bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoarchitecture of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography: imaging workflow and classification for drug testing
Authors: Salditt Tim , Reichmann Jakob , Sarrazin Clement , Schmale Sebastian , Blaurock Claudia , Schmitzer Bernhard , Balkema-Buschmann Anne 
Published: March 2024

Abstract
X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. To address these challenges, we here design and implement a novel integrated and high throughput XPCT imaging and analysis workflow for 3D histology, pathohistology and drug testing. Our approach uses semi-automated data acquisition, reconstruction and statistical quantification. We demonstrate its capability for the example of lung pathohistology in Covid-19. Using a small animal model, different Covid-19 drug candidates are administered after infection and tested in view of restoration of the physiological cytoarchitecture, specifically the alveolar morphology. To this end, we then use morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing quantitative insights into the pathological progression and partial recovery due to drug treatment. Finally, we stress that the XPCT image chain implemented here only used synchrotron radiation for validation, while the data used for analysis was recorded with laboratory µCT radiation, more easily accessible for pre-clinical research.
Ignoring cost of living misses the true level of energy burden
Authors: Zhang Jingjing , Nock Destenie , Li Xiatong 
Published: March 2024

Abstract

Energy burden, which measures the percentage of a household's income allocated to energy expenses, is a widely used metric for identifying a form energy or fuel poverty. A blind spot in energy burden calculations is an omission of the cost of living impacts on ability to spend money on energy bills. There has been a significant nationwide increase in housing burden since 1980, especially among renters. Currently, at least half of all renters face financial strain due to housing costs. Our research reveals that excluding housing cost from the energy burden calculation results in the omission of 21% of burdened census regions (2197 out of 10327 under our method) facing financial strain. Furthermore, this approach identifies more regions with household incomes above the national median (about $75,000 in 2022) experiencing energy burden when housing cost is included. These patterns are particularly pronounced in humid and cold regions. Re-thinking energy burden to include housing affordability is critical to reflect the true level of energy poverty.
Unlocking Biological Activity and Metabolomics Insights: Primary Screening of Cyanobacterial Biomass from a Tropical Reservoir
Authors: Médice Rhuana Valdetário , Arruda Renan Silva , Yoon Jaewon , Borges Ricardo Moreira , Noyma Natalia Pessoa , Lurling Miquel , Crnkovic Camila Manoel , Marinho Marcelo Manzi , Pinto Ernani 
Published: March 2024

Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) can pose risks to ecosystems and human health worldwide due to their capacity to produce natural toxins. Nevertheless, the potential danger associated with numerous metabolites produced by cyanobacteria remains undisclosed. Only select classes of cyanopeptides have been extensively studied to yield substantial evidence regarding their toxicity, resulting in their inclusion in risk management and water quality regulations. Information about exposure concentrations, co-occurrence, and toxic impacts of several cyanopeptides remains largely unexplored. This research utilized LC-MS-based metabolomics to ascertain the chemical profile of environmental cyanobacterial biomass collected from a eutrophic reservoir in Brazil. Using NP Analyst and Data Fusion-based Discovery (DAFdiscovery) platforms, we examined the correlation between the various cyanopeptides identified in the cyanobacterial crude extract, fractions, and the acute toxicity of these samples against the Artemia. salina microcrustacean. Four classes of cyanopeptides were revealed through metabolomics: microcystins, microginins, aeruginosins, and cyanopeptolins. The bioinformatics tools showed high bioactivity correlation scores for compounds of the cyanopeptolin class, in some cases even higher than those attributed to microcystins. These results emphasize the pressing need for a comprehensive evaluation of the (eco)toxicological risks associated with different cyanopeptides, considering their potential for exposure. This work also demonstrates the feasibility of conducting risk assessments using a more efficient approach involving LC-MS/MS-based metabolomics and chemometric techniques that require less time and reagents.
The effect of habitat fragmentation on Malay tapir relative abundance in Thailand’s protected areas
Authors: Suwannaphong Thanaphon , Radeloff Volker , Limmun Wanida , Suttidate Naparat 
Published: March 2024

