bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mild Thrombocytopenia, a Predictor of Outcomes After Laparoscopic Cholecystectomy
Authors: Reiche William S. , Walters Ryan W. , Schutte Bryce F. , Mukherjee Sandeep , Buaisha Haitam M. 
Published: September 2023

Background:
A common cause of mild thrombocytopenia is chronic liver disease, the most common etiology being metabolic dysfunction–associated steatotic liver disease (MASLD). Mild thrombocytopenia is a well-defined, independent marker of hepatic fibrosis in patients with chronic liver disease. Currently, there is a paucity of information available to characterize perioperative risk in patients with MASLD; therefore, the characterization of perioperative morbidity is paramount. We used a platelet threshold of 150×109 as a surrogate for fibrosis in patients undergoing laparoscopic cholecystectomy to study its effect on perioperative complications and mortality.

Patients and Methods:
We queried the American College of Surgeons National Surgical Quality Improvement Program database for laparoscopic cholecystectomies occurring from 2005 through 2018. Demographic differences between patients with and without thrombocytopenia were evaluated using the t test or the χ2 test, whereas adjusted and unadjusted differences in outcome risk were evaluated using log-binomial regression models.

Results:
We identified 437,630 laparoscopic cholecystectomies of which 6.9% included patients with thrombocytopenia. Patients with thrombocytopenia were more often males, older, and with chronic disease. Patients with thrombocytopenia and higher Aspartate Aminotransferase to Platelet Ratio Index scores had 30-day mortality rates risk ratio of 5.3 (95% CI: 4.8-5.9), with higher complication rates risk ratio of 2.4 (95% CI: 2.3-2.5). The most frequent complications included the need for transfusion, renal, respiratory, and cardiac.

Conclusions:
Perioperatively, patients with mild thrombocytopenia undergoing laparoscopic cholecystectomy had higher mortality rates and complications compared with patients with normal platelet counts. Thrombocytopenia may be a promising, cost-effective tool to identify patients with MASLD and estimate perioperative risk, especially if used in high-risk populations.
Unique clinical challenges for the teenager with congenital heart disease
Authors: Pastor Tony , Elder Robert W. 
Published: September 2023

Purpose of review
On top of existing rites of passage, adolescents with congenital heart disease (CHD) face additional challenges as related to their underlying medical condition. These include compliance with medications and appointments, establishing heart-healthy behaviors, navigating potential at-risk situations, and transition to adult-oriented care.

Recent findings
Teenagers with CHD should focus on the importance of exercise as this seems to have important long-term benefits and may help improve weight management. Mental health concerns are a major issue for teens with CHD and awareness and appropriate screening are critical. Discussion regarding sexual health, contraception, pregnancy, and CHD risk in offspring occur rarely in clinical practice, and their absence sets up the CHD adolescent for potential complications. Establishing patterns of trust and communication between physicians and teenage CHD patients are critical to enable the appropriate transition of care to adult congenital care, yet gaps in transition remain common.

Summary
The outpatient cardiologist has a critical role to help the teenager with CHD navigate difficult terrain. Returning to the roots of careful history taking, motivational interviewing, and open-ended questions may be of great benefit in warding off complications and helping steer the adolescent with CHD towards a life as a successful adult living with CHD.
Incidence and Clinicopathologic Characteristics of Human Papillomavirus–independent Invasive Squamous Cell Carcinomas of the Cervix
Authors: Stolnicu Simona , Allison Douglas , Praiss Aaron M. , Tessier-Cloutier Basile , Momeni Boroujeni Amir , Flynn Jessica , Iasonos Alexia , Serrette Rene , Hoang Lien , Patrichi Andrei , Terinte Cristina , Pesci Anna , Mateoiu Claudia , Lastra Ricardo R. , Kiyokawa Takako , Ali-Fehmi Rouba , Kheil Mira , Oliva Esther , Devins Kyle M. , Abu-Rustum Nadeem R. , Soslow Robert A. 
Published: September 2023

