bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanofibrils from oil palm trunk: effect of delignification and fibrillation technique
Authors: Zaini Lukmanul Hakim , Gindl-Altmutter Wolfgang , Gusenbauer Claudia , Rahayu Istie Sekartining , Lubis Muhammad Adly Rahandi , Mautner Andreas , Veigel Stefan 
Published: April 2024

AbstractOil palm trunk (OPT) is an inexpensive, abundantly available by-product of palm oil production which is typically not put to material use. Due to its comparably high cellulose content, OPT represents a suitable raw material for the preparation of cellulose nanofibrils (CNFs). Aiming for full utilization of the raw material and minimized energy demand, non-delignified and partially delignified (alkali-pretreated) OPT was subjected to mechanical fibrillation in the present study. As compared to CNFs from fully delignified OPT, the lignin-rich microfibrils obtained by this approach generally showed higher average fibril diameters, lower thermal stability as well as lower viscosity, and higher sedimentation rate in suspension. However, the combination of alkali-pretreatment and fibrillation by disc-grinding and subsequent high-pressure homogenization resulted in fibrils with properties similar to those of CNFs from fully delignified OPT. As proven by IR-spectroscopy, thermogravimetry and chemical composition analysis, alkali-treated OPT fibrils still contained substantial amounts of residual lignin which could, for instance, act as a natural coupling agent or binder in composite applications. Moreover, the facile delignification process applied herein requires far less chemicals and energy than conventional pulping and is thus beneficial from both the economic and ecological perspective.
Characterizing land use/land cover change dynamics by an enhanced random forest machine learning model: a Google Earth Engine implementation
Authors: Pande Chaitanya Baliram , Srivastava Aman , Moharir Kanak N. , Radwan Neyara , Mohd Sidek Lariyah , Alshehri Fahad , Pal Subodh Chandra , Tolche Abebe Debele , Zhran Mohamed 
Published: April 2024

AbstractLand use and land cover (LULC) analysis is crucial for understanding societal development and assessing changes during the Anthropocene era. Conventional LULC mapping faces challenges in capturing changes under cloud cover and limited ground truth data. To enhance the accuracy and comprehensiveness of the descriptions of LULC changes, this investigation employed a combination of advanced techniques. Specifically, multitemporal 30 m resolution Landsat-8 satellite imagery was utilized, in addition to the cloud computing capabilities of the Google Earth Engine (GEE) platform. Additionally, the study incorporated the random forest (RF) algorithm. This study aimed to generate continuous LULC maps for 2014 and 2020 for the Shrirampur area of Maharashtra, India. A novel multiple composite RF approach based on LULC classification was utilized to generate the final LULC classification maps utilizing the RF-50 and RF-100 tree models. Both RF models utilized seven input bands (B1 to B7) as the dataset for LULC classification. By incorporating these bands, the models were able to influence the spectral information captured by each band to classify the LULC categories accurately. The inclusion of multiple bands enhanced the discrimination capabilities of the classifiers, increasing the comprehensiveness of the assessment of the LULC classes. The analysis indicated that RF-100 exhibited higher training and validation/testing accuracy for 2014 and 2020 (0.99 and 0.79/0.80, respectively). The study further revealed that agricultural land, built-up land, and water bodies have changed adequately and have undergone substantial variation among the LULC classes in the study area. Overall, this research provides novel insights into the application of machine learning (ML) models for LULC mapping and emphasizes the importance of selecting the optimal tree combination for enhancing the accuracy and reliability of LULC maps based on the GEE and different RF tree models. The present investigation further enabled the interpretation of pixel-level LULC interactions while improving image classification accuracy and suggested the best models for the classification of LULC maps through the identification of changes in LULC classes.
OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies
Authors: Ernst Terrence R. , Blischak John D. , Nordlund Paul , Dalen Joe , Moore Justin , Bhamidipati Akshay , Dwivedi Pankaj , LoGrasso Joe , Curado Marco Rocha , Engelmann Brett Warren 
Published: April 2024

AbstractBackgroundThe results of high-throughput biology (‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features.ResultsWe present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access.ConclusionsOmicNavigator can be found athttps://github.com/abbvie-external/OmicNavigator
Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data
Authors: Wei Weideng , Xia Xiaoqiang , Li Taiwen , Chen Qianming , Feng Xiaodong 
Published: April 2024

Abstract
Background
In recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited researchers, without such expertise, exploring information from scRNA-seq data. Therefore, there is a tremendous need to develop easy-to-use software, covering all the aspects of scRNA-seq data analysis.

