bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing adipose-derived stromal vascular fraction storage: Temperature and time impact on cell viability in regenerative medicine
Authors: Jović Darko , Preradović Ljubiša , Jović Filip , Kremenović Mićo , Lukić Darko , Antonić Milica , Unčanin Nikola , Jović Matija 
Published: September 2024

Background:
The adipose-derived stromal vascular fraction (SVF) plays a crucial role in regenerative medicine owing to its regenerative and immunomodulatory properties. However, the effective utilization of SVF in therapeutic applications requires careful consideration of storage conditions to maintain cell viability.

Methods:
We conducted a research on 43 patients of different ages and sexes who were older than 18 years. This study explored the impact of different temperatures (‐80, ‐20, and 4 °C) on SVF storage in platelet-poor plasma for 1 and 6 months. SVF extracted using a semi-UNISTATION™ system was subjected to rigorous analysis of cell count and viability using a LUNA-STEM™ Dual Fluorescence Cell Counter.

Results:
The results indicated a significant correlation between the storage conditions and SVF viability. Notably, storing SVF at 4 °C demonstrated the highest cell viability and count, while ‐80 °C storage exhibited the least favorable outcomes. This study emphasizes the importance of minimizing storage time to preserve SVF viability, as evidenced by a decline in both cell count and viability over a 6-month period. Comparisons with the existing literature underscore the need for precise protocols for SVF storage, with considerations for temperature and cryoprotective agents. These findings provide valuable insights for developing optimal SVF storage protocols to enhance therapeutic outcomes and reduce the need for repeated adipose tissue harvesting. Despite the limitations of the study, such as the use of a cell counter instead of flow cytometry, the results establish the foundation for further research on refining SVF storage methods.

Conclusion:
The ideal storage temperature is from 4 °C, while the length of storage time inversely affects the viability of SVF; the longer the storage time, the lower the number and the viability of SVF cells, regardless of the temperature at which they are preserved.
Impact of Geopolitical Unrest on Surgical Delays and Outcomes in Immigrant Populations With Cleft Lip and Palate
Authors: Güray Şeyda , Evin Nuh , Sifil Melih K. , Yildiz Kemalettin , Güneren Ethem 
Published: September 2024

Background:
Geopolitical conflicts in the Middle East have led to mass migrations, with Turkey becoming a major host country. This influx has strained the health care system, particularly regarding specialized care for conditions like cleft lip and palate (CLP). Timely intervention is crucial for optimal outcomes, but cultural, socioeconomic, and logistical barriers often cause delays, impacting physical, functional, and psychosocial development.

Methods:
This retrospective study analyzed 72 immigrant pediatric CLP patients treated in Turkey between 2012 and 2022. Data on demographics, medical history, surgical interventions, complications, and treatment delays were collected. Surgical timing was compared with American Cleft Palate Craniofacial Association guidelines, and the impact of socioeconomic status on delays was assessed.

Results:
Seventy-two patients underwent a total of 91 surgical interventions, including 29 cleft lip repairs, 22 cleft palate repairs, 6 pharyngeal flaps, 15 fistula closures, 8 corrections of secondary lip scars and whistling deformities, and 11 alveolar bone graftings. A majority (73.6%) had poor socioeconomic status. The average delays for cleft lip, cleft palate, and alveolar bone grafting surgeries were 5.3±4, 7.3±6.1, and 34.1±23.5 months, respectively, and were significantly longer for patients with poor socioeconomic status (P=0.00502, 0.030741, and 0.041878). The average delay for pharyngeal flap surgery, performed in patients with poor socioeconomic status (except for one), was 43.7±14.1 months.

