bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-expanded Local Flaps: Optimal Choice for Repairing Defects Following Extensive Benign Tumor Resection in the Head and Face
Authors: Cui Jiangbo , Zhang Yu , Tang Yinke , Chu Feifei , Liu Wei , Bai Ruoxue , Li Yang , Ma Xianjie 
Published: October 2024

Background:
Treating extensive benign tumors of the head and face presents a longstanding challenge, necessitating efficacy at the lesion site, and postoperative esthetic considerations for the donor area.

Objective:
This study aims to explore the clinical outcomes of pre-expanded local flap reconstruction for extensive benign tumors of the head and face post resection.

Method:
From March 2018 to March 2023, a total of 18 patients with extensive benign tumors of the head and face were admitted, including 13 cases of nevus, 2 cases of hemangioma, 2 cases of neurofibroma, and 1 case of verruca. Based on the location and size of the lesions, suitable local areas were selected for tissue expansion, and expanders were implanted for regular saline injections over 8 to 16 weeks. After reaching the desired expansion, resection of the head and facial tumors and local flap reconstruction were performed. Postoperatively, data on patients’ information, tumor types, tumor area, expansion volume, postexpander complications, vascular condition after flap transfer, and donor site condition were collected.

Result:
In this series of 18 patients, benign tumors of the head and face were completely repaired through 1 to 2 stages of tissue expansion surgeries. Postimplantation complications included hematoma in 1 case and infections in 2 cases, with one instance of expander infection leading to surgical failure. However, all other patients achieved adequate expansion, successful flap survival post-transfer, and experienced no other complications. Follow-up over 6 to 24 months showed no recurrence at the lesion sites, with flaps maintaining consistent color, texture, and thickness matching surrounding skin tissue. In addition, donor site healing was excellent, with no obvious surgical scars.

Conclusions:
Pre-expanded local flap reconstruction is an ideal method for repairing extensive benign tumors of the head and face postresection.
Surgical Reconstruction of the Congenital Absent Earlobe
Authors: Guillen-Martinez Edgar Alan , Davila-Diaz Rodrigo , Barlandas-Quintana Erika , Marquez-Espriella Cuahutemoc , Garcia-Corral Jesus Ricardo , Barbosa-Villarreal Fernando 
Published: October 2024

Introduction:
A simple technique for earlobe reconstruction in a single stage, with satisfactory esthetic results and minimal morbidity.

Cases:
Two patients with congenital absent earlobe are presented. In both cases, a bilobed flap comprising skin, subcutaneous tissue, and fat was used to reconstruct the lower border of the earlobe.

Discussion:
Different techniques for earlobe reconstruction are discussed, including flap overlap, the use of skin and cartilage grafts, and double-bilobed flaps.

Conclusion:
The procedure described in this article is based on a modification of Gavello’s surgical technique, supplying a simple and effective approach for earlobe reconstruction in a single procedure.
Investigation of the Effects of Ozon and Propolis on the Healing of Bone Defects: An Experimental Study
Authors: Durmuş Halil İbrahim , Gunes Nedim 
Published: October 2024

Background/aim:
This study explores the effects of ozone and propolis on the healing of critically sized bone defects at both the histologic and molecular levels, and the locations and concentrations of osteopontin and osteonectin during healing; both proteins play roles during bone healing.

Materials and methods:
This study used 56 adult male Sprague-Dawley rats of an average weight of 350 g, divided into four groups of 14: a control group, a topical ozone group (O), a topical ozone + systemic propolis (O + PO) group, and a systemic propolis group (PO). Seven rats from each group were sacrificed at the end of week 4 and the other seven at the end of week 6. Tissues were subjected to histologic and immunohistochemical examinations in a fixative solution. The results were analyzed using the statistical software package SPSS 23 (Statistical Package for the Social Sciences—IBM). Results were considered significant at the 95% confidence level (P<0.05).

Results:
Graft sections were immunostained for osteonectin. Staining was low in the control group but moderate in the other three groups; the differences were significant. The three experimental groups did not differ significantly. Graft sections were also immunostained for osteonectin. At 4 weeks, staining was low in the control group but moderate in the other 3 groups. At 6 weeks, stronger staining was apparent in the 3 experimental groups. At both 4 and 6 weeks, the differences between the control and experimental groups were significantly different, but the differences among the experimental groups were not.

