bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploratory analyses of biomarkers in blood and stratum corneum in patients with atopic dermatitis
Authors: Maruyama Ayano , Tamagawa-Mineoka Risa , Nishigaki Hiromi , Masuda Koji , Katoh Norito 
Published: October 2022

Background:
The pathogenesis of atopic dermatitis (AD) involves various mediators, including cytokines and chemokines, which are produced by immune cells, such as dendritic cells and lymphocytes, and non-immune cells, such as epidermal cells. Several mediators, including thymus and activation-regulated chemokine (TARC), are used as biomarkers for AD severity and activity. However, additional local and systemic biomarkers of AD are required.

Methods:
This study will include 10 male patients with AD and 5 healthy adult males (age range: 20–80 years). The Eczema Area and Severity Index will be used to objectively evaluate the clinical findings. In addition, the severity of eruptions will be assessed on a 5-point scale by scoring symptoms (erythema, edema/papules, oozing/crusting, excoriation, lichenification, and xerosis), and the total intensity will be calculated by adding the symptom scores together. Subjective symptoms will be assessed using a peak pruritus numerical rating scale. Laboratory tests, including measurements of peripheral eosinophil count and serum total immunoglobulin E, TARC, and lactate dehydrogenase levels, will be performed. Using blood samples and extracts of stratum corneum samples obtained by tape stripping, we will conduct an exploratory analysis of protein expression using an antibody array to identify mediators whose levels are significantly altered in patients with AD. After 4 to 8 weeks, blood samples and stratum corneum samples will be collected again from AD patients. Moreover, we will examine whether the candidate proteins can be quantified using enzyme-linked immunosorbent assays.

Discussion:
This is an important study exploring potential local and systemic biomarkers of AD. The results of this study will be clinically meaningful for the discovery of new biomarkers for diagnosing and assessing the severity of AD.
Association between the risk of hepatitis virus-related hepatocellular carcinoma and EGF polymorphism: A PRISMA-compliant updated meta-analysis
Authors: Wang Qinjing , Xu Lingling , Wu Qianbo , Zhang Min , Zhang Jing 
Published: October 2022

Background:
The study aims to provide a comprehensive account of the association between the epidermal growth factor (EGF) + 61A/G polymorphism (rs4444903) and susceptibility to virus-related hepatocellular carcinoma (HCC).

Methods:
Electronic searching of the Chinese National Knowledge Infrastructure, Wanfang, Chinese Scientific Journal Database (VIP), PubMed, Web of Science, and Embase was conducted to select eligible studies. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated to assess the strength of the association.

Results:
In this study, a total of 18 articles were included with 2692 cases and 5835 controls for assessing the association between rs4444903 and HCC risk. The pooled results showed that the EGF + 61A/G polymorphism was significantly associated with the risk of virus-related HCC in all genetic models. Stratified analyses were conducted based on ethnicity, study quality, source of controls, type of controls, number of cases and genotyping method. The results showed that EGF + 61A/G polymorphisms significantly affect HCC susceptibility in different stratified populations. High heterogeneity was observed across included studies, and meta-regression analysis demonstrated that race, type of controls, and study quality contribute to the observed heterogeneity.

Conclusion:
This pooled analysis found that EGF + 61A/G polymorphism was significantly associated with the risk of HCC.
Diagnostic dilemma of celiac disease presenting with weight loss and secondary amenorrhea: A case report
Authors: Mumtaz Arif , Khan Qaisar Ali , Asim Nowshad , Baqi Abdul , Iram Sumaira , Majeed Abdul , Tahir Muhammad Junaid , Islam Md. Saiful , Yousaf Zohaib 
Published: October 2022

Rationale:
Celiac disease (CD) is autoimmune enteropathy affecting the proximal small intestinal mucosa. It is caused by insensitivity to gluten, a protein predominantly presented in wheat. CD is classically associated with gastrointestinal symptoms. The non-classic clinical presentation of CD can present with other organ involvement. Non-human leukocyte antigens genes are associated with atypical forms.

Patients concern:
We reported a case of 30-year-old female who presented with progressive pallor, amenorrhea, and unexplained weight loss with generalized body weakness. Her body mass index was 20. The patient was having no other systemic manifestations.

Diagnosis:
This paper reports a case of a female patient having CD without its typical features. Her laboratory evaluation revealed microcytic anemia. Anti-TTg IgA and Anti-TTG IgG antibodies were raised, ferritin and folate were low, and there was mild hyperbilirubinemia. However, follicle-stimulating hormone, luteinizing hormone, and serum estradiol levels were normal. She was diagnosed with a case of anemia resulting from malabsorption caused by CD.

Interventions:
A management plan was devised based on a strict gluten-free diet. The patient received supplements containing folates, iron, calcium, zinc, and vitamins A, D, E, B6, and B12.

