bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microstructural Analysis of Collagenous Structures in Relapsed Clubfoot Tissue
Authors: Vondrášek David , Hadraba Daniel , Přibyl Jan , Eckhardt Adam , Ošťádal Martin , Lopot František , Jelen Karel , Doubková Martina , Knitlová Jarmila , Novotný Tomáš , Janáček Jiří 
Published: January 2023

Abstract
Talipes equinovarus congenitus (clubfoot) is frequently defined as a stiff, contracted deformity, but few studies have described the tissue from the point of view of the extracellular matrix, and none have quantified its mechanical properties. Several researchers have observed that clubfoot exhibits signs of fibrosis in the medial side of the deformity that are absent in the lateral side. Our study aims to quantify the differences between the medial and lateral side tissue obtained from relapsed clubfoot during surgery in terms of the morphological and mechanical properties of the tissue. Combining methods of optical and atomic force microscopy, our study revealed that the medial side has a higher Young’s modulus, contains more collagen and less adipose tissue and that the collagen fibers propagate at a higher frequency of the crimp pattern after surgical dissection of the tissue. Our study offers a multi-correlative approach that thoroughly investigates the relapsed clubfoot tissue.
Automated Sarcomere Structure Analysis for Studying Cardiotoxicity in Human Pluripotent Stem Cell-Derived Cardiomyocytes
Authors: Cao Lu , Schoenmaker Linde , Ten Den Simone A , Passier Robert , Schwach Verena , Verbeek Fons J 
Published: January 2023

Abstract
Drug-induced cardiotoxicity is one of the main causes of heart failure (HF), a worldwide major and growing public health issue. Extensive research on cardiomyocytes has shown that two crucial features of the mechanisms involved in HF are the disruption of striated sarcomeric organization and myofibril deterioration. However, most studies that worked on extracting these sarcomere features have only focused on animal models rather than the more representative human pluripotent stem cells (hPSCs). Currently, there are limited established image analysis systems to specifically assess and quantify the sarcomeric organization of hPSC-derived cardiomyocytes (hPSC-CMs). Here, we report a fully automated and robust image analysis pipeline to detect z-lines and myofibrils from hPSC-CMs with a high-throughput live-imaging setup. Phenotype measurements were further quantified to evaluate the cardiotoxic effect of the anticancer drug Doxorubicin. Our findings show that this pipeline is able to capture z-lines and myofibrils. The pipeline filters out disrupted sarcomere structures and irrelevant noisy signals, which allows us to perform automated high-throughput imaging for accurate quantification of cardiomyocyte injury.
Modeling Curved Fibers by Fitting R-vine Copulas to their Frenet Representations
Authors: Weber Matthias , Grießer Andreas , Glatt Erik , Wiegmann Andreas , Schmidt Volker 
Published: January 2023

AbstractIn the present paper, we propose a novel single-fiber model which exploits a description of fibers as a sequence of bond and torsion angles. Using the Frenet–Serret formulas, this representation can be translated into three-dimensional (3D) space and vice-versa. While the precise locations of points along a fiber do not directly convey information about the inner material properties of the fiber, the distribution of bond, and torsion angles may be related to various material characteristics and, thus, our model may form a direct link between inner material properties and emerging microstructure properties. More precisely, we model curved fibers in the 3D Euclidean space R3 as polygonal tracks that we represent by their local curvature and torsion at each sampling point. The 2D sequences of curvatures and torsions obtained in this way are then considered as realizations of a Markov chain with finite memory which takes its values in R2. The transition kernel of this Markov chain is given by a family of conditional multivariate probability distributions. They are constructed using so-called R-vine copulas, which are fitted and validated by means of experimental data.
Fine Structure of the Compound Eyes of Male and FemaleHeortia vitessoidesMoore (Lepidoptera: Crambidae)
Authors: Pan Zijian , Wen Chao , Liu Chuanhe , Woodgate Joseph L , Chen Zhiyun , Yang Wenjuan , Li Yizhen , Ma Tao 
Published: January 2023

