bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bipotential B-neutrophil progenitors are present in human and mouse bone marrow and emerge in the periphery upon stress hematopoiesis
Authors: Shahbaz Shima , Rosero Eliana Perez , Syed Hussain , Hnatiuk Mark , Bozorgmehr Najmeh , Rahmati Amirhossein , Zia Sameera , Plemel Jason , Osman Mohammed , Elahi Shokrollah 
Published: July 2024

ABSTRACT

Hematopoiesis is a tightly regulated process that gets skewed toward myelopoiesis. This restrains lymphopoiesis, but the role of lymphocytes in this process is not well defined. To unravel the intricacies of neutrophil responses in COVID-19, we performed bulk RNAseq on neutrophils from healthy controls and COVID-19 patients. Principal component analysis revealed distinguishing neutrophil gene expression alterations in COVID-19 patients. ICU and ward patients displayed substantial transcriptional changes, with ICU patients exhibiting a more pronounced response. Intriguingly, neutrophils from COVID-19 patients, notably ICU patients, exhibited an enrichment of immunoglobulin (Ig) and B cell lineage-associated genes, suggesting potential lineage plasticity. We validated our RNAseq findings in a larger cohort. Moreover, by reanalyzing single-cell RNA sequencing (scRNAseq) data on human bone marrow (BM) granulocytes, we identified the cluster of granulocyte-monocyte progenitors (GMP) enriched with Ig and B cell lineage-associated genes. These cells with lineage plasticity may serve as a resource depending on the host’s needs during severe systemic infection. This distinct B cell subset may play a pivotal role in promoting myelopoiesis in response to infection. The scRNAseq analysis of BM neutrophils in infected mice further supported our observations in humans. Finally, our studies using an animal model of acute infection implicate IL-7/GM-CSF in influencing neutrophil and B cell dynamics. Elevated GM-CSF and reduced IL-7 receptor expression in COVID-19 patients imply altered hematopoiesis favoring myeloid cells over B cells. Our findings provide novel insights into the relationship between the B-neutrophil lineages during severe infection, hinting at potential implications for disease pathogenesis.

IMPORTANCE
This study investigates the dynamics of hematopoiesis in COVID-19, focusing on neutrophil responses. Through RNA sequencing of neutrophils from healthy controls and COVID-19 patients, distinct gene expression alterations are identified, particularly in ICU patients. Notably, neutrophils from COVID-19 patients, especially in the ICU, exhibit enrichment of immunoglobulin and B cell lineage-associated genes, suggesting potential lineage plasticity. Validation in a larger patient cohort and single-cell analysis of bone marrow granulocytes support the presence of granulocyte-monocyte progenitors with B cell lineage-associated genes. The findings propose a link between B-neutrophil lineages during severe infection, implicating a potential role for these cells in altered hematopoiesis favoring myeloid cells over B cells. Elevated GM-CSF and reduced IL-7 receptor expression in stress hematopoiesis suggest cytokine involvement in these dynamics, providing novel insights into disease pathogenesis.
Complete genome sequence of the probiotic
Lacticaseibacillus paracasei
LPC100 strain from the NORDBIOTIC collection isolated from a human fecal sample
Authors: Szczepankowska Agnieszka K. , Cukrowska Bożena , Aleksandrzak-Piekarczyk Tamara 
Published: July 2024

ABSTRACT

We report the genome sequence of the human fecal isolate
Lacticaseibacillus paracasei
LPC100 from the NORDBIOTIC collection, comprising a 3.075 Mb chromosome and three plasmids (61 kb, 12 kb, and 7 kb). Genetic content reveals the strain’s beneficial features—complete lactose metabolic pathway, potential production of bacteriocins, and short-chain fatty acids.
Metagenome-assembled genome sequence of
Spiroplasma phoeniceum
, assembled from the hindgut of
Locusta migratoria
, a migration grasshopper species
Authors: Kim Jaeha , Murakami Takumi , Toyoda Atsushi , Mori Hiroshi 
Published: July 2024