Conclusions:
This study highlights the challenges and disparities in CLP care for immigrant children in Turkey due to geopolitical conflict. While surgical complication rates are similar to established data, delays in treatment, especially among those with lower socioeconomic status, are a significant concern. The findings emphasize the need for comprehensive, culturally sensitive care and systemic interventions to improve access and outcomes for this vulnerable population.
First Case Report of Disseminated Gonococcal Arthritis in Newfoundland & Labrador
Authors: Karsenti Nessika , Nelder Matthew , LeMeissurier Jennifer , Bourassa-Blanchette Samuel , Taylor Robert 
Published: September 2024

Introduction: Disseminated gonococcal infections (DGIs) are a rare but often debilitating complication of N. gonorrhoeae infections. Often presenting as arthritis-dermatitis syndrome, true suppurative joint infections are an even more rare form of DGI. Here, we present the first known case of DGI in Newfoundland and Labrador in over 10 years.
Case report: A 50-year-old man who is known to inject drugs with multiple housing and social challenges presented to the emergency department with a two-day history of an isolated painful, erythematous knee. After being assessed by orthopedics and undergoing an operative debridement, intraoperative cultures grew N. gonorrhoeae. He was treated with intravenous (IV) ceftriaxone, and his course in hospital was complicated by inadequate pain control and a lack of stable housing.
Conclusion: DGIs, while rare, need to remain on any clinician’s differential for septic arthritis given the increasing prevalence of gonorrheal infections in Canada, and in Newfoundland and Labrador. In addition, patients who are at risk of delaying accessing care, such as people who inject drugs and unhoused individuals, are at higher risk of complicated hospital stays.
Harmonization of Margin of Stability Calculations and Investigation of the Impact of Foot Length, Foot Width, Gait Speed, and Body Mass
Authors: Dussault-Picard Cloé , Robidou Claire , Tisserand Romain , Cherni Yosra 
Published: September 2024

AbstractThe margin of stability (MoS), the minimum distance between the extrapolated center of mass and the edges of the base of support (BoS), is one of the most widely used metric to describe the mechanical stability during gait. In the current literature, the markers used to define the edges of the BoS are variable and the MoS model neglects the influence of anthropometric factors, such as foot length, foot width, and body mass. This study aimed to evaluate differences between anteroposterior (AP) and mediolateral (ML) MoS measures using various BoS edge definitions (AP: n = 3 methods, ML: n = 4 methods) and to investigate the impact of foot length, foot width, gait speed, and body mass on the MoS measures. Results show that the BoS edges definition affects the resulting MoS across the entire stance phase (AP: p<0.001 between the 3 methods; ML: p<0.001 between the 4 methods). Moreover, the AP MoS is influenced by foot length (p<0.029), as well as gait speed and body mass on both the AP (gait speed: p<0.001; body mass: p<0.038) and ML (gait speed: p<0.032; body mass: p<0.001) MoS. This study proposes a new approach based on optimal foot markers for defining the edges of the BoS, which may contribute to better assess mechanical stability during gait. Finally, the results suggest that normalizing the MoS (i.e., the AP MoS by foot length, gait speed, and body mass, and the ML MoS by gait speed and body mass) can facilitate comparisons between populations.
The utility of environmental data from traditional varieties for climate-adaptive maize breeding
Authors: Li Forrest , Gates Daniel J. , Buckler Edward S. , Hufford Matthew B. , Janzen Garrett M. , Rellán-Álvarez Rubén , Rodríguez-Zapata Fausto , Navarro J. Alberto Romero , Sawers Ruairidh J. H. , Snodgrass Samantha J. , Sonder Kai , Willcox Martha C. , Hearne Sarah J. , Ross-Ibarra Jeffrey , Runcie Daniel E. 
Published: September 2024

ABSTRACTMaintaining crop yields in the face of climate change is a major challenge facing plant breeding today. Considerable genetic variation exists inex-situcollections of traditional crop varieties, but identifying adaptive loci and testing their agronomic performance in large populations in field trials is costly.Here, we study the utility of climate and genomic data for identifying promising traditional varieties to incorporate into maize breeding programs. To do so, we use phenotypic data from more than 4,000 traditional maize varieties grown in 13 trial environments. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be locally adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify genetic loci associated with historical divergence along climatic gradients, such as the putative heat shock proteinhsftf9and the large-scale adaptive inversionInv4m.Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genomic data, and that envGWAS-identified variants provide little direct predictive information over patterns of population structure. We also find that adding environment-of-origin variables does not improve yield component prediction over kinship or population structure alone, but could be a useful selection proxy in the absence of sequencing data. While our results suggest little utility of environmental data for selecting traditional varieties to incorporate in breeding programs, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci for maize improvement, especially when coupled with high density genotyping.
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
Authors: Hingerl Johannes C. , Martens Laura D. , Karollus Alexander , Manz Trevor , Buenrostro Jason D. , Theis Fabian J. , Gagneur Julien 
Published: September 2024

AbstractUnderstanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build unifying models of gene regulation capturing sequence determinants across steps of gene expression. However, current models, developed primarily for bulk omics data, fail to capture the cellular heterogeneity and dynamic processes revealed by single-cell multi-modal technologies. Here, we introduce scooby, the first model to predict scRNA-seq coverage and scATAC-seq insertion profiles along the genome from sequence at single-cell resolution. For this, we leverage the pre-trained multi-omics profile predictor Borzoi as a foundation model, equip it with a cell-specific decoder, and fine-tune its sequence embeddings. Specifically, we condition the decoder on the cell position in a precomputed single-cell embedding resulting in strong generalization capability. Applied to a hematopoiesis dataset, scooby recapitulates cell-specific expression levels of held-out genes and cells, and identifies regulators and their putative target genes through in silico motif deletion. Moreover, accurate variant effect prediction with scooby allows for breaking down bulk eQTL effects into single-cell effects and delineating their impact on chromatin accessibility and gene expression. We anticipate scooby to aid unraveling the complexities of gene regulation at the resolution of individual cells.
BTFBS: binding-prediction of bacterial transcription factors and binding sites based on deep learning
Authors: Jin Bingbing , Liang Song , Liu Xiaoqian , Zhang Rui , Zhu Yun , Chen Yuanyuan , Liu Guangjin , Yang Tao 
Published: September 2024

AbstractBackgroundThe binding of transcription factors (TFs) to TF-binding sites plays a vital role in the process of regulating gene expression and evolution. With the development of machine learning and deep learning, some successes have been achieved in predicting transcription factors and binding sites. Then a natural question arises: for a given transcription factor and a binding site, do they bind? This is the main motivation of this work.ResultsIn this paper, we develop a model BTFBS, which predicts whether the bacterial transcription factors and binding sites combine or not. The model takes both the amino acid sequences of bacterial transcription factors and the nucleotide sequences of binding sites as inputs, and extracts features through convolutional neural network and MultiheadAttention.For the model inputs, we use two negative sample sampling methods: RS and EE. On the test dataset of RS, the accuracy, sensitivity, specificity, F1-score and MCC of BTFBS are 0.91446, 0.89746, 0.93134, 0.91264 and 0.82946, respectively. And on the test dataset of EE, the accuracy, sensitivity, specificity, F1-score and MCC of BTFBS are 0.87868, 0.89354, 0.86394, 0.87996 and 0.75796, respectively. Meanwhile, our findings indicate that the optimal approach for obtaining negative samples in the context of bacterial research is to utilize the whole genome sequences of the corresponding bacteria, as opposed to the shuffling method.ConclusionsThe above results on the test dataset have shown that the proposed BTFBS model has a good performance in predicting the combination of bacterial transcription factors and their binding sites and provides an experimental guide. BTFBS is publicly available athttps://github.com/Vceternal/BTFBS.
Nocturia as a Risk Factor for Developing Frailty in Older Adults: Results of the Berlin Aging Study II
Authors: König Maximilian , Malsch Carolin , Mariño Joany , Vetter Valentin Max , Komleva Yulia , Demuth Ilja , Steinhagen-Thiessen Elisabeth 
Published: September 2024

