bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating bulk and single-cell RNA sequencing data reveals epithelial-mesenchymal transition molecular subtype and signature to predict prognosis, immunotherapy efficacy, and drug candidates in low-grade gliomas
Authors: Wang Chengcheng , He Zheng 
Published: November 2023

Objective: Epithelial-mesenchymal transition (EMT) is a tightly regulated and dynamic process occurring in both embryonic development and tumor progression. Our study aimed to comprehensively explore the molecular subtypes, immune landscape, and prognostic signature based on EMT-related genes in low-grade gliomas (LGG) in order to facilitate treatment decision-making and drug discovery.Methods: We curated EMT-related genes and performed molecular subtyping with consensus clustering algorithm to determine EMT expression patterns in LGG. The infiltration level of diverse immune cell subsets was evaluated by implementing the single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE algorithms. The distinctions in clinical characteristics, mutation landscape, and immune tumor microenvironment (TME) among the subtypes were subjected to further investigation. Gene Set Variation Analysis (GSVA) was performed to explore the biological pathways that were involved in subtypes. The chemo drug sensitivity and immunotherapy of subtypes were estimated through GDSC database and NTP algorithm. To detect EMT subtype-related prognostic gene modules, the analysis of weighted gene co-expression network (WGCNA) was performed. The LASSO algorithm was utilized to construct a prognostic risk model, and its efficacy was verified through an independent CGGA dataset. Finally, the expression of the hub genes from the prognostic model was evaluated through the single-cell dataset and in-vitro experiment.Results: The TCGA-LGG dataset revealed the creation of two molecular subtypes that presented different prognoses, clinical implications, TME, mutation landscapes, chemotherapy, and immunotherapy. A three-gene signature (SLC39A1, CTSA and CLIC1) based on EMT expression pattern were established through WGCNA analysis. Low-risk patients showed a positive outlook, increased immune cell presence, and higher expression of immune checkpoint proteins. In addition, several promising drugs, including birinapant, fluvastatin, clofarabine, dasatinib, tanespimycin, TAK−733, GDC−0152, AZD8330, trametinib and ingenol-mebutate had great potential to the treatment of high risk patients. Finally, CTSA and CLIC1 were highly expressed in monocyte cell through single-cell RNA sequencing analysis.Conclusion: Our research revealed non-negligible role of EMT in the TME diversity and complexity of LGG. A prognostic signature may contribute to the personalized treatment and prognostic determination.
Transitions in sense of coherence among middle-aged women raising adolescents before and during the COVID-19 pandemic
Authors: Omiya Tomoko , Sankai Tomoko , Miyazaki Akari , Abe Yoshiki , Deguchi Naoko Kumada 
Published: November 2023

ObjectiveA longitudinal study was conducted among Japanese women raising adolescents to determine how the COVID-19 pandemic has affected their sense of coherence (SOC) and to provide suggestions for supporting them.MethodsThe SOC scores of 138 pairs of middle-aged women and their children (junior high school students) were compared at two time points: 2019 (before the pandemic, T1) and 2020 (during the pandemic, T2).ResultsOverall, the women’s SOC did not change, whereas the adolescents’ SOC increased. In contrast, 44% of the women’s SOC scores decreased during the pandemic; no differences were detected between the SOC maintenance and increase group (G1) and the SOC decrease group (G2) in mental health, subjective physical health, social capital, and job status, and the child variables were not related. Multiple regression analysis of G1 and G2 with SOC at T2 as the dependent variable showed that for G2, at T1, having good mental and physical health conditions, a rich social capital, and having a job were positively associated with SOC during the pandemic.ConclusionMiddle-aged Japanese women, who often work as informal workers, are easily laid off and are involved in care work. Thus, the change in their socioeconomic status due to the pandemic may have been severe. Given the long-term social impact of the pandemic, it is necessary to consider support for women, including economic and social support such as employment and building human connections.
Self-pacing ameliorates recall deficit when listening to vocoded discourse: a cochlear implant simulation
Authors: Hansen Thomas A. , O’Leary Ryan M. , Svirsky Mario A. , Wingfield Arthur 
Published: November 2023