Abstract

Habitat fragmentation threatens the persistence of mammals in tropical regions. Malay tapir (Tapirus indicus) is a globally-endangered species, and its distribution is largely confined to fragmented habitats within protected areas. However, it is unclear how that fragmentation affects its relative abundance. Here, we investigated the effects of habitat fragmentation on Malay tapir relative abundance in Thailand. We first quantified the spatial patterns of habitat fragmentation within nine of Thailand’s protected areas. Second, we assessed the relationship of fragmentation metrics and the relative abundance of Malay tapirs. Third, we identified the relative importance of the fragmentation metrics in explaining the relative abundance. We found high Malay tapir relative abundance in the Southern forest complex despite the fact that tapir habitats were significantly more fragmented there than in the protected areas in the Western forest complex (P < 0.05). Additionally, we found that the patch density, clumpiness index, proportion of habitat, and landscape shape index explained the relative abundance patterns well (R2 = 0.79) with the patch density explaining most of the variance (39.55%). Our finding highlights the urgent need to increase connectivity of forest habitats within the protected areas to support the long-term viability of Malay tapirs in Thailand.
Prediction and pathogenesis of gallstone disease based on clinical metabolomics
Authors: Li Xiang , Liu Zhengtao , Yin Xiaodan , Xu Jun , Zheng Shusen , Lei Geng 
Published: March 2024

Abstract
Gallstone is a common disease of biliary system at present. At present, our research on its pathogenesis is still at a single analysis stage. In this study, we collected peripheral serum samples from patients with gallstones and non-biliary diseases, obtained the difference of metabolites in the peripheral blood of both sides through omics technology, and established a clinical risk prediction model for gallstones based on the clinical information of patients. The weighted gene co-expression network analysis was applied to find the metabolite set with high correlation with the pathogenesis of gallstone, and the KEGG enrichment analysis was used to find the relevant enrichment pathway, so as to obtain the metabolic pathway related to the pathogenesis of gallstone. Among them, Pantothenate and CoA biosynthesis, Linoleic acid metabolism path, Citrate cycle (TCA cycle), Glyoxylate and dicarboxylate metabolism are screened that they set with high correlation with the pathogenesis of gallstone. We found in combination with other studies that these highly correlated pathways increase the incidence of gallstones by up-regulating cholesterol synthesis raw materials, reducing cholesterol breakdown, and affecting glucose and lipid metabolism. Therefore, blocking or inhibiting the related pathways or metabolites of GSD formation has guiding significance for the clinical prevention and treatment of this disease.
Changes of respiratory pathogen and clinical features of in acute exacerbation of chronic obstructive pulmonary disease after COVID-19 pandemic
Authors: Kim Soo Jung , Kim Taehee , Choi Hayoung , Shin Tae Rim , Kim Hwan Il , Jang Seung Hun , Hong Ji Young , Lee Chang Youl , Chung Soojie , Choi Jeong-Hee , Sim Yun Su 
Published: March 2024

Abstract

Respiratory infections are common causes of acute exacerbation of chronic obstructive lung disease (AECOPD). We explored whether the pathogens causing AECOPD and clinical features changed from before to after the coronavirus disease 2019 (COVID-19) outbreak. We reviewed the medical records of patients hospitalized with AECOPD at four university hospitals between January 2017 and December 2018 and between January 2021 and December. We evaluated 1,180 patients with AECOPD for whom medication histories were available. After the outbreak, the number of patients hospitalized with AECOPD was almost 44% lower compared with before the outbreak. Patients hospitalized with AECOPD after the outbreak were younger (75 vs. 77 years, p = 0.003) and more often stayed at home (96.6% vs. 88.6%, p < 0.001) than patients of AECOPD before the outbreak. Hospital stay was longer after the outbreak than before the outbreak (10 vs. 8 days. p < 0.001). After the COVID-19 outbreak, the identification rates of S. pneumoniae (15.3 vs. 6.2%, p < 0.001) and Hemophilus influenzae (6.4 vs. 2.4%, p = 0.002) decreased, whereas the identification rates of P. aeruginosa (9.4 vs. 13.7%, p = 0.023), Klebsiella pneumoniae (5.3 vs. 9.8%, p = 0.004), and methicillin-resistant Staphylococcus aureus (1.0 vs. 2.8%, p = 0.023) increased. After the outbreak, the identification rate of influenza A decreased (10.4 vs. 1.0%, p = 0.023). After the outbreak, the number of patients hospitalized with AECOPD was lower and the identification rates of community-transmitted pathogens tended to decrease, whereas the rates of pathogens capable of chronic colonization tended to increase. During the period of large-scale viral outbreaks that require quarantine, patients with AECOPD should consider treatment against strains that can colonize chronic respiratory disease rather than community acquired pathogens.
RfaA (YqhY), a novel adaptor protein, controls metabolite-sensitive protein degradation
in Bacillus subtilis
Authors: Stulke Jorg , Wicke Dennis , Lentes Sabine , Herrfurth Cornelia , Tödter Dominik , Stannek-Goebel Lorena , Commichau Fabian , Feussner Ivo 
Published: March 2024

