bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and pathological characteristics and expression of related molecules in patients with airway disseminated lung adenocarcinoma
Authors: Luan Wei , Liu Shuai , Zhang Kai , He Yin-Zai 
Published: June 2024

Abstract

Objective
Lung adenocarcinoma exhibits diverse genetic and morphological backgrounds, in addition to considerable differences in clinical pathology and molecular biological characteristics. Among these, the phenomenon of spread through air space (STAS), a distinct mode of lung cancer infiltration, has rarely been reported. Therefore, this study aimed to explore the relationship between STAS tumor cells and the clinical and molecular characteristics of patients with lung adenocarcinoma, as well as their impact on prognosis.

Methods
This study included 147 patients who were diagnosed with lung adenocarcinoma at the Inner Mongolia Autonomous Region Cancer Institute between January 2014 and December 2017. Surgical resection specimens were retrospectively analyzed. Using univariate and multivariate Cox analyses, we assessed the association between STAS and the clinicopathological features and molecular characteristics of patients with lung adenocarcinoma. Furthermore, we investigated the effects on patient prognosis. In addition, we developed a column–line plot prediction model and performed internal validation.

Results
Patients with positive STAS had a significantly higher proportion of tumors with a diameter ≥2 cm, with infiltration around the pleura, blood vessels, and nerves, and a pathological stage >IIB than in STAS-negative patients (P < 0.05). Cox multivariate survival analysis revealed that clinical stage, STAS status, tumor size, and visceral pleural invasion were independent prognostic factors influencing the 5-year progression-free survival in patients with lung adenocarcinoma. The predictive values and P values from the Hosmer-Lemeshow test were 0.8 and 0.2, respectively, indicating no statistical difference. Receiver operating characteristic curve analysis demonstrated areas under the curve of 0.884 and 0.872 for the training and validation groups, respectively. The nomogram model exhibited the best fit with a value of 192.09.

Conclusions
Clinical stage, pleural invasion, vascular invasion, peripheral nerve invasion, tumor size, and necrosis are independent prognostic factors for patients with STAS-positive lung adenocarcinoma. The nomogram based on the clinical stage, pleural invasion, vascular invasion, peripheral nerve invasion, tumor size, and necrosis showed good accuracy, differentiation, and clinical practicality.
TCGA-based analysis of oncogenic signaling pathways underlying oral squamous cell carcinoma
Authors: Gao Xing , Liu Dan-Dan , Liu Jin-Zhong , Wang Rui 
Published: June 2024

Abstract

Background
Oral squamous cell carcinoma (OSCC) represents a prevalent malignancy in the oral and maxillofacial area, having a considerable negative impact on both the quality of life and overall survival of affected individuals. Our research endeavors to leverage bioinformatic approaches to elucidate oncogenic signaling pathways, with the ultimate goal of gaining deeper insights into the molecular underpinnings of OSCC pathogenesis, and thus laying the groundwork for the development of more effective therapeutic and preventive strategies.

Methods
Differential expression analysis was performed on mRNA data from tumor and normal tissue groups to identify genes associated with OSCC, using The Cancer Genome Atlas database. Predictions of oncogenic signaling pathways linked to differentially expressed mRNAs were made, and these results were presented visually using R software, using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichments.

Results
GO and KEGG analyses of 2938 differentially expressed genes in OSCC highlighted their significant involvement in various biological processes. Notably, these processes were related to the extracellular matrix, structural organization, connective tissue development, and cell cycle regulation.

Conclusions
The comprehensive exploration of gene expression patterns provides valuable insights into potential oncogenic mechanisms in OSCC.
Resource sustainability and challenges in the supply chain: implications for infection prevention
Authors: Mehrotra Preeti , Desai Angel 
Published: June 2024

Purpose of review
Infection prevention and control practices remain the bedrock of healthcare associated infection prevention and outbreak and epidemic control efforts. However, issues in supply chain management can hinder these efforts, as exemplified by various public health emergencies. This review explores the key role of supply chains in infection prevention and explores specific challenges.

Recent findings
In all of the critical components of infection prevention and control – hand hygiene, personal protective equipment, sterile supplies, environmental disinfection, and waste management – disruptions in supply chains have led to limited availability and dissemination.

