bluuebunny/crossref_metadata_2025_split huggingface dataset:
A platform supporting generation and isolation of random transposon mutants in
Chlamydia trachomatis
Authors: Hawk Caroline , Hamdzah Nur , Dimond Zoe , Fields Kenneth A. 
Published: February 2025

ABSTRACT

Chlamydia
species represent a paradigm for understanding successful obligate intracellular parasitism. Despite limited genetic malleability, development of genetic tools has facilitated the elucidation of molecular mechanisms governing infectivity. Random mutagenesis approaches provide one of the most powerful strategies available to accomplish untargeted elucidation of gene function. Unfortunately, initial progress in transposon-mediated mutagenesis of
Chlamydia
has been challenging. To increase efficiency, we developed a plasmid-based system that couples conditional plasmid maintenance with a previously described strategy leveraging inducible expression of the
Himar1
-derived C9 transposase. Our pOri-Tn(Q) construct was maintained in
Chlamydia trachomatis
cultivated with antibiotics but was rapidly cured in the absence of antibiotic selection. pOri-Tn(Q) supported transposition events when transposase expression was induced during infection. Induction was accompanied by loss of the plasmid backbone when penicillin G was used to select for only the transposable element. C9 induction during iterative passaging was used to increase the overall insertion frequency and accumulate an expanded pool of transposon mutants. The approach supported isolation of individual mutant strains from the mixed pool, and whole-genome sequencing confirmed that the recovered strains harbored single insertions.

IMPORTANCE

Chlamydia trachomatis
is a prevalent human pathogen exerting a tremendous negative impact on human health. A complete understanding of how these bacteria create and maintain an intracellular niche and avoid/subvert host defense mechanisms to cause disease is lacking. The utility of transposon-mediated, random mutagenesis in supporting forward genetic studies is well established in a multitude of genetically tractable systems. This study reports the development of a plasmid-based system capable of generating mutant pools and supporting subsequent isolation of individual transposon mutants. This step is an important advance in providing a mechanism capable of supporting downstream studies interrogating chlamydial biology.
Rickettsial pathogen augments tick vesicular-associated membrane proteins for infection and survival in the vector host
Authors: Namjoshi Prachi , Kolape Jaydeep , Patel Avni , Sultana Hameeda , Neelakanta Girish 
Published: February 2025

ABSTRACT

Anaplasma phagocytophilum
is an obligate intracellular rickettsial pathogen that infects humans and animals. The black-legged tick
Ixodes scapularis
acts as a vector and transmits this bacterium to the vertebrate host. Upon entry into a host cell,
A. phagocytophilum
resides and multiplies in a host-derived vacuole called morulae. There is not much information available on the molecules that play an important role(s) in
A. phagocytophilum
entry and formation of these morulae in tick cells. In this study, we provide evidence that tick vesicular-associated membrane proteins, VAMP3 and VAMP4, play important roles in this phenomenon. Quantitative real-time polymerase chain reaction (QRT-PCR) analysis showed that both
vamp3
and
vamp4
transcripts are significantly upregulated at early time points of
A. phagocytophilum
infection in tick cells. We noted that both VAMP3 and VAMP4 predominantly localized to the
A. phagocytophilum
-containing vacuole. RNAi-mediated silencing of
vamp3
and/or
vamp4
expression, followed by confocal microscopy and expression analysis, indicated an impairment in
A. phagocytophilum
morulae formation in tick cells. We also noted that VAMP3 and VAMP4 play a role in the
A. phagocytophilum
persistent infection of ticks and tick cells. Furthermore, RNAi-mediated silencing of expression of arthropod
vamp3
and
vamp4
affected bacterial acquisition from an infected murine host to ticks. Collectively, this study not only provides evidence on the role of arthropod vesicular-associated membrane proteins in
A. phagocytophilum
morulae formation in tick cells but also demonstrates that these proteins are important for bacterial acquisition from an infected vertebrate host into ticks.