ABSTRACT

Spiroplasma phoeniceum
is a plant pathogen and a mesophilic microaerophile. Here, we report the metagenome-assembled genome (MAG) sequence of
S. phoeniceum
binned from hindgut contents of the wild-type male
Locusta migratoria
, a grasshopper species. The MAG sequence comprises 1,059,205 bp in 91 contigs with a 26.3% of GC content.
Distinct prophage gene profiles of
Staphylococcus aureus
strains from atopic dermatitis patients and healthy individuals
Authors: Wang Zhongjie , Peng Xue , Hülpüsch Claudia , Khan Mirzaei Mohammadali , Reiger Matthias , Traidl-Hoffmann Claudia , Deng Li , Schloter Michael 
Published: July 2024

ABSTRACT

Staphylococcus aureus
strains exhibit varying associations with atopic dermatitis (AD), but the genetic determinants underpinning the pathogenicity are yet to be fully characterized. To reveal the genetic differences between
S. aureus
strains from AD patients and healthy individuals (HE), we developed and employed a random forest classifier to identify potential marker genes responsible for their phenotypic variations. The classifier was able to effectively distinguish strains from AD and HE. We also uncovered strong links between certain marker genes and phage functionalities, with phage holin emerging as the most pivotal differentiating factor. Further examination of
S. aureus
gene content highlighted the genetic diversity and functional implications of prophages in driving differentiation between strains from AD and HE. The HE group exhibited greater gene content diversity, largely influenced by their prophages. While strains from both AD and HE universally housed prophages, those in the HE group were distinctively higher at the strain level. Moreover, although prophages in the HE group exhibited variously higher enrichment of differential functions, the AD group displayed a notable enrichment of virulence factors within their prophages, underscoring the important contribution of prophages to the pathogenesis of AD-associated strains. Overall, prophages significantly shape the genetic and functional profiles of
S. aureus
strains, shedding light on their pathogenic potential and elucidating the mechanisms behind the phenotypic variations in AD and HE environments.

IMPORTANCE

Through a nuanced exploration of
Staphylococcus aureus
strains obtained from atopic dermatitis (AD) patients and healthy controls (HE), our research unveils pivotal genetic determinants influencing their pathogenic associations. Utilizing a random forest classifier, we illuminate distinct marker genes, with phage holin emerging as a critical differential factor, revealing the profound impact of prophages on genetic and pathogenic profiles. HE strains exhibited a diverse gene content, notably shaped by unique, heightened prophages. Conversely, AD strains emphasized a pronounced enrichment of virulence factors within prophages, signifying their key role in AD pathogenesis. This work crucially highlights prophages as central architects of the genetic and functional attributes of
S. aureus
strains, providing vital insights into pathogenic mechanisms and phenotypic variations, thereby paving the way for targeted AD therapeutic approaches and management strategies by demystifying specific genetic and pathogenic mechanisms.
Imbalanced temporal states of cortical blood-oxygen-level-dependent signal variability during rest in episodic migraine
Authors: Veréb Dániel , Szabó Nikoletta , Kincses Bálint , Szücs-Bencze Laura , Faragó Péter , Csomós Máté , Antal Szabolcs , Kocsis Krisztián , Tuka Bernadett , Kincses Zsigmond Tamás 
Published: July 2024

Abstract
Background
Migraine has been associated with functional brain changes including altered connectivity and activity both during and between headache attacks. Recent studies established that the variability of the blood-oxygen-level-dependent (BOLD) signal is an important attribute of brain activity, which has so far been understudied in migraine. In this study, we investigate how time-varying measures of BOLD variability change interictally in episodic migraine patients.