Conclusion:
The authors' results are compatible with the literature. Ozone and propolis, given separately or together, improved bone healing, increased bone formation, and reduced bone destruction. However, further research is required.
EARLY ANALYSIS OF ENDOTHELIAL MARKERS TO PREDICT SEPSIS IN THE EMERGENCY DEPARTMENT
Authors: Galtung Noa , Stein Vanessa , Prpic Monika , Boyraz Burak , Ulke Jannis , Kurz Stephan , Dernedde Jens , Diehl-Wiesenecker Eva , Bauer Wolfgang , Kappert Kai 
Published: October 2024

ABSTRACT

Background: Acute infections and sepsis are a leading cause of death. These patients are primarily encountered at the emergency department (ED), where early assessment for sepsis is necessary to improve outcome. In sepsis, the inflammatory response causes several characteristic pathophysiological changes, including a dysregulated and generalized activation of the endothelium. This study aimed to analyze endothelial markers released to the blood as diagnostic biomarkers for acute infection and sepsis in the ED, as smaller studies have previously shown promising results in other settings. Methods: Serum samples from n = 312 adult patients with suspected acute infections at presentation to the ED were utilized. Patients’ courses of disease and outcomes were assessed by clinical adjudication. E-selectin, P-selectin, ICAM-1, and VCAM-1 were measured by ELISAs. The accuracy of each marker for predicting bacterial infection, sepsis, and in-hospital mortality was evaluated. Results: For sepsis, E-selectin and ICAM-1 both showed an area under the receiver operating characteristic (AUROC) of 0.62, lower than procalcitonin with 0.77 (both P < 0.01) and lactate with 0.73 (P = 0.030 and 0.046, respectively), but similar to CRP with 0.60 (P = 0.758 and 0.876, respectively). For 28-day in-hospital mortality among patients with infection, ICAM-1 performed best with an AUROC of 0.75. Conclusions: Despite promising results in small studies and specific cohorts, particularly in intensive care units, this large-scale evaluation of four endothelial biomarkers highlights their limited diagnostic utility in a broader inclusion setup design at the earliest possible time point of evaluation.
Primary care follow-up improves outcomes in older adults following emergency general surgery admission
Authors: Guttman Matthew P. , Tillmann Bourke W. , Nathens Avery B. , Bronskill Susan E. , Saskin Refik , Jaakkimainen Liisa , Huang Anjie , Haas Barbara 
Published: October 2024

BACKGROUND
While preoperative optimization improves outcomes for older adults undergoing major elective surgery, no such optimization is possible in the emergent setting. Surgeons must identify postoperative interventions to improve outcomes among older emergency general surgery (EGS) patients. The objective of this cohort study was to examine the association between early follow-up with a primary care physician (PCP) and the risk of nursing home acceptance or death in the year following EGS admission among older adults.

METHODS
Using population-based administrative health data in Ontario, Canada (2006–2016), we followed all older adults (65 years or older) for 1 year after hospital admission for EGS conditions. A multivariable Cox model was used to identify the association between early postdischarge follow-up with a patient's PCP and the time to nursing home acceptance or death while adjusting for confounders.

RESULTS
Among 76,568 older EGS patients, 32,087 (41.9%) were seen by their usual PCP within 14 days of discharge, and 9,571 (12.5%) were accepted to a nursing home or died within 1 year. Primary care physician follow-up was associated with a 13% reduced risk of nursing home acceptance or death compared with no follow-up (hazard ratio 0.87; 95% confidence interval 0.84–0.91). This effect was consistent across age and frailty strata, patients managed operatively and nonoperatively, and patients who had both high and low baseline continuity of care with their PCP.

CONCLUSION
Early follow-up with a familiar PCP was associated with a reduced risk of nursing home acceptance or death among older adults following EGS admission. Structures and processes of care are needed to ensure that such follow-up is routinely arranged at discharge.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level III.
Translational Neuroscience Contributes to Understanding Neurodevelopmental Outcomes of Dostoyevsky's “Brothers Karamazov” With Treatment Implications
Authors: Deutsch Stephen I. , Burket Jessica A. , Elikan Jeffrey , Spiegel David R. 
Published: October 2024

Abstract
Dostoyevsky's novels raise profound ethical, moral, philosophical and theological issues and, as a result, both he and his novels serve as fertile subjects of scholarly inquiry across a variety of academic disciplines. In particular, major characters in “The Brothers Karamazov” lend themselves to classical psychodynamic formulations, such as the influence of adverse childhood experiences on adult social and occupational outcomes, which in the case of Dmitry, the eldest son of Fyodor Pavlovich Karamazov, are considered in exquisitely fine detail. Prosecutor and defense attorney provide differing interpretations of how early traumas, largely due to paternal neglect and abuse, affected Dmitry's adult outcome in the climactic trial over his alleged patricide. The novel also captures an extreme, and perhaps fanciful, description of an Oedipal rivalry between Dmitry and his father for the affection of a love interest leading to tragic and unpredictable consequences for both. The novel has been dissected by scholars across a variety of diverse and seemingly unrelated disciplines and continues to serve as a springboard for collaborative discussion. Re-reading the novel led the authors to wonder if translational developments in clinical neuroscience could further understanding of poor developmental trajectories of the novel's characters, as well as offer therapeutic recommendations for promoting more favorable occupational and social outcomes. Advances in basic neuroscience have been translated into actionable individualized, interdisciplinary, multimodal treatment plans leading to improved functional outcomes for children like Dmitry, Ivan, and Smerdyakov. Translational neuroscience enriches understanding of neurodevelopmental outcomes of characters in Dostoyevsky's novel “The Brothers Karamazov,” especially in the context of genetic risk and in utero environmental insults.
Food intake enhances hippocampal sharp wave-ripples
Authors: Kaya Ekin , Wegienka Evan , Akhtarzandi-Das Alexandra , Do Hanh , Eban-Rothschild Ada , Rothschild Gideon 
Published: October 2024