Summary
Strategies to mitigate these resource constraints in the inter-epidemic period will also be highlighted. The infection prevention workforce is well poised to inform supply chain dynamics. Without robust and adequate supply chains, infection prevention and control efforts suffer which perpetuates healthcare-associated infections, clusters, and epidemics.
Infrapopliteal Endovascular Interventions for Claudication Are Associated with Poor Long-Term Outcomes in Medicare-Matched Registry Patients
Authors: Bose Sanuja , McDermott Katherine M. , Dun Chen , Mao Jialin , Solomon Alex J. , Black James H. , Columbo Jesse A. , Conte Michael S. , Deery Sarah E. , Goodney Philip P. , Kalathiya Rohan , Kalbaugh Corey A. , Siracuse Jeffrey J. , Woo Karen , Makary Martin A. , Hicks Caitlin W. 
Published: June 2024

Background:
There are limited data supporting or opposing the use of infrapopliteal peripheral vascular interventions (PVI) for the treatment of claudication.

Objectives:
We aimed to evaluate the association of infrapopliteal PVI with long-term outcomes compared with isolated femoropopliteal PVI for the treatment of claudication.

Methods:
We conducted a retrospective analysis of all patients in the Medicare-matched Vascular Quality Initiative database who underwent an index infrainguinal PVI for claudication from January 2004-December 2019 using Cox proportional hazards models.

Results:
Of 14,261 patients (39.9% female; 85.6% age ≥65 years, 87.7% non-Hispanic white) who underwent an index infrainguinal PVI for claudication, 16.6% (N=2,369) received an infrapopliteal PVI. The median follow-up after index PVI was 3.7 years (IQR 2.1-6.1). Compared to patients who underwent isolated femoropopliteal PVI, patients receiving any infrapopliteal PVI had a higher 3-year cumulative incidence of conversion to CLTI (33.3% vs. 23.8%; P<0.001); repeat PVI (41.0% vs. 38.2%; P<0.01); and amputation (8.1% vs. 2.8%; P<0.001). After risk-adjustment, patients undergoing infrapopliteal PVI had a higher risk of conversion to CLTI (aHR 1.39, 95% CI, 1.25-1.53); repeat PVI (aHR 1.10, 95% CI, 1.01-1.19); and amputation (aHR 2.18, 95% CI, 1.77-2.67). Findings were consistent after adjusting for competing risk of death; in a 1:1 propensity-matched analysis; and in subgroup analyses stratified by TASC disease, diabetes, and end-stage kidney disease.

Conclusions:
Infrapopliteal PVI is associated with worse long-term outcomes than femoropopliteal PVI for claudication. These risks should be discussed with patients.
Surgical Intelligence Can Lead to Higher Adoption of Best Practices in Minimally Invasive Surgery
Authors: Fried Gerald M. , Ortenzi Monica , Dayan Danit , Nizri Eran , Mirkin Yuval , Maril Sari , Asselmann Dotan , Wolf Tamir 
Published: June 2024

Objective:
To examine the use of surgical intelligence for automatically monitoring critical view of safety (CVS) in laparoscopic cholecystectomy (LC) in a real-world quality initiative.

Background:
Surgical intelligence encompasses routine, artificial intelligence-based capture and analysis of surgical video, and connection of derived data with patient and outcomes data. These capabilities are applied to continuously assess and improve surgical quality and efficiency in real-world settings.

Methods:
Laparoscopic cholecystectomies conducted at 2 general surgery departments between December 2022 and August 2023 were routinely captured by a surgical intelligence platform, which identified and continuously presented CVS adoption, surgery duration, complexity, and negative events. In March 2023, the departments launched a quality initiative aiming for 75% CVS adoption.

Results:
Two hundred seventy-nine procedures were performed during the study. Adoption increased from 39.2% in the 3 preintervention months to 69.2% in the final 3 months (P < 0.001). Monthly adoption rose from 33.3% to 75.7%. Visualization of the cystic duct and artery accounted for most of the improvement; the other 2 components had high adoption throughout. Procedures with full CVS were shorter (P = 0.007) and had fewer events (P = 0.011) than those without. OR time decreased following intervention (P = 0.033).