Methods
Two independent resting state functional MRI datasets acquired on 3T (discovery cohort) and 1.5T MRI scanners (replication cohort) including 99 episodic migraine patients (n3T = 42, n1.5T=57) and 78 healthy controls (n3T = 46, n1.5T=32) were analyzed in this cross-sectional study. A framework using time-varying measures of BOLD variability was applied to derive BOLD variability states. Descriptors of BOLD variability states such as dwell time and fractional occupancy were calculated, then compared between migraine patients and healthy controls using Mann-Whitney U-tests. Spearman’s rank correlation was calculated to test associations with clinical parameters.

Results
Resting-state activity was characterized by states of high and low BOLD signal variability. Migraine patients in the discovery cohort spent more time in the low variability state (mean dwell time: p = 0.014, median dwell time: p = 0.022, maximum dwell time: p = 0.013, fractional occupancy: p = 0.013) and less time in the high variability state (mean dwell time: p = 0.021, median dwell time: p = 0.021, maximum dwell time: p = 0.025, fractional occupancy: p = 0.013). Higher uptime of the low variability state was associated with greater disability as measured by MIDAS scores (maximum dwell time: R = 0.45, p = 0.007; fractional occupancy: R = 0.36, p = 0.035). Similar results were observed in the replication cohort.

Conclusion
Episodic migraine patients spend more time in a state of low BOLD variability during rest in headache-free periods, which is associated with greater disability. BOLD variability states show potential as a replicable functional imaging marker in episodic migraine.
Interstitial lung diseases (ILD) in common variable immunodeficiency (CVID) patients: a study from Iran
Authors: Khanbabaee Ghamartaj , khazaii Fatemeh , Chavoshzadeh Zahra , Rekabi Mahsa , Ghomi Zahra , Zeinali Vahide , Pourghasem Matin , Soflaee Maedeh , Ghadrdan Mahsa 
Published: July 2024

Abstract
Introduction
Interstitial lung disease (ILD) is a prevalent complication in patients with common variable immunodeficiency (CVID) and is often related to other characteristics such as bronchiectasis and autoimmunity. Because the term ILD encompasses a variety of acute and chronic pulmonary conditions, diagnosis is usually based on imaging features. Histopathology is less available. This study was conducted with the aim of investigating the ILD in patients with CVID.

Materials and methods
In this retrospective cross-sectional study, sixty CVID patients who referred to the pulmonology and immunodeficiency clinics of Mofid Children’s Hospital between 2013 and 2022 were included. The diagnosis of ILD were based on transbronchial lung biopsy (TBB) or clinical and radiological symptoms. The prevalence of ILD in CVID patients was determined. Also, the CVID patients with and without ILD were compared in terms of demographic characteristics, clinical, laboratory and radiologic findings.

Results
Among all patients, ten patients had ILD (16.6%). In terms of laboratory parameters, there was a significant difference between platelets in the two groups of CVID patients with and without ILD, and the level of platelets was higher in the group of patients with ILD. Moreover, in terms of clinical symptoms, pneumonia, diarrhea and hepatomegaly were significantly different between the two groups and were statistically higher in the group of patients with ILD (P < 0.05). Autoimmunity and malignancy were not significantly different in two groups. There was a significant difference in, hyperinflation between the two groups of CVID patients with and without ILD, and the frequency of, hyperinflation was higher in the patients without ILD (P = 0.040).

Conclusion
Understanding the pathogenesis of ILD plays an essential role in revealing non-infectious pulmonary complications that occur in CVID patients. Increasing efforts to understand ILD not only shed light on its hidden pathogenesis and clinical features, but also enhance our understanding of CVID in a broader sense.
Pain management after thoracotomy with dexamethasone and bupivacaine through a peripleural cather: a randomized controlled trial
Authors: Talebzadeh Hamid , Eslamian Mohammad , Sheikhbahaei Erfan , Esparham Ali , Zefreh Hamidreza , Sarblook Pooria , Firouzfar Alireza 
Published: July 2024

Abstract
Introduction
Thoracotomy procedures can result in significant pain and cause nausea/vomiting. Glucocorticoids have anti-emetic and analgesic effects due to their anti-inflammatory and nerve-blocking properties. This study investigates the additive effect of local dexamethasone with bupivacaine as sole analgesic medication through a peripleural catheter after thoracotomy.

