bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Report: Transition Preparation and Post-Transition Evaluation Practices at Adult Clinics That Care for Young Adults With Perinatally Acquired HIV in Massachusetts, United States
Authors: Tassiopoulos Katherine , John Betsey , Khadraoui Anisa , Salomon Liz , Vergara Eduardo , Fukuda H. Dawn , Siminski Suzanne M. , Van Dyke Russell , DeMaria Alfred 
Published: October 2024

Background:
Most young adults with perinatal HIV (PHIV) transition from pediatric or adolescent to adult clinical care. Although guidelines to increase transition success have been recommended, we know little about uptake of these guidelines, particularly by adult care clinics.

Methods:
We administered web-based surveys to adult care providers of young adults with PHIV in Massachusetts to evaluate transition preparation and post-transition evaluation practices. We compared transition practices and HIV care continuum outcomes by clinic setting.

Results:
Twenty-four providers submitted information on 23 adult care clinics. Ten were hospital-based and 13 were community-based clinics. Community-based clinics were more likely than hospital-based clinics to conduct pre-transition (33% vs. 10%) and post-transition (67% vs. 30%) evaluation of patients' readiness to self-manage health care, and to share health outcome information with the pediatric/adolescent care team (50% vs. 20%). Community-based clinics were also more likely to have personnel dedicated to the transition process and to facilitate communication between the patient and pediatric/adolescent care team. Engagement in care was similar for young adults with PHIV seen at community-based and hospital-based clinics (88.2% vs. 85.5%; P = 1.00), but retention in care (76.5% vs. 50.5%; P = 0.05) and viral suppression (88.2% vs. 65.1%; P = 0.08) were higher in community-based than in hospital-based clinics.

Conclusions:
In Massachusetts, transition practices vary across adult clinics that care for young adults with PHIV. Recommended practices, and HIV care continuum outcomes, were more likely to be met at community-based clinics than hospital-based clinics. Community-based adult care may provide more comprehensive transition practices and serve as a model for hospital-based clinics.
Diagnostic and Therapeutic Approach to Rare Tongue Lipoma
Authors: Guo Xin-Ran , Liu Zi-Xiu , Jia Jun , Yu Zi-Li 
Published: October 2024

Lipomas are benign soft tissue tumors composed of mature adipocytes, commonly found in subcutaneous tissues. Despite their prevalence in various body regions, they are relatively rare in the oral and maxillofacial regions. This study retrospectively analyzed the clinical and imaging characteristics, as well as the treatment outcomes of 57 patients diagnosed with lipoma. Among these, 42 cases (73.7%) were located in the oral-maxillofacial and head-neck regions, predominantly in areas with relatively abundant adipose tissue, including the facial/cheek area, parotid region, submental/submandibular area, and neck. In addition, this study presents a rare case of tongue lipoma in a 57-year-old male, highlighting the clinical features, diagnostic challenges, and treatment approach. The patient presented with a painless mass on the left side of the tongue that had gradually increased in size over 5 months. Physical examination revealed a firm, well-defined, moderately mobile mass measuring ~3.0×1.5 m. Imaging, including enhanced magnetic resonance imaging, suggested a diagnosis of lipoma, leading to surgical excision. The excised mass was yellowish, encapsulated, and soft. Intraoperative frozen section biopsy confirmed it as a fat-derived tumor consistent with a lipoma, and postoperative pathological examination further identified it as a spindle cell/pleomorphic lipoma. The patient experienced a smooth recovery without complications, with normal tongue function restored. This case underscores the significance of including lipoma in the differential diagnosis of tongue masses and demonstrates the efficacy of surgical excision in managing such rare tumor.
Risk Reduction of Severe Anastomotic Leakage by Evaluation of Blood Perfusion Using Indocyanine Green After Minimally Invasive Esophagectomy Followed by Narrow Gastric Tube Reconstruction
Authors: Kitadani Junya , Hayata Keiji , Goda Taro , Tominaga Shinta , Fukuda Naoki , Nakai Tomoki , Nagano Shotaro , Ojima Toshiyasu , Kawai Manabu 
Published: October 2024

Background:
Anastomotic leakage (AL) is a major complication after esophagectomy and gastric tube reconstruction. This retrospective study aims to reveal the factors in prevention of AL and in reduction of its severity.

