bluuebunny/crossref_metadata_2025_split huggingface dataset:
From confusion to clarity: a case report of hypertensive and autoimmune encephalopathy in an elderly woman
Authors: Adhikari Pratik 
Published: August 2024

Introduction and importance:
Hypertensive encephalopathy is a critical condition characterized by acute hypertension-induced cerebral dysfunction, while autoimmune encephalitis involves immune-mediated neuronal damage. Distinguishing between these entities is crucial due to overlapping clinical features and distinct management approaches.

Case presentation:
The authors present a case of a 70-year-old woman with poorly controlled hypertension who initially presented with confusion and severe headache. Despite treatment for a hypertensive emergency, including intravenous labetalol, her neurological status deteriorated. She developed seizures and fever, prompting further investigations. Initial imaging and cerebrospinal fluid (CSF) analysis suggested hypertensive encephalopathy, but negative microbiological findings and persistent symptoms necessitated consideration of autoimmune causes.

Clinical discussion:
Clinical evaluation, EEG findings, and autoimmune panels were pivotal in diagnosing autoimmune encephalitis, supported by positive anti-NMDA receptor antibodies. Prompt initiation of high-dose intravenous immunoglobulin (IVIG) led to clinical improvement, underscoring the role of targeted immunotherapy.

Conclusion:
This case highlights the diagnostic complexities and therapeutic challenges of hypertensive and autoimmune encephalopathy overlap in elderly patients. Early recognition and tailored immunotherapy were instrumental in achieving favorable outcomes, advocating for a multidisciplinary approach to managing such complex neurological conditions.
Postcesarean section abdominal wall endometriosis: a rare case report
Authors: Ibrahim Rana , Fadel Abbas , Dika Zakaria 
Published: August 2024

Introduction and importance:
Abdominal wall endometriosis (AWE) is a rare but significant complication following cesarean sections. It manifests with recurring right lower quadrant pain, particularly during menstruation, and palpable masses at the cesarean scar site. Recognizing these symptoms is critical for timely diagnosis and effective management. This report discusses the clinical manifestations, diagnostic approach, surgical intervention, and postoperative outcomes of AWE in a specific patient.

Case presentation:
A 28-year-old female presented with recurrent right lower quadrant pain, exacerbated during menstruation, and a palpable mass at her previous cesarean scar. Imaging revealed a well-defined 3.6 ×3 cm mass infiltrating through all layers of the abdominal wall.

Clinical discussion:
This case highlights the challenges of diagnosing AWE, often presenting with vague symptoms like cyclic pain and palpable masses. The primary diagnostic tool was a CT scan, with histopathological examination confirming the diagnosis. Surgical excision was performed, resulting in significant symptom relief and a low recurrence rate.

Conclusion:
This case underscores the importance of vigilance for AWE symptoms in patients with prior cesarean sections. Early recognition and surgical intervention are paramount for effective management and symptom alleviation
A case report on incidentally detected pulmonary sclerosing pneumocytoma: a diagnostic challenge
Authors: Mursalin Golam , Sawon Mehede H. , Alam Md. Kamrul , Islam Salwa 
Published: August 2024

Introduction and importance:
Pulmonary sclerosing pneumocytoma (PSP) is a rare non-cancerous lung tumor that is usually asymptomatic, but may cause respiratory distress if it becomes large. PSPs are often detected incidentally because of their slow growth, lack of symptoms, characteristic radiographic features, and increased use of imaging studies. Although it is not a malignant tumor, it can mimic malignancy on imaging and histology, leading to misdiagnosis and unnecessary surgery.

Case presentation:
A 23-year-old asymptomatic female was incidentally diagnosed with PSP during evaluation for a breast fibroadenoma. A chest CT revealed a 3 cm lobulated mass in the left upper lobe. Cytology showed malignant cells with necrotic debris. Immunohistochemistry was positive for TTF-1 and EMA, negative for p63 and AE1/AE3. Histopathology confirmed a well-circumscribed benign neoplasm, consistent with pulmonary sclerosing pneumocytoma. There was no mediastinal lymph node invasion, and the post-surgery prognosis was good.