IntroductionIn spite of its apparent ease, comprehension of spoken discourse represents a complex linguistic and cognitive operation. The difficulty of such an operation can increase when the speech is degraded, as is the case with cochlear implant users. However, the additional challenges imposed by degraded speech may be mitigated to some extent by the linguistic context and pace of presentation.MethodsAn experiment is reported in which young adults with age-normal hearing recalled discourse passages heard with clear speech or with noise-band vocoding used to simulate the sound of speech produced by a cochlear implant. Passages were varied in inter-word predictability and presented either without interruption or in a self-pacing format that allowed the listener to control the rate at which the information was delivered.ResultsResults showed that discourse heard with clear speech was better recalled than discourse heard with vocoded speech, discourse with a higher average inter-word predictability was better recalled than discourse with a lower average inter-word predictability, and self-paced passages were recalled better than those heard without interruption. Of special interest was the semantic hierarchy effect: the tendency for listeners to show better recall for main ideas than mid-level information or detail from a passage as an index of listeners’ ability to understand the meaning of a passage. The data revealed a significant effect of inter-word predictability, in that passages with lower predictability had an attenuated semantic hierarchy effect relative to higher-predictability passages.DiscussionResults are discussed in terms of broadening cochlear implant outcome measures beyond current clinical measures that focus on single-word and sentence repetition.
Effects of environmental and genetic interactions on job burnout in coal miners: interactions between occupational stress, coping styles, and NR3C2 gene polymorphisms
Authors: Lin Xin , Ma Xiaofan , Yi Xiaoting , Qu Chao , Li Fuye 
Published: November 2023

ObjectivesTo investigate the current situation regarding occupational burnout among coal miners, explore the relationship between NR3C2 gene polymorphism and occupational burnout, and analyze the influence of the interaction between environment and gene on occupational burnout. This study provides a scientific basis for formulating health strategies to combat job burnout.MethodsA total of 1,500 first-line coal mine workers were selected by cluster random sampling, and the job burnout scale, job content questionnaire (JCQ), and simplified coping style questionnaire (SCSQ) were used for the questionnaire survey. A total of 150 workers were randomly selected from the high burnout group and the low burnout group, and a total of 300 workers were selected as the research objects to examine the relationship between gene polymorphism, environment-gene interactions and burnout. This study employed iMLDRTM genotyping technology for NR3C2 gene (rs5522, rs2070950) polymorphism analysis. The relationship between the occurrence of job burnout, occupational stress, coping styles and the NR3C2 gene was analyzed.ResultsFinally, a total of 1,282 valid questionnaires were retrieved, with an effective recovery rate of 85.5%. The study included 128 participants (10%) with zero burnout, 400 (31.2%) with mild burnout, 649 (50.6%) with moderate burnout and 105 (8.2%) with severe burnout. There were significant differences in the rate of burnout among miners with respect to sex, age, working years, educational level, shifts, and marital status (P &lt; 0.05). The difference in occupational stress between the different job burnout groups was statistically significant (P &lt; 0.05). Compared with the GG genotype of rs2070950 of the NR3C2 gene, the CC genotype was identified as a susceptibility gene for occupational burnout (P &lt; 0.05). In respect to rs5522, rs2070950, occupational stress, positive coping, and negative coping, the low-risk group was unlikely to suffer from job burnout compared with the high-risk group (OR = 0.103, 95%CI: 0.058–0.182).ConclusionIn addition to demographic characteristics, occupational stress and negative coping styles were also identified as risk factors for job burnout. The interaction between locus rs5522, locus rs2070950, occupational stress, positive response, and negative response were found to affect the incidence of occupational burnout.
Occupational exposure and health surveys at metal additive manufacturing facilities
Authors: Assenhöj Maria , Almstrand Ann-Charlotte , Kokelj Spela , Ljunggren Stefan A. , Olin Anna-Carin , Karlsson Helen 
Published: November 2023

