bluuebunny/crossref_metadata_2025_split huggingface dataset:
Congenital hemivertebrae combined with situs inversus totalis: A rare case report
Authors: Guo Zheng , Li Donglai , Zang Xuehui 
Published: March 2024

Rationale:
Situs inversus totalis is a rare malposition of organs that typically involves lesions in the respiratory, circulatory, or urinary systems. Cases of congenital hemivertebrae combined with situs inversus totalis are extremely rare and have limited reports.

Patient concerns:
We report a 2.5 years old girl with 2 congenital hemipyramids and complete visceral inversion who ultimately underwent hemilaminectomy.

Diagnosis:
Congenital hemivertebrae combined with situs inversus totalis.

Intervention:
The patient underwent hemilaminectomy.

Outcomes:
The spinal deformity was corrected.

Lessons:
For patient with spinal deformities combined with situs inversus totalis, surgery can be an effective treatment method. But we also need to be vigilant about the dysfunction of various systems.
Sarcomatoid hepatocellular carcinoma: A case report and review of the literature
Authors: Hu Chengyin , Zhao Mingwei , Wei Qiang , Chen Zhuo , Zhao Baolei 
Published: March 2024

Rationale:
Sarcomatoid hepatocellular carcinoma (SHC) is a rare malignant tumor composed of both carcinoma and sarcoma components. It has atypical clinical symptoms and a high degree of malignancy, with rapid progression and a poor prognosis.

Patient concerns:
A 63-year-old female patient was admitted to our hospital with a chief complaint of fatigue present for more than 1 month and fever for 10 days.

Diagnoses:
This patient underwent an upper abdominal MRI plain scan and enhanced scan showed a solid tumor in the right lobe of the liver, with a size of approximately 4.7 cm × 4.0 cm × 6.5 cm, present as low signal on T1WI, slightly high signal on T2WI, and heterogeneous high signal on DWI. Multi-phase dynamic contrast-enhanced MR scan showed significant enhancement in the arterial phase and low enhancement in the portal and delayed phases. The pathology showed the tumor cells to be positive for cytokeratin (CK), Vimentin, EMA, CD34, cyclinD1, negative for CK8, CK19, CK20, SMA, Desmin, S-100, CD117, Dog-1, Hepar-1, SOX-10 and ALK, and Ki-67 approximately 50%, which confirmed the diagnosis of SHC.

Interventions:
Laparoscopic right posterior lobe of liver resection was conducted, and the postoperative pathology revealed the presence of SHC.

Outcomes:
The patient was discharged 9 days after the surgery without any complications. There has been no evidence of recurrence at the 1 month, however bilateral pleural metastases appeared during the follow-up 3 months after surgery.

Lessons:
SHC is a rare and aggressive liver cancer. So far, there is still a lack of effective therapeutic strategy, and the prognosis was dismal even though patients received radical surgical resection.
The Rhinoplasty Rosetta Stone: Using Rasch Analysis to Create and Validate Crosswalks between the NOSE and the SCHNOS Functional Subscale
Authors: van Zijl Floris V. W. J. , Declau Frank , Rizopoulos Dimitris , Datema Frank R. 
Published: March 2024

Background:
The Nasal Obstruction Symptom Evaluation (NOSE) and the Functional subscale of the Standardized Cosmesis and Health Nasal Outcomes Survey (SCHNOS-O) are widely used patient-reported outcome measures to measure functional outcomes of rhinoplasty. However, as different instruments produce scores on different metrics, results of these instruments cannot be linked directly, thus hindering comparison and aggregating of rhinoplasty outcome data from practices using either instrument. The aim of this study was to develop and validate crosswalks between the NOSE and the SCHNOS-O.

Methods:
In a sample of 552 rhinoplasty patients who completed both instruments, the NOSE and SCHNOS-O scales were co-calibrated onto a common interval-scaled metric using Rasch analysis. Separate Rasch models were run per instrument, and the latent constructs were estimated using the calibrated item parameters. By anchoring original patient-reported outcome measure scores of both instruments to this Rasch computed measurement scale, the scores of both instruments were linked. A second independent sample was used to validate the created crosswalks.