We aimed to determine the frequency of human papillomavirus–independent (HPVI) cervical squamous cell carcinoma (SCC) and to describe clinicopathologic characteristics. Among 670 patients with surgically treated SCCs in an established multi-institutional cohort, 447 had available tissue. Tissue microarrays were constructed and studied by in situ hybridization (ISH) for high-risk and low-risk human papillomavirus (HPV) mRNA and immunohistochemistry for p16 and p53. Tumors were HPVI if negative by HPV ISH and they failed to show diffuse p16 positivity by immunohistochemistry, and human papillomavirus–associated (HPVA) if positive by HPV ISH. Ten HPVI SCCs and 435 HPVA SCCs were identified; 2 cases were equivocal and excluded from analysis. The overall rate of HPVI SCC was low (2%) but was higher among older patients (7% in patients above 60 y of age and 17% in patients above 70 y of age). Compared with HPVA, patients with HPVI SCC were significantly older (median age, 72 vs. 49, P<0.001) and diagnosed at a higher stage (40% vs. 18% with stage III/IV disease, P=0.055). p53 expression was varied; 2 cases (20%) had null expression and 8 (80%) had wild-type expression. HPVI SCCs were heterogenous, with keratinizing, nonkeratinizing, and warty morphologies observed. Several cases had a precursor lesion reminiscent of differentiated vulvar intraepithelial neoplasia, with prominent basal atypia and hypereosinophilia or a basaloid-like morphology. Two patients (20%) had distant recurrences within 12 months, and 3 (30%) died of disease during follow-up. HPVI SCCs are rare tumors that are more common among older patients with higher stage disease and have important clinical and histologic differences from HPVA SCCs.
Neurologic infections in people with HIV: shifting epidemiological and clinical patterns
Authors: Wan Miranda Mengyuan , Gill M. John , Fonseca Kevin , Krentz Hartmut , Power Christopher , Lang Raynell 
Published: September 2023

Objectives:
The aim of this study was to define the frequency, risk factors, and clinical outcomes of both AIDS-defining and non-AIDS-defining neurologic infections among people with HIV (PWH).

Design:
We conducted a retrospective observational cohort study by linking the clinical database at the Southern Alberta HIV Clinic (SAC) with the regional hospital and microbiology databases to identify cases and the associated morbidity and mortality for these neurologic infections from 1995 to 2018.

Methods:
Neurologic infections were categorized into AIDS-defining and non-AIDS defining. Annual incidence rates per 1000 person-years were calculated. Cox proportional hazards models estimated adjusted hazard ratios (aHR) and 95% confidence intervals of risk factors for neurologic infections in PWH and mortality outcomes.

Results:
Among 2910 PWH contributing 24 237 years of follow-up, 133 (4.6%) neurologic infections were identified; 107 (80%) were AIDS-defining and 26 (20%) non-AIDS defining. While the incidence of AIDS-defining neurologic infections declined over time, no change was seen in incidence of non-AIDS defining infections. The risk of having any neurologic infection was greater among black PWH (aHR = 2.5 [1.6–4.0]) (vs. white PWH) and those with a CD4+ T-cell nadir of less than 200 cells/μl (aHR = 6.6 [4.0–11.1]) (vs. ≥200 cells/μl). More AIDS-defining neurologic infections occurred in PWH with lower CD4+ T-cell counts and higher HIV viral loads. PWH with any neurologic infections experienced more seizures, strokes, all-cause mortality (aHR = 2.2 [1.5–3.2] and HIV-related mortality (aHR = 6.4 [3.9–10.7] (vs. no neurologic infection).

Conclusion:
Both AIDS and non-AIDS defining neurologic infections continue to occur in PWH resulting in significant morbidity and mortality. Early diagnosis and initiation of ART remain crucial in preventing neurological infections in PWH.
Using serial cross-sectional surveys to create a retrospective nested cohort to determine HIV incidence from 20 US cities
Authors: Burnett Janet C. , Broz Dita , Berg Julie , Callens Steven , Wejnert Cyprian 
Published: September 2023

Objective:
To estimate HIV incidence using successive cross-sectional surveys by creating retrospective nested cohorts among MSM, people who inject drugs (PWID), and heterosexually active persons (HET).

Design:
Cohorts were created among participants who had at least one repeat observation across four surveillance cycles from National HIV Behavioral Surveillance in 20 US cities.