Method
The study was conducted as a randomized control trial on 82 patients. Participants were allocated to receive either 2.5 mg/kg of bupivacaine plus 0.2 mg/kg of dexamethasone or 2.5 mg/kg of bupivacaine plus the same amount of normal saline as placebo through a 6 French peripleural catheter implemented above the parietal pleura and beneath the musculoskeletal structure of the chest wall. The primary outcome was the severity of pain 24 h after the operation in the visual analogue scale (VAS) score. Secondary outcomes were the incidence of nausea/vomiting, opioid consumption for pain control, and incidence of any adverse effects.

Results
: A total of 50 participants were randomized to each group, and the baseline characteristics were similar between the groups. Median of VAS score (6 (3-8) vs. 8 (6-9), p < 0.001), postoperative opioid consumption (9 (36%) vs. 17 (68%) patients, p=0.024), and median length of hospital stay (4 (3-8) vs. 6 (3-12) days, p < 0.001) were significantly lower in the dexamethasone group. However, postoperative nausea/vomiting (p=0.26 for nausea and p=0.71 for vomiting) and surgical site infection (p = 0.55) were similar between the two groups.

Conclusion
In thoracotomy patients, administering local dexamethasone + bupivacaine through a peripleural catheter can reduce postoperative pain, analgesic consumption, and length of hospital stay.

Trial Registration
Iranian Registry of Clinical Trials (IRCT20220309054226N1, registration date: 3/21/2022.
Evaluation of preoperative difficult airway prediction methods for adult patients without obvious airway abnormalities: a systematic review and meta-analysis
Authors: Wang Zhichen , Jin Yile , Zheng Yueying , Chen Hanjian , Feng Jingyi , Sun Jing 
Published: July 2024

Abstract
Background
This systematic review aims to assist clinical decision-making in selecting appropriate preoperative prediction methods for difficult tracheal intubation by identifying and synthesizing literature on these methods in adult patients undergoing all types of surgery.

Methods
A systematic review and meta-analysis were conducted following PRISMA guidelines. Comprehensive electronic searches across multiple databases were completed on March 28, 2023. Two researchers independently screened, selected studies, and extracted data. A total of 227 articles representing 526 studies were included and evaluated for bias using the QUADAS-2 tool. Meta-Disc software computed pooled sensitivity (SEN), specificity (SPC), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). Heterogeneity was assessed using the Spearman correlation coefficient, Cochran’s-Q, and I2 index, with meta-regression exploring sources of heterogeneity. Publication bias was evaluated using Deeks’ funnel plot.

Results
Out of 2906 articles retrieved, 227 met the inclusion criteria, encompassing a total of 686,089 patients. The review examined 11 methods for predicting difficult tracheal intubation, categorized into physical examination, multivariate scoring system, and imaging test. The modified Mallampati test (MMT) showed a SEN of 0.39 and SPC of 0.86, while the thyromental distance (TMD) had a SEN of 0.38 and SPC of 0.83. The upper lip bite test (ULBT) presented a SEN of 0.52 and SPC of 0.84. Multivariate scoring systems like LEMON and Wilson’s risk score demonstrated moderate sensitivity and specificity. Imaging tests, particularly ultrasound-based methods such as the distance from the skin to the epiglottis (US-DSE), exhibited higher sensitivity (0.80) and specificity (0.77). Significant heterogeneity was identified across studies, influenced by factors such as sample size and study design.