IntroductionAdditive manufacturing is a novel state-of-the art technology with significant economic and practical advantages, including the ability to produce complex structures on demand while reducing the need of stocking materials and products. Additive manufacturing is a technology that is here to stay; however, new technologies bring new challenges, not only technical but also from an occupational health and safety perspective. Herein, leading Swedish companies using metal additive manufacturing were studied with the aim of investigating occupational exposure and the utility of chosen exposure- and clinical markers as predictors of potential exposure-related health risks.MethodsExposure levels were investigated by analysis of airborne dust and metals, alongside particle counting instruments measuring airborne particles in the range of 10 nm−10 μm to identify dusty work tasks. Health examinations were performed on a total of 48 additive manufacturing workers and 39 controls. All participants completed a questionnaire, underwent spirometry, and blood and urine sampling. A subset underwent further lung function tests.ResultsExposure to inhalable dust and metals were low, but particle counting instruments identified specific work tasks with high particle emissions. Examined health parameters were well within reference values on a group level. However, statistical analysis implied an impact on workers kidney function and possible airway inflammation.ConclusionThe methodology was successful for investigating exposure-related health risks in additive manufacturing. However, most participants have been working &lt;5 years. Therefore, long-term studies are needed before we can conclusively accept or reject the observed effects on health.
Impact of multiparametric magnetic resonance imaging targeted biopsy on functional outcomes in patients following robot-assisted laparoscopic radical prostatectomy
Authors: Leitsmann Conrad , Uhlig Annemarie , Bremmer Felix , Mohr Mirjam Naomi , Trojan Lutz , Leitsmann Marianne , Reichert Mathias 
Published: November 2023

IntroductionMultiparametric magnetic resonance imaging guided prostate biopsy (mpMRI PBx) leads to a higher rate of successful nerve-sparing in robot-assisted laparoscopic prostatectomy (ns-RALP) for prostate cancer (PCa). This study aimed to evaluate the impact of mpMRI PBx compared to standard ultrasound-guided PBx on functional outcomes focusing on erectile function in patients following ns-RALP.Material and methodsAll RALPs performed between 01/2016 and 06/2021 were retrospectively stratified according to (attempted) ns vs. non ns RALPs and were then categorized based on the PBx technique (mpMRI PBx vs. standard PBx). We compared RALP outcomes such as pathological tumor stage, rates of secondary nerve resection (SNR) and positive surgical margin status (PSM). Furthermore, we explored the association between PBx-technique and patient-reported outcomes assessed 12 months after RALP using the prospectively collected 26-item Expanded Prostate Cancer Index Composite (EPIC-26) questionnaire. Chi-square tests and logistic regression analysis were conducted.ResultsA total of 849 RALPs included 517 (61%) procedures with (attempted) ns. Among these, 37.5% were diagnosed via preoperative mpMRI PBx. Patients with a preoperative standard PBx had a 57% higher association of PSM (p = 0.030) compared to patients with mpMRI PBx and a 24% higher risk of erectile dysfunction (ED) 12 months post RALP (p = 0.025). When ns was attempted, we observed a significantly higher rate of SNR in patients who underwent a standard PBx compared to those who received a mpMRI PBx (50.8% vs. 26.7%, p &lt; 0.001) prior RALP. In comparison, upgrading occurred more often in the standard PBx group (50% vs. 40% mpMRI PBx, p = 0.008).ConclusionThe combination of mpMRI PBx for PCa diagnosis followed by ns-RALP resulted in significantly fewer cases of SNR, better oncological outcomes and reduced incidence of ED 1 year after surgery. This included fewer PSM and a lower rate of postoperative tumor upgrading.
Machine Learning Approach to Analyze the Heavy Quark Diffusion Coefficient in Relativistic Heavy Ion Collisions
Authors: Guo Rui , Li Yonghui , Chen Baoyi 
Published: November 2023

The diffusion coefficient of heavy quarks in a deconfined medium is examined in this research using a deep convolutional neural network (CNN) that is trained with data from relativistic heavy ion collisions involving heavy flavor hadrons. The CNN is trained using observables such as the nuclear modification factor RAA and the elliptic flow v2 of non-prompt J/ψ from the B-hadron decay in different centralities, where B meson evolutions are calculated using the Langevin equation and the instantaneous coalescence model. The CNN outputs the parameters, thereby characterizing the temperature and momentum dependence of the heavy quark diffusion coefficient. By inputting the experimental data of the non-prompt J/ψ(RAA,v2) from various collision centralities into multiple channels of a well-trained network, we derive the values of the diffusion coefficient parameters. Additionally, we evaluate the uncertainty in determining the diffusion coefficient by taking into account the uncertainties present in the experimental data (RAA,v2), which serve as inputs to the deep neural network.
Sage Essential Oil as an Antimicrobial Agent against Salmonella enterica during Beef Sous Vide Storage
Authors: Gál Robert , Čmiková Natália , Kačániová Miroslava , Mokrejš Pavel 
Published: November 2023

