bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emerging perspectives in the management of IgA nephropathy: a comprehensive review
Authors: Gomes Ana Marta , Schau Bruno , Farinha Ana 
Published: November 2024

Abstract
IgA nephropathy (IgAN) is the most prevalent form of primary glomerulonephritis worldwide and a leading cause of chronic kidney disease and renal failure. This disorder is characterized by the deposition of immune complexes containing galactose-deficient forms of IgA and complement C3 in the glomeruli. Until now, disease management relied mainly on optimized supportive care. Systemic corticosteroid therapy is proposed for patients at high risk of disease progression, but the effectiveness and safety of this approach are under debate. A significant proportion of patients do not respond to current therapies and require kidney replacement therapy at a young age, with substantial costs and impact on quality of life. Recently, there have been multiple joint efforts to improve the understanding of IgAN pathophysiology. International collaborations resulted in multiple ongoing clinical trials that are providing new insights toward innovative therapeutic options such as SGLT2 inhibitors, dual endothelin and angiotensin receptor blockers, targeted-release budesonide, B-cell proliferation and differentiation inhibitors, and complement system blockers. Based on this new evidence, revision of the guidelines to manage IgAN is expected to occur in the near future. In addition to the novelty in therapeutic agents, there is also a growing interest in new noninvasive biomarkers for IgAN screening, risk stratification to monitor the course of the disease, and the response to treatment. In this review, we discuss current knowledge on the pathophysiology of IgAN, disease management, and emerging advances in clinical translation of IgAN research.
What do you need to know when preparing to give a talk at an international dermatology conference? Insights and practical recommendations
Authors: Shah Hemali , Parisi Rose , Polo Silveira Luísa , Dodiuk-Gad Roni P. 
Published: November 2024

Objectives:
To provide a checklist for presentation preparation at dermatology conferences, discuss important factors to consider when preparing a presentation, and recommend strategies for effective presentations and networking.

Data Sources:
With a combination of personal experience and literature review of PubMed database and dermatology society resources, this article serves as the first comprehensive guide for how to prepare a talk for an international dermatology conference.

Conclusion:
Conferences are an excellent opportunity to learn more about yourself, your field, and others throughout the world. Well-prepared presentations have the potential to greatly impact your audience and expand your connections. The authors provide a step-by-step discussion and checklist that thoroughly addresses the logistics, operations, scientific content, and social aspects that are important to know when preparing to give a presentation in the field of dermatology.
An overview of Helicobacter pylori infections, diagnostic methods and treatment
Authors: Mohammadi Mohammad Reza , Omidi Amir Hossein , Mohsenzadeh Amin , Sabati Hoda , Daliri Layegheh 
Published: November 2024

Background:Helicobacter pyloriis one of the most common infectious diseases in the world, causing peptic ulcers and gastric cancer in humans.Methods:Here, we used the words ‘Helicobacter pylori’, ‘identification’ and ‘treatment’ from the published data in PubMed, Scopus, and Google Scholar databases for this study.Results:Methods of identification ofH. pyloriare divided into two categories: invasive and noninvasive. Invasive methods detect bacteria directly from gastric biopsy, but noninvasive methods examine different samples. The key to effective treatment forH. pyloriinfection is the use of combination therapy, similar to the treatment for bacterial meningitis or endocarditis. Although alternative therapies, including herbal remedies and probiotics, have been used to improve eradication, current treatments still rely on a combination of antimicrobial agents such as amoxicillin, clarithromycin, metronidazole, and levofloxacin, as well as antisecretory agents such as proton pump inhibitors.Conclusion:Both invasive and noninvasive diagnostic methods identifyH. pylori. Combination therapies are more efficient in eradicating the bacterium.
Bacterial contamination on the white coats of medical laboratory students at a tertiary care hospital
Authors: Nayak Kusumakshi , Shetty Seema , Poojary Akshaya , Prabhu Thejaswini 
Published: November 2024

Background:
White coats might be a potential source of infection and play a huge role in transmitting pathogenic bacteria in hospital setup as well as in the community.

Objective:
This cross-sectional study was conducted to evaluate the bacterial contamination on white coats of students working in diagnostic laboratories and determine their antibacterial susceptibility.

Methods:
Swabs were collected from the sleeves and pockets of the white coat of 96 students working in various diagnostic labs in a tertiary care hospital and processed for bacteriological analysis based on standard procedures.

