bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lower li1mb mesenchymal hamartoma masquerading as hemangioma: a case report of AA2 atypical presentation and diagnostic challenges
Authors: Puduru Nikhil , KA Dilip Vasant , Shaikh Faiza A. , Shaikh Humaira , Acharya Bimarsh , Sydhom Pishoy 
Published: June 2024

Introduction and importance:
Hamartomas are abnormal growths that consist of various types of mesenchymal tissues, including cartilage, fat, connective tissue, and smooth muscle. These tumors can occur in almost any organ system within the body. While head and neck hamartomas have been frequently documented, cases involving the lower limbs are relatively rare. However, a unique instance of a mesenchymal hamartoma located in the leg has recently emerged.

Case presentation:
A 30-year-old woman presented with a painless, gradually growing swelling on her left leg, diagnosed as a subcutaneous hemangioma preoperatively. Despite unsuccessful propranolol treatment, surgical excision revealed a mesenchymal hamartoma. Postoperative examination confirmed the diagnosis, and the patient recovered smoothly without recurrence after a week of hospitalization.

Clinical discussion:
Cutaneous mesenchymal hamartomas are benign tissue growths with unknown etiology, associated with syndromes like Cowden and Peutz-Jeghers. Smooth muscle hamartoma can be acquired after skin trauma. Hemartoma can be misdiagnosed as hemangiomas. Cutaneous mesenchymal hamartomas presents as painless swellings in various locations, occasionally in adulthood. Differential diagnoses include lipomas and fibromas. Surgical excision is recommended for symptomatic cases to prevent recurrence.

Conclusion:
This case highlights the atypical presentation of the hamartoma and emphasizes the importance of accurate diagnosis and management.
A 23-year-old male patient with Kimura’s disease without renal transplantation: a rare case report from Syria
Authors: Alsmoudi Hasan , Sleiay Mouhammed , Almohamed Ahmad , Hamsho Suaad , Alhadla Ahmad , Alqreea Mohammed , Alakhras Abdulkareem 
Published: June 2024

Introduction and importance:
Kimura’s disease (KD) is a chronic, nonmalignant inflammatory disorder that primarily affects subcutaneous tissue. It is typically characterized by painless nodules in the head and neck regions, accompanied by elevated eosinophil and serum IgE levels. The purpose of this case study is to elucidate this rare disease, particularly in the Asian region and Syria, and to explore diagnostic and therapeutic methodologies with the objective of mitigating the number of undiagnosed patients suffering from this disease.

Case presentation:
A 23-year-old male patient presented to the Ear, Nose, and Throat (ENT) Department of the hospital with symptoms that had been initiated 7 months prior. The primary symptoms were pain and swelling in the left preauricular area, followed by subsequent swelling in the right preauricular area the next day. The patient experienced severe, intermittent pain, generalized pruritus, and systemic manifestations, including fever, chills, fatigue, malaise, anorexia, and a weight loss of 20 kg over the course of seven months. A fine-needle aspiration of the left parotid gland revealed the presence of lymphocytes at various maturation stages, with no evidence of abnormal cells. A diagnosis of KD was subsequently confirmed.

Clinical discussion:
To our knowledge, this case represents the second documented instance of KD in Syria. Furthermore, our case is among the extremely rare instances of KD in a patient without a history of renal transplantation.

Conclusion:
Further research is essential to ascertain the actual prevalence of this condition and to identify the most effective management strategies.
Utilizing Data and Alarm Champions to Enhance Alarm Management
Authors: Mullen Joellan , Sattari Sulimon , Rauch Melissa , Stein Fernando , Roy Kevin , Acorda Darlene E. 
Published: June 2024

Background:
Nuisance and false alarms distract clinicians from urgent alerts, raising patient safety risks.

Local Problem:
High alarm rates in a pediatric progressive care unit resulted in experiencing 180-250 alarms per day or 1 alarm every 3 to 4 minutes per clinician.

Methods:
Through Plan-Do-Study-Act cycles, environmental, policy, and technology changes were implemented to decrease the average alarms/day/bed and percentage of time in alarm.

Interventions:
Alarm settings tailored to patient needs using features embedded within the patient monitoring system were implemented and monitored with the assistance of alarm champions.