Conclusion
No single preoperative prediction method shows clear superiority for predicting difficult tracheal intubation. The evidence supports a combined approach using multiple methods tailored to specific patient demographics and clinical contexts. Future research should focus on integrating advanced technologies like artificial intelligence and deep learning to improve predictive models. Standardizing testing procedures and establishing clear cut-off values are essential for enhancing prediction reliability and accuracy. Implementing a multi-modal predictive approach may reduce unanticipated difficult intubations, improving patient safety and outcomes.
Use of the Ishii Test for screening sarcopenia in older adults: a systematic review with meta-analysis of diagnostic test accuracy (DTA) studies
Authors: Macêdo Sabrina Gabrielle Gomes Fernandes , de Souza Macêdo Pedro Rafael , Barbosa Weslley Sales , Maciel Álvaro Campos Cavalcanti 
Published: July 2024

Abstract
Background
The Ishii Test is recommended by the European Working Group on Sarcopenia in Older People (EWGSOP2), however the use of this technique is still little explored in the clinical context and the scientific literature.

Objective
We aimed to verify the use of the Test of Ishii in screening for sarcopenia in older adults.

Methods
We searched three electronic databases and two reviewers independently screened and assessed the studies. Studies with older adults (60 years or more) of both genders, no year or language restriction and which aimed to evaluate sarcopenia using the Ishii Test and another diagnostic criteria were selected. A summary of the ROC curve, sensitivity and specificity were performed using the MedCalc and SPSS software programs, respectively.

Results
A total of 3,298 references were identified in the database, 278 by manually searching, and finally 11 studies were included for the review. The screening test showed good sensitivity and specificity in both genders. All studies showed values above the considered value for the Area Under the Curve (AUC) results, without discriminating power (0.500). Four studies used the original values, and five studies developed a new cut-off point. A summary of the AUC curve showed the diamond close to one, indicating that the Ishii test has good performance for screening sarcopenia (I2=83,66%; p<0.001; 95%CI: 69.38 to 91.28 for men; and I2=60.04%; p<0.001; 95%CI: 13.06 to 81.63 for women).

Conclusion
The Ishii Test can be considered a useful tool for the early identification of sarcopenia in older adults. However, further studies are still needed to understand the behavior of this screening tool.

Trial registration
CRD42023424392.
Insights into inflammation and implications for the pathogenesis and long-term outcomes of endometrial cancer: genome-wide surveys and a clinical cohort study
Authors: Wang Jing , Chen Zhichao , Lai Yaozhen , Ma Zebiao , Wang Luanhong , Fiori Pier Luigi , Carru Ciriaco , Capobianco Giampiero , Zhou Li 
Published: July 2024

Abstract
Background
Despite evidence showing a connection between inflammation and endometrial cancer (EC) risk, the surveys on genetic correlation and cohort studies investigating the impact on long-term outcomes have yet to be refined. We aimed to address the impact of inflammation factors on the pathogenesis, progression and consequences of EC.

Methods
For the genetic correlation analyses, a two-sample of Mendelian randomization (MR) study was applied to investigate inflammation-related single-nucleotide polymorphisms involved with endometrial cancer from GWAS databases. The observational retrospective study included consecutive patients diagnosed with EC (stage I to IV) with surgeries between January 2010 and October 2020 at the Cancer Hospital of Shantou University Medical College.

Results
The 2-sample MR surveys indicated no causal relationship between inflammatory cytokines and endometrial cancer. 780 cases (median age, 55.0 years ) diagnosed with EC were included in the cohort and followed up for an average of 6.8 years. Increased inflammatory parameters at baseline were associated with a higher FIGO stage and invasive EC risk (odds ratios [OR] 1.01 to 4.20). Multivariate-cox regression suggested that multiple inflammatory indicators were significantly associated with overall survival (OS) and progression-free survival (PFS) (P < 0.05). Nomogram models based on inflammatory risk and clinical factors were developed for OS and PFS with C-index of 0.811 and 0.789, respectively. LASSO regression for the validation supported the predictive efficacy of inflammatory and clinical factors on the long-term outcomes of EC.

Conclusions
Despite the fact that the genetic surveys did not show a detrimental impact of inflammatory cytokines on the endometrial cancer risk, our cohort study suggested that inflammatory level was associated with the progression and long-term outcomes of EC. This evidence may contribute to new strategies targeted at decreasing inflammation levels during EC therapy.