AbstractEffective regulation of energy metabolism is critical for survival. Metabolic control involves various nuclei within the hypothalamus, which receive information about the body’s energy state and coordinate appropriate responses to maintain homeostasis, such as thermogenesis, pancreatic insulin secretion, and food-seeking behaviors. It has recently been found that the hippocampus, a brain region traditionally associated with memory and spatial navigation, is also involved in metabolic regulation. Specifically, hippocampal sharp wave ripples (SWRs), which are high-frequency neural oscillations supporting memory consolidation and foraging decisions, have been shown to reduce peripheral glucose levels. However, whether SWRs are enhanced by recent feeding– when the need for glucose metabolism increases, and if so, whether feeding-dependent modulation of SWRs is communicated to other brain regions involved in metabolic regulation, remains unknown. To address these gaps, we recorded SWRs from the dorsal CA1 region of the hippocampus of mice during sleep sessions before and after consumption of meals of varying caloric values. We found that SWRs occurring during sleep are significantly enhanced following food intake, with the magnitude of enhancement being dependent on the caloric content of the meal. This pattern occurred under both food-deprived andad libitumfeeding conditions. Moreover, we demonstrate that GABAergic neurons in the lateral hypothalamus, which are known to regulate food intake, exhibit a robust SWR-triggered increase in activity. These findings identify the satiety state as a factor modulating SWRs and suggest that hippocampal-lateral hypothalamic communication is a potential mechanism by which SWRs could modulate peripheral metabolism and food intake.
Privacy-Preserving Visualization of Brain Functional Connectivity
Authors: Tao Ye , Sarwate Anand D. , Panta Sandeep , Plis Sergey , Calhoun Vince D. 
Published: October 2024

AbstractPrivacy protection is important in visualization due to the risk of leaking personal sensitive information. In this paper, we study the problem of privacy-preserving visualizations using differential privacy, employing biomedical data from neuroimaging as a use case. We investigate several approaches based on perturbing correlation values and characterize their privacy cost and the impact of pre- and post-processing. To obtain a better privacy/visual utility tradeoff, we propose workflows for connectogram and seed-based connectivity visualizations, respectively. These workflows successfully generate visualizations similar to their non-private counterparts. Experiments show that qualitative assessments can be preserved while guaranteeing privacy. These results show that differential privacy is a promising method for protecting sensitive information in data visualization.
A Streamlined High-Throughput LC-MS Assay for Quantifying Peptide Degradation in Cell Culture
Authors: Rozans Samuel J. , Moghaddam Abolfazl S. , Pashuck E. Thomas 
Published: October 2024

AbstractPeptides are widely used in biomaterials due to their easy of synthesis, ability to signal cells, and modify the properties of biomaterials. A key benefit of using peptides is that they are natural substrates for cell-secreted enzymes, which creates the possibility of utilizing cell-secreted enzymes for tuning cell-material interactions. However, these enzymes can also induce unwanted degradation of bioactive peptides in biomaterials, or in peptide therapies. Liquid chromatography-mass spectrometry (LC-MS) is a widely used, powerful methodology that can separate complex mixtures of molecules and quantify numerous analytes within a single run. There are several challenges in using LC-MS for the multiplexed quantification of cell-induced peptide degradation, including the need for non-degradable internal standards and the identification of optimal sample storage conditions. Another problem is that cell culture media and biological samples typically contain both proteins and lipids that can accumulate on chromatography columns and degrade their performance. However, removing these constituents can be expensive, time consuming, and increases sample variability. Here we show that directly injecting samples onto the LC-MS without any purification enables rapid and accurate quantification of peptide concentration, and that hundreds of LC-MS runs can be done on a single column without a significantly diminish the ability to quantify the degradation of peptide libraries. We also show that column failure is evident when hydrophilic peptides fail to be retained on the column, and this can be easily identified using standard peptide mixtures for column benchmarking. In total, this work introduces a simple and effective method for simultaneously quantifying the degradation of dozens of peptides in cell culture. By providing a streamlined and cost-effective method for the direct quantification of peptide degradation in complex biological samples, this work enables more efficient assessment of peptide stability and functionality, facilitating the development of advanced biomaterials and peptide-based therapies.
Balanced polymorphisms in gamete-binding genes are not associated with human infertility
Authors: Hart M. W. , Crespi B. , Seethram K. 
Published: October 2024