Conclusions:
Surgical intelligence facilitated a steady increase in CVS adoption, reaching the goal within 6 months. Low initial adoption stemmed from a single CVS component, and increased adoption was associated with improved OR efficiency. Real-world use of surgical intelligence can uncover new insights, modify surgeon behavior, and support best practices to improve surgical quality and efficiency.
Mixed ctDNA dynamics and decreased detection rates in early-stage lung cancer patients during radiation treatment
Authors: Boniface Christopher , Baker Kathryn , Deig Christopher , Halsey Carol , Kelley Taylor , Rahmani Ramtin , Tormoen Garth , Spellman Paul T , Nabavizadeh Nima 
Published: June 2024

AbstractQuantification and detection of circulating tumor DNA (ctDNA) has been used to identify the presence of cancers. Ablative radiation therapy kills tumor cells to reduce tumor burden and it follows that these dying tumor cells could lead to increased ctDNA abundance. We carried out deep, error-corrected sequencing of cell-free DNA collected serially from 12 stage I, and 2 stage II/III non-small cell lung cancer (NSCLC) patients undergoing external-beam radiation treatment (EBRT) after initial diagnosis. We found that ctDNA detection rates decreased at the first blood draw as compared to baseline (43% to 7% of patients). Total ctDNA abundance decreased in 6 patients and increased in 5 patients between those same blood draws, with one patient showing evidence of tumoral heterogeneity. Both patients with stage II/III disease had the largest increases in ctDNA abundance from baseline. Multiple blood draws improved ctDNA detection rates from 43% to 50% with a second blood draw and to 71% with 4 blood draws. Additionally, EGFR mutations were detectable in 6 patients during EBRT that were not detected prior to treatment. Taken together, these results provide an early-stage NSCLC counterpoint to previous work that reported improved ctDNA detection after radiation therapy in more advanced disease.
Competing Risk Survival analysis of time to in-hospital mortality or Recovery among Covid-19 Patients in South-East Ethiopia: a hospital-based multisite study
Authors: Wordofa Addis , Demissie Ayalneh , Kalu Abdurehman , Tune Abdurehman , Suleiman Mohammed , Kibret Abay , Abera Zerihun , Mulugeta Yonas 
Published: June 2024

AbstractBackgroundTo date, survival data on risk factors for COVID-19 mortality in south- Ethiopia is limited, and none of the published survival studies have used a competing risk approach. This study aims to identify risk factors for in-hospital mortality in COVID-19 patients hospitalized at one of the six hospitals in southeast -Ethiopia, considering recovery as a competing risk.MethodsThis observational multisite study included a medical record of 827 confirmed SARS-CoV-2 cases hospitalized at one of the six hospitals in southeast-Ethiopia from October 1, 2022 to May 31, 2023. We compiled data on the patients’ socio-demographic characteristics, clinical manifestation, comorbidity, treatment status, treatment outcomes, and length of stay. We performed a Cox regression analysis for competing risks, presenting cause-specific hazard ratios (HRcs) for the effect of preselected factors on the absolute risk of death and recovery.Results827 patients were included (51.9% male; median age 50 years, IQR: 38—65). Patients were hospitalized for a median duration of 5 days (IQR: 1—7); 139 (17%) of them died, while 516 (62%) were recovered and discharged alive, the rest 172 (21%) were censored. Patients with higher age (HRcs 2.62, 95% CI 1.29—5.29), immune- compromised state (HRcs 1.46, 95% CI 1.08—1.98) had increased risk of death, whereas male sex paradoxically (HRcs 0.45, 95% CI 0.22—0.91) associated with decreased risk of death. We found no increased mortality risk in diabetes patients.ConclusionThis competing risk survival analysis allows us to corroborate specific pattern of risk factors about COVID-19 mortality and its progression among different groups of individuals (differentiated by age and immune-compromised state). 62% presenting cases recovered within a median duration of 5 days; where as 17% die within the first 72 hours, most with immune-compromised conditions. This should be considered while planning and allocating the distribution of care services for effective health service delivery
The Relationships of Resting-state Brain Entropy (BEN), Ovarian Hormones and Behavioral Inhibition and Activation Systems (BIS/BAS)
Authors: Song Dong-Hui , Wang Ze 
Published: June 2024

