bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Sequencing-by-Synthesis and Avidity Base Chemistry Next-Generation Sequencing Platforms in Identifying Somatic Variants of Hematological Malignancies
Authors: Lim Min Hui , Kim Juwuk , Tu Zheng Jin , Cheng Yu-Wei 
Published: February 2025

Abstract

Background
This study evaluates the performance of the Illumina NextSeq™ 550 and the Element Biosciences AVITI™ next-generation sequencing (NGS) system, in detecting single nucleotide variants (SNVs) and gene fusions.

Methods
A set of 66 NGS libraries, consisting of 33 DNA, 24 cDNA, and triplicates of 3 control libraries, were prepared from bone marrow samples targeting 63 genes and related fusions, and initially sequenced using the NextSeq 550 in the Cleveland Clinic's molecular diagnostic laboratory. The same libraries were subsequently sequenced on the AVITI. The resulting data were analyzed using a combination of Cleveland Clinic developed pipelines and ArcherDx virtual machine software.

Results
The study found that all 105 SNVs and 39 gene fusions identified by the NextSeq 550 were also detected in the AVITI, demonstrating a high degree of concordance between the platforms. The analyses revealed R2 values of 0.86 for read depth and 0.96 for VAF of the 105 DNA variants, and 0.95 for read depth and 0.97 for fusion percentage of the 39 fusion variants. In the reproducibility studies, the VAF and fusion percentage of all variants were within 2 standard deviations of the mean when the same positive controls were sequenced 3 times on the AVITI.

Conclusions
These results indicate that the NextSeq 550 and the AVITI provide comparable performance in terms of accuracy and sensitivity for variant detection. Notably, the AVITI chemistry requires substantially lower PhiX input than the NextSeq 550 needs for this application. This results in substantial cost and efficiency benefits.
Efficacy of supplemental amino acids with Corynebacterium glutamicum cell mass on growth and health of nursery pigs
Authors: Cheng Yi-Chi , Duarte Marcos Elias , Kim Sung Woo 
Published: February 2025

Abstract
Removing filtration and crystallization provides amino acids with reduced purity because Corynebacterium glutamicum cell mass (CGCM) is not removed. This study aimed to evaluate nutritional and functional values of granulated Threonine (Thr) and Valine (Val) with CGCM in diets for growth performance, jejunal mucosa-associated microbiota, nutrient digestibility, and health of nursery pigs. Seventy-two newly weaned pigs (28 d-of-age; initial body weight (BW) of 8.2 ± 0.4 kg) were allotted to 9 treatments (n = 8) based on a randomized complete block design with sex and initial BW as blocks. Treatments consisted of a basal diet with different levels of standardized ileal digestible (SID) Thr and Val: NC (SID Thr and SID Val at 70% of NRC requirement), CT (95% SID Thr using crystalline Thr); CV (95% SID Val using crystalline Val); PT (95% SID Thr using ThrPro); PV (95% SID Val using ValPro); HCT (5 × crystalline Thr used in CT); HCV (5 × crystalline Val used in CV); HPT (5 × ThrPro used in PT); HPV (5 × ValPro used in PV). Diets were fed to nursery pigs for 25 d in 2 phases (10 d and 15 d, respectively). Feed intake and BW were recorded at the end of each phase. Blood samples were collected to measure serum proteins, metabolites, and electrolytes on d 21. Pigs were euthanized at d 25 to collect liver and jejunal tissues for morphological evaluation and jejunal mucosa to measure intestinal health biomarkers. Data were analyzed by SAS using MIXED procedure. Pigs with 95% SID Thr or 95% SID Val tended to have greater average daily gain (P = 0.078) and gross energy digestibility (P = 0.058), had greater (P &lt; 0.05) jejunal villus height, and had lower (P &lt; 0.05) plasma urea nitrogen and liver fibrosis than pigs with 70% SID Thr or 70% SID Val, respectively. Pigs fed a diet with HAAPro had increased (P &lt; 0.05) alpha diversity of jejunal mucosa-associated microbiota than pigs fed a diet with AAPro. Pigs fed a diet with HAAPro had increased (P &lt; 0.05) relative abundance of Bifidobacterium and decreased (P &lt; 0.05) relative abundance of Comamonas than pigs fed a diet with AAPro. In conclusion, increasing the supplementation of AAPro by five folds than typical level did not negatively affect growth performance whereas beneficially modulated the jejunal mucosa-associated microbiota. Results suggest that AAPro can effectively replace the use of crystalline amino acids in pig diets whilst potentially reducing feed costs due to reduced cost of producing such amino acids.
Multi-messenger emission from magnetic reconnection in blazar jets: the case of TXS 0506+056
Authors: de Gouveia Dal Pino E M , Rodríguez-Ramírez J C , del Valle M V 
Published: February 2025