Methods:
Repeat participants were identified using a combination of date of birth, race/ethnicity, metropolitan statistical area, and gender. The analysis was limited to participants who tested negative for HIV at baseline and were assumed to be at risk between cycles. We calculated person-years at risk from the individual time between cycles and used the total number of seroconversions to estimate incidence and a Poisson distribution to approximate variance. Rate ratios were calculated using age, gender, race/ethnicity, and region.

Results:
From 2008 to 2019, successive surveys recaptured nested cohorts of 1747 MSM, 3708 PWID, and 1396 HET. We observed an incidence rate of 2.5 per 100 person-years [95% confidence interval (CI) 2.1–2.8) among MSM; 0.6 per 100 person-years (95% CI 0.5–0.7) among PWID; and 0.3 per 100 person-years (95% CI 0.1–0.4) among HET. HIV incidence was higher among younger MSM, black MSM (compared with white MSM), and PWID residing in the South and territories (compared with the Midwest).

Conclusion:
These estimates are consistent with previously published incidence estimates from prospective cohort studies among these populations. Using repeat cross-sectional surveys to simulate a cohort, may serve as another strategy in estimating HIV incidence.
Incidental Uptake in a Subacute Stroke on 18F-Piflufolastat PSMA PET/CT
Authors: Lewis Miles C. , Wale Daniel J. , Liao Eric , Viglianti Benjamin L. 
Published: September 2023

Abstract
Prostate-specific membrane antigen (PSMA) PET/CT has proven to be effective in the evaluation of prostate cancer and has become increasingly used clinically as multiple radiopharmaceuticals have become commercially available. With increasing use, incidental uptake from a variety of nononcologic processes will be encountered and considered interpretive pitfalls. We outline a case of a 71-year-old man who underwent imaging with PSMA PET/CT, which demonstrated uptake in the left parietal-temporal junction that was shown to be a subacute stroke. This case demonstrates a reported cause of uptake on PSMA PET for which the underlying mechanism is not yet well understood.
Thyroid Accumulation of 99mTc-DTPA in Graves Disease
Authors: Zhong Peng , Yang Jiahuan , Wang Yimiao , Wei Li , Chen Libo 
Published: September 2023

Abstract

99mTc-DTPA dynamic renal scintigraphy for evaluating glomerular filtration rate was performed in a 29-year-old woman with hyperuricemia and Graves disease. Subsequently, 99mTc-DTPA orbital scintigraphy was conducted to determine the activity of Graves ophthalmopathy. Thyroid accumulation of 99mTc-DTPA was incidentally identified. This should be cautiously distinguished from 99mTc-pertechnetate uptake, considering that the salivary glands, oral cavity, and stomach were not visualized. Our case demonstrates that augmentation of blood supply, enhancement of capillary permeability, and accumulation of inflammatory exudate may be involved in the pathological process of Graves disease.
Comparing Rationale for Opioid Prescribing Decisions after Surgery with Subsequent Patient Consumption: A Survey of the Highest Quartile of Prescribers
Authors: Beaulieu-Jones Brendin R , Marwaha Jayson S , Kennedy Chris J , Le Danny , Berrigan Margaret T , Nathanson Larry A , Brat Gabriel A 
Published: September 2023

Background:
Opioid prescribing patterns, including those after surgery, have been implicated as a significant contributor to the US opioid crisis. A plethora of interventions–from nudges to reminders–have been deployed to improve prescribing behavior, but reasons for persistent outlier behavior are often unknown.

Study Design:
Our institution employs multiple prescribing resources and a near real-time, feedback-based intervention to promote appropriate opioid prescribing. Since 2019, an automated system has emailed providers when a prescription exceeds the 75 th percentile of typical opioid consumption for a given procedure–as defined by institutional data collection. Emails include population consumption metrics and an optional survey on rationale for prescribing. Responses were analyzed to understand why providers choose to prescribe atypically large discharge opioid prescriptions. We then compared provider prescriptions against patient consumption.

