bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dog sniffing biomechanic responses in an odor detection test of odorants with differing physical properties
Authors: Burnett Lydia R , Hebdon Nick R , Stevens Pete A , Moljo Monica D , Waldrop Lindsay D , DeGreeff Lauryn E 
Published: November 2024

Abstract
Dogs are utilized in forensic science for their extensive scent-detection capabilities. They are often considered the “gold standard” in-field detection for targets such as illicit drugs and explosives. Despite their prevalence in the field, relatively little is known about how dogs interact with and transport volatile organic compounds through their olfactory system. In this study, 2 groups of dogs were utilized—Sport detection dogs (n = 19) that participate in the National Association of Canine Scent Work and have achieved advanced standing through training and successful search competitions and law enforcement explosive detection dogs (n = 8) which were included for comparison. Both groups were presented with 2 target odorants having differing molecular properties, 2-ethyl-1-hexanol and ammonia, 2 non-target odorants, 1-bromooctane and methyl benzoate, and a negative control. Canines were tested prior to experience with the target odorants, when all odorants were novel, after some brief training with the target odorants, and after a longer training time with the target odorants. The non-target odorants were never used in training. Sniffing was measured using flow sensors embedded in a wall immediately in front of the odorants held in a closed cylinder. Sensor data were used to calculate sniff flow rate, frequency (sniffs per seconds), and volume. Results indicated no difference in sniffing dynamics between target odorants; however, sniffing frequency increased significantly with increased experience with the target odorants (Wilcoxon rank sum exact test, W = 148, P = 6 × 10−5). Sniff volume and flow rate showed a positive correlation to body mass for all sport detection dogs (slope = 2.71, F(1,17) = 9.48, P = 0.007, R2 = 0.32), though the R2 was low, indicating other factors at play. Law enforcement detection dogs were shown to take in significantly higher mean total sniff volumes (Wilcoxon rank sum exact test: W = 0. 7, P = 10−4) and volume flow rates (Wilcoxon rank sum exact test: W = 5, P = 6 × 10−5) compared to the sport detection dogs, but the sniff frequency remained similar for both groups.
Performance of Abbreviated Breast MRI in High-Risk Patients in a Tertiary Care Academic Medical Center
Authors: Zaza Tamara , Chandora Kapil , Yalniz Ceren , Zamora Kathryn Watts , Zalasin Stefanie , Li Yufeng , Woodard Stefanie 
Published: November 2024

Abstract

Introduction
The development of abbreviated breast MRI (AB-MRI) protocols reduce scan times. This paper reports the performance of AB-MRI at a tertiary care public academic medical center in comparison with established literature.

Methods
This HIPAA-compliant IRB-approved retrospective study reviewed 413 AB-MRI screenings in high-risk patients from June 2020 to March 2023. Data were collected from 3 databases (MagView, Cerner PowerChart, and Prism Primordial). Demographics and overall BI-RADS assessment were recorded. For all positive (BI-RADS 0, 3, 4, 5) examinations, manual review of each case was performed. Performance metrics (sensitivity, specificity, cancer detection rate [CDR], recall rate, positive predictive value [PPV] 3 and negative predictive value [NPV]) were calculated. PubMed and Google Scholar were used to review similar AB-MRI studies to compare performance metrics.

Results
There were 413 AB-MRI examinations from 413 unique patients. The majority of cases were audit-negative BI-RADS 1 or 2 (83.8%, 346/413). There were 67 (16.2%, 67/413) audit-positive cases with 3.6% (15/413) BI-RADS 3, 10.9% (45/413) BI-RADS 4, 0.7% (3/413) BI-RADS 5, and 1.0% (4/413) BI-RADS 0. Performance metrics showed a sensitivity of 100.0% (95% CI, 63.1%-100.0%) and a specificity of 85.7% (95% CI, 81.9%-88.9%). The PPV3 was 14.3% (95% CI, 5.1%-23.5%), and the NPV was 100.0% (95% CI, 99.0%-100.0%). The CDR was 19.4 per 1000 screenings. The results are comparable to prior literature and benchmark data.