Results:
The average number of alarms/day/bed decreased from 177.69 to 96.94 over the course of 10 years, a 45.45% reduction. The percentage of time in alarm decreased from 7.52% to 2.83%, a 62.37% reduction.

Conclusions:
Arming clinicians with technology to analyze real-time clinical data made alarms meaningful and actionable, decreasing false alarms without compromising patient safety.
Point-of-Care Ultrasound Evaluation of Pediatric Osteomyelitis in the Emergency Department
Authors: Tsung James W. , Rizvi Munaza B. , Rabiner Joni E. 
Published: June 2024

Abstract
Musculoskeletal and soft tissue complaints commonly present to the pediatric emergency department and literature supports the use point-of-care ultrasound (POCUS) in the diagnosis of these complaints. The diagnosis of osteomyelitis typically involves laboratory testing with inflammatory biomarkers, imaging with x-ray, and often magnetic resonance imaging with test results often not immediately available. We report a case series of children initially evaluated with POCUS for osteomyelitis. The POCUS may expedite diagnosis and treatment when used as the initial test in children with suspected osteomyelitis in the emergency department.
Sleep, Sleep Apnea, and Fatigue in People Living With HIV
Authors: Orr Jeremy E. , Velazquez Jazmin , Schmickl Christopher N. , Bosompra Naa-Oye , DeYoung Pamela N. , Gilbertson Dillon , Malhotra Atul , Grant Igor , Ancoli-Israel Sonia , Karris Maile Young , Owens Robert L. 
Published: June 2024

Background:
People living with HIV (PLWH) often report fatigue even when viral load is suppressed. Obstructive sleep apnea (OSA), which is often associated with fatigue, is common in PLWH, but whether OSA explains fatigue in this population is unknown.

Setting:
Academic university-affiliated HIV and Sleep Medicine Clinics.

Methods:
PLWH, aged 18–65 years, with a body mass index of 20–35 kg/m2 and viral suppression (RNA <200 copies per mL), were recruited to undergo daytime questionnaires, including the Functional Assessment of Chronic Illness Therapy Fatigue Scale and Epworth Sleepiness Scale, 7 days of actigraphy (to determine daily sleep duration and activity amplitude and rhythms), and an in-laboratory polysomnography to assess for the presence and severity of OSA.

Results:
Of 120 subjects with evaluable data, 90 (75%) had OSA using the American Academy of Sleep Medicine 3% desaturation or arousal criteria, with an apnea–hypopnea index >5/h. There was no difference in Functional Assessment of Chronic Illness Therapy scores between those with and without OSA, although those with OSA did report more daytime sleepiness as measured using the Epworth Sleepiness Scale. In a multivariable model, predictors of fatigue included more variable daily sleep durations and decreased mean activity counts. Sleepiness was predicted by the presence of OSA.

Conclusion:
OSA was very common in our cohort of PLWH, with those with OSA reporting more sleepiness but not more fatigue. Variability in sleep duration was associated with increased fatigue. Further study is needed to determine if treatment of OSA, or an emphasis on sleep consistency and timing, improves symptoms of fatigue in PLWH.
Artificial Intelligence Methods for the Argenta Classification of Deformational Plagiocephaly to Predict Severity and Treatment Recommendation
Authors: Nguyen Huan T. , Obinero Chioma G. , Wang Ellen , Boyd Alexandra K. , Cepeda Alfredo , Talanker Michael , Mumford Danielle , Littlefield Tim , Greives Matthew R. , Nguyen Phuong D. 
Published: June 2024

Introduction
Deformational plagiocephaly (DP) can be classified into 5 severity types using the Argenta scale (AS). Patients with type III or higher require referral to craniofacial surgery for management. Primary care pediatricians (PCPs) are often the first to encounter patients with DP, but current screening methods are subjective, increasing the risk of bias, especially for clinicians with little exposure to this population. The authors propose the use of artificial intelligence (AI) to classify patients with DP using the AS and to make recommendations for referral to craniofacial surgery.

Methods
Vertex photographs were obtained for patients diagnosed with unilateral DP from 2019 to 2020. Using the photographs, an AI program was created to characterize the head contour of these infants into 3 groups based on the AS. The program was trained using photographs from patients whose DP severity was confirmed clinically by craniofacial surgeons. To assess the accuracy of the software, the AS predicted by the program was compared with the clinical diagnosis.