Results
We proposed a clear analysis framework for scRNA-seq data, which emphasized the fundamental and crucial roles of cell identity annotation, abstracting the analysis process into three stages: upstream analysis, cell annotation and downstream analysis. The framework can equip researchers with a comprehensive understanding of the analysis procedure and facilitate effective data interpretation. Leveraging the developed framework, we engineered Shaoxia, an analysis platform designed to democratize scRNA-seq analysis by accelerating processing through high-performance computing capabilities and offering a user-friendly interface accessible even to wet-lab researchers without programming expertise.

Conclusion
Shaoxia stands as a powerful and user-friendly open-source software for automated scRNA-seq analysis, offering comprehensive functionality for streamlined functional genomics studies. Shaoxia is freely accessible at http://www.shaoxia.cloud, and its source code is publicly available at https://github.com/WiedenWei/shaoxia.
Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study
Authors: Jeong Sohyun , Liao Yi-Tyng , Tsai Min-Hsuan , Wang Yao-Kuang , Wu I-Chen , Liu Chung-Jung , Wu Ming-Shun , Chan Tze-Sian , Chen Ming-Yao , Hu Ping-Jen , Kao Wei-Yu , Liu Hsiang-Chin , Tsai Ming-Ju , Liu Cheng-Yuan , Chang Chun-Chao , Wu Deng-Chyang , Hsu Yi-Hsiang 
Published: April 2024

Abstract
Background
Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

Results
A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543). In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

Conclusion
Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.
High prevalence of multidrug-resistant Enterobacterales carrying extended-spectrum beta-lactamase and AmpC genes isolated from neonatal sepsis in Ahvaz, Iran
Authors: Mansouri Sima , Savari Mohammad , Malakian Arash , Abbasi Montazeri Effat 
Published: April 2024

Abstract
Objectives
In the recent years, multidrug resistant (MDR) neonatal septicemia-causing Enterobacterales has been dramatically increased due to the extended-spectrum beta-lactamases (ESBLs) and AmpC enzymes. This study aimed to assess the antibiotic resistance pattern, prevalence of ESBLs/AmpC beta-lactamase genes, and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) fingerprints in Enterobacterales isolated from neonatal sepsis.

Results
In total, 59 Enterobacterales isolates including 41 (69.5%) Enterobacter species, 15 (25.4%) Klebsiella pneumoniae and 3 (5.1%) Escherichia coli were isolated respectively. Resistance to ceftazidime and cefotaxime was seen in all of isolates. Furthermore, all of them were multidrug-resistant (resistant to three different antibiotic categories). The phenotypic tests showed that 100% of isolates were ESBL-positive. Moreover, AmpC production was observed in 84.7% (n = 50/59) of isolates. Among 59 ESBL-positive isolates, the highest percentage belonged to blaCTX−M−15 gene (66.1%) followed by blaCTX−M (45.8%), blaCTX−M−14 (30.5%), blaSHV (28.8%), and blaTEM (13.6%). The frequency of blaDHA, blaEBC, blaMOX and blaCIT genes were 24%, 24%, 4%, and 2% respectively. ERIC-PCR analysis revealed that Enterobacterales isolates were genetically diverse. The remarkable prevalence of MDR Enterobacterales isolates carrying ESBL and AmpC beta-lactamase genes emphasizes that efficient surveillance measures are essential to avoid the more expansion of drug resistance amongst isolates.
Overexpression of the WRKY transcription factor gene NtWRKY65 enhances salt tolerance in tobacco (Nicotiana tabacum)
Authors: Zhang Xiaoquan , Zhang Yaxuan , Li Man , Jia Hongfang , Wei Fengjie , Xia Zongliang , Zhang Xuelin , Chang Jianbo , Wang Zhaojun 
Published: April 2024

Abstract
Background
Salt stress severely inhibits plant growth, and the WRKY family transcription factors play important roles in salt stress resistance. In this study, we aimed to characterize the role of tobacco (Nicotiana tabacum) NtWRKY65 transcription factor gene in salinity tolerance.