AbstractEntropy measures the irregularity or complexity of a system. Recent research on brain entropy (BEN) based on resting-state fMRI has provided complementary information to other metrics such as low-frequency fluctuations and cerebral blood flow. It has been established that neural plasticity, both pharmacological and nonpharmacological, as well as brain stimulation can influence BEN. However, it remains unknown whether BEN can reflect the effects of hormones. Furthermore, recent studies have indicated that ovarian hormones influence both the behavioral inhibition and activation systems. In our study, we utilized open-access available data from OpenNeuro to investigate the effects of ovarian hormones on BEN and their impact on BIS/BAS.Our results indicated a negative correlation between progesterone (PROG) and BEN in the frontal-parietal network and limbic system, while BEN showed a significant positive correlation with BAS-drive in the DLPFC. Additionally, a significant negative correlation was observed between PROG and BAS-drive. Further analysis revealed that DLPFC BEN mediates the negative correlation between PROG and BAS-drive. This suggests that PROG reduces BAS-drive by increasing the executive and inhibitory functions of DLPFC. We also analyzed the FC between DLPFC and the whole brain. DLPFC-IPL FC showed a significant positive correlation with BAS-drive, while DLPFC-LOFC FC exhibited a significant negative correlation with BAS-fun-seeking. Moreover, DLPFC-AG FC demonstrated a significant positive correlation with BAS-rewards. These results are consistent with the relationship between executive functions of the frontal-parietal network and impulsivity representation of BAS.Our study is the first to demonstrate that BEN can also reflect the impact of hormones on brain function. Additionally, we identified that the negative correlation between PROG and BAS-drive is mediated by left DLPFC BEN, providing new insights into our understanding of the effects of PROG on the brain and behavior.
Abnormal local cortical functional connectivity due to interneuron dysmaturation after neonatal intermittent hypoxia
Authors: Goussakov Ivan , Synowiec Sylvia , Fabres Rafael Bandeira , Almeida Gabriela Dias , Takada Silvia Honda , Aksenov Daniil , Drobyshevsky Alexander 
Published: June 2024

ABSTRACTBackgroundPremature infants often experience frequent hypoxic episodes due to immaturity of respiratory control that may result in disturbances of gray and white matter development and long-term cognitive and behavioral abnormalities. We hypothesize that neonatal intermittent hypoxia alters cortical maturation of excitatory and inhibitory circuits that can be detected early with functional MRI.MethodsC57BL/6 mouse pups were exposed to an intermittent hypoxia (IH) regimen consisting of 12 to 20 daily hypoxic episodes of 5% oxygen exposure for 2 min at 37C from P3 to P7, followed by MRI at P12 and electrophysiological recordings in cortical slices and in vivo at several time points between P7 and P13. Behavioral tests were conducted at P41-P50 to assess animal activity and motor learning.ResultsAdult mice after neonatal IH exhibited hyperactivity in open field test and impaired motor learning in complex wheel tasks. Patch clamp and evoked field potential electrophysiology revealed increased glutamatergic transmission accompanied by elevation of tonic inhibition.A decreased synaptic inhibitory drive was evidenced by miniature IPSC frequency on pyramidal cells, multi-unit activity recording in vivo in the motor cortex with selective GABAAreceptor inhibitor picrotoxin injection, as well as by the decreased interneuron density at P13. There was also an increased tonic depolarizing effect of picrotoxin after IH on principal cells’ membrane potential on patch clamp and direct current potential in extracellular recordings. The amplitude of low-frequency fluctuation on resting-state fMRI was larger, with a larger increase after picrotoxin injection in the IH group.ConclusionsIncreased excitatory glutamatergic transmission, decreased numbers, and activity of inhibitory interneurons after neonatal IH may affect the maturation of connectivity in cortical networks, resulting in long-term cognitive and behavioral changes, including impaired motor learning and hyperactivity. Functional MRI reveals increased intrinsic connectivity in the sensorimotor cortex, suggesting neuronal dysfunction in cortical maturation after neonatal IH. The increased tonic inhibition, presumably due to tonic extrasynaptic GABA receptor drive, may be compensatory to the elevated excitatory glutamatergic transmission.
Comparative connectomics of the descending and ascending neurons of theDrosophilanervous system: stereotypy and sexual dimorphism
Authors: Stürner Tomke , Brooks Paul , Capdevila Laia Serratosa , Morris Billy J. , Javier Alexandre , Fang Siqi , Gkantia Marina , Cachero Sebastian , Beckett Isabella R. , Champion Andrew S. , Moitra Ilina , Richards Alana , Klemm Finja , Kugel Leonie , Namiki Shigehiro , Cheong Han S.J. , Kovalyak Julie , Tenshaw Emily , Parekh Ruchi , Schlegel Philipp , Phelps Jasper S. , Mark Brandon , Dorkenwald Sven , Bates Alexander S. , Matsliah Arie , Yu Szi-chieh , McKellar Claire E. , Sterling Amy , Seung Sebastian , Murthy Mala , Tuthill John , Lee Wei-Chung A. , Card Gwyneth M. , Costa Marta , Jefferis Gregory S.X.E. , Eichler Katharina 
Published: June 2024