Results
Nineteen patients were assessed by the AI software. All 3 patients with type I DP were correctly classified by the program (100%). In addition, 4 patients with type II were correctly identified (67%), and 7 were correctly classified as type III or greater (70%).

Conclusions
Using vertex photographs and AI, the authors were able to objectively classify patients with DP based on the AS. If converted into a smartphone application, the program could be helpful to PCPs in remote or low-resource settings, allowing them to objectively determine which patients require referral to craniofacial surgery.
Improving communication among nursing staff at a children's hospital in the southern United States: a best practice implementation project
Authors: Keith Brandi B. , Upchurch Linda , Palokas Michelle , Christian Robin 
Published: June 2024

Introduction:
Ineffective communication between health care professionals is one of the leading causes of medical errors and can result in adverse events and patient harm. Improving the effectiveness of communication in health care is a worldwide necessity.

Objective:
The aim of this project was to promote evidence-based practices regarding general communication principles among the nursing staff in one unit of a children's hospital in the southern United States.

Methods:
The project used JBI's Evidence Implementation Framework, together with two JBI audit tools (Practical Application of Clinical Evidence System and Getting Research into Practice). A baseline audit was conducted, followed by the implementation of targeted strategies. The project was completed with a follow-up audit to determine changes in practice.

Results:
Baseline data revealed 61% adherence with four audit criteria for effective communication in health care. Barriers included a lack of education of nursing staff regarding communication skills and less than optimal use of a structured communication tool. Targeted strategies to address the barriers included providing an educational module on communication to nursing staff and moving the structured communication tool to a more convenient location to increase its use. The post-implementation data revealed 81% adherence with the four audit criteria, a 20% increase from baseline results.

Conclusions:
Optimizing communication and monitoring the use of a structured communication tool has the potential to decrease the risk of medical errors among health care providers.

Spanish abstract:

http://links.lww.com/IJEBH/A217
Peripheral bloodGATA2expression impactsRNF213mutation penetrance and clinical severity in moyamoya disease
Authors: Mineharu Yohei , Kamata Takahiko , Tomoto Mei , Sato Noriaki , Tamada Yoshinori , Funaki Takeshi , Oichi Yuki , Harada Kouji H , Koizumi Akio , Kimura Tetsuaki , Inoue Ituro , Okuno Yasushi , Miyamoto Susumu , Arakawa Yoshiki 
Published: June 2024

ABSTRACTBackgroundThe p.R4810K founder mutation in theRNF213gene confers susceptibility to moyamoya disease (MMD) and non-MMD intracranial artery disease. However, penetrance is incomplete, and the underlying molecular mechanism remains unknown.Methods and ResultsTranscriptome analysis of peripheral blood was conducted with 9 MMD patients and 5 unaffected mutation carriers from 4 familial MMD pedigrees. Bayesian network analysis identified upregulated gene modules associated with lipid metabolism and leukocyte development (includingGATA2andSLC45A3), and EGFR signaling (UBTD1). It also identified downregulated gene modules related to mitochondrial ribosomal proteins (RPS3AandRPL26), and cytotoxic T cell immunity (GZMAandTRGC1). TheGATA2network was replicated through WGCNA analysis and further examined in a case-control study, comprising 43 MMD patients, 16 non-MMD patients, 19 unaffected carriers, and 35 healthy controls.GATA2exhibited a significant linear correlation withSLC45A3and was significantly higher in MMD patients compared to age- and sex-matched unaffected carriers or wild-type controls. Among patients with the p.R4810K mutation, higherGATA2expression was associated with an earlier age of onset, bilateral involvement, and symptomatic disease onset.ConclusionsPeripheral bloodGATA2expression was associated with increased penetrance of theRNF213mutation and more severe clinical manifestations in MMD.
The differential immunological impact of photon vs proton radiation therapy in high grade lymphopenia
Authors: Heather James M. , Kim Daniel W. , Sepulveda Sean M. , van Seventer Emily E. , Fish Madeleine G. , Corcoran Ryan , Hacohen Nir , Hong Theodore S. , Cobbold Mark 
Published: June 2024