AbstractBackground & AimThe current study examined cross-sectional and longitudinal associations between nocturia and frailty in a cohort of men and women aged 60 years and older, as evidence on this topic was lacking.MethodsBaseline and follow-up data from the Berlin Aging Study II (n=1671) assessed on average 7.1 (IQR 6.2-8.7) years apart were analyzed. Self-reported nocturia was dichotomized into </≥ 2 micturitions per night, and frailty was assessed using the Fried Frailty Phenotype. Covariables were identified a priori based on a review of the existing literature.ResultsAt baseline, 70.2% of the participants were robust, 28.9% were pre-frail, and 0.9% were frail; 254 participants (23.6%) had self-reported nocturia. In longitudinal analyses, the prevalence and incidence of frailty at follow-up significantly increased when nocturia was present at baseline. Over the median follow-up of 7.1 years, there were 41 incident frailty cases (IR 5.15, 95% CI 3.79-7.00 per 1000 person-years). After adjusting for age, sex, morbidity burden, and baseline frailty status, baseline nocturia was associated with a 2.23-fold increased risk (95% CI 1.17-4.18) of frailty at follow-up.ConclusionNocturia is linked to a higher risk of developing frailty in older adults, both women and men.
Diastolic dysfunction in aortic stenosis is associated with greater damping of left ventricular recoil, and not myocardial stiffness
Authors: Salman Katrin , Sundqvist Martin G , Stevenson Jonathan , Cain Peter A , Ugander Martin 
Published: September 2024

AbstractBackgroundAortic stenosis (AS) is associated with increasing severity of diastolic dysfunction as measured by conventional echocardiographic grading. The parameterized diastolic filling (PDF) method can describe diastolic function mechanistically, by analyzing filling using the physics of classical mechanics for spring recoil. The study aimed to use the PDF method to describe the mechanics of how diastolic dysfunction manifests in AS.MethodsPatients (n=73) undergoing echocardiography were included according to AS of varying severity (normal/mild AS: maximum Doppler velocity across aortic valve (Vmax) <3.0 m/s, moderate/severe AS: Vmax≥3.0 m/s). PDF analysis of pulsed wave Doppler transmitral E-waves was performed using freely available software.ResultsCompared to normal/mild AS (n=41), patients with moderate/severe AS (n=32) had a left ventricle with a greater interventricular septal thickness (p=0.02) and higher E/e’ (p=0.007), but similar left ventricular ejection fraction (p=0.10) and left atrial volume index (p=0.21). PDF analysis showed that moderate/severe AS did not differ in myocardial stiffness (p=0.70), but had a higher myocardial damping (p=0.02), higher load (p=0.04), longer derived time constant of isovolumetric pressure decay (tau, p=0.004), higher filling energy (p=0.02), higher peak driving (p=0.02) and resistive (p=0.004) force of filling, lower kinematic filling efficiency index (p<0.001), but no difference in the load-independent index of diastolic function (p=0.62).ConclusionsAS was primarily associated with a greater damping of LV recoil (increased viscoelasticity) and load, but without a change in myocardial stiffness. This provides novel insight into the mechanics of how diastolic dysfunction manifests in AS.
Characterization of Clinical MRI Findings in Moderately-Late Preterm Infants Diagnosed with Cerebral Palsy: A Single Center Retrospective Study
Authors: Fisher Elizabeth , Tartakovsky Jessica , Bliss Laura A. , Jaju Alok , Aw-Zoretic Jessie , Vernon Laura , Mithal Divakar S. 
Published: September 2024

I.AbstractCerebral Palsy is the most common movement disorder in childhood and is commonly associated with brain injury and prematurity. At least 10% of patients have a normal brain MRI and current practices suggest genetic testing may be indicated for those patients. However, given that prematurity itself is a risk factor for CP, which MRI patterns are present in premature infants and which genetic causes are present remains unclear. In the present study, a cohort of moderate-late preterm infants born between 32 and 34 weeks gestational age was analyzed to determine whether CP disease severity, comorbid conditions, and genetic testing are associated with particular MRI findings. We identified that comorbid conditions and CP severity are similar across imaging patterns regardless of the perceived severity of the imaging findings. Genetic diagnoses were identified in 13% of all patients. In patients with MRI concerning for injuries, over 20% had genetic testing sent. Abnormal MRI findings in moderate-late preterm infants with CP are common, but are not a strong predictor of disease severity and may be associated with underlying genetic causes that are underdiagnosed due to unclear practice guidelines.
Physical therapy in patients with Parkinson’s disease treated with Deep Brain Stimulation: a Delphi panel study
Authors: Guidetti M. , Marceglia S. , Bocci T. , Duncan R. , Fasano A. , Foote K.D. , Hamani C. , Krauss J.K. , Kühn A. A. , Lena F. , Limousin P. , Lozano A.M. , Maiorana N.V. , Modugno N. , Moro E. , Okun M.S. , Oliveri S. , Santilli M. , Schnitzler A. , Temel Y. , Timmermann L. , Visser-Vandewalle V. , Volkmann J. , Priori A. 
Published: September 2024