Abstract
The carboxylation of acetyl-CoA is the committed step of fatty acid synthesis catalyzed by the multisubunit acetyl-CoA carboxylase (ACCase). However, the mechanisms that control the activity of this enzyme are poorly understood. Here, we identify the so far unknown protein RfaA (YqhY) of the model bacterium Bacillus subtilis as a regulator of fatty acid acquisition that targets the AccC subunit of ACCase for degradation. RfaA interacts with both AccC and the ClpE unfoldase subunit of the ClpEP protease complex. While the former interaction is not sensitive to the physiological conditions, RfaA interacts with ClpE only in the absence of the global amino group donor glutamate. This results in the degradation of AccC in the absence of glutamate. The inactivation of the rfaA gene results in the accumulation of fatty acids in the cell and in the formation of lipid droplets which are toxic for the bacteria. The reduced fatty acid synthesis in the absence of glutamate as a result of RfaA- and ClpEP-dependent degradation of AccC thus prevents intoxication of the cells by fatty acids. Our findings suggest that the degradation of enzymes that catalyze the committed step of biosynthetic pathways might be an important mechanism to control cellular homeostasis.
Astrocytic NHERF-1 increases seizure susceptibility by inhibiting surface expression of TREK-1
Authors: Hwang Eun Mi , Bae Yeonju , Kim Ajung , Lee Shinae , seongseop kim , Park Sunyoung , Ryoo Kanghyun , Yi Gwan-Su , Park Jae-Yong 
Published: March 2024

Abstract
Mature hippocampal astrocytes exhibit a linear current-to-voltage (I-V) K + membrane conductance, which is called passive conductance. It is estimated to enable astrocytes to keep potassium homeostasis in the brain. We previously reported that the TWIK-1/TREK-1 heterodimeric channels are crucial for astrocytic passive conductance. However, the regulatory mechanism of these channels by other binding proteins still remains elusive. Here, we identified Na+/H + exchange regulator-1 (NHERF-1), a protein highly expressed in astrocytes, as a candidate interaction partner for these channels. NHERF-1 endogenously bound to TWIK-1/TREK-1 in hippocampal cultured astrocytes. When NHERF-1 is overexpressed or silenced, surface expression and activity of TWIK-1/TREK-1 heterodimeric channels were inhibited or enhanced, respectively. Furthermore, we confirmed that reduced astrocytic passive conductance by NHERF-1 overexpressing in the hippocampus increases kainic acid (KA)-induced seizure sensitivity. Taken together, these results suggest that NHERF-1 is a key regulator of TWIK-1/TREK-1 heterodimeric channels in astrocytes and suppression of TREK-1 surface expression by NHERF-1 increases KA-induced seizure susceptibility via reduction of astrocytic passive conductance.
A Potential Toxicological Risk Assessment of Heavy Metals and Pesticides in Irrigated Rice Cultivars near Industrial Areas of Dhaka, Bangladesh
Authors: Huda Muhammad Nurul , Hosen Anowar , Akter Mahfuga , Islam Md. Mominul , Emon Sharmin Zaman , Rahman Asma , Harun-Ur-Rashid Mohammad , Jashim Zuairia Binte , Shahrukh Saif , Ismail Mohammad 
Published: March 2024