Abstract
Measurements from astroparticle experiments, such as the 2017 flare associated with the source TXS 0506+056, indicate that blazars act as multi-messenger (MM; radiation and neutrinos) factories. Theoretically, the particle acceleration mechanisms responsible for blazar emissions and the precise location within the jet where this occurs remain undetermined. This paper explores MM emission driven by magnetic reconnection in a blazar jet. Previous studies have shown that reconnection in the magnetically dominated regions of these relativistic jets can efficiently accelerate particles to very high energies (VHE). Assuming that turbulent-driven magnetic reconnection accelerates cosmic-ray protons and electrons by a Fermi process, we developed a lepto-hadronic radiation model without the influence of external soft-photons to explain the 2017 MM flare from TXS 0506+056. In the proposed scenario, the emission blob moves downstream in the jet from ∼2 to 4 pc from the central engine, which is a supermassive black hole (SMBH) of 3 × 108 M⊙ launching a jet with 150LEdd power. As the blob moves, we observe a sequence of spectral energy distribution (SED) profiles that match the observed arrival of the high energy neutrino and electromagnetic emission from TXS 0506+056. This arrival coincides with the high state of intermediate energy γ-rays (E ∼ 1 GeV) detection, followed by the subsequent appearance of the VHE γ-ray signal and then no further significant neutrino detection. We obtain a time delay between the neutrino and VHE events ≃ 6.4 days, which is consistent with that observed in the 2017 MM flare.
The XXL Survey LIV. X-ray luminosity function and Luminosity-Mass Relation of optically selected galaxy groups
Authors: Wood C , Maughan B J , Crossett J P , Eckert D , Pierre M , Ramos-Ceja M E , Robotham A S G , Adami C , Faccioli L , Koulouridis E , McGee S L , Pacaud F , Phillipps S 
Published: February 2025

Abstract
The overlap between the GAMA spectroscopic survey and the XXL X-ray survey was used to study the X-ray properties of optically-selected groups of galaxies. Forced X-ray aperture photometry was applied to an optically-selected sample of 235 groups (containing at least five member galaxies) to measure their X-ray luminosities in the regime of low signal to noise X-ray data. The sample encompasses X-ray luminosities over an order of magnitude fainter than typical X-ray selected samples, and avoids X-ray selection biases. This gives access to low mass groups where the effects of non-gravitational processes, such as AGN-feedback, should be most apparent and could inhibit their detection in an X-ray survey. We measured the X-ray luminosity function (XLF) of the sample, and found it to be consistent with the extrapolation of the XLF from X-ray selected samples at higher luminosities. The XLF was combined with a theoretical halo mass function to infer the form of the scaling relation between X-ray luminosity and mass (LM relation) for the GAMA groups. We found a slope of 1.87 ± 0.12, which is steeper than self similarity in this mass regime. When comparing with other measurements of the LM relation, we find evidence for a steepening of the slope in the low mass regime, likely due to the impact of non-gravitational processes. Our approach can be translated to eROSITA data using multi-wavelength surveys to constrain the X-ray properties of galaxy groups in the limits of high redshift and low mass.
Individualized and targeted coagulation management in bleeding trauma patients
Authors: Hofmann Nikolaus , Schöchl Herbert , Gratz Johannes 
Published: February 2025

Purpose of review
This review aims to summarize current evidence on hemostatic management of bleeding trauma patients, with a focus on resuscitation strategies using either coagulation factor concentrates or fixed-ratio transfusion concepts. It discusses the potential benefits and limitations of both approaches.

Recent findings
Recent studies have shown that coagulopathy caused by massive traumatic hemorrhage often cannot be reversed by empiric treatment. During initial resuscitation, a fixed-ratio transfusion approach uses the allogeneic blood products red blood cells, plasma, and platelets to mimic ‘reconstituted whole blood’. However, this one-size-fits-all strategy risks both overtransfusion and undertransfusion in trauma patients.
Many European trauma centers have shifted toward individualized hemostatic therapy based on point-of-care diagnostics, particularly using viscoelastic tests. These tests provide rapid insight into the patient’s hemostatic deficiencies, enabling a more targeted and personalized treatment approach.