Outcomes:
After 3 months of treatment with strict gluten-free diet patient showed remarkable improvement. Her hemoglobin level raised with weight gain. Her normal menstrual cycle was restored with complete resolution of symptoms at 1 year follow-up.

Lessons:
The pathogenesis of the atypical CD is multifactorial, but impaired uptake of micronutrients from the duodenum is the most likely cause, even if other common features of classical forms, such as bloating and diarrhea, are absent. Lack of awareness about atypical forms may lead to under-diagnoses of the disease. The physicians should consider the atypical presentations of CD to avoid the under-diagnoses of this multisystem disorder.
Rare magnetic resonance imaging findings of intracranial solitary fibrous tumor: A case report
Authors: Huang Zhicheng , Dai Dongqin , Tang Guangcai 
Published: October 2022

Rationale:
Solitary fibrous tumor (SFT) is a rare mesenchymal spindle cell tumor. SFT in the central nervous system (CNS) is rare. This case reports rare magnetic resonance imaging (MRI) findings of intracranial SFT (ISFT).

Patient concerns:
We report a 47-year-old female patient who was found to have weakness in her right limb with walking instability 2 months before the visit.

Diagnoses:
Based on imaging, the provisional diagnosis was meningioma. Postsurgical histopathological diagnosis confirmed World Health Organization (WHO) grade I SFT/hemangiopericytoma (HPC).

Interventions:
The lesion was totally excised. The patient improved remarkably after the operation, without any signs of associated limb movement disorder.

Outcomes:
No local recurrence or metastases were observed in the follow-up 3 months after the surgery.

Lessons:
Intracranial SFT is a rare mesenchymal tumor. Due to different tumor components, imaging manifestations are diverse and lack of characteristics, so preoperative diagnosis is challenging. Our case provides a rare ISFT with significantly decreased signal intensity in T2 weighted images (T2WI), which is an important supplement to the rare imaging findings of intracranial SFT.
Clinical Application of a Modified Local Transposition Flap (Parallelogram Flap) Surgery in Repairing Fingertip Defects
Authors: Zhang Yingkai , Wang Yao , Zhou Jiaqi , He Xianwei , Wu Rongbo 
Published: October 2022

Objective
Parallelogram flap was performed for transverse finger amputation with the loss of distal pulp, nails, and bone. This study aimed to compare the clinical effects of parallelogram flap, antegrade homodigital island flaps, and reverse digital artery island flaps in fingertip reconstruction.

Patients and Methods
From January 2017 to January 2021, clinical patient data with parallelogram flaps (78 cases), antegrade homodigital island flaps (78 cases), and reverse digital artery island flaps (78 cases) to repair fingertip defects were collected and analyzed. Two hundred thirty-four cases (234 fingers) were included in our study. All operations were performed by one surgical team. The operation time, 2-point discrimination, total active movement, and the Michigan Hand Questionnaire (MHQ) of the injured fingers were recorded to evaluate the therapeutic effect.

Results
Parallelogram flaps (group A), antegrade homodigital island flaps (group B), and reverse digital artery island flaps (group C) had survived postoperatively. The operative duration of group A is the shortest (A < B < C, P < 0.05). At the last 6-month follow-up, there was no difference with the 2-point discrimination of the palmar part of the flaps in group A and group B but better than group C (P < 0.05). There was no difference with the total active movement of injured figures in 3 groups (P > 0.05). The MHQ summary scores in group A were much higher than those in group B and group C (P < 0.05). Evaluation of the MHQ subscale performance showed that the overall hand function, activities of daily living, work performance, and pain score had no differences (P > 0.05), but aesthetics and satisfaction score was the highest in group A (A > B > C, P < 0.05).

Conclusions
The reconstruction of transverse finger amputation using parallelogram flaps can achieve a shorter operation time, a more satisfying appearance. Parallelogram flaps and antegrade homodigital island flaps can both achieve a better sensory recovery. Parallelogram flaps is a better choice for reconstruction of transverse finger amputation with the loss of distal pulp, nails, and bone.
Closed-Incision Negative Pressure Therapy Prevents Major Abdominal Donor-Site Complications in Autologous Breast Reconstruction
Authors: Limpiado MarcArthur , Guest Rachel , Egan Katie G. , Elver Ashlie A. , Johnson Braden M. , Cullom Melissa E. , Nazir Niaman , Holding Julie , Lai Eric C. , Butterworth James A. 
Published: October 2022

Background
Outcomes in autologous breast reconstruction continue to improve with refinements in microsurgical techniques; however, donor-site morbidity remains a concern. Closed-incision negative pressure therapy (ciNPT) has been shown to reduce wound complications. Limited evaluation in abdominal donor sites has shown promising results. We hypothesize that ciNPT will reduce abdominal donor-site complications.