Results
This study characterized the role of tobacco (Nicotiana tabacum) NtWRKY65 transcription factor gene in salinity tolerance using four NtWRKY65 overexpression lines. NtWRKY65 is localized to the nucleus, has transactivation activity, and is upregulated by NaCl treatment. Salinity treatment resulted in the overexpressing transgenic tobacco lines generating significantly longer roots, with larger leaf area, higher fresh weight, and greater chlorophyll content than those of wild type (WT) plants. Moreover, the overexpressing lines showed elevated antioxidant enzyme activity, reduced malondialdehyde content, and leaf electrolyte leakage. In addition, the Na+ content significantly decreased, and the K+/Na+ ratio was increased in the NtWRKY65 overexpression lines compared to those in the WT. These results suggest that NtWRKY65 overexpression enhances salinity tolerance in transgenic plants. RNA-Seq analysis of the NtWRKY65 overexpressing and WT plants revealed that NtWRKY65 might regulate the expression of genes involved in the salt stress response, including cell wall component metabolism, osmotic stress response, cellular oxidant detoxification, protein phosphorylation, and the auxin signaling pathway. These results were consistent with the morphological and physiological data. These findings indicate that NtWRKY65 overexpression confers enhanced salinity tolerance.

Conclusions
Our results indicated that NtWRKY65 is a critical regulator of salinity tolerance in tobacco plants.
Patients’ expectations of primary health care from both patients’ and physicians’ perspectives: a questionnaire study with a qualitative approach
Authors: Oster Andreas , Wiking Eivor , Nilsson Gunnar H , Olsson Christina B 
Published: April 2024

Abstract
Background
Patients’ ideas, concerns, and expectations are three important concepts in consultation techniques. Limited studies on these concepts include responses from both health care providers and care recipients of the same consultation. Highlighting both perspectives provides an increased understanding of the consultation. This study aims to explore the perspectives of patients and health care professionals about patients’ expectations of primary health care during consultations with primary care physicians and compare the two sets of perspectives.

Methods
A cross-sectional study. Patients (n = 113) and physicians (n = 67) from five primary health care centers completed a questionnaire after planned consultations. Their responses to open-ended questions about patients’ expectations, from patients’ and physicians’ perspectives were analyzed with qualitative content analyses.

Results
The patients expected a personal journey, through the primary health care system where they were the subject of interest. A journey, with ready access to a health care provider followed by a consultation with the physician, medical measures administered, their outcomes discussed, and a plan developed for continued health care. The physicians observed patients’ expectations to concern the responsibilities placed on primary health care where patients were the object of interest. Patients’ short-term expectations were described in a similar way by both patients and physicians. Patients expressed their long-term expectations as more personal and interpersonal whereas physicians observed them from a more professional and organizational standpoint.

Conclusions
Patients and physicians have different views of what patients expect of primary health care. While patients’ short-term expectations were perceived by physicians, their long-term expectations were not. Patients expected more of a personal journey through the primary health care system while physicians observed patients’ expectations to concern the responsibilities placed on primary health care. Identifying and meeting patients’ expectations is an important part of patient-centered care, and a better understanding of patients’ expectations is needed to improve health professionals’ consultation skills.
Soil-transmitted helminths and associated factors among pregnant women in Doreni district, Oromia region, Ethiopia: a cross-sectional study
Authors: Mekonen Adamu Tesfa , Hirpha Teshome Bekana , Zewdie Asrat 
Published: April 2024

Abstract
Background
Soil-transmitted helminthiasis (STH) refers to a set of parasitic illnesses caused by nematode worms and spread to people through faeces-contaminated soil. It is highly prevalent in low- and middle-income countries due to a lack of environmental sanitation and personal hygiene. Pregnant women are among the risk groups for infection by soil-transmitted helminths. Former studies of the disease burden among pregnant women in Ethiopia didn’t indicate the intensity of parasitic infection. The aim of this study was to assess the prevalence and associated factors of soil-transmitted helminths among pregnant women.

Methods
An institution-based cross-sectional study was conducted among 416 randomly selected pregnant women. The data were collected using a structured interview-administered questionnaire and a laboratory test. The Kato-Katz technique was used to diagnose soil-transmitted helminthiasis and determine the intensity of the infection. The collected data were entered into Epi-Data version 4.6 and exported to SPSS version 25 for analysis. Multivariate logistic regression analysis was used to identify independent predictors of soil-transmitted helminths at a p-value < 0.05.