Summary
Individualized, goal-directed hemostatic management offers several advantages over fixed-ratio transfusion therapy for trauma patients. However, there is a paucity of data regarding the direct comparison of these two approaches.
Host Response Stratification in Malarial and Non-malarial Sepsis: A Prospective, Multicenter Analysis From Uganda
Authors: Cummings Matthew J. , Lutwama Julius J. , Owor Nicholas , Tomoiaga Alin S. , Ross Jesse E. , Muwanga Moses , Nsereko Christopher , Nayiga Irene , Kyebambe Stephen , Shinyale Joseph , Ochar Thomas , Nie Kai , Xie Hui , Miake-Lye Sam , Villagomez Bryan , Qi Jingjing , Reynolds Steven J. , Nakibuuka Martina Cathy , Lu Xuan , Kayiwa John , Haumba Mercy , Nakaseegu Joweria , Che Xiaoyu , Byakika-Kibwika Pauline , Wayengera Misaki , Achan Jane , Kim-Schulze Seunghee , Lipkin W. Ian , O’Donnell Max R. , Bakamutumaho Barnabas 
Published: February 2025

Objectives:
Globally, the burden of sepsis is highest in malaria endemic areas of sub-Saharan Africa. The influence of malaria on biological heterogeneity inherent to sepsis in this setting is poorly understood. We sought to determine shared and distinct features of the host response in malarial and non-malarial sepsis in sub-Saharan Africa.

Design and Setting:
Analysis of Olink proteomic data from prospective observational cohort studies of sepsis conducted at public hospitals in Uganda (discovery cohort [Entebbe, urban], n = 238; validation cohort [Tororo, rural], n = 253).

Patients:
Adults (age ≥ 18 yr) hospitalized with sepsis.

Interventions:
None.

Measurements and Main Results:
The frequency of malaria-associated (malarial) sepsis was 20% in the discovery cohort and 28% in the validation cohort. In both cohorts, a shared host response was predominant, with less than or equal to 8% of proteins differentially expressed (Benjamini-Hochberg-adjusted p ≤ 0.05) between malarial and non-malarial sepsis, after adjustment for demographic variables and HIV and tuberculosis coinfection. In both cohorts, malarial sepsis was associated with increased expression of immunosuppressive proteins (interleukin-10, leukocyte immunoglobulin-like receptor B1, killer cell immunoglobulin-like receptor 3DL1), including those associated with Tcell exhaustion and apoptosis (lymphocyte activation gene 3, T cell immunoglobulin and mucin domain containing 4). A classifier model including these immunosuppressive proteins showed reasonable discrimination (area under the receiver operating characteristic curves, 0.73 [95% CI, 0.65–0.81] and 0.72 [0.65–0.79]) and calibration (Brier scores 0.14 and 0.18) for stratification of malarial sepsis in the discovery and validation cohorts, respectively.

Conclusions:
Host responses are largely conserved in malarial and non-malarial sepsis but may be distinguished by a signature of relative immunosuppression in the former. Further investigations are needed to differentiate mechanisms of malarial and non-malarial sepsis, with the goal of informing pathogen-stratified and pathogen-agnostic treatment strategies.
Incidence and management of accidental dural puncture and postdural puncture headache in parturients
Authors: Cohen Stav , Greenberger Chaim , Aptekman Boris , Rabkin Victor , Weiniger Carolyn F. 
Published: February 2025

BACKGROUND
Postdural puncture headache (PDPH) is a common complication of neuraxial block resulting from either intentional dural puncture (IDP) or accidental dural puncture (ADP).

OBJECTIVES
The primary objective was to estimate the rate of PDPH and ADP following introduction of a real-time documentation system in April 2018. Secondary objectives included examining the use of epidural blood patch (EBP) and investigating risk factors associated with ADP and PDPH.

DESIGN
Retrospective cohort study.

SETTING
Secondary care at a tertiary hospital from January 2017 to April 2022.

PATIENTS
Three hundred and eleven adult parturients after neuraxial block, with PDPH or a reported ADP, were identified during the procedure or postpartum.

INTERVENTIONS
Implementation of a real-time documentation system in April 2018 to improve PDPH and ADP documentation.

MAIN OUTCOME MEASURES
Rates of PDPH and ADP, performance of epidural blood patch, and risk factors associated with PDPH and ADP.