AbstractHeortia vitessoides is a destructive pest of the economically important plant Aquilaria sinensis in China. We investigated the external morphology and ultrastructure of H. vitessoides compound eyes using scanning and transmission electron microscopy. We found that H. vitessoides has superposition eyes, made up of a mean of 3,671 and 3,428 ommatidia in males and females, respectively. The mean ommatidial diameter for males and females was 18.87 and 16.81 µm, respectively. Each ommatidium was capped by a convexly curved corneal facet lens of about 13.85 µm thickness. Corneal nipples measuring 226.36 nm in height in males and 295.48 nm in females, covered the surface of the eyes. Heortia vitessoides eyes are eucone, with each ommatidium having a crystalline cone comprising four cone cells, surrounded by two primary pigment cells. The centrally fused rhabdom of each ommatidium was formed by 8–11 of retinal cells, somewhat more than are typically found in Lepidoptera. The relatively large size of the compound eyes, the large number of ommatidia, large number of retinula cells, and high corneal nipples all suggest that H. vitessoides eyes are adapted to optimize visual sensitivity under dim light conditions.
Benchmark Tests of Atom Segmentation Deep Learning Models with a Consistent Dataset
Authors: Wei Jingrui , Blaiszik Ben , Scourtas Aristana , Morgan Dane , Voyles Paul M 
Published: January 2023

AbstractThe information content of atomic-resolution scanning transmission electron microscopy (STEM) images can often be reduced to a handful of parameters describing each atomic column, chief among which is the column position. Neural networks (NNs) are high performance, computationally efficient methods to automatically locate atomic columns in images, which has led to a profusion of NN models and associated training datasets. We have developed a benchmark dataset of simulated and experimental STEM images and used it to evaluate the performance of two sets of recent NN models for atom location in STEM images. Both models exhibit high performance for images of varying quality from several different crystal lattices. However, there are important differences in performance as a function of image quality, and both models perform poorly for images outside the training data, such as interfaces with large difference in background intensity. Both the benchmark dataset and the models are available using the Foundry service for dissemination, discovery, and reuse of machine learning models.
Evaluation of prognostic factors for patients with eosinophilic granulomatosis with polyangiitis recruited at the pneumonological centre and mainly ANCA negativity: A retrospective analysis of a single cohort in Poland
Authors: Fijolek Justyna , Wiatr Elzbieta , Bujnowski Pawel , Piotrowska-Kownacka Dorota , Roszkowski-Sliz Kazimierz 
Published: January 2023

ABSTRACT

Objectives
The aim was to investigate the risk factors for relapse and death in patients with eosinophilic granulomatosis with polyangiitis (EGPA) recruited at the pneumonological centre and mainly antineutrophil cytoplasmic antibody negativity.

Methods
We retrospectively recruited 86 patients. Relapse was defined as the recurrence or appearance of new organ symptoms. The study end-point included the final examination.

Results
Relapses occurred in 34.9% of the patients, while 9.3% died. Immunosuppressive therapy (P = 0.042), prolonged low-dose corticosteroid treatments (mainly for asthma) (P = 0.006), and longer follow-up duration (P = 0.004) were associated with a higher relapse risk, while advanced EGPA severity (P = 0.0015) and activity (P = 0.044), older age of onset (P = 0.030), symptomatic cardiac involvement (P = 0.007), and postinflammatory cardiac fibrosis (P = 0.038) were associated with a higher risk of death. Sinusitis (P = 0.028) and prolonged low-dose corticosteroid treatments (P = 0.025) correlated with a better prognosis. Relapses did not have an impact on the mortality (P = 0.693).