ABSTRACTGenes expressed in gametes that mediate sperm interaction with the mammalian egg are of considerable interest to evolutionary biologists because the evolution of such genes can account for variation in reproductive compatibility between mates and reproductive isolation between species. The human orthologs of such genes are also potential targets for both contraception and treatment of infertility. One gene system of particular interest is the sperm-binding genes of the inner egg coat or zona pellucida (Zp2, Zp3) and their cognate protein in the mouse sperm acrosome (Zp3r). Previous population genetic analyses in humans pointed toward three balanced polymorphisms (one in each geneZP2, ZP3, andZP3R) as potential targets of some form of balancing selection in the evolution of human fertility. We tested that association using genetic analysis of couples seeking fertility assistance, but we could not reject the null hypothesis of no association between balanced polymorphisms and infertility. Our study was based on a small sample of couples, but the data were sound: the allele frequencies at those three balanced polymorphisms were not different from random expectation in that clinical sample. If an effect of those allele frequencies on infertility exists it is probably small. Our study was based in part on an old error in gene annotation that was only recently discovered (after the start of participant recruitment for this genetic analysis), and this error may account for our results, which argue against a role for balancing selection on those three genes in humans.
SeqDance: A Protein Language Model for Representing Protein Dynamic Properties
Authors: Hou Chao , Shen Yufeng 
Published: October 2024

AbstractProteins perform their functions by folding amino acid sequences into dynamic structural ensembles. Despite the important role of protein dynamics, their complexity and the absence of efficient representation methods have limited their integration into studies on protein function and mutation fitness, especially in deep learning applications. To address this, we present SeqDance, a protein language model designed to learn representation of protein dynamic properties directly from sequence alone. SeqDance is pre-trained on dynamic biophysical properties derived from over 30,400 molecular dynamics trajectories and 28,600 normal mode analyses. Our results show that SeqDance effectively captures local dynamic interactions, co-movement patterns, and global conformational features, even for proteins lacking homologs in the pre-training set. Additionally, we showed that SeqDance enhances the prediction of protein fitness landscapes, disorder-to-order transition binding regions, and phase-separating proteins. By learning dynamic properties from sequence, SeqDance complements conventional evolution- and static structure-based methods, offering new insights into protein behavior and function.
TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline
Authors: Kelsey Maxfield M.G. , Kalekar Radha L. , Sedivy John M. 
Published: October 2024

AbstractThe recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this mobile ‘dark genome’. The TE-Seq pipeline conducts an end-to-end analysis of RNA-sequencing data, examining both genes and TEs. It implements the most current computational methods tailor-made for TEs, enabling a comprehensive analysis of TE expression at both the individual element level and at the TE clade level. If supplied with long-read DNA sequencing data, it creates a TE-complete genome incorporating non-reference (polymorphic) TE-loci, enabling the functional characterization of the evolutionarily youngest mobile elements in the genome.
New QTLs involved in the control of stigma position in tomato
Authors: Riccini Alessandro , Olivieri Fabrizio , Farinon Barbara , Bitton Frederique , Diouf Isidore , Carretero Yolande , Soler Salvador , del Rosario Figàs Maria , Prohens Jaime , Monforte Antonio Jose , Granell Antonio , Causse Mathilde , Mazzucato Andrea 
Published: October 2024

AbstractThe tomato mating system was strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in domesticated forms retaining a non-inserted or a heat-inducible SP needs elucidation. To widen the possibility of identifying SP genetic determinants, we analysed the trait in four populations (two germplasm collections, a multiparental recombinant inbred and a biparental progeny) under different environmental conditions (normal and heat stressed). Overall, 36 markers significantly associated with the trait were discovered. Several co-localizations were found, both among regions firstly reported in this work and among them and previously reported positions. This supported the reliability of the analysis. Three of such regions, in the long arms of chromosome 1, 8 and 11, were validated in an independent segregating population and candidate genes in confidence intervals were identified among transcription factors and hormone, stress and cell-wall-related genes. In conclusion, the work supported the hypothesis that the SP phenotype is controlled by different key-genes in tomato, paving the way to identifying novel players and novel mechanisms involved in the regulation of herkogamy.HighlightThe study of three germplasm collections in tomato allowed the identification new significant markers for the stigma position trait while confirmed several previously reported QTLs.