Conclusion
This study demonstrates high sensitivity (100.0%) and NPV (100.0%) of AB-MRI with comparable specificity (85.7%) and CDR (19.4/1000) to the literature, adding support to the use of AB-MRI. Further research is needed to optimize AB-MRI protocols.
The macrostructure of narratives produced by children acquiring Finnish Sign Language
Authors: Pietarinen Heta , Kanto Laura 
Published: November 2024

Abstract
This article investigates the narrative skills of children acquiring Finnish Sign Language (FinSL). Producing a narrative requires vocabulary, the ability to form sentences, and cognitive skills to construct actions in a logical order for the recipient to understand the story. Research has shown that narrative skills are an excellent way of observing a child’s language skills, for they reflect both grammatical language skills and the ability to use the language in situationally appropriate ways. This study was conducted using the FinSL Narrative Skills Production Test assessment to observe how narrative skills develop in children between the ages of 4 and 11 who acquire FinSL in their natural language environments. The results show that the narrative skills of children acquiring FinSL develop following the same guidelines found in other signed and spoken languages. Narrative structure and content increase with age.
“Being alone for a whole year [is hard]” Families reflect on the emotional toll of stem cell transplantation for sickle cell disease
Authors: Steinberg Dara M , Mulinda Carly , Castaño Katerina , DiCola Katie , Tanenbaum Molly L , Onderwyzer Gold Abigail , Beauchemin Melissa P , Bhatia Monica 
Published: November 2024

Abstract

Objective
Sickle cell disease (SCD) is associated with significant morbidity and mortality. Hematopoietic stem cell transplantation (HCT) can improve health-related quality of life (HRQOL) but may be physically and emotionally challenging. Thus, the aim of this study was to understand the experience of HCT from the perspective of youth and young adults (YYAs) post-HCT for SCD and their parents.

Methods
YYAs were recruited from an urban hospital. Sociodemographic and HCT-specific information was analyzed for all enrolled. YYAs and/or their primary caregivers during HCT, participated in semi-structured interviews (e.g., pre-HCT knowledge, challenges, advice for families/health care providers). Interviews were audio-recorded, transcribed, and analyzed using content analysis.

Results
There were 19 YYAs enrolled (63.2% male; 68.4% Black or African American; 47.4% Hispanic or Latino; M days post-HCT = 1946.53 ± 1329.13; M age at HCT = 10.95 ± 6.10 years old; M current age 15.74 ± 5.78 years old). Interviews were done with six YYAs alone, five YYA-caregiver dyads, and eight caregivers alone. The caregivers were all mothers. Participants reported underestimating the emotional impact HCT would have on themselves and their family members. They experienced challenges related to isolation, academics, finances, and post-HCT medical needs. In contrast, they felt well prepared for physiological aspects of HCT. They sought HCT to improve YYAs’ HRQOL and encouraged others to consider it, but to be cognizant of the potential psychosocial impact.

Conclusions
This study highlights the importance of preparing families for the psychosocial effects of HCT. Incorporating psychosocial assessment, education, and intervention throughout HCT has the potential to promote HRQOL for YYAs and their families.
Penile length after penile implant surgery is determined by stretched penile length before surgery
Authors: van Renterghem Koenraad , De Bruyn Helene , Jorissen Cedric , Van Huele Andries , D’Anna Maurizio , Torremadé Josep , Martinez-Salamanca Juan I , Prieto Matienzo Laura , Moncada Ignacio 
Published: November 2024

Abstract

Background
While various treatment modalities exist, penile prosthesis (PP) implantation offers a permanent solution for patients that do not respond to or are not suitable for other treatment options for erectile dysfunction.

Aim
The aim of this study was to establish stretched penile length before surgery as a reliable determining factor of penile length after penile implant surgery.

Methods
For this study, data on penile length before and after PP surgery from three European centers was analyzed. Penile length measurements were conducted preoperatively and postoperatively in different conditions using standardized techniques. Only virgin cases were included and a complete case analysis was performed.

Outcome
The outcome of this study was the comparison of stretched penile length before and the inflated penile length after PP surgery.