Results:
During the study period, 10,672 eligible post-surgical patients were discharged. 2,013 prescriptions (29.4% of opioid prescriptions) exceeded our institutional guideline. Surveys were completed by outlier prescribers for 414 (20.6%) encounters. Among patients where both consumption data and prescribing rationale surveys were available, 35.2% did not consume any opioids after discharge and 21.5% consumed <50% of their prescription. Only 93 (39.9%) patients receiving outlier prescriptions were outlier consumers. Most common reasons for prescribing outlier amounts were attending preference (34%) and prescriber analysis of patient characteristics (34%).

Conclusions:
The top quartile of opioid prescriptions did not align with, and often far exceeded, patient post-discharge opioid consumption. Providers cite assessment of patient characteristics as a common driver of decision-making, but this did not align with patient usage for approximately 50% of patients.
BBSdb, an open resource for bacterial biofilm-associated proteins
Authors: Zhang Zhiyuan , Pan Yuanyuan , Hussain Wajid , Li Qingqing , Li Erguang 
Published: September 2023

AbstractSummaryBacterial biofilms are organized heterogeneous assemblages of microbial cells encased within a self-produced matrix of exopolysaccharides, extracellular DNA and proteins. Over the last decade, more and more biofilm-associated proteins have been discovered and investigated. Furthermore, omics techniques such as transcriptomes, proteomes also play important roles in identifying new biofilm-associated genes or proteins. However, those important data have been uploaded separately to various databases, which creates obstacles for biofilm researchers to have a comprehensive access to these data. In this work, we constructed BBSdb, a state-of-the-art open resource of bacterial biofilm-associated protein. It includes 48 different bacteria species, 105 transcriptome datasets, 21 proteome datasets, 1205 experimental samples, 57,823 differentially expressed genes (DEGs), 13,605 differentially expressed proteins (DEPs), 1,930 ‘Top 5% differentially expressed genes’ and a predictor for prediction of biofilm-associated protein. In addition, 1,781 biofilm-associated proteins, including annotation and sequences, were extracted from 942 articles and public databases via text-mining analysis. We usedE. colias an example to represent how to explore potential biofilm-associated proteins in bacteria. We believe that this study will be of broad interest to researchers in field of bacteria, especially biofilms, which are involved in bacterial growth, pathogenicity, and drug resistance.Availability and implementationThe BBSdb is freely available athttp://124.222.145.44/#!/.
Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
Authors: Hoshino Masakazu , Cossard Guillaume , Haas Fabian B. , Kane Emma I. , Kogame Kazuhiro , Jomori Takahiro , Wakimoto Toshiyuki , Coelho Susana M. 
Published: September 2023

AbstractSexual reproduction is widespread among eukaryotes, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of taxa. Despite extensive research on the evolution of asexuality from sexual ancestors, the molecular changes underpinning the switch to asexual reproduction remain elusive, particularly in organisms with haploid sexual systems such as bryophytes, and red and brown algae in which males and females are haploid and multicellular. Here, we investigate independent events in which asexuality has emerged from sexual ancestor lineages in species of the brown algalScytosiphon, we examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that individuals from asexual, female-only (‘Amazon’) populations lose their ability to produce and sex pheromone and, consequently, are unable to attract and fuse with male gametes, whereas they gain the ability to trigger parthenogenic (asexual) development from large, unfertilized eggs. This independent and convergent decline in pheromone production and optimization of asexual traits is accompanied by convergent changes in gene expression, including de-feminization and masculinization of the Amazon gamete transcriptomes. These data are consistent with the idea that decay of female functions, rather than relaxation of sexual antagonism, is the dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we identify a locus on an autosomal protein-coding gene that is associated with the switch to asexuality. We propose that the sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
Dynamic Inference by Model Reduction
Authors: Priorelli Matteo , Stoianov Ivilin Peev 
Published: September 2023