AbstractRadiation therapy has long been a cornerstone of cancer treatment. More recently, immune checkpoint blockade has also been applied across a variety of cancers, often leading to remarkable response rates. However, photon-based radiotherapy – which accounts for the vast majority – is also known to frequently induce profound lymphopenia, which might limit the efficacy of immune system based combinations. Proton beam therapy is known to produce a less drastic lymphopenia, which raises the possibility of greater synergy with immunotherapy.In this study we aimed to explore the exact nature of the differential impact of the two radiation modalities upon the immune system. We used multiparametric flow cytometry and deep sequencing of rearranged TCRb loci to investigate a cohort of 20 patients with gastrointestinal tumors who received either therapy. Proton-treated patients remained relatively stable throughout treatment for most metrics considered, whereas those who received photons saw a profound depletion in naïve T cells, increase in effector/memory populations, and loss of TCR diversity. The repertoires of photon-treated patients underwent oligoclonal expansion after their lymphocyte count nadirs, particularly of CD8+ Temra cells, driving this reduction in diversity. Across the entire cohort, this reduction in post-nadir diversity inversely correlated with the overall survival time of those patients who died. This raises the possibility that increased adoption of proton-based or other lymphocyte sparing radiotherapy regimes may lead to better survival in cancer patients.
BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis
Authors: Ostner Johannes , Kirk Tim , Olayo-Alarcon Roberto , Thöming Janne Gesine , Rosenthal Adam Z. , Häussler Susanne , Müller Christian L. 
Published: June 2024

AbstractBacterial single-cell RNA sequencing has the potential to elucidate within-population heterogeneity of prokaryotes, as well as their interaction with host systems. Despite conceptual similarities, the statistical properties of bacterial single-cell datasets are highly dependent on the protocol, making proper processing essential to tap their full potential. We present BacSC, a fully data-driven computational pipeline that processes bacterial single-cell data without requiring manual intervention. BacSC performs data-adaptive quality control and variance stabilization, selects suitable parameters for dimension reduction, neighborhood embedding, and clustering, and provides false discovery rate control in differential gene expression testing. We validated BacSC on a broad selection of bacterial single-cell datasets spanning multiple protocols and species. Here, BacSC detected subpopulations inKlebsiella pneumoniae, found matching structures ofPseudomonas aeruginosaunder regular and low-iron conditions, and better represented subpopulation dynamics ofBacillus subtilis. BacSC thus simplifies statistical processing of bacterial single-cell data and reduces the danger of incorrect processing.
Deviations from normative functioning underlying emotional episodic memory revealed cross-scale neurodiverse alterations linked to affective symptoms in distinct psychiatric disorders
Authors: Xiao Yang , Li Mingzhu , Zhang Xiao , Zhang Yuyanan , Ge Yuqi , Lu Zhe , Ma Mengying , Song Yuqing , Tan Hao-Yang , Zhang Dai , Yue Weihua , Yan Hao 
Published: June 2024

AbstractBackgroundAffective symptoms are a prevalent psychopathological feature in various psychiatric disorders. However, the underlying neurobiological mechanisms are complex and not yet fully understood.MethodsWe used normative modelling to establish a reference for neurofunctional activation of functional magnetic resonance imaging based on an emotional episodic memory task, which is frequently used to study affective symptoms in psychiatric disorders. This normative reference was derived from a large dataset of healthy individuals (n = 409), and used to evaluate individualized functional alterations by calculating deviations from this reference in a clinical dataset of 328 participants, which included 168 healthy controls and patients with major depressive disorder (MDD, n = 56), bipolar disorder (BD, n = 31), and schizophrenia (SZ, n = 73). The neurofunctional deviations were mapped to emotional networks with specific emotional functions and used to predict affective symptoms in different mental disorders. The microscale cellular signatures underlying macroscale variations were identified using imaging transcriptomic analysis, and associated with affective symptoms.ResultsWe observed distinct patterns of cross-scale neural alterations linked to affective symptoms in three psychiatric disorders. Macroscale neural dysfunctions in distinct disorders were embedded into non-overlapping emotional networks and significantly associated with affective symptoms. The oligodendrocytes may mediate the network-specific impairments, and microglia for MDD, astrocytes for BD, and excitatory neurons for SZ as replicable cell-type correlates of affective symptoms.ConclusionsThese findings have potential implications for the understanding of unique neuropathological patterns of affective symptoms in distinct psychiatric disorders and improving individualized treatment response.
AllergenAI: a deep learning model predicting allergenicity based on protein sequence
Authors: Yang Chengyuan , Negi Surendra S , Schein Catherine H , Braun Werner , Kim Pora 
Published: June 2024