Results
Data on penile length before and after PP of 361 patients was analyzed. Preoperative stretched penile length was equal to postoperative inflated penile length in 33% of patients. The absolute mean difference between pre-surgery stretched and postoperative inflated lengths was 1.1 cm. No correlation was found between implanted cylinder length and postoperative penile length. Additionally, the choice of implant type did not significantly affect postoperative penile length outcomes.

Clinical implications
Our findings confirm the reliability of preoperative stretched penile length as a tool for proper patient counseling before PP surgery.

Strengths & Limitations
Although our study is overpowered, our results show that preoperative stretched penile length serves as a reliable predictor of postoperative penile length outcomes after PP surgery. By providing clinicians with a tool for patient counseling, our findings contribute to enhancing satisfaction and quality of life outcomes in patients undergoing PP implantation.

Conclusion
Preoperative stretched penile length serves as a reliable predictor of postoperative penile length outcomes after PP surgery.
Streaming Large-Scale Microscopy Data to a Supercomputing Facility
Authors: Welborn Samuel S , Harris Chris , Ribet Stephanie M , Varnavides Georgios , Ophus Colin , Enders Bjoern , Ercius Peter 
Published: November 2024

Abstract
Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s−1 (87,000 frames s−1), producing a 700 GB dataset in 15 s. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera’s data acquisition system to supercomputing nodes at the National Energy Research Scientific Computing Center, bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a postmortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.
Prior Musculoskeletal Injury and Components of Physical Fitness in Military Personnel: A Systematic Review with Meta-analysis
Authors: Garcia Rafael Chieza Fortes , Muniz Adriane Mara de Souza , Jacinto Douglas de Castro , Bunn Priscila Dos Santos 
Published: November 2024

ABSTRACT

Introduction
Military personnel confront heightened risks of musculoskeletal injuries (MSIs) because of the demanding nature of their duties, contributing to restricted active duty and financial burdens. Although preventable factors like training and physical fitness influence some injuries, understanding the enduring effects of previous MSIs on physical fitness in military personnel remains a critical gap. This study aimed to systematically review and meta-analyze this impact.

Materials and Methods
In accordance with PRISMA guidelines, a systematic review with meta-analysis was conducted, focusing on military personnel with and without a history of MSIs. Physical fitness components were assessed via observational studies, with isokinetic peak torque values as primary metrics. Quality assessments utilized the NIH Quality Assessment Tool and GRADE framework.

Results
Out of 36 papers, 6 met inclusion criteria, with 4 included in the meta-analysis. Across 1,267 participants, individuals with prior MSIs exhibited a significant reduction in the pooled effect size for isokinetic peak muscle force, with d+ = −0.25 (95% CI: −0.36 to −0.13), notably affecting knee and shoulder regions. These findings underscore the pervasive impact of MSIs on military personnel’s physical performance, necessitating targeted interventions.

Conclusion
Military personnel with prior MSIs exhibit enduring deficits in isokinetic peak muscle force, particularly in knee and shoulder regions. However, evidence on the impact of previous injuries on other physical fitness components remains limited. Further research is crucial to understanding the multifaceted impact of MSIs on diverse aspects of physical performance, informing comprehensive injury prevention strategies and optimizing performance outcomes among military personnel.
Can the affected intestinal segment visualized on abdominal ultrasound predict gastrointestinal tract bleeding in immunoglobulin A vasculitis?
Authors: Polat Merve Cansu , Ekici Tekin Zahide , Keçeli Avni Merter , Çelikel Elif , Güngörer Vildan , Karagöl Cüneyt , Kaplan Melike Mehveş , Öner Nimet , Öztürk Didem , Özçelik Emine , Işıklar Ekici Mehveş , Uğur Es Yasemin , Yoğun Sultan Nilay , Çelikel Acar Banu 
Published: November 2024

ABSTRACT

Objectives
The study aimed to evaluate immunoglobulin A vasculitis (IgAV) patients with gastrointestinal (GI) tract involvement and to reveal the relationship between the location and extent of the affected intestinal segment detected on the initial abdominal ultrasound and GI tract bleeding.