Methods:
Enrolled in this study were the 183 patients diagnosed with esophageal cancer who underwent minimally invasive esophagectomy followed by narrow gastric tube reconstruction at Wakayama Medical University Hospital between January 2018 and March 2023. Evaluation of blood perfusion using indocyanine green began in September 2020.

Results:
AL occurred in 42 patients (22%) and did not occur in 141 patients (78%). Patient characteristics were not significantly different between patients with and without AL. Evaluation of blood perfusion of the gastric tube was performed in 69 of the 183 patients (37.7%), and after its introduction the rates of AL decreased from 28.0% to 14.4%. Blood perfusion was less evaluated in the AL group than in the non-AL group (23.8% vs. 41.8%, P=0.034). Multivariate analysis demonstrated that non-evaluation of blood perfusion using indocyanine green (odds=3.115) was an independent risk factor for AL. For the patients with AL, active interventions (eg, tube insertion into the gastric tube through the nose or fistula, embolization of cyanoacrylate) were performed significantly more often in the group without evaluation of blood perfusion than in the group with evaluation. Without evaluation of blood perfusion, there was significantly longer time from onset to resumption of diet and significantly longer postoperative hospital stays.

Conclusions:
Evaluation of qualitative blood perfusion can lead to both risk reduction and prevention of severe AL after narrow gastric tube reconstruction for esophageal cancer.
Feasibility of Using a Novel, Multimodal Motor Function Assessment Platform With Machine Learning to Identify Individuals With Mild Cognitive Impairment
Authors: Hall Jamie B. , Akter Sonia , Rao Praveen , Kiselica Andrew , Ranum Rylea , Thomas Jacob M. , Guess Trent M. 
Published: October 2024

Introduction:
Early identification of clinical conditions associated with Alzheimer disease and related dementias (ADRD) is vital for intervention. One promising early detection method is the use of instrumented assessment to identify subtle motor declines associated with ADRD. This pilot study sought to establish the feasibility of building a machine learning model to identify individuals with mild cognitive impairment (MCI) using motor function data obtained from an inexpensive, portable device.

Methods:
Our novel, multimodal motor function assessment platform integrates a depth camera, forceplate, and interface board. Healthy older adults (n=28) and older adults with MCI (n=19) were assessed during static balance, gait, and sit-to-stand activities in both single- and dual-task conditions. Three machine learning models (ie, support vector machine, decision trees, and logistic regression) were trained and tested with the goal of classification of MCI.

Results:
Our best model was decision trees, which demonstrated an accuracy of 83%, a sensitivity of 0.83, a specificity of 1.00, and an F1 score of 0.83. The top features were extracted and ranked on importance.

Discussion:
This study demonstrates the feasibility of building a machine learning model capable of identifying individuals with mild cognitive impairment using motor function data obtained with a portable, inexpensive, multimodal device.
Evaluating Long-Term Autonomic Dysfunction and Functional Impacts of Long COVID: A Follow-Up Study
Authors: Eastin Ella F. , Machnik Jannika V. , Larsen Nicholas W. , Seliger Jordan , Geng Linda N. , Bonilla Hector , Yang Phillip C. , Stiles Lauren E. , Miglis Mitchell G. 
Published: October 2024