Results:
Among 96 white coats, bacterial contamination was observed in 63 white coats. Pockets of the white coats were highly contaminated with pathogenic bacteria than sleeves. Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus were isolated only from 13 white coats. The majority were Staphylococcus epidermidis, followed by Micrococcus luteus. All isolates of S. aureus were susceptible to antibiotics used. Few isolates of A. baumannii were resistant to ampicillin and amoxicillin. One isolate of P. aeruginosa exhibited resistance to Cefoperazone.

Conclusion:
White coats of students working in diagnostic labs were contaminated with both pathogenic and nonpathogenic bacteria, which can cause cross contamination and increase the spread of nosocomial infection. Bacteria resistant to antibiotics can lead to treatment complications. Thus, policies should be prepared and followed to reduce the risk of infectious disease transmission by following routine laboratory practices such as hand washing, frequent cleaning of white coats and disinfecting other fomites.
Sequencing analysis of efflux pump and porin genes among Pseudomonas aeruginosa isolated from different sources
Authors: Saidmurad Mustafa Azm , AL-Jubori Sawsan Sajid 
Published: November 2024

Background:
Efflux pumps are multidrug resistance mechanisms that play a crucial role in the antibiotic resistance of Pseudomonas aeruginosa. In this study, we aimed to investigate the prevalence of efflux pump genes among P. aeruginosa isolated from different sources.

Methods:
Forty clinical isolates that were primarily identified as P. aeruginosa were obtained from different laboratories of teaching hospitals in Baghdad/Iraq. Their identification was confirmed by using 16s rDNA as a housekeeping gene (HKG). To study different six types of efflux pump and porin genes, specific primers were used to detect mex A1, mex R, mex X, mex Y, oprD1, and oprJ1 genes followed by sequencing the amplified fragment, which was analyzed by Geneious software.

Results:
The results of amplification showed that all the 40 isolates (100%) were compatible with P. aeruginosa. Antibiotic sensitivity test (AST) for 14 antimicrobial agents was tested using Kirby–Bauer disc diffusion method and the result of the resistance pattern was as follows: 100% for SXT and F, 95% for TGC, 80% for CIP, 60% for LEV, 55% for FEP, 50% for AK, 47.5% for TOB, 40% for CAR, 35% for PRL, 27.5% for IMP, 25% for CAZ, 22.5% for ATM, 7.5% for COL, while the percentage of EP and porin genes among the total isolates as following: mex X 100%, 97.5% for oprD1, 95% for mexR, 92.5% for each mex Y and oprJ1, mex A 82.5%. The results explained that the most resistant six isolates in AST were resistant to 11–13 antimicrobial agents that harbored all six types of efflux pumps and porin genes and these isolates were obtained from urine and burn specimens.
Conclusion: our study demonstrated a high prevalence of efflux pumps and porin genes among P. aeruginosa isolates from different sources, indicating the significant role of efflux pumps in antibiotic resistance. These findings highlight the need for continuous surveillance of antibiotic resistance mechanisms and the development of new strategies to combat MDR P. aeruginosa infections.
Exceptional prevalence of blaNDM-1 gene producing Enterobacter cloacae ssp. dissolvens isolated from hospitals in Baghdad
Authors: Shakir Sinaa Mahdi , Hussein Nadheema Hammood , Al-Kadmy Israa M.S. , Taha Butheina Mohammed , Hussein Jumaah Dakel , Batiha Gaber El-Saber , Hetta Helal F. 
Published: November 2024

Background and aim:
Hereine, we report for the first time the spread of balNDM-1 and other Extended spectrum B lactemase (ESβL) related genes among carbapenem-resistant Enterobacter cloacae ssp. dissolvens isolated from hospitals in Baghdad/Iraq.

Methods:
Thirty-one clinical and environmental Enterobacter spp. were isolated. Antimicrobial susceptibility testing was done by VITEK-2 system, Uniplex PCR amplification was carried out for detection of blaNDM-1 and bla
OXA-48, Multiplex PCR for detection other Metalo B lactemase (MBL) genes For the detection of genes, which are blaIMP, blaVIM, blaSIM, blaGIM, and blaSPM.