Methods
This medical record review study was conducted on 117 IgAV patients with GI tract involvement between January 2016 and June 2023. Patients were divided into two groups: those with (n = 28) and without (n = 89) GI tract bleeding. Predictors of GI tract bleeding were investigated by comparing demographic, clinical characteristics, and laboratory findings.

Results
Gender, age at diagnosis, symptoms at admission, rash distribution, GI tract complaints, and the elapsed time until the development of GI tract symptoms were similar in both groups. There was no difference between small intestinal, large intestinal, or small + large intestinal involvement (P = .89). The ileum was the most commonly affected intestinal segment in patients with and without GI tract bleeding (P = .37). Jejunal wall thickening (P = .04) and the number of affected intestinal segments (P = .008) were higher in patients with GI tract bleeding.

Conclusions
In IgAV patients, jejunum involvement and affected multiple intestinal segments shown by abdominal ultrasound are associated with GI tract bleeding.
dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
Authors: Yao Lantian , Guan Jiahui , Xie Peilin , Chung Chia-Ru , Zhao Zhihao , Dong Danhong , Guo Yilin , Zhang Wenyang , Deng Junyang , Pang Yuxuan , Liu Yulan , Peng Yunlu , Horng Jorng-Tzong , Chiang Ying-Chih , Lee Tzong-Yi 
Published: November 2024

Abstract
Antimicrobial resistance is one of the most urgent global health threats, especially in the post-pandemic era. Antimicrobial peptides (AMPs) offer a promising alternative to traditional antibiotics, driving growing interest in recent years. dbAMP is a comprehensive database offering extensive annotations on AMPs, including sequence information, functional activity data, physicochemical properties and structural annotations. In this update, dbAMP has curated data from over 5200 publications, encompassing 33,065 AMPs and 2453 antimicrobial proteins from 3534 organisms. Additionally, dbAMP utilizes ESMFold to determine the three-dimensional structures of AMPs, providing over 30,000 structural annotations that facilitate structure-based functional insights for clinical drug development. Furthermore, dbAMP employs molecular docking techniques, providing over 100 docked complexes that contribute useful insights into the potential mechanisms of AMPs. The toxicity and stability of AMPs are critical factors in assessing their potential as clinical drugs. The updated dbAMP introduced an efficient tool for evaluating the hemolytic toxicity and half-life of AMPs, alongside an AMP optimization platform for designing AMPs with high antimicrobial activity, reduced toxicity and increased stability. The updated dbAMP is freely accessible at https://awi.cuhk.edu.cn/dbAMP/. Overall, dbAMP represents a comprehensive and essential resource for AMP analysis and design, poised to advance antimicrobial strategies in the post-pandemic era.
SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain
Authors: Chandrasekaran Thyagarajan T , Choudalakis Michel , Bröhm Alexander , Weirich Sara , Kouroukli Alexandra G , Ammerpohl Ole , Rathert Philipp , Bashtrykov Pavel , Jeltsch Albert 
Published: November 2024

Abstract
SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a major protein lysine methyltransferase trimethylating lysine 9 on histone H3 (H3K9) which is involved in heterochromatin formation and silencing of repeat elements (REs). It contains a unique Triple Tudor Domain (3TD), which specifically binds the dual modification of H3K14ac in the presence of H3K9me1/2/3. Here, we explored the role of the 3TD H3–tail interaction for the H3K9 methylation activity of SETDB1. We generated a binding reduced 3TD mutant and demonstrate in biochemical methylation assays on peptides and recombinant nucleosomes containing H3K14ac and H3K14ac analogs, respectively, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also observe this effect in cells where SETDB1 binding and activity is globally correlated with H3K14ac, and knockout of the H3K14 acetyltransferase HBO1 causes a drastic reduction in H3K9me3 levels at SETDB1 dependent sites. Regions with DNA hypomethylation after SETDB1 knockout also show an enrichment in SETDB1-dependent H3K9me3 and H3K14ac. Further analyses revealed that 3TD is particularly important at specific target regions like L1M REs, where H3K9me3 cannot be efficiently reconstituted by the 3TD mutant of SETDB1. In summary, our data demonstrate that the H3K9me3 and H3K14ac are not antagonistic marks but rather the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac regions and establishment of H3K9me3.
Acquired and genetic drivers of C3 and C5 convertase dysregulation in C3 glomerulopathy and immunoglobulin-associated MPGN
Authors: Roquigny Julia , Meuleman Marie-Sophie , El Sissy Carine , Martins Paula Vieira , Meri Seppo , Duval Anna , Le Quintrec Moglie , Fakhouri Fadi , Chauvet Sophie , Frémeaux-Bacchi Véronique 
Published: November 2024