Sous-vide is a process comprising vacuum-sealing food, heating it to the desired temperature, and circulating it in a water bath in a sous vide machine. This cooking technique is increasingly common in homes and catering establishments due to its simplicity and affordability. However, manufacturers and chef’s recommendations for low-temperature and long-term sous-vide cooking in media raise food safety concerns, particularly when preparing beef tenderloin. In this study, Salmonella enterica was found to be inactivated by heat and sage essential oil (EO) in beef samples from musculus psoas major that had been sous vide processed. To determine whether heat treatment was likely to increase the sous vide efficiency, S. enterica and sage EO were mixed. After being vacuum-packed and injected with S. enterica, the samples were cooked at 50–65 °C through the sous vide technique for the prescribed time. On days 1, 3, and 6, the amounts of S. enterica, total bacteria, and coliform bacteria were measured in the control and treated groups of beef processed sous vide. Mass spectrometry was used to identify bacterial isolates on different days. On each day that was measured, a higher number of all the microbiota was found in the samples exposed to 50 °C for 5 min. The most frequently isolated microorganisms from both groups of samples were Pseudomonas fragi (17%), Pseudomonas cedrina (8%), and Proteus vulgaris (8%); in the treated group, also S. enterica (21%), Pseudomonas fragi (13%), and Pseudomonas veronii (6%). After the heat treatment of samples at 65 °C for 20 min, the total count of bacteria and coliform bacteria was zero. It has been shown that adding sage essential oil (EO) in combination with sous vide processing technique leads to the stabilization and safety of beef tenderloin.
Antioxidant Activity of Selected Medicinal Plants Used by Traditional Herbal Practitioners to Treat Cancer in Malawi
Authors: Masumbu Friday Fosta Fred , Kamanula John Finias , Mwakikunga Anthony , Mwamatope Bonface , Tembo David 
Published: November 2023

This study evaluated the phytochemical composition and antioxidant activity of Piliostigma thonningii (Schumach.) Milne-Redh, Psorospermum febrifugum Spach, Inula glomerata Oliv. and Hiern, Zanthoxylum chalybeum Engl. and Monotes africanus A.DC., claimed to treat cancer by Malawian traditional herbal practitioners. Ground and dried plant extracts were analyzed for total phenolic content (TPC), total flavonoid content (TFC), total alkaloid content (TAC), ferric reducing antioxidant power (FRAP) and 2,2-Diphenyl-1-Picrylhydrazyl (DPPH) using standard assays. The TPC, TFC, and TAC ranged from 539 ± 2.70 to 4602 ± 32 mg GAE/g DW, 6.18 ± 0.03 to 64.04 ± 0.16 mg QE/g DW and 19.25 ± 0.07 to 76.05 ± 0.36 mg CE/g DW, respectively, and the variations were significant, p < 0.05. FRAP values ranged from 82.15 ± 0.7 to 687.28 ± 0.71 mg TEAC/g DW and decreased in the following order: P. thoningii (Schumach.) Milne-Redh > P. febrifugum Spach > M. africanus A.DC > Z. chalybeum Engl > I. glomerata Oliv. and Hiern. The scavenging activity (SA50) of the extracts ranged from 0.09 ± 0.01 to 1.57 ± 0.01 μg/mL of extract with P. thonningii (Schumach.) Milne-Redh showing the lowest value. Based on the levels of phenolic compounds and their antioxidant activity, the plants in this study could be considered for use as medicinal agents and sources of natural bioactive compounds and antioxidants.
A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles
Authors: Su Yating , Zeeshan Ul Haq Muhammad , Liu Xiaofeng , Li Yang , Yu Jing , Yang Dongmei , Wu Yougen , Liu Ya 
Published: November 2023