ABSTRACTInnovations in protein engineering can help redesign allergenic proteins to reduce adverse reactions in sensitive individuals. To accomplish this aim, a better knowledge of the molecular properties of allergenic proteins and the molecular features that make a protein allergenic is needed. We present a novel AI-based tool, AllergenAI, to quantify the allergenic potential of a given protein. Our approach is solely based on protein sequences, differentiating it from previous tools that use some knowledge of the allergens’ physicochemical and other properties in addition to sequence homology. We used the collected data on protein sequences of allergenic proteins as archived in the three well-established databases, SDAP 2.0, COMPARE, and AlgPred 2, to train a convolutional neural network and assessed its prediction performance by cross-validation. We then used Allergen AI to find novel potential proteins of the cupin family in date palm, spinach, maize, and red clover plants with a high allergenicity score that might have an adverse allergenic effect on sensitive individuals. By analyzing the feature importance scores (FIS) of vicilins, we identified a proline-alanine-rich (P-A) motif in the top 50% of FIS regions that overlapped with known IgE epitope regions of vicilin allergens. Furthermore, using∼ 1600 allergen structures in our SDAP database, we showed the potential to incorporate 3D information in a CNN model. Future, incorporating 3D information in training data should enhance the accuracy. AllergenAI is a novel foundation for identifying the critical features that distinguish allergenic proteins.
Population History and Admixture of the Fulani People from the Sahel
Authors: Fortes-Lima Cesar A. , Diallo Mame Yoro , Janoušek Václav , Černý Viktor , Schlebusch Carina M. 
Published: June 2024

SummaryThe Fulani people, one of the most important pastoralist groups in sub-Saharan Africa, are still largely underrepresented in population genomic research. They speak a Niger-Congo language called Fulfulde or Pulaar and live in scattered locations across the Sahel/Savannah Belt, from the Atlantic Ocean to Lake Chad. According to historical records, their ancestors spread from Futa Toro in the Middle Senegal Valley to Futa-Jallon in Guinea, and then eastward into the Sahel belt over the past 1500 years. However, the earlier history of this traditionally pastoral population has not been well studied. To uncover the genetic structure and ancestry of this widespread population, we gathered genome-wide genotype data from 460 individuals across 18 local Fulani populations, along with comparative data from both modern and ancient worldwide populations. This represents the most geographically wide-scaled genome-wide study of the Fulani to date. We revealed a genetic component closely associated with all local Fulani populations, suggesting a shared ancestral component possibly linked to the beginning of African pastoralism in the Green Sahara. Comparison to ancient DNA results also identified the presence of an ancient Iberomaurusian associated component across all Fulani groups, providing novel insights into their deep genetic history. Additionally, our genetic data indicate a later Fulani expansion from the western to the eastern Sahel, characterized by a clinal pattern and admixture with several other African populations north of the equator.
Increasing the representation of minoritized youth for inclusive and reproducible brain-behavior associations
Authors: Ramduny Jivesh , Uddin Lucina Q. , Vanderwal Tamara , Feczko Eric , Fair Damien A. , Kelly Clare , Baskin-Sommers Arielle 
Published: June 2024

AbstractPopulation neuroscience datasets allow researchers to estimate reliable effect sizes for brain-behavior associations because of their large sample sizes. However, these datasets undergo strict quality control to mitigate sources of noise, such as head motion. This practice often excludes a disproportionate number of minoritized individuals. We employ motion-ordering and motion-ordering+resampling (bagging) to test if these methods preserve functional MRI (fMRI) data in the Adolescent Brain Cognitive Development Study (N=5,733). Black and Hispanic youth exhibited excess head motion relative to data collected from White youth, and were discarded disproportionately when using conventional approaches. Both methods retained more than 99% of Black and Hispanic youth. They produced reproducible brain-behavior associations across low-/high-motion racial/ethnic groups based on motion-limited fMRI data. The motion-ordering and bagging methods are two feasible approaches that can enhance sample representation for testing brain-behavior associations and fulfill the promise of consortia datasets to produce generalizable effect sizes across diverse populations.