IMPORTANCE

Anaplasma phagocytophilu
m is a tick-borne pathogen primarily transmitted by black-legged Ixodes scapularis ticks to humans and animals. This bacterium enters host cells, forms a host-derived vacuole, and multiplies within this vacuole. The molecules that are critical in the formation of host-derived vacuole in tick cells is currently not well-characterized. In this study, we provide evidence that arthropod vesicular-associated membrane proteins, VAMP3 and VAMP4, are critical for
A. phagocytophilum
early and persistent infection in tick cells. These arthropod proteins are important for the formation of host-derived vacuoles in tick cells. Our study also provides evidence that these proteins are important for
A. phagocytophilum
acquisition from the infected murine host into ticks. Characterization of tick molecules important in bacterial entry and/or survival in the vector host could lead to the development of strategies to target this and perhaps other rickettsial pathogens.
Altitude-induced central sleep apnea does not affect mean sleep oxygen saturation in young healthy males
Authors: Heiniger G. , Raemy F. , Solelhac G. , Imler T. , Waeber A. , Lambercy K. , Bradley B. , Lecciso G. , Degache F. , Heinzer Raphael C 
Published: February 2025

At high-altitude, periodic breathing (PB) can occur during sleep in healthy individuals. PB is characterized by a cyclical ventilatory pattern that alternates between central sleep apnea and brief episodes of hyperventilation. The aim of this study was to evaluate the effect of periodic breathing on sleep SpO2. 36 healthy males subjects (median-age:26[24-28]years old, median BMI:22.7[21.1-23.8]Kg/m2) underwent a polysomnography at a simulated altitude of 3,500 meters(FiO2:13%). Correlations were sought between the Apnea-Hypopnea Index(AHI), Oxygen Desaturation Index(ODI), percentage of total sleep time spent in PB, and mean SpO2 throughout the entire sleep period by calculating the Spearman's rank correlation test. We identified 20 participants who had experienced at least 3 minutes of PB adjacent to at least 3 minutes of regular breathing(RB). We compared the mean SpO2 between the two respiratory patterns using Wilcoxon signed-rank test. At simulated-altitude, the subjects spent a median-IQR of 43.9[12.5-79.1]% of sleep in PB and the median-AHI was 77.3[31.4-127.5]/h. Median awake and asleep SpO2 were 75.4[24-28]% and 68.5[66.4-72.5]% respectively. We found no within subject difference in SpO2 between RB and PB periods (median-IQR RB vs PB: 67.2%{63.8-74.8%} vs 67.5%{64.5-73.9%},p=0.43). No significant correlation was found between the mean sleep SpO2 and AHI(n=36,rs=-0.19,p=0.26), ODI(n=36,rs=-0.23,p=0.18) or PB(n=36,rs=-0.07,p=0.67). Awake SpO2 was correlated with mean SpO2 during sleep(n=36,rs=0.55;p=0.001). PB per se does not have a detrimental effect on mean SpO2 in young healthy males. Correlation between awake and sleep SpO2, suggests that sleep SpO2 at high-altitude is primarily determined by baseline oxygen saturation rather than the respiratory pattern developed during sleep.
Incidentally Discovered Duodenal Gastrointestinal Stromal Tumour (GIST): Operative Treatment and Problems After Surgery—A Case Report and Literature Review
Authors: Lüthje Peter , Nurmi-Lüthje Ilona 
Published: February 2025

Background: Gastrointestinal stromal tumours (GISTs) are mesenchymal tumours of the digestive tract that can involve any part of the tract. The tumours can be harmless or life‐threatening.Materials and Methods: A case report of a surgeon who fell in a Finnish sauna, and he immediately felt that some ribs were broken. Magnetic resonance imaging and ultrasound showed three fractured ribs and an intrasplenic haematoma. Contrast‐enhanced computed tomography (CT) demonstrated a small intrasplenic anomaly but no haematoma. Incidentally, an incidentaloma in the left adrenal gland was diagnosed. Three months later, a control CT scan was performed. The radiological findings on the adrenal gland and laboratory examinations matched those of a benign adenoma. Incidentally, a small duodenal tumour was diagnosed. At the same time, anaemia (haemoglobin: 104 g/L) and iron deficiency (ferritin: 8 μg/L) were noticed. An esophagogastroduodenoscopy showed an intramural tumour localised after the bulb‐descending junction. Because the tumour was submucosal, the pathological diagnosis failed. Three months later, a radical surgical resection of the tumour with a resection margin of 2 mm and primary closing of the duodenum was performed. Pathological examination showed a well‐circumscribed submucosal mesenchymal tumour with spindle cells. A tumour‐free margin was uncertain. Immunohistochemistry findings showed a GIST. Due to the uncertain margin, an esophagogastroduodenoscopy control was planned at 2 years postoperatively. The patient disagreed with the decision and ordered a private control CT 3 months after the operation. The new CT found no local recurrence or metastasis. The patient contacted the head surgeon of the clinic, who ordered a 1‐year postoperative CT. The 1‐year follow‐up CT finding agreed with the previous findings.Conclusion: The aftertreatment of a radical‐operated GIST is extremely important if histologic examination of the tumour‐free margin is uncertain. In that case, CT controls should be considered once a year for at least 3 years.
Establishment of a Lactylation‐Related Gene Signature for Hepatocellular Carcinoma Applying Bulk and Single‐Cell RNA Sequencing Analysis
Authors: Yu Lianghe , Shi Yan , Zhi Zhenyu , Li Shuang , Yu Wenlong , Zhang Yongjie 
Published: February 2025

