bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drought characterization using different indices, theory of run and trend analysis in bilate river watershed, rift valley of Ethiopia
Authors: Burka Ashenafi , Biazin Birhanu , Bewket Woldeamlak 
Published: June 2023

Droughts have become more powerful and frequent, affecting more people for longer periods than any other natural disaster, particularly in eastern Africa. The unprecedented climate change has increased the severity, duration, and frequency of droughts. The objectives of this study were to evaluate performances of different drought indices for spatiotemporal drought characterization in the Bilate river watershed that represents part of the rift valley drylands in Ethiopia. Historical data for 39 years (1981–2019) from seven stations were used for drought analyses using the following indices: Standardized Precipitation Index (SPI), Standardized Precipitation Evapotranspiration Index (SPEI), Reconnaissance Drought Index (RDI), enhanced Reconnaissance Drought Index (eRDI) with different time scale and Self-Calibrated Palmer Drought Severity Index (scPDSI). Among them, SPI, SPEI, RDI and eRDI with 6-month and 9-month time scales were found to be the best correlated drought indices to characterize the historical drought events. Then, using the selected drought indices, temporal drought analysis showed occurrence of major drought events in the years: 1984/85, 1999/2000, 2002/3, and 2009. Some of these years are well known as famine years in some parts of Ethiopia including the study area. The results revealed spatial variation the severity of drought with extreme droughts occurred in the southern part of the Bilate watershed. Application of the theory of run confirmed that the maximum severity and duration of drought were observed at the Bilate Tena station that is located in the southern part of the watershed; the most severe being observed on a 9-month scale during 1984/85. Hossana and Wulbareg stations showed the highest frequency of drought over the study period. The Mann-Kendal trend test statistics showed an increasing trend of drought conditions in the study watershed.
The transcriptome response of astronaut leukocytes to long missions aboard the International Space Station reveals immune modulation
Authors: Stratis Daniel , Trudel Guy , Rocheleau Lynda , Pelchat Martin , Laneuville Odette 
Published: June 2023

IntroductionSpaceflight leads to the deconditioning of multiple body systems including the immune system. We sought to characterize the molecular response involved by capturing changes in leukocyte transcriptomes from astronauts transitioning to and from long-duration spaceflight.MethodsFourteen male and female astronauts with ~6-month- long missions aboard the International Space Station (ISS) had 10 blood samples collected throughout the three phases of the study: one pre-flight (PF), four in-flight (IF) while onboard the ISS, and five upon return to Earth (R). We measured gene expression through RNA sequencing of leukocytes and applied generalized linear modeling to assess differential expression across all 10 time points followed by the analysis of selected time points and functional enrichment of changing genes to identify shifts in biological processes.ResultsOur temporal analysis identified 276 differentially expressed transcripts grouped into two clusters (C) showing opposite profiles of expression with transitions to and from spaceflight: (C1) decrease-then-increase and (C2) increase-then-decrease. Both clusters converged toward average expression between ~2 and ~6 months in space. Further analysis of spaceflight transitions identified the decrease-then-increase pattern with most changes: 112 downregulated genes between PF and early spaceflight and 135 upregulated genes between late IF and R. Interestingly, 100 genes were both downregulated when reaching space and upregulated when landing on Earth. Functional enrichment at the transition to space related to immune suppression increased cell housekeeping functions and reduced cell proliferation. In contrast, egress to Earth is related to immune reactivation.ConclusionThe leukocytes’ transcriptome changes describe rapid adaptations in response to entering space followed by opposite changes upon returning to Earth. These results shed light on immune modulation in space and highlight the major adaptive changes in cellular activity engaged to adapt to extreme environments.
Gene set enrichment analysis identifies immune subtypes of kidney renal clear cell carcinoma with significantly different molecular and clinical properties
Authors: Chen Zuobing , Cao Wenxiu , Luo Jiangti , Abdelrahman Zeinab , Lu Qiqi , Wang Huafen , Wang Xiaosheng 
Published: June 2023