Results:
Among thirty-one Enterobacter spp. isolates, 5 (16.12%) isolates classified as resistant to imipenem and meropenem together, according to MIC results, all isolates show high level of resistance 31 (100%) isolates to (amoxicillin/clavulanic acid and cefazolin, amikacin, ciprofloxacin), while resistance level ranged from 25 (80.6%) isolates to (ampicillin), 19 (61.3%) isolates resistant to trimethoprim/sulfamethoxazole, 17 (54.8%) resistant to gentamicin,15 (48.4%) resistant to ceftriaxone,11 (35.5%) isolates resistant to nitrofurantoin, 8 (25.8%)isolates resistant to cefepime piperacillin/tazobactam and tetracycline, whereas 6 (19.4%) islates resistant to aztreonam, 5 (16.1%) isolates resistant to meropenem, and finally 2 (6.5%) isolates resistant to levofloxacin.
One isolate out of 5 which resistant to imipenem gave positive result in bla

NDM−1
and Pre-

NDM-1
gene, 2 isolates show positive result in bla

VIM
gene, all 5 isolates show positive resistant to IMI gene, While, none of these isolates gave any result in SIM, GIM, SPM and bla
OXA-48 genes

Conclusion:
Carbapenem consider the last treatment to ESβL resistant isolates, but recently reported these isolates developed resistance towards antibiotics and produce carbapenemase and especially new-delhi-metallo-β-lactamase-1 (blaNDM-1) and cause increase the epidemiological situation resistance around the world.
Benign, but Ominous, Pseudotumor in the Post-Sleeve Gastrectomy Hiatal Hernia: A Case Series
Authors: Consul Nikita , Cheng Monica , Scholz Francis J. 
Published: November 2024

Abstract
We have incidentally observed a finding not yet described in the literature, on both cross-sectional imaging and fluoroscopy, to correlate with increased obstructive symptoms in our post sleeve gastrectomy patients. This case series aims to show postsurgical imaging cases with the common underlying finding of a pseudotumor associated with hiatal herniae and obstructive symptoms. Because this clinical presentation may, in some cases, warrant postsurgical revision, knowledge of the imaging findings and their potential clinical significance is useful to radiologists who interpret routine cross-sectional imaging examinations as well as fluoroscopic evaluations of these post sleeve gastrectomy patients.
COMPARATIVE CHARACTERISTICS OF THE ACCUMULATION OF DIFFERENT VARIANTS OF THE SARS-COV-2 VIRUS (WUHAN, DELTA, OMICRON) IN THE ORGANS OF MODEL ANIMALS
Authors: Chernov A.S. , Kazakov V.A. , Gogleva I.S. , Savenko S.V. , Schukina V.N. , Loginova S.Ya. , Borisevich S.V. , Smirnov I.V. , Telegin G.B. , Belogurov A.A. 
Published: November 2024

ABSTRACTBackgroundThe genotypic variability of the SARS-CoV-2 virus has proven to be extremely high, and the emergence of new strains raises concerns about their possible high virulence, transmissibility, and ability to bypass responses of the body’s immune system induced by previous infection or vaccination. Therefore, one of the main tasks is to study the pathogenesis of various variants of the virus using experimental animal biomodels of SARS-CoV-2 to quickly find methods and approaches to fighting new viruses.Methods60 humanized mice of the C57BL/6-Tgtn (CAG-human AEC2-IRES-Luciferase-WPRE-polyA) line (hACE2) were used. Mice were infected intranasally at different doses with three variants of the SARS-CoV-2 virus: Wuhan, Delta and Omicron.ResultsWe showed that humanized hACE2 mice, when infected with all three variants of the SARS-CoV-2 virus, showed typical pathological changes in lung consistency comparable to those found in COVID-19 in humans. All mice developed interstitial pneumonia, characterized by inflammatory cell infiltration and thickening of the alveolar septa, characteristic of vascular damage.ConclusionsAt a dose of 4 lg plaque-forming unit (PFU), all variants showed 100% mortality. A dose-dependent effect was established only for the Wuhan and Delta variants. In a comparative assessment of different variants of the SARS-CoV-2 virus in a humanized mouse model of hACE2, it was found that the Delta variant leads to more severe damage compared to Wuhan or Omicron.
Is an earlier onset of focal epilepsy associated with atypical language lateralization? A systematic review, meta-analysis and new data
Authors: Prentice Freya , Chehabeddine Lara , Eriksson Maria Helena , Murphy Jennifer , Sepeta Leigh N. , Gaillard William D. , Berl Madison M. , Liégeois Frédérique , Baldeweg Torsten 
Published: November 2024