AbstractBackgroundThe longitudinal prevalence and autonomic symptom burden in Long COVID patients is not well-established.ObjectiveAssess the duration and severity of autonomic dysfunction in adults with Long COVID and evaluate its impact on function and quality of life.DesignA follow-up survey of a subset of participants from a cross-sectional online survey of adults with Long COVID. Multivariable logistic regression identified predictors of moderate to severe autonomic dysfunction.Participants526 adults (ages 20-65) with a history of Long COVIDMain measuresThe Composite Autonomic Symptom 31 (COMPASS-31) score, the RAND 36-Item Health Survey, the prevalence of new postural orthostatic tachycardia syndrome (POTS), and predictors of autonomic dysfunction, including POTSKey results71.9% of Long COVID patients had a COMPASS-31 score >20, suggestive of moderate to severe autonomic dysfunction. The median symptom duration was 36 [30-40] months, reaching up to 3.5 years after SARS-CoV-2 infection. 37.5% of Long COVID patients could no longer work or had to drop out of school due to their Long COVID illness. 40.5% were newly diagnosed with POTS following SARS-CoV-2 infection.ConclusionsEvidence of persistent moderate to severe autonomic dysfunction was seen in 71.9% of Long COVID patients in our study, with a 36-month median symptom duration, suggesting that enduring autonomic dysfunction is highly prevalent in the Long COVID population. Moderate to severe autonomic dysfunction was significantly correlated with impaired function and capacity, highlighting the need to address POTS and other manifestations of autonomic dysfunction as a key component of Long COVID management.
B cells imprinted by ancestral SARS-CoV-2 develop pan-sarbecovirus neutralization in immune recalls
Authors: Chen Xixian , Li Ling , Du Ruiping , Wang Zuowei , Li Yunjian , Sun Yi , Qin Rongrong , Feng Hualong , Hu Lin , Chen Xuanyi , Lu Maosheng , Huang Xueyan , Jiang Liwei , Zuo Teng 
Published: October 2024

AbstractA key question on ancestral SARS-CoV-2 immune imprinting is to what extent imprinted B cells can develop neutralizing breadth and potency in immune recalls. Here, we longitudinally tracked B cells recognizing wild-type spike in two individuals, who were sequentially infected by Omicron variants after receiving mRNA vaccines. Functional and genetic analysis of 632 monoclonal antibodies (mAbs) from those B cells reveals that mAbs cloned after second infection have dramatically enhanced neutralizing breadth and potency, which is attributed to recall and maturation of pre-existing memory B cells. Among the 11 mAbs that potently neutralize SARS-CoV-2 variants from wild-type to KP.3, 5 mAbs are classified into public clonotypes encoded by IGHV3-53 or IGHV3-66, whereas the rest belong to a rarely reported clonotype encoded by IGHV3-74. Notably, IGHV3-74 mAbs can also broadly neutralize other sarbecoviruses by targeting a novel epitope on receptor-binding domain of spike. These results support that ancestral SARS-CoV-2 immune imprinting can be harnessed in developing pan-SARS-CoV-2 and even pan-sarbecovirus vaccines.SummaryChen et al. demonstrate that B cells imprinted by ancestral SARS-CoV-2 have tremendous potential to develop neutralizing breadth and potency in repeated immune recalls driven by Omicron variants, implicating that ancestral SARS-CoV-2 immune imprinting can be harnessed in developing pan-SARS-CoV-2 and even pan-sarbecovirus vaccines.
End-to-end multimodal deep learning for real-time decoding of months-long neural activity from the same cells
Authors: He Yichun , Marin-Llobet Arnau , Sheng Hao , Liu Ren , Liu Jia 
Published: October 2024

AbstractLong-term, stable, and real-time decoding of behavior-dependent neural dynamics from the same cells is critical for brain-computer interfaces (BCIs) and for understanding neural evolution during learning, and memory, and disease progression. Recent advances in flexible and high-density electrodes have enabled the stability required for long-term tracking but generate vast datasets that challenge existing analysis methods. Current spike sorting approaches rely heavily on manual curation and lack scalability for large-scale, real-time processing. Here, we introduce AutoSort, an end-to-end multimodal deep neural network-based method that enables real-time tracking and decoding of the same neurons over months. AutoSort uses a scalable strategy by learning deep representations from initial recordings and applying the trained model in real-time. It integrates multimodal features, including waveform features, distribution patterns, and inferred neuron spatial locations, to ensure robustness and accuracy. AutoSort outperforms existing methods in both simulated and long-term recordings, reducing computational demands by using only 10% of the time and 25% of the memory compared to conventional methods. By combining AutoSort with high-density flexible probes, we track neural dynamics in real-time during motor learning and skill acquisition over 2 months, capturing intrinsic neural manifold drift, stabilization, and post-learning representational drift. AutoSort offers a promising solution for studying long-term neural intrinsic dynamics and enabling real-time BCI decoding.
Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation
Authors: Fricke Michel , Mechel Anna , Twellsieck Björn , Grein Jessica M. , Cima-Omori Maria-Sol , Zweckstetter Markus , Holzbaur Erika L.F. , Boecker C. Alexander 
Published: October 2024