BackgroundKidney renal clear cell carcinoma (KIRC) is the most prevalent renal malignancy, marked by a high abundance of tumor-infiltrating lymphocytes (TILs) and an unfavorable prognosis upon metastasis. Numerous studies have demonstrated that KIRC possesses a tumor microenvironment that is highly heterogeneous, and this is associated with significant variations in the effectiveness of most first-line drugs administered to KIRC patients. Therefore, it is crucial to classify KIRC based on the tumor microenvironment, although these subtyping techniques are still inadequate.MethodsBy applying gene set enrichment scores of 28 immune signatures, we conducted a hierarchical clustering of KIRC and determined its immune subtypes. In addition, we conducted a comprehensive exploration of the molecular and clinical features of these subtypes, including survival prognosis, proliferation, stemness, angiogenesis, tumor microenvironment, genome instability, intratumor heterogeneity, and pathway enrichment.ResultsThrough cluster analysis, two immune subtypes of KIRC were identified and termed Immunity-High (Immunity-H) and Immunity-Low (Immunity-L). This clustering outcome was consistent in four independent KIRC cohorts. The subtype Immunity-H exhibited elevated levels of TILs, tumor aneuploidy, homologous recombination deficiency, stemness, and proliferation potential, along with a poorer prognosis for survival. Despite this, the Immunity-L subtype demonstrated elevated intratumor heterogeneity and a stronger angiogenesis signature in contrast to Immunity-H. According to the results of pathway enrichment analysis, the Immunity-H subtype was found to be highly enriched in immunological, oncogenic, and metabolic pathways, whereas the Immunity-L subtype was highly enriched in angiogenic, neuroactive ligand-receptor interaction, and PPAR pathways.ConclusionsBased on the enrichment of immune signatures in the tumor microenvironment, KIRC can be categorized into two immune subtypes. The two subtypes demonstrate considerably distinct molecular and clinical features. In KIRC, an increase in immune infiltration is linked to a poor prognosis. Patients with Immunity-H KIRC may exhibit active responses to PPAR and immune checkpoint inhibitors, whereas patients with Immunity-L may manifest favorable responses to anti-angiogenic agents and immune checkpoint inhibitors. The immunological classification provides molecular insights into KIRC immunity, as well as clinical implications for the management of this disease.
The neutrophil-to-lymphocyte ratio and lactate dehydrogenase combined in predicting liver metastasis and prognosis of colorectal cancer
Authors: Chen Qin , Li Guo-lin , Zhu Hong-quan , Yu Jian-Dong , Chen Zhi-Ping , Wu Jia-Yan , Lin Ze-Yu , Wan Yun-Le 
Published: June 2023

BackgroundThe neutrophil-to-lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) level are inflammatory markers related to tumor growth and metabolism. This study investigated the value of preoperative NLR, LDH and the combination of NLR and LDH (NLR-LDH) for predicting colorectal cancer liver metastasis (CRLM) and tumor prognosis in the early stages of colorectal cancer (CRC).Materials and methodsThree hundred patients undergoing CRC resection were included. Logistic regression analysis was used to estimate the correlation between CRLM time and inflammatory markers, and Kaplan–Meier survival and Cox regression analyses were used to estimate overall survival (OS). Forest plots were prepared based on the multivariate Cox analysis model and evaluated by receiver operating characteristic (ROC) curve analysis.ResultsThe NLR cut-off value was 2.071 according to the ROC curve. The multivariate analysis showed that the elevated LDH level and a high NLR-LDH level were independent predictors of synchronous CRLM and OS (p &lt; 0.05). The combination of a high NLR and elevated LDH and NLR-LDH levels suggested a poor prognosis and a significantly shorter median survival time than a low NLR and low levels of LDH and NLR-LDH. The ROC curve analysis results illustrated that the predictive value of the NLR-LDH score for synchronous CRLM [area under the curve (AUC) = 0.623, p &lt; 0.001] and OS (AUC = 0.614, p = 0.001) was superior to that of the NLR or LDH score used alone.ConclusionLDH and NLR-LDH are reliable, easy-to-use, independent biomarkers for predicting synchronous or metachronous CRLM and OS in CRC patients. The NLR is an important monitoring index for CRLM. Preoperative NLR, LDH and NLR-LDH may help to guide the use of therapeutic strategies and cancer surveillance.
Distribution of drug-resistant genes in alveolar lavage fluid from patients with psittacosis and traceability analysis of causative organisms
Authors: Lu Huiqun , Yuan Jing , Wu Zeming , Wang Lingwei , Wu Shuang , Chen Qiongcheng , Zhang Zhen , Chen Zhigao , Zou Xuan , Hu Qinghua , Feng Tiejian , Lu Jianhua , Ji Liyin , Qiu Shuxiang , Xu Shiqin , Jiang Min , Li Yinghui , Peng Bo , Bai Qinqin , Cai Rui , Geng Yijie , Shi Xiaolu 
Published: June 2023