AbstractIn most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and information bottleneck connecting the brain and the ventral nerve cord (VNC, spinal cord analogue) and comprises diverse populations of descending (DN), ascending (AN) and sensory ascending neurons, which are crucial for sensorimotor signalling and control.Integrating three separate EM datasets, we now provide a complete connectomic description of the ascending and descending neurons of the female nervous system ofDrosophilaand compare them with neurons of the male nerve cord. Proofread neuronal reconstructions have been matched across hemispheres, datasets and sexes. Crucially, we have also matched 51% of DN cell types to light level data defining specific driver lines as well as classifying all ascending populations.We use these results to reveal the general architecture, tracts, neuropil innervation and connectivity of neck connective neurons. We observe connected chains of descending and ascending neurons spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analysis of circuits implicated in sex-related behaviours, including female ovipositor extrusion (DNp13), male courtship (DNa12/aSP22) and song production (AN hemilineage 08B). Our work represents the first EM-level circuit analyses spanning the entire central nervous system of an adult animal.
Protein Sequence Domain Annotation using Language Models
Authors: Sarkar Arpan , Krishnan Kumaresh , Eddy Sean R. 
Published: June 2024

AbstractProtein function inference relies on annotating protein domains via sequence similarity, often modeled through profile Hidden Markov Models (profile HMMs), which capture evolutionary diversity within related domains. However, profile HMMs make strong simplifying independence assumptions when modeling residues in a sequence. Here, we introduce PSALM (Protein Sequence Annotation using Language Models), a hierarchical approach that relaxes these assumptions and uses representations of protein sequences learned by protein language models to enable high-sensitivity, high-specificity residue-level protein sequence annotation. We also develop the Multi-Domain Protein Homology Benchmark (MDPH-Bench), a benchmark for protein sequence domain annotation, where training and test sequences have been rigorously split to share no similarity between any of their domains at a given threshold of sequence identity. Prior benchmarks, which split one domain family at a time, do not support methods for annotating multi-domain proteins, where training and test sequences need to have multiple domains from different families. We validate PSALM’s performance on MDPH-Bench and highlight PSALM as a promising alternative to HMMER, a state-of-the-art profile HMM-based method, for protein sequence annotation.
Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen
Authors: Hoang-Phou Steven , Pal Sukumar , Slepenkin Anatoli , Abisoye-Ogunniyun Abisola , Zhang Yuliang , Gilmore Sean F. , Shelby Megan , Bourguet Feliza , Mohagheghi Mariam , Noy Aleksandr , Rasley Amy , de la Maza Luis M. , Coleman Matthew A. 
Published: June 2024

AbstractChlamydia trachomatisis the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and de-centralized production of recombinant protein vaccine antigens. Here, we use CFPS to produce the putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for use as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were primed with CT584 adjuvanted with CpG-1826 intranasally (i.n.) or CpG-1826 + Montanide ISA 720 intramuscularly (i.m.), followed four-weeks later by an i.m. boost before respiratory challenge with 104inclusion forming units (IFU) ofChlamydia muridarum. Immunization with CT584 generated robust antibody responses but weak cell mediated immunity and failed to protect against i.n. challenge as demonstrated by body weight loss, increased lungs’ weights and the presence of high numbers of IFUs in the lungs. While CT584 alone may not be the ideal vaccine candidate, the speed and flexibility with which CFPS can be used to produce other potential chlamydial antigens makes it an attractive technique for antigen production.