Results:
Total scores on the NOSE and SCHNOS-O were strongly correlated. The Rasch-based co-calibration of the NOSE and SCHNOS-O items resulted in a model that adequately fitted the data. Back-and-forth crosswalk tables were created from the NOSE to the SCHNOS-O. For patients with moderate nasal obstruction, predicted SCHNOS-O scores were slightly higher for a given level of the NOSE. Intraclass correlation coefficients between predicted and actual scores were 0.93 for both directions, indicating adequate agreement for group-level comparisons.

Conclusions:
This study developed and validated Rasch-based crosswalks from the NOSE to the SCHNOS-O and vice versa. The provided crosswalks enhance comparison and harmonization of functional rhinoplasty outcomes.
A National Analysis of Targeted Muscle Reinnervation following Major Upper Extremity Amputation
Authors: Valentine Lauren , Weidman Allan A. , Foppiani Jose , Hernandez Alvarez Angelica , Kim Erin , Hassell Natalie E. , Elmer Nicholas , Engmann Toni F. , Lin Samuel J. , Dowlatshahi Sammy 
Published: March 2024

Background:
Postamputation pain is a debilitating sequela of upper extremity (UE) amputation. Targeted muscle reinnervation (TMR) is a relatively novel treatment that can help prevent pain and improve quality of life. The purpose of this study was to evaluate national trends in the application of immediate TMR following UE amputations.

Methods:
An analysis of the Nationwide Inpatient Sample database was conducted from 2016 to 2019. International Classification of Diseases, 10th Revision, codes were used to identify encounters involving UE amputation with and without TMR. Nationwide Inpatient Sample weights were used to estimate national estimates of incidence. Patient-specific and hospital-specific factors were analyzed to assess associations with use of TMR.

Results:
A total of 8945 weighted encounters underwent UE amputation, and of those, only 310 (3.5%) received TMR. The majority of TMR occurred in urban hospitals (>95%). Younger patients (47 years versus 54 years; P = 0.008) and patients located in New England were significantly more likely to undergo TMR. There was no difference in total cost of hospitalization among patients who underwent TMR ($55,241.0 versus $59,027.8; P = 0.683) but significantly shorter lengths of hospital stay when undergoing TMR versus other management (10.6 days versus 14.8 days; P = 0.012).

Conclusions:
TMR has purported benefits of pain reduction, neuroma prevention, and increased prosthetic control. Access to this beneficial procedure following UE amputation varies by demographics and geographic region. Given that TMR has not been shown to increase cost while simultaneously decreasing patient length of stay, increased efforts to incorporate this procedure into training and practice will help to ensure equitable care for amputation patients.
Smoking Primes the Metabolomic Response in Trauma
Authors: Gallagher Lauren T. , Erickson Christopher , D’Alessandro Angelo , Schaid Terry , Thielen Otto , Hallas William , Mitra Sanchayita , Stafford Preston , Moore Ernest E. , Silliman Christopher C. , Calfee Carolyn S. , Cohen Mitchell J. 
Published: March 2024

ABSTRACT

Introduction
Smoking is a public health threat due to its well described link to increased oxidative stress-related diseases including peripheral vascular disease and coronary artery disease. Tobacco use has been linked to risk of inpatient trauma morbidity including acute respiratory distress syndrome, however its mechanistic effect on comprehensive metabolic heterogeneity has yet to be examined.

Methods
Plasma was obtained on arrival from injured patients at a Level 1 Trauma Center and analyzed with modern mass spectrometry-based metabolomics. Patients were stratified by non-smoker, passive smoker and active smoker by lower, inter-quartile and upper quartile ranges of cotinine intensity peaks. Patients were sub-stratified by High Injury/High Shock (Injury Severity Score ≥ 15, Base Excess<-6) and compared to healthy controls. P-value <0.05 following FDR correction of t-test was considered significant.

Results
48 patients with High Injury/High Shock (7 (15%) non-smokers, 25 (52%) passive smokers and 16 (33%) active smokers) and 95 healthy patients who served as controls (30 (32%) non-smokers, 43 (45%) passive smokers and 22 (23%) active smokers) were included. Elevated metabolites in our controls who were active smokers include enrichment in chronic inflammatory and oxidative processes. Elevated metabolites in active smokers in high injury/high shock include enrichment in the malate-aspartate shuttle, tyrosine metabolism, carnitine synthesis, and oxidation of very long-chain fatty acids.