BackgroundChlamydia psittaci is a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains of C. psittaci respond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes of C. psittaci have relatively stable hosts and different pathogenicity.MethodsMacrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients’ alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of the C. psittaci ompA gene were used, and a phylogenetic tree was constructed with C. psittaci genotypic sequences from other sources, including Chinese published sources. The C. psittaci found in each patient were genotyped by comparing ompA gene sequences. In addition, to better illustrate the relationship between genotype and host of C. psittaci, 60 bird fecal samples were collected from bird-selling stores for screening and C. psittaci typing.ResultsMacrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, including C. psittaci resistance gene sequences from two patients that matched those previously published on NCBI. Based on ompA genotyping, two patients were infected with C. psittaci genotype A and one patient was infected with genotype B. All five C. psittaci-positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of the C. psittaci genotype A in this study were derived from parrots, while genotype B was probably derived from chickens.ConclusionThe presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes of C. psittaci may help prevent transmission to humans.
Generation of a monoclonal antibody against duck circovirus capsid protein and its potential application for native viral antigen detection
Authors: Li Jinxin , Liu Fengli , Ren Zhihao , Fu Guanghua , Shi Jizhen , Zhao Naiyu , Huang Yu , Su Jingliang 
Published: June 2023

IntroductionDuck circovirus (DuCV) infection is currently recognized as an important immunosuppressive disease in commercial duck flocks in China. Specific antibodies against DuCV viral proteins are required to improve diagnostic assays and understand the pathogenesis of DuCV infection.Methods and resultsTo generate DuCV-specific monoclonal antibodies (mAbs), a recombinant DuCV capsid protein without the first 36 N-terminal amino acids was produced in Escherichia coli. Using the recombinant protein as an immunogen, a mAb was developed that reacted specifically with the DuCV capsid protein, expressed in E. coli and baculovirus systems. Using homology modeling and recombinant truncated capsid proteins, the antibody-binding epitope was mapped within the region of 144IDKDGQIV151, which is exposed to solvent in the virion capsid model structure. To assess the applicability of the mAb to probe the native virus antigen, the murine macrophage cell line RAW267.4 was tested for DuCV replicative permissiveness. Immunofluorescence and Western blot analysis revealed that the mAb recognized the virus in infected cells and the viral antigen in tissue samples collected from clinically infected ducks.DiscussionThis mAb, combined with the in vitro culturing method, would have widespread applications in diagnosing and investigating DuCV pathogenesis.
The correlation between the severity of cerebral microbleeds and serum HMGB1 levels and cognitive impairment in patients with cerebral small vessel disease
Authors: Wang Minghua , Liu Junli , Wang Fan , Li Qing , Zhang Jian , Ji Sibei , Li Shaomin , Lu Chengbiao , Zhao Jianhua 
Published: June 2023

ObjectiveThe study investigated the correlation and predictive value between the severity of cerebral microbleeds (CMBs) and the level of serum High Mobility Group Protein B1 (HMGB1) and the occurrence of cognitive impairment in patients with cerebral small vessel disease (CSVD).MethodsA total of 139 patients with CSVD admitted to the Department of Neurology of the First Affiliated Hospital of Xinxiang Medical University from December 2020 to December 2022 were selected as study subjects. The Montreal Cognitive Assessment (MoCA) scale was used to assess the cognitive function and was divided into the cognitive impairment group and the cognitive normal group. Magnetic Resonance Imaging (MRI) and Susceptibility Weighted Imaging (SWI) were used to screen and assess the severity of CMBs. Serum HMGB1 levels of CSVD patients were measured by enzyme linked immunosorbent assay (ELISA). Multivariable logistic regression analysis was used to explore risk factors for cognitive impairment and CMBs. Pearson correlation analysis was used to investigate the correlation between HMGB1 and cognitive function. Receiver Operating Characteristics (ROC) curves were used to assess the predictive value of HMGB1 for the occurrence of cognitive impairment in patients with CMBs.ResultsHigh Mobility Group Protein B1, uric acid (UA), glycosylated hemoglobin (HbA1c), CMBs, lacunar cerebral infarction (LI), years of education, and history of hypertension were risk factors for cognitive impairment (P &lt; 0.05); HMGB1 was significantly and negatively associated with total MoCA score, visuospatial/executive ability, and delayed recall ability (P &lt; 0.05). HMGB1 was significantly and positively correlated with the number of CMBs (P &lt; 0.05). The area under the ROC curve for HMGB1 predicting cognitive impairment in patients with CMBs was 0.807 (P &lt; 0.001).ConclusionSerum HMGB1 levels are associated with the development of cognitive impairment in CSVD patients, and serum HMGB1 levels have a high predictive value for the development of cognitive impairment in CSVD patients with combined CMBs, which can be used for early clinical identification and intervention of vascular cognitive impairment.
Balance and gait in progressive supranuclear palsy: a narrative review of objective metrics and exercise interventions
Authors: Dale Marian L. , Silva-Batista Carla , de Almeida Filipe Oliveira , Horak Fay B. 
Published: June 2023