RESULTS
The overall rate of PDPH was 0.4% (164/39888), 95% confidence intervals (CI) 0.0036 to 0.0049, and the rate of ADP was 0.9% (284/31635), 95% CI 0.0078 to 0.0099. During the real-time documentation period, the rates were 0.44% (157/35376), 95% CI 0.0038 to 0.0052, and 0.99% (279/28121), 95% CI 0.0088 to 0.0111, for PDPH and ADP respectively. Thirty-two (10.3%) cases had IDP, and 279 (89.7%) had ADP. Among 279 ADP cases, 76.3% were identified during the procedure, 10.4% suspected and 13.3% identified postpartum. Cases of ADP identified postpartum had more emergency room visits (19%). Epidural blood patch (EBP) was administered in 72% of PDPH cases, with a high first-time success rate (89.5%); 11 women received epidural blood patch after IDP.

CONCLUSIONS
Postdural puncture headache remains a significant concern. In our cohort, 13.3% of ADP cases were detected postpartum, posing an increased challenge and underscoring the critical importance of follow-up care. We confirm that epidural blood patch may be required following any neuraxial block.

TRIAL REGISTRATION
Not applicable.
Chondrocutaneous Advancement Flap and Postauricular Skin Flap: An Effective Combination for Large Helical Rim Defect Reconstruction
Authors: De Rosa Anna , Grieco Michele P. , D’Antonio Santolo , Rullo Vincenzo , Castellaneta Francesco , Fabrizio Tommaso 
Published: February 2025

Background:
Defects of the ear helix are a frequent challenge in plastic surgery, with more than 5% of all skin cancers occurring in this region. The Antia-Buch flap is a single-stage reconstruction technique utilizing chondrocutaneous flaps for helix repair. However, for defects exceeding 2 cm, it can lead to auricular distortion. To address this limitation, we propose a modified Antia-Buch technique combining chondrocutaneous advancement with a postauricular skin flap to optimize outcomes.

Methods:
A retrospective review was conducted of 15 patients who underwent our modified Antia-Buch flap procedure between 2019 and 2022. This approach incorporated chondrocutaneous advancement for primary defect closure and a postauricular skin flap for improved contouring. Functional and aesthetic outcomes were assessed using a questionnaire developed in collaboration with a clinical psychologist. The questionnaire evaluated surgical satisfaction, cosmetic results, self-image, and social integration postreconstruction.

Results:
No complications, including ischemic necrosis or the need for surgical revision, were observed in any case. The technique demonstrated excellent vascularity, with no occurrences of flap failure. Patient-reported outcomes revealed high satisfaction rates, with no evidence of self-image distortion or social barriers. Aesthetic results were rated as superior, with minimal risk of auricular distortion even for larger defects.

Conclusions:
The modified Antia-Buch technique is a reliable and effective method for helical rim reconstruction, particularly for defects larger than 2 cm. It offers technical simplicity, low complication rates, patient convenience, and excellent cosmetic outcomes, making it a preferred option for many auricular defect reconstructions.
The Use of BODY-Q to Assess Factors Impacting Satisfaction and Quality-of-life Postabdominoplasty in Kenya
Authors: Nyakiongora Sarah , Laspro Matteo , Dele-Oni Oluchukwu , Abdullahi Adan A. , Nangole Ferdinand W. , Pusic Andrea L. 
Published: February 2025

Background:
Massive weight loss can often lead to skin redundancy and affect a patient’s quality of life. Abdominoplasty has grown in popularity due to its cosmetic and functional effects. There is currently a paucity in the patient-reported outcome measures literature in low-resource areas. As such, this study aimed to apply the BODY-Q measure to evaluate factors impacting abdominoplasty outcomes in Kenya.

Methods:
Patients undergoing abdominoplasty were asked to complete BODY-Q scales before and after surgery. Patient demographics, medical history, and postoperative care were retrospectively collected from patient records. Inference statistics were used to assess predictors of improvement in postsurgical BODY-Q scores and seroma formation. Student t tests were used to compare means; chi-square tests were used to assess differences between proportions, and R
2 was used to determine the proportion of variance.

Results:
Thirty-nine patients underwent abdominoplasty, of whom 38 answered both surveys. Mean age and body mass index (BMI) were 38.30 (±6.35) years and 30.80 (±6.35) kg/m2, respectively. The difference in pre- and postoperative BODY-Q scores was −73.5, with an effect size of −6.67 and a minimal clinically important difference of −2.00. Positive predictors of BODY-Q score improvement were concurrent liposuction (P = 0.004), preoperative BMI (P = 0.001), and patient-rated scar quality (P = 0.003). Other factors were not significantly predictive.