Conclusions
Smoking promotes a state of oxidative stress leading to mitochondrial dysfunction which is additive to the inflammatory milieu of trauma. Smoking is associated with impaired mitochondrial substrate utilization of long-chain fatty acids, aspartate and tyrosine all of which accentuate oxidative stress following injury. This altered expression represents an ideal target for therapies to reduce oxidative damage toward the goal of personalized treatment of trauma patients.

Level of Evidence
Level III, Prognostic/Epidemiological
Impact of Preformed Donor-specific Antibodies in Comparison to ABO Incompatibility in Living Donor Liver Transplantation: A Propensity Score–Matched Analysis
Authors: Kim Jiyoung , Hong Suk Kyun , Kim Jae-Yoon , Lee Jaewon , Choi Hyun Hwa , Kim Minseob , Kim Youngjin , Hong Su young , Lee Jeong-Moo , Choi YoungRok , Yi Nam-Joon , Lee Kwang-Woong , Suh Kyung-Suk 
Published: March 2024

Background.
Immunological factors play a pivotal role in the outcomes of solid organ transplantation. We aimed to elucidate the effects of donor-specific antibodies (DSAs) and ABO compatibility on living donor liver transplantation (LDLT) outcomes.

Methods.
A retrospective analysis was conducted on 584 LDLT recipients from 2015 to 2020. The recipients were stratified into 3 groups: ABO-compatible recipients without DSAs (group 1), ABO-compatible recipients with DSAs (group 2), and ABO-incompatible recipients without DSAs (group 3). Propensity score matching was used for balanced comparisons.

Results.
In the matched comparisons, group 2 exhibited a higher incidence of T cell–mediated rejection compared with group 1 (22.7% versus 4.5%, P = 0.030). Despite this, the 5-y survival rates were similar between groups 1 and 2 (81.6% versus 95.5%, P = 0.085). Group 3, in comparison with group 1, showed elevated rates of cytomegalovirus infection (23.2% versus 7.3%, P = 0.008), T cell–mediated rejection (28.0% versus 7.3%, P = 0.001), and antibody-mediated rejection (13.4% versus 0%, P = 0.001). However, the survival rates were comparable between group 3 and group 1 (82.0% versus 86.5%, P = 0.220, respectively). Comparisons between group 2 and group 3 did not reveal significant differences in postoperative outcomes or survival rates (P > 0.05).

Conclusions.
DSA positivity and ABO incompatibility contribute to distinct posttransplant complications in LDLT. The integrated consideration of both factors in pretransplant assessment may enhance risk stratification and inform tailored interventions. Further research is required to corroborate these findings and provide mechanistic insights.
Optimizing ODE-derived Synthetic Data for Transfer Learning in Dynamical Biological Systems
Authors: Zabbarov Julian , Witzke Simon , Kleissl Maximilian , Iversen Pascal , Renard Bernhard Y. , Baum Katharina 
Published: March 2024

AbstractMotivationSuccessfully predicting the development of biological systems can lead to advances in various research fields, such as cellular biology and epidemiology. While machine learning has proven its capabilities in generalizing the underlying non-linear dynamics of such systems, unlocking its predictive power is often restrained by the limited availability of large, curated datasets. To supplement real-world data, informing machine learning by transfer learning with data simulated from ordinary differential equations has emerged as a promising solution. However, the success of this approach highly depends on the designed characteristics of the synthetic data.ResultsWe optimize dataset characteristics such as size, diversity, and noise of ordinary differential equation-based synthetic time series datasets in three relevant and representative biological systems. To achieve this, we here, for the first time, present a framework to systematically evaluate the influence of such design choices on transfer learning performance in one place. We achieve a performance improvement of up to 92% in mean absolute error for our optimized simulation-based transfer learning compared to non-informed deep learning. We find a strong interdependency between dataset size and diversity effects. The optimal transfer learning setting heavily relies on real-world data characteristics as well as its coherence with the synthetic data’s dynamics, emphasizing the relevance of such a framework.Availability and ImplementationThe code is available athttps://github.com/DILiS-lab/opt-synthdata-4tl.
Inflammation induced Th17 cells synergize with the inflammation-trained microbiota to mediate host-resiliency against intestinal injury
Authors: Golob JL , Hou G , Swanson BJ , Bishu S , Grasberger H , El Zataari M , Lee A , Kao J , Kamada N , Bishu S 
Published: March 2024