Abstract

Rice intake represents a significant pathway through which humans accumulate heavy metals. This study presents a comprehensive analysis of heavy metal and pesticide contamination in rice cultivars irrigated with industrial wastewater near Dhaka, Bangladesh, a region heavily influenced by industrial activities. We employed a unique methodology that not only quantified the concentrations of heavy metals and pesticide residues in rice grains but also extended to evaluating the physicochemical properties of rice stems, husks, soil, and irrigation water. Our findings revealed alarmingly high levels of heavy metals such as lead, cadmium, chromium, nickel, and mercury in the soil and irrigation water, with concentrations in some cases exceeding the World Health Organization safety thresholds by 2 to 15 times. Notably, the rice grains also exhibited significant contamination, including substantial amounts of Diazinon and Fenitrothion pesticides, exceeding the established safety limits. The study employed hazard quotients (HQs) and cancer risk (CR) assessments to evaluate the potential health risks associated with the consumption of contaminated rice. The results indicated HQ values were greater than 1 for rice grains across the sampled fields, suggesting a considerable non-carcinogenic health risk, particularly from lead exposure, which was found at levels twice the standard limit in all the sampling fields. Moreover, the CR values for As, Pb, Cd, Co, and Mn highlighted a significant carcinogenic risk in several instances.
Latent profile analysis and burnout study of Work addiction among clinical nurses
Authors: Liang Xinhui , Liu Xiaoxia , Yin yue , Liu fang , Zhang La Ting , Hu Mengyi , jia yao , Gao lijuan , Jiang xue 
Published: March 2024

Abstract
Background: Work addiction in clinical nurses is associated with burnout.However, the classification of work addiction in this group remains unclear. The purpose of this study was to clarify the subtypes of work addiction in Chinese clinical nurses, explore the factors influencing the subtypes, and explore the relationship between job burnout and work addiction to provide a reference for improving the work addiction of nurses.
Methods: From July to October 2023, 524 clinical nurses from five tertiary general hospitals in Shaanxi Province were selected for a cross-sectional survey. They filled out questionnaires online through the questionnaire star, which included the General Information Questionnaire, the Burnout Scale, and the Work Addiction Scale. Data analysis included latent feature analysis, analysis of variance, chi-square test, binary logistic regression,and hierarchical regression analysis.
Results: Two potential traits were identified - low-grade work addiction(grade 1) and high work addiction (grade 3), representing 67.9% and 32.1%of the total number of nurses surveyed, respectively. Nurses' job titles and emotional exhaustion had an impact on the potential categories of work addiction in clinical nurses (P<0.05). Burnout is a significant predictor of work addiction and can independently explain the 18.70%difference in work addiction in clinical nurses.
Conclusion: There are different classification characteristics of work addiction in clinical nurses in China. More than half of clinical nurses have low levels of burnout, and work addiction is an essential predictor of nurses' burnout. Hospital administrators should actively focus on nurses with high work addiction to help them reduce burnout.
RETRACTED: Phenotypic and genotypic characterization of biofilm formation in Staphylococcus haemolyticus isolated from urinary tract infections and their antibiotic resistance patterns.
Authors: Rafik Aniba , Asmaa Dihmane , Habiba Raqraq , Amina Ressmi , Kaotar Nayme , Mohammed Timinouni , Abouddihaj Barguigua 
Published: March 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
Association of Exhaled Breath Volatile Organic Compounds with Surgical Traumatic Stress during General Anaesthesia: An Exploratory Study
Authors: Wang Qifeng , Zhao Yuyi , Li Shikuo , Li Xuehan , Wang Haiyan , Zuo Yunxia 
Published: March 2024