ABSTRACTAlthough deep brain stimulation of the subthalamic nucleus (STN-DBS) induces motor benefits in people with Parkinson’s disease (PwPD), the size and duration of the effects of STN-DBS on motor axial (e.g., postural instability, trunk posture alterations) and gait impairments (e.g., freezing of gait – FOG) are still ambiguous. Physical therapy (PT) effectively complements pharmacological treatment to improve postural stability, gait performance, and other dopamine-resistant symptoms (e.g. festination, hesitation, axial motor dysfunctions, and FOG) in PwPD who are non-surgically treated. Despite the potential for positive adjuvant effects of PT following STN-DBS surgery, there is a paucity of science available on the topic. In such a scenario, gathering the opinion and expertise of leading investigators worldwide was pursued to study motor rehabilitation in PwPD following STN-DBS. After summarizing the few available findings through a systematic review, we identified clinical and academically experienced DBS clinicians (n=21) to discuss the challenges related to PT following STN-DBS. A 5-point Likert scale questionnaire was used and based on the results of the systematic review along with a Delphi method. Thirty-nine questions were submitted to the panel – half related to general considerations on PT following STN-DBS, half related to PT treatments. Despite the low-to-moderate quality, the few available rehabilitative studies suggested that PT could improve dynamic and static balance, gait performance and posture. Similarly, panellists strongly agreed that PT might help in improving motor symptoms and quality of life, and it may be possibly prescribed to maximize the effects of the stimulation. The experts agreed that physical therapists could be part of the multidisciplinary team taking care of the patients. Also, they agreed on prescribing of conventional PT, but not massage or manual therapy. Our results will inform the rehabilitation and the DBS community to engage, publish and deepen this area of research. Such efforts may spark guidelines for PT following STN-DBS.GRAPHICAL ABSTRACT
Gaps and Opportunities for Data Systems and Economics to Support Priority Setting for Climate-Sensitive Infectious Diseases in Sub-Saharan Africa: A Rapid Scoping Review
Authors: Delight Ellie A. , Brunn Ariel A. , Ruiz Francis , Gerard Jessica , Falconer Jane , Liu Yang , Bah Bubacarr , Bett Bernard , Uzochukwu Benjamin , Oloko Oladeji K. , Njuguna Esther , Murray Kris A. 
Published: September 2024

AbstractClimate change alters risks associated with climate-sensitive infectious diseases (CSIDs) with pandemic potential. This poses additional threats to already vulnerable populations, further amplified by intersecting social factors, such as gender and socioeconomic status. Currently, critical evidence gaps and inadequate institutional and governance mechanisms impact on the ability for African States to prevent, detect and respond to CSIDs. The aim of this study was to explore the role of data systems and economics to support priority setting for CSID preparedness in sub-Saharan Africa.We conducted a rapid scoping review to identify existing knowledge and gaps relevant to economics and data systems. A literature search was performed across six bibliographic databases in November 2023. A list of 14 target pathogens, identified by the World Health Organization as Public Health Emergencies of International Concern or R&D Blueprint Pathogens, was adopted and compared to a database of CSIDs to determine relevant inclusion criteria. Extracted data were synthesised using bibliometric analysis, thematic topic categorisation, and narrative synthesis to identify research needs, evidence gaps, and opportunities for priority setting.We identified 68 relevant studies. While African author involvement has been increasing since 2010, few studies were led by senior authors from African institutions. Data system studies (n = 50) showed broad coverage across CSIDs and the WHO AFRO region but also a high degree of heterogeneity, indicating a lack of clearly defined standards for data systems related to pandemic preparedness. Economic studies (n = 18) primarily focused on COVID-19 and Ebola and mostly originated from South Africa. Both data system and economic studies identified limited data sharing across sectors and showed a notable absence of gender sensitivity analyses. These significant gaps highlight important opportunities to support priority setting and decision-making for pandemic preparedness, ultimately leading to more equitable health outcomes.