ABSTRACTParkinson disease-causing mutations in theLRRK2gene hyperactivate LRRK2 kinase activity, leading to increased phosphorylation of a subset of RAB GTPases, which are master regulators of intracellular trafficking. In neurons, processive retrograde transport of autophagosomes is essential for autophagosome maturation and effective degradation of autophagosomal cargo in the axon. We found that knockout of the LRRK2-counteracting RAB phosphatase PPM1H resulted in a gene dose-dependent disruption of the axonal transport of autophagosomes, leading to impaired degradation of axonal alpha-synuclein (aSyn), a key protein in Parkinson disease pathophysiology. Defective autophagosome transport and impaired aSyn degradation also correlated with increased aSyn aggregation in primaryPPM1Hknockout neurons exposed to preformed fibrils of aSyn, an effect that was dependent on LRRK2 kinase activity. Thus, our results link LRRK2-mediated RAB hyperphosphorylation to aSyn pathology in Parkinson disease and further establish a role for impaired autophagy in Parkinson disease pathophysiology.
A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV
Authors: Sajadi Mohammad M. , Abbasi Abdolrahim , Tehrani Zahra Rikhtegaran , Siska Christine , Clark Rutilio , Chi Woo , Seaman Michael S. , Mielke Dieter , Wagh Kshitij , Liu Qingbo , Jumpa Taylor , Ketchem Randal R. , Nguyen Dung N. , Tolbert Willaim D. , Pierce Brian G. , Atkinson Ben , Deming Derrick , Sprague Megan , Asakawa Andrew , Ferrer David , Dunn Yasmin , Calvillo Sarah , Yin Rui , Guest Johnathan D. , Korber Bette , Mayer Bryan T. , Sato Alicia H. , Ouyang Xin , Foulke Scott , Habibzadeh Parham , Karimi Maryam , Aslanabadi Arash , Hojabri Mahsa , Saadat Saman , Zareidoodeji Roza , Kędzior Mateusz , Pozharski Edwin , Heredia Alonso , Montefiori David , Ferrari Guido , Pazgier Marzena , Lewis George K. , Jardine Joseph G. , Lusso Paolo , DeVico Anthony 
Published: October 2024

AbstractAnti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with “first generation” bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of “enhanced” antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.
Semisynthetic Simulation for Microbiome Data Analysis
Authors: Sankaran Kris , Kodikara Saritha , Li Jingyi Jessica , Cao Kim-Anh Lê 
Published: October 2024

AbstractHigh-throughput sequencing data lie at the heart of modern microbiome research. Effective analysis of these data requires careful preprocessing, modeling, and interpretation to detect subtle signals and avoid spurious associations. In this review, we discuss how simulation can serve as a sandbox to test candidate approaches, creating a setting that mimics real data while providing ground truth. This is particularly valuable for power analysis, methods benchmarking, and reliability analysis. We explain the probability, multivariate analysis, and regression concepts behind modern simulators and how different implementations make trade-offs between generality, faithfulness, and controllability. Recognizing that all simulators only approximate reality, we review methods to evaluate how accurately they reflect key properties. We also present case studies demonstrating the value of simulation in differential abundance testing, dimensionality reduction, network analysis, and data integration. Code for these examples is available in an online tutorial (https://go.wisc.edu/8994yz) that can be easily adapted to new problem settings.
eQTL in diseased colon tissue identifies novel target genes associated with IBD
Authors: Nishiyama Nina C. , Silverstein Sophie , Darlington Kimberly , Kennedy Ng Meaghan M. , Clough Katelyn M. , Bauer Mikaela , Beasley Caroline , Bharadwaj Akshatha , Ganesan Rajee , Kapadia Muneera R. , Lau Gwen , Lian Grace , Rahbar Reza , Sadiq Timothy S. , Schaner Matthew R. , Stem Jonathan , Friton Jessica , Faubion William A. , Sheikh Shehzad Z. , Furey Terrence S. 
Published: October 2024