Background: Lactylation is closely involved in cancer progression, but its role in hepatocellular carcinoma (HCC) is unclear. The present work set out to develop a lactylation‐related gene (LRG) signature for HCC.Methods: The lactylation score of tumor and normal groups was calculated using the gene set variation analysis (GSVA) package. The single‐cell RNA sequencing (scRNA‐seq) analysis of HCC was performed in the “Seurat” package. Prognostic LRGs were selected by performing univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses to develop and validate a Riskscore model. Functional enrichment analysis was conducted by gene set enrichment analysis (GSEA) using the “clusterProfiler” package. Genomic characteristics between different risk groups were compared, and tumor mutational burden (TMB) was calculated by the “Maftools” package. Immune cell infiltration was assessed by algorithms of cell‐type identification by estimating relative subsets of RNA transcript (CIBERSORT), microenvironment cell populations‐counter (MCP‐counter), estimating the proportions of immune and cancer cells (EPIC), tumor immune estimation resource (TIMER), and single‐sample gene set enrichment analysis (ssGSEA). Immunotherapy response was predicted by the tumor immune dysfunction and exclusion (TIDE) algorithm. Drug sensitivity was analyzed using the “pRRophetic” package. A nomogram was established using the “rms” package. The expressions of the prognostic LRGs in HCC cells were verified by in vitro test, and cell counting kit‐8 (CCK‐8), wound healing, and transwell assays were carried out to measure the viability, migration, and invasion of HCC cells.Results: The lactylation score, which was higher in the tumor group than in the normal group, has been confirmed as an independent factor for the prognostic evaluation in HCC. Six prognostic LRGs, including two protective genes (FTCD and APCS) and four risk genes (LGALS3, C1orf43, TALDO1, and CCT5), were identified to develop a Riskscore model with a strong prognostic prediction performance in HCC. The scRNA‐seq analysis revealed that LGALS3 was largely expressed in myeloid cells, while APCS, FTCD, TALDO1, CCT5, and C1orf43 were mainly expressed in hepatocytes. The high‐risk group was primarily enriched in the pathways involved in tumor occurrence and development, with higher T cell infiltration. Moreover, the high‐risk group was found to be less responsive to immunotherapy but was more sensitive to chemotherapeutic drugs. By integrating Riskscore and clinical features, a nomogram with a high predictive accuracy was developed. Additionally, C1orf43, CCT5, TALDO1, and LGALS3 were highly expressed in HCC cells. Silencing CCT5 inhibited the viability, migration, and invasion of HCC cells.Conclusion: The present work developed a novel LRG gene signature that could be considered a promising therapeutic target and biomarker for HCC.
Homograft Root Replacement Does Not Provide Superior Outcomes in Invasive Aortic Valve Endocarditis Compared With Prosthetic Valve Conduits
Authors: Farrington Woodrow J. , Lou Xiaoying , Zurcher Jonathan R. , Chen Edward P. , Keeling William Brent , Leshnower Bradley G. 
Published: February 2025