Conclusions
Relapses in EGPA remain frequent, although they do not impact mortality. Cardiac involvement is common, but clinically symptomatic cardiomyopathy is associated with a higher risk of death. Asthma requiring chronic corticosteroid treatments is associated with a lower risk of death, although the risk of EGPA recurrence is significantly higher.
Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine
Authors: Kovalenko Ganna , Yakovleva Anna , Smyrnov Pavlo , Redlinger Matthew , Tymets Olga , Korobchuk Anna , Kolodiazieva Anna , Podolina Anna , Cherniavska Svitlana , Skaathun Britt , Smith Laramie R , Strathdee Steffanie A , Wertheim Joel O , Friedman Samuel R , Bortz Eric , Goodfellow Ian , Meredith Luke , Vasylyeva Tetyana I 
Published: January 2023

Abstract
Internally displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly stigmatized group, internally displaced people who inject drugs (IDPWIDs). We inform the framework by Nanopore generated HIV pol sequences and IDPWID migration history. In June–September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly available sequences (N = 359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data shows that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.
The Impact of Social Determinants of Health on Pressure Injury Progression: A Retrospective Chart and Scoping Review
Authors: Sasson Daniel C. , Duan Kaiti , Patel Seema M. , Junn Alexandra , Hsia Henry C. 
Published: January 2023

ABSTRACT

OBJECTIVE
To understand the effects of nutrition security and social determinants of health (SDOHs) on pressure injury (PI) progression through a scoping review and retrospective review of patients reporting to New England’s largest healthcare system.

METHODS
Authors performed a scoping review for full-text, original articles reporting outcomes data specific to PIs in patients with socially informed nutrition insecurity. Investigators also performed a retrospective review of all patients from 2012 to 2021 to search for patients with PI documentation and International Classification of Diseases, Tenth Revision Z codes related to the SDOHs.

RESULTS
A full-text review of 2,323 articles from 1965 to 2020 failed to locate any eligible studies. Investigators identified 1,044 patients who met the inclusion criteria; 50.7% were men, 74.3% were White, and 13.3% had evidence of detrimental SDOHs. The average PI duration was 12.13 days (interquartile range, 6 days). Multivariate regression analysis revealed that PI duration was longer in men, Black patients, and patients with evidence of detrimental SDOHs compared with their converse counterparts (P < .0001). The presence of detrimental SDOHs independently predicted an increased duration of disease by 13.07 days (95% CI, 8.99–17.15; t = 6.29, P < .0001).

CONCLUSIONS
A patient’s SDOH history has a significant and considerably stronger correlation with disease progression than predictors that are traditionally studied such as sex, race, or body mass index. These findings are novel, as highlighted by the absence of data uncovered in the literature. These data carry relevance for plastic surgeons wishing to prevent early recurrence following operative closure of PI-related wounds.
Impact of Early Tracheostomy Versus Late or No Tracheostomy in Nonneurologically Injured Adult Patients: A Systematic Review and Meta-Analysis*
Authors: Villemure-Poliquin Noémie , Lessard Bonaventure Paule , Costerousse Olivier , Rouleau-Bonenfant Thierry , Zarychanski Ryan , Lauzier François , Audet Nathalie , Moore Lynne , Gagnon Marc-Aurèle , Turgeon Alexis F. 
Published: January 2023

OBJECTIVE:
The optimal timing of tracheostomy in nonneurologically injured mechanically ventilated critically ill adult patients is uncertain. We conducted a systematic review of randomized controlled trials to evaluate the effect of early versus late tracheostomy or prolonged intubation in this population.

DATA SOURCES:
We searched MEDLINE, Embase, CENTRAL, CINAHL, and Web of science databases for randomized controlled trials comparing early tracheostomy (<10 d of intubation) with late tracheostomy or prolonged intubation in adults.

DATA SELECTION:
We selected trials comparing early tracheostomy (defined as being performed less than 10 d after intubation) with late tracheostomy (performed on or after the 10th day of intubation) or prolonged intubation and no tracheostomy in nonneurologically injured patients. The primary outcome was overall mortality. Secondary outcomes included ventilator-associated pneumonia, duration of mechanical ventilation, ICU, and hospital length of stay.

DATA EXTRACTION:
Two reviewers screened citations, extracted data, assessed the risk of bias, and classification of Grading of Recommendations, Assessment, Development, and Evaluation independently.