Casparian strip membrane domain protein-like (CASPL) genes are key genes for the formation and regulation of the Casparian strip and play an important role in plant abiotic stress. However, little research has focused on the members, characteristics, and biological functions of the patchouli PatCASPL gene family. In this study, 156 PatCASPL genes were identified at the whole-genome level. Subcellular localization predicted that 75.6% of PatCASPL proteins reside on the cell membrane. A phylogenetic analysis categorized PatCASPL genes into five subclusters alongside Arabidopsis CASPL genes. In a cis-acting element analysis, a total of 16 different cis-elements were identified, among which the photo-responsive element was the most common in the CASPL gene family. A transcriptome analysis showed that p-hydroxybenzoic acid, an allelopathic autotoxic substance, affected the expression pattern of PatCASPLs, including a total of 27 upregulated genes and 30 down-regulated genes, suggesting that these PatCASPLs may play an important role in the regulation of patchouli continuous cropping obstacles by affecting the formation and integrity of Casparian strip bands. These results provided a theoretical basis for exploring and verifying the function of the patchouli PatCASPL gene family and its role in continuous cropping obstacles.
Laboratory Surveillance of Acinetobacter spp. Bloodstream Infections in a Tertiary University Hospital during a 9-Year Period
Authors: Spiliopoulou Anastasia , Giannopoulou Ioanna , Assimakopoulos Stelios F. , Jelastopulu Eleni , Bartzavali Christina , Marangos Markos , Paliogianni Fotini , Kolonitsiou Fevronia 
Published: November 2023

Multidrug-resistant Acinetobacter baumannii infections have become a threat for public health worldwide. The aim of the present study was to follow-up resistance patterns of Acinetobacter spp. bloodstream isolates in a Tertiary University Hospital over the last nine years, from 2014 to 2022. Susceptibility patterns were followed for the following antimicrobial agents: amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, imipenem, meropenem, tigecycline, trimethoprim/sulfamethoxazole, and colistin. Minimal inhibitory concentration (MIC) values to ampicillin/sulbactam, cefepime, ceftazidime, minocycline, piperacillin/tazobactam were evaluated from 2020 to 2023. During the study period, 853 Acinetobacter spp. bloodstream infections (BSIs) were recorded, accounting for 5.36% of all BSIs. A. baumannii was isolated in 795 cases (93.2%), during the study period. Most BSIs were recorded in adult intensive care units (ICU) (46.2%) and medical wards (42%). Among A. baumannii isolates, 4.5% were multidrug-resistant, 84.7% were extensively drug-resistant, and 8.5% were pandrug-resistant. Resistance to carbapenems was over 95%. Resistance to tigecycline increased significantly during the last years of the study (2020–2022); A. baumannii isolates with MIC ≤ 2 μg/mL accounted for 28.5% of all isolates. Resistance to colistin exhibited an increasing pattern up to 42.2% in 2022. Increasing resistance rates and the evolution of pandrug-resistant isolates call for the urgent application of preventive and response actions.
The DAWN antivirals trial: process evaluation of a COVID-19 trial in general practice
Authors: Tare Dajana , Coenen Samuel , De Sutter An , Heytens Stefan , Devroey Dirk , Buret Laetitia , Schoenmakers Birgitte , Delvaux Nicolas , Verbakel Jan Y , Bogaerts Kris , van den Bruel Ann 
Published: November 2023

Background
The DAWN antivirals trial was a multicentric, randomised placebo-controlled trial evaluating antiviral medication for COVID-19 in general practice. The trial was prematurely terminated because of insufficient recruitment.

Aim
To explore which factors contributed to the premature termination.

Design & setting
General practice in Belgium.

Method
Patients were randomised to camostat or placebo (patients and physicians blinded) between June 2021 and July 2022; a third arm evaluating molnupiravir (open label) was opened in March 2022. The outcome assessor was blinded for all comparisons except for the patient reported outcomes in case of molnupiravir. The authors analysed available trial data and evaluated trial context, implementation, and mechanisms of impact based on semi-structured interviews with trial stakeholders.

Results
The trial recruited 44 participants; 19 were allocated to camostat (median age 55 years), 8 to molnupiravir (median age 60 years), and 17 to placebo (median age 56 years). There were no serious adverse events in either group. Most difficulties were related to the pandemic context: disruption to routine clinical services; multiple changes to the service model for COVID-19 patients; overwhelmed clinical staff; delays of trial medication; and staff shortages in the sponsor and clinical team. In addition, regulatory approval processes were lengthy and led to additional study procedures. It was felt that the trial started too late, when vaccinations had already begun.

Conclusion
The DAWN antivirals trial was stopped prematurely. Although many barriers were related to the pandemic itself, hurdles such as a small and inexperienced sponsor and clinical teams, delays in regulatory processes, and research capacity in routine settings could be overcome by established research infrastructure and standardisation of processes.