Conclusions:
Kenyan patients seem to be highly satisfied with abdominoplasty procedures, which result in significant improvements in quality of life. Factors significantly associated with higher satisfaction include concurrent liposuction, higher preoperative BMI, and postoperative scar quality.
Multimodal analgesia with thoracic paravertebral block decrease pain and side effects in mastectomy patients.
Authors: Liu Pei-Chin , Su Fu-Wei , Tsai Yi-Fang , Lin Yen-Shu , Sung Chun-Sung , Tseng Ling-Ming , Teng Wei-Nung 
Published: February 2025

Background:
Enhanced recovery after surgery (ERAS) protocols incorporating multimodal analgesia (MMA) have become increasingly popular for breast cancer surgery. Our study evaluated an ERAS approach that combined nonintubated general anesthesia with thoracic paravertebral block (TPVB) as part of the MMA and compared it to traditional general anesthesia (GA). Postoperative outcomes were assessed using numerical rating scale (NRS) pain scores, total analgesic consumption, and nausea and vomiting (PONV).

Methods:
We reviewed the medical records of 60 female patients aged 30–85 years who underwent unilateral mastectomy with or without sentinel lymph node biopsy (SLNB). Thirty patients received nonintubated general anesthesia with a regional block (MMA group), whereas the remaining 30 patients received conventional GA and were matched based on their anesthesia records. Postoperative analgesics, including pethidine and tramadol, were converted into intravenous morphine equivalents. We compared the groups using paired t tests for age, height, weight, operation duration, NRS scores, total analgesic dosage, and the Fisher exact test for PONV rates.

Results:
The MMA group showed significantly lower NRS scores (p < 0.001) and total analgesic consumption (p < 0.001) than the GA group. Although PONV rates were lower in the MMA group (0% vs 13%, p = 0.112), this difference was not statistically significant, likely due to the effective PONV management in the GA group with dexamethasone or 5HT-3 antagonists. There was no significant difference in pain scores (p = 0.722) or the need for additional analgesics (p = 0.419) between double- and triple-level TPVB.

Conclusion:
Nonintubated general anesthesia with TIVA and MMA using TPVB is a viable and safe alternative for breast cancer surgery. It results in reduced pain scores and analgesic needs compared with conventional GA, with PONV outcomes comparable to those managed with standard intravenous medications.
Establishing a threshold for maximum standardized uptake value on 18F-fluorodeoxyglucose PET/CT to predict high-grade lung adenocarcinoma and its prognostic significance
Authors: Huang Miao , Wang Yaqi , Yang Xin , Li Nan , Liu Bing , Li Xiang , Zhang Shanyuan , Lu Fangliang , Li Shaolei , Yan Shi , Lin Dongmei , Wu Nan 
Published: February 2025

Objective:
The objective of this study is to determine an optimal threshold for the maximum standardized uptake value (SUVmax) of 18F-fluorodeoxyglucose PET/CT to predict the newly proposed high-grade tumor classification and assess its prognostic significance in invasive lung adenocarcinoma (LUAD).

Methods:
Surgical specimens from 185 patients with pathological stage I invasive LUAD in the training group, along with 90 patients in the validation group, were analyzed using the novel IASLC grading system. The receiver operating characteristic curve was used to determine the optimal SUVmax threshold and assess its predictive accuracy. Disease-free survival (DFS) and overall survival (OS) were analyzed using Kaplan–Meier survival curves and Cox regression analysis.

Results:
Linear correlation analysis demonstrated a significant positive association between SUVmax and the proportion of high-grade histological patterns (R² = 0.346, P < 0.001). The optimal SUVmax cutoff for predicting grade 3 tumors was 3.8, with an area under the curve of 0.866 in the training dataset and 0.899 in the validation dataset. Multivariate logistic regression analysis identified an SUVmax >3.8 as an independent predictor of grade 3 tumors (P < 0.001). In Cox regression analysis, SUVmax >3.8 was independently associated with reduced DFS (HR = 4.009, 95% CI: 1.568–10.250, P = 0.004) and OS (HR = 5.536, 95% CI: 1.175–26.075, P = 0.030).

Conclusion:
As a noninvasive preoperative parameter, SUVmax >3.8 is a significant indicator of high-grade tumors as classified by the IASLC grading system and is strongly associated with worse DFS and OS.