ABSTRACTBackground and AimsInflammation can generate pathogenic Th17 cells and cause a inflammatory dysbiosis. In the context of Inflammatory Bowel Disease (IBD) these inflammatory Th17 cells and dysbiotic microbiota may perpetuate injury to intestinal epithelial cells (IECs). However, many models of IBD like T-cell transfer colitis and IL-10-/-mice rely on the absence of regulatory pathways, so it is difficult to tell if inflammationcan also induce protective Th17 cells.MethodsWe subjected C57BL6, RAG1-/-or JH-/-mice to systemic or gastrointestinal (GI)Citrobacter rodentium(Cr). Mice were then subject to 2.5% dextran sodium sulfate to cause epithelial injury. Fecal microbiota transfer was performed by bedding transfer and co-housing. Flow cytometry, qPCR, 16s sequencing and histology were used to assess parameters.ResultsTransient inflammation with GI but not systemicCrwas protective from subsequent intestinal injury. This was replicated with sequential DSS collectively indicating that transient inflammation provides tissue-specific protection. Inflammatory Th17 cells that have a tissue resident memory signature expanded in the intestine. Experiments with reconstituted RAG1-/-, JH-/-mice and cell trafficking inhibitors showed that inflammation induced Th17 cells were required for protection. Fecal microbiota transfer showed that the inflammation-trained microbiota was necessary for protection, likely by maintaining protective Th17 cellsin situ.ConclusionInflammation can generate protective Th17 cells which synergize with the inflammation-trained microbiota to provide host resiliency against subsequent injury, indicating that inflammation induced Th17 tissue resident memory T cells are heterogenous and contain protective subsets.
PIM kinase control of CD8 T cell protein synthesis and cell trafficking
Authors: Marchingo Julia M , Spinelli Laura , Pathak Shalini , Cantrell Doreen A 
Published: March 2024

AbstractIntegration of a large network of kinase signalling pathways co-ordinates changes in the transcription, translation and metabolic events required for T cell activation and differentiation. The present study explores the role of the Serine/Threonine kinases PIM1 and PIM2 in controlling murine CD8 T lymphocyte antigen receptor-mediated activation and differentiation in response to the cytokines Interleukin 2 (IL-2) or IL-15. We show that PIM kinases are dispensable for the differentiation programs controlled by the antigen-receptor and IL-15. There is however a selective role for the PIM kinases in the context of IL-2 regulation of CD8 T cell fate. One key insight was that the PIM kinases controlled the migratory capabilities of effector CD8 T cells, withPim1/Pim2-deficient CD8 T cells unable to fully switch off the naïve T cell chemokine and adhesion receptor program during effector differentiation. PIM kinases were also needed for IL-2 to sustain high expression of the glucose transporters SLC2A1 and SLC2A3 and to maintain activity of the nutrient sensing kinase mTORc1. Strikingly, PIM kinases did not have a dominant impact on IL-2-driven transcriptional programs but rather selectively modulated protein synthesis to shape cytotoxic T cell proteomes. This study reveals a selective role of PIM kinases in IL-2 control of CD8 T cells and highlights how regulated changes in protein synthesis can impact T cell phenotypes.
Does Haldane’s rule speciation within mimetic Poison frogs?
Authors: Lorioux-Chevalier Ugo , Chouteau Mathieu , Roland Alexandre-Benoit 
Published: March 2024

AbstractTo explain how populations with distinct warning signals coexist in close parapatry, we experimentally assessed intrinsic mechanisms acting as reproductive barriers within threeRanitomeyapoison-frog species. For all species, assortative mating did not occur, nor did a survival disadvantage for inter-population hybrids. However, inRanitomeya fantastica, these hybrids of the male sex are sterile, an outcome predicted by Haldane’s rule. Our results suggest a possible XY sex determinism inR. fantastica, and show that this process is associated with an extraordinary diversity, leading to speciation.Graphical Abstract
Bridging polarities in metabolomics: Cross-ionization mode chemical similarity prediction between tandem mass spectra
Authors: de Jonge Niek F. , Chekmeneva Elena , Schmid Robin , Joas David , Truong Lem-Joe , van der Hooft Justin J.J. , Huber Florian 
Published: March 2024