AbstractRight and bilateral language representation is common in focal epilepsy, possibly reflecting the influence of epileptogenic lesions and/or seizure activity in the left hemisphere. Atypical language lateralization is assumed to be more likely in cases of early seizure onset, due to greater language plasticity in childhood. However, evidence for this association is mixed, with most research based on small samples and heterogenous cohorts. In this preregistered meta-analysis we examined the association between age at seizure onset and fMRI-derived language lateralization in individuals with focal epilepsy. The pooled effect size demonstrated a correlation between an earlier onset and rightward language lateralization in the total sample (r=0.1, p=.005, k=58, n=1240), with no difference in the correlation between left and right hemisphere epilepsy samples (Q=62.03, p=.302). In exploratory analyses of the individual participant data (n=1157), we demonstrated strong evidence that a logarithmic model fits the data better than a linear (BF=350) or categorical model with 6 years of age as a cut-off (BF=36). These findings indicate that there is a small but significant relationship between age at seizure onset and language lateralization. The relationship was consistent with theories of language plasticity proposing an exponential decline in plasticity over early childhood. However, given that this effect was subtle and only found in larger sample sizes, an early age at seizure onset would not serve as a good indicator of atypical language lateralization on the individual patient level.
Single cell variant to enhancer to gene map for coronary artery disease
Authors: Amrute Junedh M. , Lee Paul C. , Eres Ittai , Lee Chang Jie Mick , Bredemeyer Andrea , Sheth Maya U. , Yamawaki Tracy , Gurung Rijan , Anene-Nzelu Chukwuemeka , Qiu Wei-Lin , Kundu Soumya , Li Daniel Y. , Ramste Markus , Lu Daniel , Tan Anthony , Kang Chul-Joo , Wagoner Ryan E. , Alisio Arturo , Cheng Paul , Zhao Quanyi , Miller Clint L. , Hall Ira M. , Gupta Rajat M. , Hsu Yi-Hsiang , Haldar Saptarsi M. , Lavine Kory J. , Jackson Simon , Andersson Robin , Engreitz Jesse M. , Foo Roger S-Y , Li Chi-Ming , Ason Brandon , Quertermous Thomas , Stitziel Nathan O. 
Published: November 2024

AbstractAlthough genome wide association studies (GWAS) in large populations have identified hundreds of variants associated with common diseases such as coronary artery disease (CAD), most disease-associated variants lie within non-coding regions of the genome, rendering it difficult to determine the downstream causal gene and cell type. Here, we performed paired single nucleus gene expression and chromatin accessibility profiling from 44 human coronary arteries. To link disease variants to molecular traits, we developed a meta-map of 88 samples and discovered 11,182 single-cell chromatin accessibility quantitative trait loci (caQTLs). Heritability enrichment analysis and disease variant mapping demonstrated that smooth muscle cells (SMCs) harbor the greatest genetic risk for CAD. To capture the continuum of SMC cell states in disease, we used dynamic single cell caQTL modeling for the first time in tissue to uncover QTLs whose effects are modified by cell state and expand our insight into genetic regulation of heterogenous cell populations. Notably, we identified a variant in theCOL4A1/COL4A2CAD GWAS locus which becomes a caQTL as SMCs de-differentiate by changing a transcription factor binding site for EGR1/2. To unbiasedly prioritize functional candidate genes, we built a genome-wide single cell variant to enhancer to gene (scV2E2G) map for human CAD to link disease variants to causal genes in cell types. Using this approach, we found several hundred genes predicted to be linked to disease variants in different cell types. Next, we performed genome-wide Hi-C in 16 human coronary arteries to build tissue specific maps of chromatin conformation and link disease variants to integrated chromatin hubs and distal target genes. Using this approach, we show that rs4887091 within theADAMTS7CAD GWAS locus modulates function of a super chromatin interactome through a change in a CTCF binding site. Finally, we used CRISPR interference to validate a distal gene,AMOTL2, liked to a CAD GWAS locus. Collectively we provide a disease-agnostic framework to translate human genetic findings to identify pathologic cell states and genes driving disease, producing a comprehensive scV2E2G map with genetic and tissue level convergence for future mechanistic and therapeutic studies.
Detecting PI3K and TP53 Pathway Disruptions in Early-Onset Colorectal Cancer Among Hispanic/Latino Patients
Authors: Monge Cecilia , Waldrup Brigette , Manjarrez Sophia , Carranza Francisco , Velazquez-Villarreal Enrique 
Published: November 2024