Background: Surgical dogma advocates for the use of homograft in invasive aortic valve endocarditis due to a perceived advantage in the prevention of recurrent infection. However, conclusive data to support this strategy are lacking. This study evaluated outcomes of root replacement in invasive aortic valve endocarditis using homografts or prosthetic‐valved conduits.Methods: A retrospective review of a single U.S. academic center’s aortic database identified 150 patients who underwent aortic root replacement for invasive aortic valve endocarditis from 2002 to 2022. Patients undergoing the Ross procedure or aortic valve replacement without root replacement were excluded from the study. Patients were divided into two groups based upon the type of valved conduit implanted. Preoperative characteristics, postoperative morbidity, reintervention for recurrence of infection, and short‐ and long‐term survival were compared between the two groups.Results: There were 70 patients who underwent a homograft root replacement (homograft), and 80 patients who received either a bioprosthetic or mechanical‐valved conduit (prosthetic). The mean age of patients was 53.3 ± 15.6 and 21.3% were female. The overall incidence of preoperative stroke and aortic root abscess was 42% and 71%, respectively. There was no difference between the two groups in age, gender, end‐stage renal disease, cardiogenic shock, and aortic root abscess. The prosthetic group had a higher incidence of preoperative stroke (prosthetic 52% vs. homograft 25%, p = 0.02). The incidence of preoperative prosthetic valve endocarditis was 30% for the cohort and significantly higher in the homograft group (p = 0.02). Reoperative sternotomy was 78.7% among the groups with a higher likelihood among the homograft group. Cardiopulmonary bypass and cross clamp times were shorter in the prosthetic group (p < 0.05). There was no difference in postoperative stroke or renal failure between the two groups. The 30‐day mortality for the entire cohort was 20.1% and was increased in the homograft group (homograft 25.7% vs. prosthetic 16.3%, p = 0.15). At 7 years follow‐up, survival was 62% in the prosthetic group and 53% in the homograft group. The need for reintervention due to recurrence of infection was 3.2% for the entire series and equivalent (homograft 3.5%, vs. prosthetic 4.2%, p = 0.82) between the groups.Conclusions: The use of homograft for root replacement does not provide significant improved short‐ or long‐term outcomes compared with prosthetic‐valved conduits in invasive endocarditis. In this patient population, these data refute the necessity for a more complex procedure using homograft in these high‐risk patients and conduit selection should be tailored to individual anatomy and surgeon‐specific experience.
CD103+CD56+ ILCs are associated with an altered CD8+ T-cell profile within the tumour microenvironment
Authors: Chung Douglas C. , Shakfa Noor , Vakharia Jehan , Warner Kathrin , Jacquelot Nicolas , Sayad Azin , Han SeongJun , Ghaedi Maryam , Garcia-Batres Carlos R. , Sotty Jules , Azarmina Arvin , Nowlan Ferris , Chen Edward L.Y. , Zon Michael , Elford Alisha R. , Wang Ben X. , Nguyen Linh T. , Mrkonjic Miralem , Clarke Blaise A. , Bernardini Marcus Q. , Haibe-Kains Benjamin , Ferguson Sarah E. , Crome Sarah Q. , Jackson Hartland W. , Ohashi Pamela S. 
Published: February 2025

Abstract
Immunotherapies have had unprecedented success in the treatment of multiple cancer types, albeit with variable response rates. Unravelling the complex network of immune cells within the tumour microenvironment (TME) may provide additional insights to enhance antitumour immunity and improve clinical response. Many studies have shown that natural killer (NK) cells or innate lymphoid cells (ILCs) have regulatory capacity. Here, we identified CD103 as a marker that was found on CD56+ cells that were associated with a poor proliferative capacity of tumour-infiltrating lymphocytes (TILs) in culture. We further demonstrated that CD103+CD56+ ILCs isolated directly from tumours represented a distinct ILC population that expressed unique surface markers (such as CD49a and CD101), transcription factor networks, and transcriptomic profiles compared to CD103–CD56+ NK cells. Using single-cell multi-omic and spatial approaches, we found that these CD103+CD56+ ILCs were associated with CD8+ T cells with reduced expression of granzyme B (GZMB). Thus, this study identifies a population of CD103+CD56+ ILCs with potentially inhibitory functions that are associated with a TME that includes CD8+ T cells with poor antitumour activity. Further studies focusing on these cells may provide additional insights into the biology of an inhibitory TME.
A Mechanism of Stochastic Synchronization in the Climate System: an Interpretation of the Boundary Current Synchronization as a Maxwell’s Demon
Authors: Yasuda Yuki , Kohyama Tsubasa 
Published: February 2025