AbstractMass spectrometry is a cornerstone of untargeted metabolomics, enabling the characterization of metabolites in both positive and negative ionization modes. However, comparisons across ionization modes have remained a substantial challenge due to the distinct fragmentation patterns produced by each polarity. To overcome this barrier, we present MS2DeepScore 2.0, a machine learning-based model to predict chemical similarity between mass fragmentation spectra, which works both between different and the same ionization modes. We demonstrate the utility of MS2DeepScore 2.0 in a human urine case study, where MS2DeepScore enabled cross-ionization mode molecular networking, enhancing data exploration and metabolite annotation. To ensure robustness, we have implemented a quality estimation method that flags spectra with low information content or those dissimilar to the training data, thereby minimizing false predictions. Altogether, MS2DeepScore 2.0 extends our current capabilities in organizing, exploring, and annotating untargeted metabolomics profiles.
Development of sound production inDanionella cerebrum
Authors: Groneberg Antonia H. , Dressler Lena E. , Kadobianskyi Mykola , Müller Julie , Judkewitz Benjamin 
Published: March 2024

AbstractAcoustic signaling, integral to intraspecific communication and reproductive behavior, undergoes notable changes during an animal’s ontogenetic development. The onset and progression of this maturation in fish remains poorly understood. Here, we investigate the ontogeny of acoustic communication in the micro glassfishDanionella cerebrum(DC), one of the smallest known vertebrates and an emerging model organism in neuroscience. Adult DC males produce audible clicks that appear in sequences with a repetition rate of 60 or 120 Hz, caused by consecutive unilateral or alternating bilateral compressions, respectively. To investigate the maturation of this ability, we performed long-term sound recordings and morphological studies of the DC sound production apparatus throughout its ontogenetic development. We found that DC start producing clicks during the second month of their lives and continually increase their abundance and structured repetition over the course of the following one to two months. The sound production machinery, including specialized bone and cartilage structures, start to form in male DC after approximately four weeks and prior to full maturation of the reproductive organs. While the DC clicks increase in amplitude with age and body size, click repetition rates of 60 and 120 Hz are stable throughout development. This suggests a fully developed central pattern generator in juvenile males, yet a continued maturation of the drumming apparatus capable of creating louder sounds.
Estimation of Jacquard’s genetic identity coefficients with bi-allelic variants by constrained least-squares
Authors: Graffelman Jan , Weir Bruce S. , Goudet Jérôme 
Published: March 2024

AbstractThe Jacquard genetic identity coefficients are of fundamental importance in relatedness research. We address the estimation of these coefficients as well as other relatedness parameters that derive from them such as kinship and inbreeding coefficients using a concise matrix framework. Estimation of the Jacquard coefficients via likelihood methods and the expectation–maximization algorithm is computationally very demanding for large numbers of polymorphisms. We propose a constrained least squares approach to estimate the Jacquard coefficients. A simulation study shows constrained least squares achieves root-mean-squared errors that are comparable with those of the maximum likelihood approach, in particular when founder allele frequencies are unknown, while obtaining enormous computational savings.
Retinotopic biases in contextual feedback signals to V1 for object and scene processing
Authors: Bennett Matthew A. , Petro Lucy S. , Abbatecola Clement , Muckli Lars 
Published: March 2024

AbstractIdentifying the objects embedded in natural scenes relies on recurrent processing between lower and higher visual areas. How is cortical feedback information related to objects and scenes organised in lower visual areas? The spatial organisation of cortical feedback converging in early visual cortex during object and scene processing could be retinotopically specific as it is coded in V1, or object centred as coded in higher areas, or both. Here, we characterise object and scene-related feedback information to V1. Participants identified foreground objects or background scenes in images with occluded central and peripheral subsections, allowing us to isolate feedback activity to foveal and peripheral regions of V1. Using fMRI and multivoxel pattern classification, we found that feedback of object information is projected to foveal V1 cortex with increased detail during an object identification task. Background scene information is projected to both foveal and peripheral V1 but can be disrupted by a sufficiently demanding object discrimination task. We suggest that the feedback connections during scene perception project back to earlier visual areas an automatic sketch of occluded information to the predicted retinotopic location. In the case of a cognitive task however, feedback pathways project content to foveal retinotopic space, potentially for introspection, functioning as a cognitive active blackboard and not necessarily predicting the object’s location. This feedback architecture could reflect the internal mapping in V1 of the brain’s endogenous models of the visual environment that are used to predict perceptual inputs.