with oligodendrocyte- lineage cells rather than with astrocytes, highlighting an important species difference. Overall, this study further highlights cerebral astrocytic abnormalities as a consistent feature of depression in humans.
A Method for Optimizing Imaging Parameters to Record Neuronal and Cellular Activity at Depth with Bioluminescence
Authors: Silvagnoli Alexander D. , Taylor Kaylee A. , Slaviero Ashley N. , Petersen Eric D. 
Published: November 2023

AbstractOptical imaging of activity has provided valuable insight into brain function and accelerated the field of neuroscience in recent years. Genetically encoded fluorescent activity sensors of calcium, neurotransmitters and voltage have been tools of choice for optical recording of neuronal activity. However, photon scattering and absorbance limits fluorescence imaging to superficial regions forin vivoactivity imaging. This limitation prevents recording of population level activity in lower brain regions of experimental animals without implanted hardware. Single and multiphoton methods find maximal use in the cortex and experience loss of signal at greater depths. Successful efforts have been made to increase the depth of fluorescence imaging using fiber photometry and gradient reflective index lenses. However, these methods are highly invasive, requiring an implant within the brain. Bioluminescence imaging offers a promising alternative to achieve activity imaging in deeper brain regions without hardware implanted within the brain. Bioluminescent reporters can be genetically encoded and produce photons without external excitation. The use of enzymatic photon production also enables prolonged imaging sessions without the risk of photobleaching or phototoxicity. These characteristics render bioluminescence suitable to non-invasive imaging of deep neuronal populations. To facilitate the adoption of bioluminescent activity imaging, we sought to develop a low cost, simplein vitromethod to optimize imaging parameters for determining optimal exposure times and optical hardware configurations to determine what frame rates can be captured with an individual lab’s imaging hardware with sufficient signal-to-noise ratios without the use of animals prior to starting anin vivoexperiment. To achieve this, we developed an assay for modelingin vivooptical conditions with a brain tissue phantom paired with engineered cells that produce bioluminescence. We then used this assay to limit-test the detection depth vs maximum frame rate for bioluminescence imaging at experimentally relevant tissue depths using off the shelf imaging hardware. With this method, we demonstrate an effective means for increasing the utility of bioluminescent tools and lowering the barrier to adoption of bioluminescence activity imaging with bioluminescent sensors.
Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types
Authors: Kumar Pradeep , Gholamalamdari Omid , Zhang Yang , Zhang Liguo , Vertii Anastassiia , van Schaik Tom , Peric-Hupkes Daan , Sasaki Takayo , Gilbert David M. , van Steensel Bas , Ma Jian , Kaufman Paul D. , Belmont Andrew S. 
Published: November 2023

AbstractGenome differential positioning within interphase nuclei remains poorly explored. We extended and validated TSA-seq to map genomic regions near nucleoli and pericentric heterochromatin in four human cell lines. Our study confirmed that smaller chromosomes localize closer to nucleoli but further deconvolved this by revealing a preference for chromosome arms below 36-46 Mbp in length. We identified two lamina associated domain subsets through their differential nuclear lamina versus nucleolar positioning in different cell lines which showed distinctive patterns of DNA replication timing and gene expression across all cell lines. Unexpectedly, active, nuclear speckle-associated genomic regions were found near typically repressive nuclear compartments, which is attributable to the close proximity of nuclear speckles and nucleoli in some cell types, and association of centromeres with nuclear speckles in hESCs. Our study points to a more complex and variable nuclear genome organization than suggested by current models, as revealed by our TSA-seq methodology.