Clinical discussion:
PSP is a slow-growing tumor that is often asymptomatic until it reaches a significant size. Owing to their well-circumscribed margins and the presence of calcifications, they are often detected incidentally during imaging studies, such as routine chest radiography or CT scans for unrelated conditions. Although these tumors are often incidental, it is important to diagnose and treat them appropriately to prevent potential complications and malignant transformation.

Conclusion:
The findings of this study contribute to the existing literature, increase awareness of this rare tumor, and provide insights into its diagnosis, treatment, and follow-up.
Comprehensive Characterization of Surface-Bound Proteins and Measurement of Fibrin Fiber Thickness on Extracorporeal Membrane Oxygenation Circuits Collected From Patients*
Authors: Cai Tengyi , Emery-Corbin Samantha J. , McCafferty Conor , Van Den Helm Suelyn , Letunica Natasha , Attard Chantal , Barton Rebecca , Horton Stephen , Bottrell Steve , Schultz Bradley , MacLaren Graeme , Chiletti Roberto , Best Derek , Johansen Amy , Newall Fiona , Butt Warwick , d’Udekem Yves , Dagley Laura F. , Yousef Jumana M. , Monagle Paul , Ignjatovic Vera 
Published: August 2024

OBJECTIVE:
To characterize surface-bound proteins and to measure the thickness of fibrin fibers bound to extracorporeal membrane oxygenation (ECMO) circuits used in children.

DESIGN:
Single-center observational prospective study, April to November 2021.

SETTING:
PICU, Royal Children’s Hospital, Melbourne, Australia.

PATIENTS:
Patients aged less than 18 years on venoarterial ECMO and without preexisting disorder.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
ECMO circuits were collected from six patients. Circuit samples were collected from five different sites, and subsequently processed for proteomic and scanning electron microscopy (SEM) studies. The concentration of proteins bound to ECMO circuit samples was measured using a bicinchoninic acid protein assay, whereas characterization of the bound proteome was performed using data-independent acquisition mass spectrometry. The Reactome Over-representation Pathway Analyses tool was used to identify functional pathways related to bound proteins. For the SEM studies, ECMO circuit samples were prepared and imaged, and the thickness of bound fibrin fibers was measured using the Fiji ImageJ software, version 1.53c (https://imagej.net/software/fiji/). Protein binding to ECMO circuit samples and fibrin networks showed significant intra-circuit and interpatient variation. The median (range) total protein concentration was 19.0 (0–76.9) μg/mL, and the median total number of proteins was 2011 (1435–2777). A total of 933 proteins were commonly bound to ECMO circuit samples from all patients and were functionally involved in 212 pathways, with signal transduction, cell cycle, and metabolism of proteins being the top three pathway categories. The median intra-circuit fibrin fiber thickness was 0.20 (0.15–0.24) μm, whereas the median interpatient fibrin fiber thickness was 0.18 (0.15–0.21) μm.

CONCLUSIONS:
In this report, we have characterized proteins and fiber fibrin thickness bound to ECMO circuits in six children. The techniques and approaches may be useful for investigating interactions between blood, coagulation, and the ECMO circuit and have the potential for circuit design.
Phase I Dose Volume Escalation of Rectally Administered PC-1005 to Assess Safety, Pharmacokinetics, and Antiviral Pharmacodynamics as a Multipurpose Prevention Technology (MTN-037)
Authors: Ho Ken , Hoesley Craig , Anderson Peter L. , Fernández-Romero Jose A. , Friedland Barbara A. , Kelly Clifton W. , Jiao Yuqing , Edick Stacey , Brand Rhonda , Kunjara Na Ayudhya Ratiya Pamela , Zyhowski Ashley , Hartman Douglas J. , Reddy Nipun B. , Al-Khouja Amer , Piper Jeanna , Bauermeister Jose A. , Teleshova Natalia , Melo Claudia , Cornejal Nadjet , Barnable Patrick , Singh Devika , Scheckter Rachel , McClure Tara , Hillier Sharon L. , Hendrix Craig W. ,   on behalf of the MTN-037 Study Team
Published: August 2024

Background:
On demand, topical PrEP is desired by those preferring episodic, nonsystemic PrEP. PC-1005 gel (MIV-150, zinc, and carrageenan) exhibits in vitro antiviral HIV-1, human papillomavirus (HPV), and herpes simplex virus type 2 (HSV-2) activity, attractive for a multipurpose prevention technology candidate. We evaluated the safety, pharmacokinetics, and antiviral effect of rectally applied PC-1005.