ABSTRACT
Dysregulation of the alternative pathway of complement plays a central role in the pathophysiology of C3 glomerulopathy (C3G). Various autoimmune and genetic factors targeting the alternative pathway have been associated with both C3G and primary immunoglobulin-associated membranoproliferative glomerulonephritis (Ig-MPGN), suggesting shared pathophysiological mechanisms. This review highlights the wide range of disease drivers identified that mainly target components or protein complexes of the alternative pathway, both in C3G and Ig-MPGN. Nephritic factors, which constitute a heterogeneous group of autoantibodies targeting the C3 or the C5 convertase, are the most common abnormalities. Monoclonal gammopathies are frequent in aging adults. They may promote complement activation and have in some cases also been found to target alternative pathway regulatory proteins. Additionally, some patients with C3G and Ig-MPGN carry rare variants in genes encoding complement activating or regulating proteins of the alternative pathway. This review provides an informative overview of pathogenetic mechanisms associated with each abnormality, acting at different steps in the complement cascade. The diversity of targets involved in the C3G pathophysiology suggests the potential benefit of therapeutical approaches tailored to the underlying disease drivers, with a pivotal impact upstream or at the level of the C3 or C5 convertase activity.
Postoperative NEOadjuvant TEMozolomide followed by chemoradiotherapy versus upfront chemoradiotherapy for glioblastoma multiforme (NEOTEM) trial: Interim results
Authors: Sharifian Azadeh , Kazemian Ali , Farzin Mostafa , Amirkhani Nikan , Farazmand Borna , Naderi Soheil , Khalilian Alireza , Pourrashidi Ahmad , Amjad Ghazaleh , Kolahdouzan Kasra , Abyaneh Romina , Jablonska Paola Anna , Ghalehtaki Reza 
Published: November 2024

Abstract

Background
Glioblastoma multiforme (GBM) is an aggressive brain tumor with poor survival rates despite current treatments. The standard of care (SOC) includes surgery, followed by radiotherapy plus concurrent and adjuvant chemotherapy with temozolomide (TMZ). This phase II trial assessed the safety and efficacy of neoadjuvant TMZ (nTMZ) before and during chemoradiotherapy in newly diagnosed GBM patients.

Methods
Newly diagnosed GBM patients who underwent maximal safe resection were randomized into 2 groups. One received nTMZ before standard chemoradiotherapy and adjuvant TMZ (intervention). The other received standard chemoradiotherapy followed by adjuvant TMZ (control). Primary endpoints were progression-free survival (PFS) at 6 and 12 months. Secondary endpoints included overall survival, radiological and clinical responses, and adverse events.

Results
Of 35 patients, 16 were in the intervention group and 19 in the control group. Median PFS was 9 months (95% CI: 3.93–14.06) versus 3 months (95% confidence interval [CI]: 1.98–4.01) in the control and intervention groups (P = .737), with a high progression rate (73.4%) during nTMZ treatment. The 6-month PFS rates were 58% versus 25% (P = .042), and 12-month PFS rates were 26% versus 25% (P = .390) in the control and intervention groups, respectively. Patients with unmethylated O6-methylguanine-DNA methyltransferase (MGMT) and those with good performance status (PS) had significantly worse PFS with nTMZ. However, those who underwent larger extent of resection exhibited significantly better PFS with nTMZ. Adverse events were similar between groups.

Conclusions
Neoadjuvant TMZ before SOC chemoradiotherapy did not improve outcomes for newly diagnosed GBM patients and is unsuitable for those with unmethylated MGMT and good PS. However, It may benefit patients with near or gross total resection. Further research is needed to refine GBM treatment strategies.