DATA SYNTHESIS:
Our search strategy yielded 8,275 citations, from which nine trials (n = 2,457) were included. We did not observe an effect on the overall mortality of early tracheostomy compared with late tracheostomy or prolonged intubation (risk ratio, 0.91, 95% CI, 0.82–1.01; I
2 = 18%). Our results were consistent in all subgroup analyses. No differences were observed in ICU and hospital length of stay, duration of mechanical ventilation, incidence of ventilator-acquired pneumonia, and complications. Our trial sequential analysis showed that our primary analysis on mortality was likely underpowered.

CONCLUSION:
In our systematic review, we observed that early tracheostomy, as compared with late tracheostomy or prolonged intubation, was not associated with a reduction in overall mortality. However, we cannot exclude a clinically relevant reduction in mortality considering the level of certainty of the evidence. A well-designed trial is needed to answer this important clinical question.
Prospective Real-Time Validation of a Lung Ultrasound Deep Learning Model in the ICU
Authors: Dave Chintan , Wu Derek , Tschirhart Jared , Smith Delaney , VanBerlo Blake , Deglint Jason , Ali Faraz , Chaudhary Rushil , VanBerlo Bennett , Ford Alex , Rahman Marwan A. , McCauley Joseph , Wu Benjamin , Ho Jordan , Li Brian , Arntfield Robert 
Published: January 2023

OBJECTIVES:
To evaluate the accuracy of a bedside, real-time deployment of a deep learning (DL) model capable of distinguishing between normal (A line pattern) and abnormal (B line pattern) lung parenchyma on lung ultrasound (LUS) in critically ill patients.

DESIGN:
Prospective, observational study evaluating the performance of a previously trained LUS DL model. Enrolled patients received a LUS examination with simultaneous DL model predictions using a portable device. Clip-level model predictions were analyzed and compared with blinded expert review for A versus B line pattern. Four prediction thresholding approaches were applied to maximize model sensitivity and specificity at bedside.

SETTING:
Academic ICU.

PATIENTS:
One-hundred critically ill patients admitted to ICU, receiving oxygen therapy, and eligible for respiratory imaging were included. Patients who were unstable or could not undergo an LUS examination were excluded.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
A total of 100 unique ICU patients (400 clips) were enrolled from two tertiary-care sites. Fifty-six patients were mechanically ventilated. When compared with gold standard expert annotation, the real-time inference yielded an accuracy of 95%, sensitivity of 93%, and specificity of 96% for identification of the B line pattern. Varying prediction thresholds showed that real-time modification of sensitivity and specificity according to clinical priorities is possible.

CONCLUSIONS:
A previously validated DL classification model performs equally well in real-time at the bedside when platformed on a portable device. As the first study to test the feasibility and performance of a DL classification model for LUS in a dedicated ICU environment, our results justify further inquiry into the impact of employing real-time automation of medical imaging into the care of the critically ill.
The Effect of Biomarkers on Clinical Trial Risk in Gastric Cancer
Authors: Dhillon Sumeet , Lopes Gilberto , Parker Jayson L. 
Published: January 2023

Objectives:
This study examined clinical trial success rates for new drug developments in gastric cancer since 1998. We also examined the clinical trial design features that may mitigate the risk of clinical trial failure.

Materials and Methods:
Clinical trial data was obtained from clinicaltrials.gov. Drugs were included if they entered testing between January 1, 1998 and January 1, 2022 and were excluded if they did not have a completed phase I trial or treated secondary effects of gastric cancer. Transition probabilities were calculated for each phase and compared with industry averages. Success rates were determined based on biomarker usage, drug target, type of therapy, and drug chemistry.

Results:
Upon screening 1990 trials, 219 drugs met our inclusion criteria. The probability of a drug completing all phases of testing and obtaining FDA approval was 7%, which is below the 11% industry average. The use of biomarkers in clinical development resulted in nearly a 2-fold increase in the cumulative success rate. Biologics also exhibited higher success rates (17%) as opposed to small molecules (1%). This was true even when we compared both drug types that shared the same target. When comparing only receptor-targeted therapies, biologics (62%) continued to outperform small molecules (18%). Similarly, when narrowed down to drugs targeting solely HER2 receptors, biologics continued to prevail (64% vs. 24%).