Methods
A retrospective chart review was performed of patients who underwent abdominally based autologous free tissue transfer for breast reconstruction by 4 microsurgeons at an academic institution from 2015 to 2020. The application of a commercial ciNPT for donor-site management was at the discretion of the operating surgeon. Demographics, operative details, and management of donor-site complications were analyzed.

Results
Four hundred thirty-three patients underwent autologous breast reconstruction; 212 abdominal donor sites were managed with ciNPT and 219 with standard dressings. Demographics were statistically similar between groups. Abdominal wound healing complications were noted in 30.2% of ciNPT patients (64/212) and 22.8% of control patients (50/219, P = 0.08); however, overall wound complications were attributed to obesity on multivariable analysis. Closed-incision negative pressure therapy significantly decreased complications requiring reoperation (ciNPT 6.2%, 4/64; control 26.5%, 13/51; P = 0.004). There were no significant differences in surgical site infection rates (P = 0.73) and rates of abdominal scar revisions (ciNPT 11.8%, 25/212; control 9.1%, 20/219; P = 0.37).

Conclusions
Use of ciNPT in abdominal donor-site management significantly decreases the incidence of delayed wound healing requiring surgical intervention, with one major wound healing complication prevented for every 6 donor sites managed with ciNPT.
Using a Business Model (the 4 Disciplines of Execution) to Improve Consistency, Efficiency, and Length of Stay in Microvascular Autologous Breast Reconstruction
Authors: Easton Joseph , Roberto Amy , Lax Elizabeth , Reyna Chantal , Dale Elizabeth 
Published: October 2022

Background
Autologous free tissue transfer is a common method of breast reconstruction in the United States, but it involves many care teams and can incur a large cost on an institution. The consistency and efficiency of performing these procedures can be improved with a method called the 4 disciplines of execution (4DX).

Methods
Patients that underwent autologous breast reconstruction between 2015 and 2020 were included. Midway through the collection period, several preoperative and intraoperative interventions were implemented using the 4DX. Then, 2 cohorts of patients were analyzed for differences in operative times, length of stay (LOS), and major complications.

Results
Thirty-two total patients were included. The median operative time before interventions were implemented was 828 minutes, and the median operative time after interventions was 619 minutes (P < 0.05). The median LOS in days before interventions was 5 days, and the median LOS after interventions was 3 days (P < 0.05). There were no statistically significant differences in complications before or after the interventions.

Conclusions
The 4DX successfully improved consistency and efficiency in the process of performing autologous breast reconstruction at our institution, as evidenced by a faster median operative time and shorter patient LOS in the hospital.
Sitagliptin Versus Placebo to Reduce the Incidence and Severity of Posttransplant Diabetes Mellitus After Kidney Transplantation—A Single-center, Randomized, Double-blind Controlled Trial
Authors: Delos Santos Rowena B. , Hagopian Jennifer C. , Chen Ling , Ramakrishnan Madhuri , Wijeweera Helen , Klein Christina L. , Brennan Daniel C. 
Published: October 2022

Background.
Postkidney transplant diabetes mellitus (PTDM) affects cardiovascular, allograft, and recipient health. We tested whether early intervention with sitagliptin for hyperglycemia (blood glucose >200 mg/dL) within the first week of transplant and discontinued at 3 mo could prevent development of PTDM in patients without preexisting diabetes.

Methods.
The primary efficacy objective was to improve 2-h oral glucose tolerance test (OGTT) by >20 mg/dL at 3 mo posttransplant. The secondary efficacy objective was to prevent new onset PTDM, defined as a normal OGTT at 3 mo.

Results.
Sixty-one patients consented, and 50 patients were analyzed. The 3-mo 2-h OGTT (end of treatment) was 141.00 ± 62.44 mg/dL in the sitagliptin arm and 165.22 ± 72.03 mg/dL (P = 0.218) in the placebo arm. The 6-mo 2-h OGTT (end of follow-up) was 174.38 ± 77.93 mg/dL in the sitagliptin arm and 171.86 ± 83.69 ng/dL (P = 0.918) in the placebo arm. Mean intrapatient difference between 3- and 6-mo 2-h OGTT in the 3-mo period off study drug was 27.56 + 52.74 mg/dL in the sitagliptin arm and −0.14 + 45.80 mg/dL in the placebo arm (P = 0.0692). At 3 mo, 61.54% of sitagliptin and 43.48% of placebo patients had a normal 2-h OGTT (P = 0.2062), with the absolute risk reduction 18.06%. There were no differences in HbA1c at 3 or 6 mo between sitagliptin and placebo groups. Participants tolerated sitagliptin well.