AbstractBackground/ObjectivesThis study aims to characterize PI3K and TP53 pathway alterations in Hispanic/Latino patients with early-onset colorectal cancer (CRC), focusing on potential differences compared to non-Hispanic White (NHW) patients. Understanding these differences may shed light on the molecular basis of CRC health disparities.MethodsUsing cBioPortal, we conducted a bioinformatics analysis to evaluate CRC mutations within the PI3K and TP53 pathways. CRC cases were stratified by age and ethnicity: (1) early-onset (<50 years) versus late-onset (≥50 years) and (2) early-onset in Hispanic/Latino patients compared to early-onset in NHW patients. Mutation frequencies were assessed using descriptive statistics, with chi-squared tests comparing proportions between early-onset Hispanic/Latino and NHW groups. Kaplan-Meier survival curves were generated to assess overall survival for early-onset Hispanic/Latino patients, stratified by the presence or absence of PI3K and TP53 pathway alterations.ResultsSignificant differences were noted when comparing early-onset CRC in Hispanic/Latino patients to early-onset CRC in NHW patients. PI3K pathway alterations were more prevalent in early-onset CRC among Hispanic/Latino patients (90.5% vs. 41.5%, p = 9.279e-5), with mTOR alterations also significantly higher in this group (14.3% vs. 1.5%, p = 0.043). No significant differences were observed between early-onset and late-onset CRC cases within the Hispanic/Latino cohort. Additionally, Hispanic/Latino patients with early-onset CRC showed improved clinical outcomes when TP53 pathway alterations were present (p =5.4e-4).ConclusionsThese findings highlight the distinct role of PI3K and TP53 pathway disruptions in early-onset CRC among Hispanic/Latino patients, suggesting that pathway-specific mechanisms may drive cancer health disparities. Insights from this study could inform the potential development of precision medicine approaches and targeted therapies aimed at addressing these disparities and improving outcomes for diverse patient populations.
Comparing machine learning models for predicting mutation status in Acute Myeloid Leukemia patients using RNA-seq data
Authors: Silva Raíssa , Riedel Cédric , Reboul Jerome , Ruffle Florence , Gallopin Mélina , Boureux Anthony , Commes Thérèse 
Published: November 2024

AbstractAcute Myeloid Leukemia (AML) is a highly heterogeneous disease. The current AML classifications are based mainly on molecular markers, including cytogenetics features, fusion genes, and the presence or absence of mutations. In this study, we investigated mutation status in AML patients through RNA-seq data in link with differential gene expression. We applied seven machine learning algorithms to identify the presence or absence of NPM1, IDH1/IDH2, and FLT3-ITD mutations, reaching 95%, 93%, and 87% accuracy, respectively. In each case, the best performing models were complex models, suggesting highly complex biological processes at work behind AML.
Anti-HIV-1 HSPC-based gene therapy with safety kill switch to defend against and attack HIV-1 infection
Authors: Guo Qi , Parikh Keval , Zhang Jian , Brinkley Alexander , Chen Grace , Jakramonpreeya Natnicha , Zhen Anjie , An Dong Sung 
Published: November 2024

AbstractHematopoietic stem/progenitor cell (HSPC)-based anti-HIV-1 gene therapy holds promise to provide life-long remission following a single treatment. Here we report a multi-pronged anti-HIV-1 HSPC-based gene therapy designed to defend against and attack HIV-1 infection. We developed a lentiviral vector capable of co-expressing three anti-HIV-1 genes. Two are designed to prevent infection, including a short-hairpin RNA (CCR5sh1005) to knock down HIV-1 co-receptor CCR5 and a membrane anchored HIV-1 fusion inhibitor (C46). The third gene is a CD4-based chimeric antigen receptor (CAR) designed to attack HIV-1 infected cells. Our vector also includes a non-signaling truncated human epidermal growth factor receptor (huEGFRt) which acts as a negative selection-based safety kill switch against transduced cells. Anti-HIV-1 vector-transduced human CD34+ HSPC efficiently reconstituted multi-lineage human hematopoietic cells in humanized bone marrow/liver/thymus (huBLT) mice. HIV-1 viral load was significantly reduced (1-log fold reduction, p <0.001) in transplanted huBLT mice. Anti-huEGFR monoclonal antibody Cetuximab (CTX) administration significantly reduced huEGFRt+ vector-modified cells (>4-fold reduction, p <0.01) in huBLT mice. These results demonstrate that our strategy is highly effective for HIV-1 inhibition, and that CTX-mediated negative selection can deplete anti-HIV-1 vector-modified cells in the event of unwanted adverse effects in huBLT mice.