Methods:
HIV-uninfected adults received a series of 3 rectal PC-1005 doses—4, 16, and 32 mL separated by 2-week washout periods. Following each dose, plasma, rectal fluid and tissue, and vaginal fluid were collected over 48 hours.

Results:
Thirteen adults enrolled; 12 completed all 3 doses. All 13 adverse events reported were grade 1 or 2; 5 were judged study drug related. Plasma MIV-150 peaked 1–2 h after dosing with a median peak concentrations range of 0.07–0.23 ng/mL and median half-life range of 4.9–7.4 hours across dose volumes; median concentrations were below assay quantitation limits (BLQ) 24 hours after dosing. Rectal tissue MIV-150 peaked 0.5–1 hours after dosing at 1.4 ng/g (ng/mL) (0.8, 1.9), 46.0 (30.7, 831.0), and 79.7 (11.9, 116.0), respectively, after each dose volume; median tissue concentrations were BLQ beyond 5 hours for all doses. All vaginal fluid samples were BLQ. Ex vivo antiviral assays showed 5 hours of antiviral HPV and HSV effects but no anti-HIV activity.

Conclusions:
MIV-150 rectal tissue concentrations were below the 100 ng/g target concentration and transient. Ex vivo assays demonstrated antiviral HSV and HPV effects but not against HIV. PC-1005 requires a more potent antiviral and longer-lasting formulation for further consideration as a multipurpose prevention technology candidate.

Clinical Trials:

NCT03408899.
Vagococcus jeotgali sp. nov., isolated from cutlassfish jeotgal, a traditional Korean fermented seafood
Authors: Joe Sung-Hong , Yang Ah-In , Kim Bora , Joe Hae-In , Hong Yeongjin , Shin Na-Ri 
Published: August 2024

A novel, Gram-positive, facultatively anaerobic, and non-motile bacterial strain, designated B2T-5T, was isolated from jeotgal, a traditional Korean fermented seafood. Colonies grown on gifu anaerobic medium agar plates were cream-coloured, irregular, and umbonate with curled margins. Optimal growth of strain B2T-5T occurred at 20 °C, pH 8.0, and in the presence of 1% (w/v) NaCl. Strain B2T-5T was negative for oxidase and catalase activity. Hippurate was not hydrolysed and acetoin was not produced. The major cellular fatty acids were C18 : 1
ω9c and C16 : 0. The cell-wall peptidoglycan was of the A4α type containing l-Lys–d-Asp. The predominant respiratory quinone was menaquinone 7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. According to the phylogenetic analysis based on 16S rRNA gene sequences, strain B2T-5T was most closely related to Vagococcus teuberi DSM 21459T, showing 98.2% sequence similarity. Genome sequencing of strain B2T-5T revealed a genome size of 2.0 Mbp and a G+C content of 33.8 mol%. The average nucleotide identities of strain B2T-5T with Vagococcus teuberi DSM 21459T, Vagococcus bubulae SS1994T, and Vagococcus martis D7T301T were 75.0, 74.7, and 75.1%, respectively. Based on the phenotypic, chemotaxonomic, and genotypic data, strain B2T-5T represents a novel species of the genus Vagococcus, for which the name Vagococcus jeotgali sp. nov. is proposed. The type strain is B2T-5T (=KCTC 21223T=JCM 35937T).
High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian
Authors: Ishiya Koji , Mizuno Fuzuki , Gojobori Jun , Kumagai Masahiko , Taniguchi Yasuhiro , Kondo Osamu , Matsushita Masami , Matsushita Takayuki , Wang Li , Kurosaki Kunihiko , Ueda Shintaroh 
Published: August 2024