Conclusions.
Although this study did not show a significant difference between groups, it can inform future studies in the use of sitagliptin in the very early posttransplant period.
Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis
Authors: Banayo Joy B. , Manese Kathlyn Louise V. , Salces Agapita J. , Yamagata Takahiro 
Published: October 2022

ABSTRACTPhilippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and Visayas, Philippines. In addition, a much-debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n=157) were collected from 10 provinces in Luzon and the Visayas, Philippines. Approximately 650 base pairs of the mtDNA d-loop control region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1-38 samples each), forming 4 haplogroups i.e. North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but the use of wild pig for interspecific hybridization was observed. This study showed that the Philippine native pigs have ancestral origin from at least 3Sus scrofalineage and that they were not domesticated from the endemic wild pigs of the Philippines.
Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing
Authors: Baker Daniel N. , Langmead Ben 
Published: October 2022

AbstractA genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing dataset. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. While existing tools can easily compare 10,000s of genomes, relevant datasets can reach millions of sequences and beyond. Popular tools also fail to considerk-mer multiplicities, making them less applicable in quantitative settings. We describe a method called Dashing 2 that builds on the SetSketch data structure. SetSketch is related to HyperLogLog, but discards use of leading zero count in favor of a truncated logarithm of adjustable base. Unlike HLL, SetSketch can perform multiplicity-aware sketching when combined with the ProbMinHash method. Dashing 2 integrates locality-sensitive hashing to scale all-pairs comparisons to millions of sequences. Dashing 2 is free, open source software available athttps://github.com/dnbaker/dashing2
Comparative Analysis of RNA Secondary Structure Accuracy on Predicted RNA 3D Models
Authors: Kulkarni Mandar , Thangappan Jayaraman , Deb Indrajit , Wu Sangwook 
Published: October 2022

ABSTRACTRNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) information is the standard prerequisite for most RNA 3D modeling. Despite several 2D and 3D structure prediction tools proposed in recent years, one of the challenges is to choose the best combination for accurate RNA 3D structure prediction. Here, we benchmarked seven small RNA PDB structures (40 to 90 nucleotides) with different topologies to understand the effects of different 2D structure predictions on the accuracy of 3D modeling. The current study explores the blind challenge of 2D to 3D conversions and highlights the performances ofde novoRNA 3D modeling from their predicted 2D structure constraints. Our results show that conformational sampling-based methods such as SimRNA and IsRNA1 depend less on 2D accuracy, whereas motif-based methods account for 2D evidence. Our observations illustrate the disparities in available 3D and 2D prediction methods and may further offer insights into developing topology-specific or family-specific RNA structure prediction pipelines.
A Machine-learning-based Method to Detect Degradation of Motor Control Stability with Applications to Diagnosis of Presymptomatic Parkinson’s Disease
Authors: Shah Vrutangkumar V. , Jadav Shail , Goyal Sachin , Palanthandalam-Madapusi Harish J. 
Published: October 2022

AbstractParkinson’s disease (PD), a neuro-degenerative disorder, is often detected by onset of its motor symptoms such as rest tremor. Unfortunately, motor symptoms appear only when approximately 40%-60% of the dopaminergic neurons in the substantia nigra are lost. In most cases, by the time PD is clinically diagnosed, the disease may already have started 4 to 6 years beforehand. So there is a need for developing a test for detecting PDbeforethe onset of the motor symptoms. This phase of PD is referred to as Presymptomatic PD (PPD). The motor symptoms of Parkinsons Disease are manifestations of instability in the sensorimotor system that develops gradually due to the neuro-degenerative process. In this paper, based on the above insight, we propose a new method that can potentially be used to detect degradation of motor control stability which can be employed for the detection of PPD. The proposed method tracks the tendency of a feedback control system to transition to an unstable state, and uses machine learning algorithm for its robust detection. This method is explored using simulations of a simple pendulum with PID controller as a conceptual representation for both healthy and PPD individuals. We also propose an example task with physiological measurements that can be used with this method and potentially be employed in a clinical setting. We present representative data collected through such a task, thereby demonstrating the feasibility to generate data for the proposed method.Author summaryParkinson’s disease (PD) is a neuro-degenerative disorder that develops and progresses over several years. Currently, one is able to diagnose PD only after the appearance of motor symptoms (symptoms in movements of body parts), which unfortunately may be 4 to 6 years after the neuro-degeneration may have started. It has been shown that there are benefits to diagnosing PD at early stages, motivating the need to explore tools for diagnosing PD in the pre-symptomatic stage referred to as Presymptomatic Parkinson’s disease (PPD). In this paper, a novel approach is explored that utilises the insight that the motor symptoms in PD may be seen as an instability in the feedback-control system that controls movements of body parts (sensory-motor loop). The proposed method uses a series of simple movement tasks performed by an individual in a clinic as the input to detect any gradual degradation of movement control that is leading to an instability, but before the instability and consequently the symptoms are manifested. This method is tested through extensive simulations and a potential experimental realisation with preliminary data. While a full-fledged validation will be undertaken as part of future work, initial results show promise and feasibility of further data collection.