AbstractGenome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such asABOandTNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.
Metabolic interplay drives population cycles in a cross-feeding microbial community
Authors: Ross Tyler D. , Klausmeier Christopher A. , Venturelli Ophelia S. 
Published: October 2024

AbstractPopulation cycles are prevalent in ecosystems and play key roles in determining their functions1,2. While multiple mechanisms have been theoretically shown to generate population cycles3–6, there are limited examples of mutualisms driving self-sustained oscillations. Using an engineered microbial community that cross-feeds essential amino acids, we experimentally demonstrate cycles in strain abundance that are robust across environmental conditions. A nonlinear dynamical model that incorporates the experimentally observed cross-inhibition of amino acid production recapitulates the population cycles. The model shows that the cycles represent internally generated relaxation oscillations, which emerge when fast resource dynamics with positive feedback drive slow changes in strain abundance. Our findings highlight the critical role of resource dynamics and feedback in shaping population cycles in microbial communities and have implications for biotechnology.
Increase of tropical seabirds (Sula) in the California Current Ecosystem with warmer ocean conditions
Authors: Russell Tamara M. , Pereksta David M. , Tietz James R. , Vernet Maria , Jahncke Jaime , Ballance Lisa T. 
Published: October 2024

ABSTRACTClimate change is impacting marine ecosystems in the California Current Ecosystem (CCE) through physical changes (e.g., an increase in the frequency and intensity of marine heatwaves) that manifest biologically at all trophic levels. We investigated range expansion into the CCE and correlations with environment for a group of tropical/sub-tropical seabirds. We assessed changes in the abundance (2002-2022) of five species from the genus,Sula(Cocos, Blue-footed, Red-footed, Masked, and Nazca Boobies), using a novel compilation of four data sources (at-sea surveys, n=82 observations, records from Southeast Farallon Island, n=600, the California Rare Birds Committee, n=593, andeBird-a citizen science mobile application, n= 20,529), and looked for relationships with the environment, including broad temporal and spatial scale dynamics (El Niño Southern Oscillation), local conditions where the bird was reported, and potential source conditions from Baja California Sur and the Gulf of California. All five species increased in abundance, and all, with the exception of Blue-footed, exhibited a northward range expansion by as much as 6.8 degrees latitude and increased range area of between 235-1013% within the CCE. There was increased abundance during warmer conditions (El Niño and warm SST) for Cocos, Red-footed, Masked, and Nazca Boobies, and all species increased by 692-3015% after the extreme marine heatwaves that began in late 2013. Our results document a tropical shift in seabirds of the CCE, which may present future challenges to resident species. As marine heatwaves are projected to increase in frequency and intensity, in addition to long-term warming, we hypothesize that these species will continue to expand their range northward in the CCE.
Negativeome in Early-Life Virome Studies: Characterization and Decontamination
Authors: Kuzub Nataliia , Kurilshikov Alexander , Zhernakova Alexandra , Garmaeva Sanzhima 
Published: October 2024

AbstractEnvironmental contamination complicates the study of low-biomass microbial communities like the human gut virome. In 1,321 early-life gut viromes and 55 negative controls (NCs) from four datasets, we identified viral contaminants and their prevalence across studies. Samples and NCs were indistinguishable in genomic and ecological features, with 71.5% of samples sharing at least one identical strain with NCs. This work demonstrates the efficacy of strain-aware decontamination for preserving biological signals.