Abstract
Surgical procedures can induce traumatic stress responses, which are associated with postoperative complications. Therefore, a perioperative monitor is needed to identify patients with a higher degree of stress responses. We explored the relationship between breath volatile organic compounds (VOCs), a non-invasive method widely explored in disease diagnosis, and surgical traumatic stress. Exhaled breath and blood samples were collected from 105 patients under general anaesthesia at three time points: prior to incision (Pre-op), 2h after incision (Intra-op), and prior to extubation (End-op). Differential VOCs between these time points were screened. Blood metabolomics analysis, traumatic stress-related biomarkers detection, and correlation analysis between VOCs and stress biomarkers were performed. We found that both the abundance of VOCs and blood metabolites changed significantly between these time points. Norepinephrine, epinephrine and cortisol all increased significantly in Intra-op and then reduced significantly in End-op. Correlation analysis showed both Comp_6 and Comp_23 were negatively correlated with norepinephrine in group comparison between Intra-op and End-op, the same trend as that in group comparison between Pre-op and Intra-op. We conclude that surgical traumatic stress resulting from surgical procedures may change the exhaled breath VOC profile in perioperative patients, providing preliminary evidence for VOC use in future monitoring.
Improvement and clinical benefit analysis of low-dose ketamine on postoperative pain and sleep after sinus surgery
Authors: Zhao Yan-ping , Lu Ji-can , Liu Chao , Fu Xun-si , Jia Yan , Zhu Feng 
Published: March 2024

Abstract

Objective
To investigate the benefits of low-dose esketamine on pain relief and sleep quality improvement after sinus surgery.
Methods
One hundred and thirty-five patients admitted to our hospital between June 2018 and September 2023 who suffered from sinusitis and were scheduled to undergo functional endoscopic sinus surgery were recruited. Three groups were divided as 0.2 mg (n = 45), 0.3 mg (n = 45), and control (n = 45) using a random number table. Three groups were tested for the Pittsburgh Sleep Quality Index (PSQI), the Visual Analogue Scale (VAS), the Hamilton Depression Scale (HAMD), the Hamilton Anxiety Scale (HAMA), the Connor-Davidson Resilience Scale (CD-RISC), and the Sino-nasal Outcome Test-20 (SNOT-20), and the related scores were analyzed by comparing their means between the groups.
Results
Esketamine affected differently the PSQI, the VAS, the HAMD, the HAMA, the CD-RISC, and the SNOT-20 scores in patients (FPSQI score treatment=67.569 FHAMD score treatment=59.593, FHAMA score treatment=71.479, FCD−RISC score treatment=65.549, F SNOT−20 score treatment=66.429, FVAS score treatment=56.73, all P < 0.05). The PSQI, the HAMD, the HAMA, the SNOT-20, and the VAS scores were in the same order at the four-time points of 1, 3, 5, and 9 days ( the order at all four-time points was: control > 0.2 mg > 0.3 mg), while the order of the CD-RISC scores at the four-time points was: control < 0.2 mg < 0.3 mg.
Conclusion
Low-dose esketamine boasts relief of postoperative anxiety, pain, and depression, reduction of patient symptoms, and improvement of sleep quality after sinus surgery.
miRNA changes associated with differentiation of human embryonic stem cells into human retinal ganglion cells
Authors: Esmaeili Maryam , Mead Ben 
Published: March 2024

Abstract

miRNA, short non-coding RNA, are rapidly emerging as important regulators in cell homeostasis, as well as potential players in cellular degeneration. The latter has led to interest in them as both biomarkers and as potential therapeutics. Retinal ganglion cells (RGC), whose axons connect the eye to the brain, are central nervous system cells of great interest, yet their study is largely restricted to animals due to the difficulty in obtaining healthy human RGC. Using a CRISPR-based reporter embryonic stem cell line, human RGC were generated and their miRNA profile characterized using NanoString miRNA assays. We identified a variety of retinal specific miRNA upregulated in ESC-derived RGC, with half of the most abundant miRNA also detectable in purified rat RGC. Several miRNA were however identified to be unique to RGC from human. The findings show which miRNA are abundant in RGC and the limited congruence with animal derived RGC. These data could be used to understand miRNA’s role in RGC function, as well as potential biomarkers or therapies in retinal diseases involving RGC degeneration.