AbstractThe migration of prehistoric humans led to intriguing interactions and changes in cultural and genetic heritage. In Eurasia, prehistoric migration and population replacement have affected present-day humans. The available high-quality genetic evidence for prehistoric migration in eastern Eurasia, particularly in the Far East, is still limited. We succeeded in obtaining low-contaminant, high-coverage genomes from middle-Yayoi (>46-fold coverage) and Initial Jomon (>67-fold coverage) individuals from mainland Japan. This study demonstrated that the Yayoi individual exhibited a genetic profile distinct from that of the indigenous Jomon population of the Japanese archipelago, suggesting that Yayoi ancestry was connected to the peopling of the Eurasian continent. Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people. The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent. Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then. The high-coverage whole-genome sequence also revealed differences in the demographic backgrounds of the two ancestral populations during the Yayoi and Jomon periods. Our results shed light on the prehistorical events and origins of related migrations from Eurasia at that time and their genetic background, cultural transformations, and links to modern Japanese people.
Associations between oral microbiota pathogens and elevated depressive and anxiety symptoms in men
Authors: Kerff Fannie , Pasco Julie A , Williams Lana J , Jacka Felice N , Loughman Amy , Dawson Samantha L 
Published: August 2024

AbstractBackgroundSystemic inflammation has been associated with depression. Certain oral bacterial species contribute to extra oral inflammation, however their potential association with mental disorders remains unclear. This study investigated the associations between oral microbiota pathogens and depressive and anxiety symptoms.MethodsData came from 436 men from the Geelong Osteoporosis Study. Using 16S rRNA gene sequencing, we characterized the oral microbiota composition and created a composite variable representing the prevalence of known oral pathogens,Porphyromonas gingivalis,Treponema denticola,Fusobacterium nucleatum, andPrevotella nigrescens. Binary variables were created representing elevated depressive and anxiety symptoms using the Hospital Anxiety and Depression Scale. Associations between oral pathogens and elevated depressive/anxiety symptoms were analyzed using logistic regression adjusted for confounders (age, socio-economic status, diet, smoking, alcohol, exercise, obesity and hypertension).ResultsWe found limited evidence for an association between the pathogen composite and elevated depressive (N = 39) but not anxiety (N = 66) symptoms. Moreover, some of the comprising species,P. nigrescens(OR 1.61 (95% CI 1.21, 2.13)) andF. nucleatum (subsp. animalis ATCC 51191(1.54 (1.13, 2.11)),subsp. animalis(1.47 (1.05, 2.08)) andsubsp. vincentii(1.47 (1.06, 2.04))) were associated with elevated depressive symptoms. Exploratory analyses revealed several other taxa associated with depression and anxiety.LimitationsThis study focuses on mental health symptoms and not diagnoses in men, and the results may not be generalizable to women.ConclusionsWe identified several taxa within the oral microbiota that were associated with depressive and anxiety symptoms. Further replication and mechanistic studies are needed.HighlightsA composite of oral pathogens is associated with depressive symptoms in adult menAssociations betweenP. nigrescens and other species and elevated depressive symptomsAssociations remain following adjustment for confoundersOral microbial diversity was not associated with depressive or anxiety symptomsFewer associations between oral microbial composition and anxiety than depression
Characteristics of human donor lungs utilized for research
Authors: Shankar Nishanth R , Garnica Lorena , Stahlschmidt Emily , Byers Derek , Kulkarni Hrishikesh 
Published: August 2024

AbstractIntroductionMany fundamental discoveries have occurred using primary cells from deceased donor lungs. These cells respond differently to injury when there are underlying co-morbidities like diabetes mellitus, hypertension, aging and exposures to cigarette smoke, cocaine and chronic alcohol use. However, the prevalence of these characteristics in donor lungs utilized for research is currently unknown.MethodsThis retrospective cohort study procured data of lung transplant donors from Mid-America Transplant from January 2017 until July 2023. The donors were characterized based on lung utilization into three groups - lungs used for research, lungs used for transplant, and lungs not recovered from donors for either research or transplantation.ResultsThe mean age of donors whose lungs were utilized for research was 41±18 years. 25% of them were expanded criteria donors (ECD) while 10% of the donors in the transplant cohort were ECD. 14% of the donors whose lungs were utilized for research had history of diabetes compared to 8% of donors whose lungs were transplanted. A quarter of the research donor population had positive history of cigarette use within the preceding 20 years. At least 40% of donors had a positive history of non-intravenous drug use, of whom a majority had a history of continued non-intravenous drug use.ConclusionsNo strict selection criteria or protocols exist when human donor lungs are obtained for ex-vivo research. There is a high prevalence of diabetes mellitus, history of smoking and non-intravenous drug use along with older age distribution in donors whose lungs used are for research.
Regulatory Roles of Long Non-Coding RNAs in Arterial Stiffness and Hypertension: Insights from Two African American Studies
Authors: Vargas Jose D. , Abbas Malak , Goodney Gabriel , Gaye Amadou 
Published: August 2024