Results
The overall prevalence of soil-transmitted helminths among pregnant women was 30%. (95%, CI: 26-34%). Living in a rural area (AOR = 3.35; 95% CI = 1.83–6.13), drinking from an unprotected water source (AOR = 2.52; 95% CI = 1.45–4.37), not washing one’s hand after the toilet (AOR = 2.75; 95% CI = 1.55–4.88), lacking health information (AOR = 1.70; 95% CI = 1.01–2.85), working as a daily labourer (AOR = 2.88; 95% CI = 1.01–8.20), and walking barefoot (AOR = 4.00; 95% CI = 2.29–7.00) were significantly associated with the presence of soil-transmitted helminths among pregnant women.

Conclusion
The prevalence of STH was significantly moderate in the study area, where pregnant women were mostly affected by ascariasis and hookworms. Living in a rural area, being a daily labourer, walking barefoot, not washing hands after the toilet, drinking from an unprotected water source, and lacking health information were the determining factors. Interventions including health education, the expansion of pure drinking water sources, the promotion of personal hygiene, and the wearing of shoes are recommended to reduce the burden of soil-transmitted helminths in the study area.
Application and evaluation of topical amphotericin B for the treatment of respiratory fungal infections
Authors: Cui Ning , Zhao Jingming 
Published: April 2024

Abstract
Background
In recent years, the prevalence of respiratory fungal diseases has increased. Polyene antifungal drugs play a pivotal role in the treatment of these conditions, with amphotericin B (AmB) being the most representative drug. This study aimed to evaluate the efficacy and safety of topical administration of AmB in the treatment of respiratory fungal infections.

Methods
We conducted a retrospective study on hospitalized patients treated with topical administered AmB for respiratory fungal infections from January 2014 to June 2023.

Results
Data from 36 patients with invasive pulmonary fungal infections treated with topical administration of AmB were collected and analyzed. Nebulization was administered to 27 patients. After the treatment, 17 patients evidenced improved conditions, whereas 10 patients did not respond and died in the hospital. One patient experienced an irritating cough as an adverse reaction. Seven patients underwent tracheoscopic instillation, and two received intrapleural irrigation; they achieved good clinical therapeutic efficacy without adverse effects.

Conclusion
The combined application of systemic antifungal treatment and topical administration of AmB yielded good therapeutic efficacy and was well-tolerated by the patients. Close monitoring of routine blood tests, liver and kidney function, and levels of electrolytes, troponin, and B-type natriuretic peptide supported this conclusion.
Longitudinal assessment of ventricular volume trajectories in early-stage schizophrenia: evidence of both enlargement and shrinkage
Authors: Svancer Patrik , Capek Vaclav , Skoch Antonin , Kopecek Miloslav , Vochoskova Kristyna , Fialova Marketa , Furstova Petra , Jakob Lea , Bakstein Eduard , Kolenic Marian , Hlinka Jaroslav , Knytl Pavel , Spaniel Filip 
Published: April 2024

Abstract
Background
Lateral ventricular enlargement represents a canonical morphometric finding in chronic patients with schizophrenia; however, longitudinal studies elucidating complex dynamic trajectories of ventricular volume change during critical early disease stages are sparse.

Methods
We measured lateral ventricular volumes in 113 first-episode schizophrenia patients (FES) at baseline visit (11.7 months after illness onset, SD = 12.3) and 128 age- and sex-matched healthy controls (HC) using 3T MRI. MRI was then repeated in both FES and HC one year later.

Results
Compared to controls, ventricular enlargement was identified in 18.6% of patients with FES (14.1% annual ventricular volume (VV) increase; 95%CI: 5.4; 33.1). The ventricular expansion correlated with the severity of PANSS-negative symptoms at one-year follow-up (p = 0.0078). Nevertheless, 16.8% of FES showed an opposite pattern of statistically significant ventricular shrinkage during ≈ one-year follow-up (-9.5% annual VV decrease; 95%CI: -23.7; -2.4). There were no differences in sex, illness duration, age of onset, duration of untreated psychosis, body mass index, the incidence of Schneiderian symptoms, or cumulative antipsychotic dose among the patient groups exhibiting ventricular enlargement, shrinkage, or no change in VV.

Conclusion
Both enlargement and ventricular shrinkage are equally present in the early stages of schizophrenia. The newly discovered early reduction of VV in a subgroup of patients emphasizes the need for further research to understand its mechanisms.