Abstract
This study has applied information thermodynamics to a bivariate linear stochastic differential equation (SDE) that describes a synchronization phenomenon of sea surface temperatures (SSTs) between the Gulf Stream and the Kuroshio Current, which is referred to as the boundary current synchronization (BCS). Information thermodynamics divides the entire system fluctuating with stochastic noise into subsystems and describes the interactions between these subsystems from the perspective of information transfer. The SDE coefficients have been estimated through regression analysis using observational and numerical simulation data. In the absence of stochastic noise, the solution of the estimated SDE shows that the SSTs relax toward zero without oscillation. The estimated SDE can be interpreted as a Maxwell’s demon system, with the Gulf Stream playing the role of the “Particle” and the Kuroshio Current playing the role of the “Demon.” The Gulf Stream forces the SST of the Kuroshio Current to be in phase. By contrast, the Kuroshio Current maintains the phase by interfering with the relaxation of the Gulf Stream SST. In the framework of Maxwell’s demon, the Gulf Stream is measured by the Kuroshio Current, whereas the Kuroshio Current performs feedback control on the Gulf Stream. When the Gulf Stream and the Kuroshio Current are coupled in an appropriate parameter regime, synchronization is realized with atmospheric and oceanic fluctuations as the driving source. This new mechanism, “stochastic synchronization,” suggests that such fluctuations can be converted into directional variations in a subsystem of the climate system through synchronization by utilizing information (i.e., information-to-energy conversion).
Assessing Patient-Reported Outcomes: A Mixed Methods Qualitative Comparison Between Obturator and Surgically Reconstructed Maxillectomy Patients
Authors: Almanaseer Ala , Dong Cecilia , Paczkowski Freeman , Laxague Francisco , Macneil S Danielle , Nichols Anthony C. , Yoo John , Fung Kevin , Aragon Cecilia , Mendez Adrian 
Published: February 2025

Objectives: Cancers of the maxillary region are often treated surgically with a maxillectomy followed by rehabilitation involving surgical reconstruction or obturator insertion to improve functional outcomes. However, there is a lack of consensus regarding the specific indications for either rehabilitation method. The objective of this study was to identify unique functional domains for maxillectomy patients who underwent surgical reconstruction or obturator insertion post-op to provide standardized data that can inform selection of either method. Methods: This mixed-methods qualitative research was conducted from January 2020 to June 2022 at London Health Sciences Centre, a tertiary care center in London, Ontario, Canada. Phase I included open-ended patient interviews through grounded theory, while phase II incorporated focus groups through the Delphi technique. Phase I identified functional domains of interest, which were further refined based on importance to patients in phase II. Inclusion criteria consisted of adults, 18 years or older who underwent maxillectomy surgery for head and neck cancer. Results: A total of 22 patients were included in phase I and 8 patients were included in phase II. The top 4 functional domains that affected patients regardless of rehabilitation method were eating difficulties, speaking difficulties, social discomfort with public eating, and numbness. The top 4 unique functional domains identified for the surgical group were dry mouth, trismus, chewing difficulties, and eye-related symptoms. The top 4 unique functional domains for the obturator group were obturator discomfort, nasal regurgitation, weight loss, and voice changes. Conclusions: This study identified functional domains affecting maxillectomy patients, which can be used to inform decisions regarding selection of rehabilitation method in clinical practice. This data can also in the future to create the first patient-reported outcomes instrument for this patient population.
Comparison of Commonly Used Fall Risk Assessment Tools in Predicting Fall Risk: A Prospective Observational Study in Older Adult Inpatients Over 80 Years of Age
Authors: Cai Lingqin , Cheng Xianzong , Zhang Kaijie , Yao Ling , Zhang Xiyue , Wang Zhang 
Published: February 2025

Background: Falls and fall-related injuries represent significant public health concerns, yet no reliable and valid assessment tool exists for evaluating fall risk in hospitalized older adults (≥80 years old). Objective: This study compared the discriminative properties of 5 commonly utilized fall risk assessment tools and comprehensive geriatric assessments for fallers and non-fallers among older adult inpatients. Methods: Comprehensive geriatric assessments, which included evaluations of fall risk, were conducted on 82 older adult inpatients. The incidence of falls during hospitalization was documented. The analysis compared the consistency of these scales with actual fall incidents, and the predictive values for fall risk were assessed using the areas under the receiver operating characteristic curve. Results: More than 30 older adult inpatients had a documented history of falls. The incidence of falls recorded in this study was 27.6 per 1000 patient days. The assessment scores of the National Health Commission Fall Scale, Morse Fall Scale, Berg Balance Scale, and Barthel Index revealed that fallers were at a significantly higher risk compared with non-fallers. The Morse Fall Scale showed the best consistency between score and fall occurrence (kappa = 0.461, P = .001). Its area under the receiver operating characteristic curve (AUC) was 0.813 (95% CI 0.676-0.949). The combined AUC for the Morse Fall Scale and Barthel Index was 0.891 (95% CI 0.784-0.998). Conclusions: Analysis of these assessment scales indicates that the Morse Fall Scale exhibits the highest predictive value for falls among older adult inpatients aged 80 years and above. Integration of the Barthel Index may enhance the predictive validity.