AbstractHow do we infer which one of several targets another agent is following? And how are we capable of grasping an object on the fly? Reducing a model as complex as the surrounding dynamic environment into a small set of simpler hypotheses is a reasonable cognitive solution, but how can the brain compare and choose among dynamic hypotheses? Recent advances in Bayesian Model Reduction have led to innovative solutions to actively infer the state of affairs of the world and perform discrete planning with continuous signals, but dealing with highly dynamic contexts is a difficult matter. We propose that choosing among flexible hypotheses is possible by using reduced priors sampled from the dynamics of a generative model. Each reduced prior corresponds to an alternative future world constantly generated from the current observations, which the agent can use to accumulate evidence for a discrete hypothesis. We tested the approach on two everyday tasks: inferring a dynamic trajectory and grasping a moving object, which the model solved with high accuracy. Our study may thus shed light on how agents can smoothly generate and infer static intentions that result in dynamic behaviors, and on the specific role of intention precisions in motor learning.
A comparison of telencephalon composition among chickens, junglefowl, and wild galliforms
Authors: Racicot Kelsey J. , Ham Jackson R. , Augustine Jacqueline , Henriksen Rie , Wright Dominic , Iwaniuk Andrew N. 
Published: September 2023

AbstractDomestication is the process of modifying animals for human benefit through selective breeding in captivity. One of the traits that often diverges is the size of the brain and its constituent regions; almost all domesticated species have relatively smaller brains and brain regions than their wild ancestors. Although the effects of domestication on the brain have been investigated across a range of both mammal and bird species, almost nothing is known about the neuroanatomical effects of domestication on the world’s most common bird: the chicken (Gallus gallus). We compared the quantitative neuroanatomy of the telencephalon of white leghorn chickens with red junglefowl, their wild counterpart, and several wild galliform species. We focused specifically on the telencephalon because telencephalic regions typically exhibit the biggest differences in size in domesticate-wild comparisons. Relative telencephalon size was larger in chickens than in junglefowl and ruffed grouse (Bonasa umbellus). The relative size of telencephalic regions did not differ between chickens and junglefowl but did differ in comparison with ruffed grouse. Ruffed grouse had larger hyperpallia and smaller entopallial, nidopallial and striatal volumes than chickens and junglefowl. Multivariate analyses that included an additional three wild grouse species corroborated these findings: chicken and junglefowl have relatively larger nidopallial and striatal volumes than grouse. Conversely, the mesopallial and hyperpallial volumes tended to be relatively smaller in chickens and junglefowl. From this suite of comparisons, we conclude that chickens do not follow a pattern of widespread decreases in telencephalic region sizes that is often viewed as typical of domestication. Instead, chickens have undergone a mosaic of changes with some regions increasing and others decreasing in size and there are few differences between chickens and junglefowl.
Comparative Analysis of Association Networks Using Single-Cell RNA Sequencing Data Reveals Perturbation-Relevant Gene Signatures
Authors: Nouri Nima , Gaglia Giorgio , Mattoo Hamid , Rinaldis Emanuele de , Savova Virginia 
Published: September 2023

SUMMARYSingle-cell RNA sequencing (scRNA-seq) data has elevated our understanding of systemic perturbations to organismal physiology at the individual cell level. However, despite the rich information content of scRNA-seq data, the relevance of genes to a perturbation is still commonly assessed through differential expression analysis. This approach provides a one-dimensional perspective of the transcriptomic landscape, risking the oversight of tightly controlled genes characterized by modest changes in expression but with profound downstream effects. We present GENIX (Gene Expression Network Importance eXamination), a novel platform for constructing gene association networks, equipped with an innovative network-based comparative model to uncover condition-relevant genes. To demonstrate the effectiveness of GENIX, we analyze influenza vaccine-induced immune responses in peripheral blood mononuclear cells (PBMCs) collected from recovered COVID-19 patients, shedding light on the mechanistic underpinnings of gender differences. Our methodology offers a promising avenue to identify genes relevant to perturbation responses in biological systems, expanding the scope of response signature discovery beyond differential gene expression analysis.HIGHLIGHTSConventional methods used to identify perturbation-relevant genes in scRNA-seq data rely on differential expression analysis, susceptible to overlooking essential genes.GENIX leverages cell-type-specific inferred gene association networks to identify condition-relevant genes and gene programs, irrespective of their specific expression alterations.GENIX provides insight into the gene-regulatory response to the influenza vaccine in naïve and recovered COVID-19 patients, expanding on previously observed gender-specific differences.GRAPHICAL ABSTRACT