Conclusions:
Implementing biomarkers, receptor-targeted therapies, and biologics in clinical development improves clinical trial success rates in gastric cancer. Thus, physicians should prioritize the enrollment of gastric cancer patients in clinical trials that incorporate the aforementioned features.
Prominin-1 promotes restitution of the murine extrahepatic biliary luminal epithelium following cholestatic liver injury
Authors: Zhong Allen , Short Celia , Xu Jiabo , Fernandez G. Esteban , Malkoff Nicolas , Noriega Nicolas , Yeo Theresa , Wang Larry , Mavila Nirmala , Asahina Kinji , Wang Kasper S. 
Published: January 2023

Background and Aims:
Restitution of the extrahepatic biliary luminal epithelium in cholangiopathies is poorly understood. Prominin-1 (Prom1) is a key component of epithelial ciliary body of stem/progenitor cells. Given that intrahepatic Prom1-expressing progenitor cells undergo cholangiocyte differentiation, we hypothesized that Prom1 may promote restitution of the extrahepatic bile duct (EHBD) epithelium following injury.

Approach and Results:
Utilizing various murine biliary injury models, we identified Prom1-expressing cells in the peribiliary glands of the EHBD. These Prom1-expressing cells are progenitor cells which give rise to cholangiocytes as part of the normal maintenance of the EHBD epithelium. Following injury, these cells proliferate significantly more rapidly to re-populate the biliary luminal epithelium. Null mutation of Prom1 leads to significantly >10-fold dilated peribiliary glands following rhesus rotavirus–mediated biliary injury. Cultured organoids derived from Prom1 knockout mice are comprised of biliary progenitor cells with altered apical-basal cellular polarity, significantly fewer and shorter cilia, and decreased organoid proliferation dynamics consistent with impaired cell motility.

Conclusions:
We, therefore, conclude that Prom1 is involved in biliary epithelial restitution following biliary injury in part through its role in supporting cell polarity.
Analysis of Imaging Results for Semisitting Compared with Supine Positioning in the Retrosigmoid Approach for Resection of Cerebellopontine Angle Vestibular Schwannomas
Authors: Arambula Alexandra M. , Wichova Helena , Lucas Jacob C. , Schelbar Natalie , Harn Nicholas , Ledbetter Luke , Chamoun Roukoz B. , Camarata Paul J. , Lin James , Staecker Hinrich 
Published: January 2023

Objective
To compare the completeness of resection of vestibular schwannomas using three-dimensional segmented volumetric analysis of pre- and postoperative magnetic resonance imaging (MRI) of patients undergoing supine and semisitting positioning for the retrosigmoid approach.

Study Design
Retrospective chart review.

Setting
Tertiary medical center.

Patients
Patients with vestibular schwannomas undergoing surgical resection via the retrosigmoid approach.

Intervention(s)
Tumor resection via the retrosigmoid approach with different patient positioning: standard supine versus semisitting.

Main Outcome Measure(s)
Preoperative versus postoperative three-dimensional segmented volumetric MRI analysis of vestibular schwannomas.

Results
A total of 43 patients (15 supine and 28 semisitting) underwent retrosigmoid craniotomy for resection of vestibular schwannomas. For the conventional supine and semisitting positioning, mean preoperative tumor volumes were 12.65 and 8.73 cm3 (p = 0.15), respectively. Postoperative mean tumor volumes for the supine and semisitting positions were 2.09 and 0.48 cm3 (p = 0.13), respectively. There were 11 cases of postoperative sigmoid sinus thrombosis, 3 in the conventional supine group and 8 in the semisitting groups, and there were 6 cases of postoperative cerebrospinal fluid leaks, all in the semisitting group. The mean House–Brackmann scores for the supine and semisitting groups were 2.9 and 2.3, respectively. There was no statistically significant difference between groups in the rates of these or any other postoperative complications.

Conclusions
The semisitting position for the suboccipital retrosigmoid approach for vestibular schwannoma resection does not compromise the ability to adequately resect the tumor as seen by volumetric MRI results. Further studies are needed to establish the safety of this position compared with the traditional supine approach.