ABSTRACTBackgroundArterial stiffness, commonly assessed via pulse wave velocity (PWV), is marked by reduced arterial elasticity and serves as a significant risk factor for cardiovascular disease and an early indicator of hypertension. This study investigated the regulatory roles of long non-coding RNAs (lncRNAs) in modulating mRNAs associated with arterial stiffness and hypertension, with a particular focus on African Americans, a population disproportionately impacted by hypertension.MethodsWe utilized whole-blood transcriptome sequencing data from two African American (AA) cohorts with high hypertension prevalence: the GENE-FORECAST study (436 subjects) and the MH-GRID study (179 subjects). Our objectives were to: (1) identify lncRNAs and mRNAs differentially expressed (DE) between the upper and lower tertiles of PWV, (2) determine DE lncRNAs associated with the expression levels of each DE mRNA, and (3) link the lncRNA-modulated mRNAs to hypertension across both datasets.ResultsDifferential expression analysis revealed 1,035 DE mRNAs and 31 DE lncRNAs between upper and lower PWV groups. Then lncRNA-mRNA pairs significantly associated were identified, involving 31 unique lncRNAs and 1,034 unique mRNAs. Finally, 22 of the lncRNA-modulated mRNAs initially linked to PWV were found associated with hypertension, in both datasets. Interestingly, 30 lncRNAs were linked to the expression of UCP2 (Uncoupling Protein 2), a gene implicated in oxidative stress and endothelial function.ConclusionsOur findings underscore the significant roles of lncRNAs in regulating gene expression associated with arterial stiffness and hypertension. The differential expression of UCP2 in relation to PWV and hypertension, along with its potential regulation by lncRNAs, offers valuable insights into the molecular mechanisms underlying arterial stiffness and its connection with hypertension.
3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility
Authors: Trang Khanh B. , Sharma Prabhat , Cook Laura , Mount Zachary , Thomas Rajan M. , Kulkarni Nikhil N. , Pahl Matthew C. , Pippin James A. , Su Chun , Kaestner Klaus H. , O’Brien Joan M. , Wagley Yadav , Hankenson Kurt D. , Jermusyk Ashley , Hoskins Jason W. , Amundadottir Laufey T. , Xu Mai , Brown Kevin M. , Anderson Stewart A. , Yang Wenli , Titchenell Paul M. , Seale Patrick , Zemel Babette S. , Chesi Alessandra , Romberg Neil , Levings Megan K. , Grant Struan F.A. , Wells Andrew D. 
Published: August 2024

ABSTRACTA portion of the genetic basis for many common autoimmune disorders has been uncovered by genome-wide association studies (GWAS), but GWAS do not reveal causal variants, effector genes, or the cell types impacted by disease-associated variation. We have generated 3D genomic datasets consisting of promoter-focused Capture-C, Hi-C, ATAC-seq, and RNA-seq and integrated these data with GWAS of 16 autoimmune traits to physically map disease-associated variants to the effector genes they likely regulate in 57 human cell types. These 3D maps of genecis-regulatory architecture are highly powered to identify the cell types most likely impacted by disease-associated genetic variation compared to 1D genomic features, and tend to implicate different effector genes than eQTL approaches in the same cell types. Most of the variants implicated by thesecis-regulatory architectures are highly trait-specific, but nearly half of the target genes connected to these variants are shared across multiple autoimmune disorders in multiple cell types, suggesting a high level of genetic diversity and complexity among autoimmune diseases that nonetheless converge at the level of target gene and cell type. Substantial effector gene sharing led to the common enrichment of similar biological networks across disease and cell types. However, trait-specific pathways representing potential areas for disease-specific intervention were identified. To test this, we pharmacologically validated squalene synthase, a cholesterol biosynthetic enzyme encoded by theFDFT1gene implicated by our approach in MS and SLE, as a novel immunomodulatory drug target controlling inflammatory cytokine production by human T cells. These data represent a comprehensive resource for basic discovery of genecis-regulatory mechanisms, and the analyses reported reveal mechanisms by which autoimmune-associated variants act to regulate gene expression, function, and pathology across multiple, distinct tissues and cell types.