BackgroundThe use of objective gait and balance metrics is rapidly expanding for evaluation of atypical parkinsonism, and these measures add to clinical observations. Evidence for rehabilitation interventions to improve objective measures of balance and gait in atypical parkinsonism is needed.AimOur aim is to review, with a narrative approach, current evidence on objective metrics for gait and balance and exercise interventions in progressive supranuclear palsy (PSP).MethodsLiterature searches were conducted in four computerized databases from the earliest record up to April 2023: PubMed, ISI’s Web of Knowledge, Cochrane’s Library, and Embase. Data were extracted for study type (cross-sectional, longitudinal, and rehabilitation interventions), study design (e.g., experimental design and case series), sample characteristics, and gait and balance measurements.ResultsEighteen gait and balance (16 cross-sectional and 4 longitudinal) and 14 rehabilitation intervention studies were included. Cross-sectional studies showed that people with PSP have impairments in gait initiation and steady-state gait using wearable sensors, and in static and dynamic balance assessed by posturography when compared to Parkinson’s disease (PD) and healthy controls. Two longitudinal studies observed that wearable sensors can serve as objective measures of PSP progression, using relevant variables of change in turn velocity, stride length variability, toe off angle, cadence, and cycle duration. Rehabilitation studies investigated the effect of different interventions (e.g., balance training, body-weight supported treadmill gait, sensorimotor training, and cerebellar transcranial magnetic stimulation) on gait, clinical balance, and static and dynamic balance assessed by posturography measurements. No rehabilitation study in PSP used wearable sensors to evaluate gait and balance impairments. Although clinical balance was assessed in 6 rehabilitation studies, 3 of these studies used a quasi-experimental design, 2 used a case series, only 1 study used an experimental design, and sample sizes were relatively small.ConclusionWearable sensors to quantify balance and gait impairments are emerging as a means of documenting progression of PSP. Robust evidence for improving balance and gait in PSP was not found for rehabilitation studies. Future powered, prospective and robust clinical trials are needed to investigate the effects of rehabilitation interventions on objective gait and balance outcomes in people with PSP.
Disrupted topological organization of white matter structural networks in high myopia patients revealed by diffusion kurtosis imaging and tractography
Authors: Wang Huihui , Wen Hongwei , Li Jing , Chen Qian , Li Shanshan , Wang Zhenchang 
Published: June 2023

IntroductionHigh myopia (HM) is a public health issue that can lead to severe visual impairment. Previous studies have exhibited widespread white matter (WM) integrity damage in HM patients. However, how these WM damages are topologically related, and the network-level structural disruptions underlying HM has not been fully defined. We aimed to assess the alterations of brain WM structural networks in HM patients using diffusion kurtosis imaging (DKI) and tractography in the present study.MethodsIndividual whole-brain and ROI-level WM networks were constructed using DKI tractography in 30 HM patients and 33 healthy controls. Graph theory analysis was then applied to explore the altered global and regional network topological properties. Pearson correlations between regional properties and disease duration in the HM group were also assessed.ResultsFor global topology, although both groups showed a small-world network organization, HM patients exhibited significant decreased local efficiency and clustering coefficient compared with controls. For regional topology, HM patients and controls showed highly similar hub distributions, except for three additional hub regions in HM patients including left insula, anterior cingulate and paracingulate gyri (ACG), and median cingulate and paracingulate gyri (DCG). In addition, HM patients showed significantly altered nodal betweenness centrality (BC) mainly in the bilateral inferior occipital gyrus (IOG), left superior occipital gyrus (SOG), caudate nucleus, rolandic operculum and right putamen, pallidum, and gyrus rectus compared with controls. Intriguingly, the nodal BC of left IOG was negatively correlated with disease duration in HM patients.DiscussionOur findings suggest that HM exhibited alterations in WM structural networks as indicated by decreased local specialization. This study may advance the current understanding of the pathophysiological mechanisms underlying HM.
A two-branch trade-off neural network for balanced scoring sleep stages on multiple cohorts
Authors: Zhang Di , Sun Jinbo , She Yichong , Cui Yapeng , Zeng Xiao , Lu Liming , Tang Chunzhi , Xu Nenggui , Chen Badong , Qin Wei 
Published: June 2023

IntroductionAutomatic sleep staging is a classification process with severe class imbalance and suffers from instability of scoring stage N1. Decreased accuracy in classifying stage N1 significantly impacts the staging of individuals with sleep disorders. We aim to achieve automatic sleep staging with expert-level performance in both N1 stage and overall scoring.MethodsA neural network model combines an attention-based convolutional neural network and a classifier with two branches is developed. A transitive training strategy is employed to balance universal feature learning and contextual referencing. Parameter optimization and benchmark comparisons are conducted using a large-scale dataset, followed by evaluation on seven datasets in five cohorts.ResultsThe proposed model achieves an accuracy of 88.16%, Cohen’s kappa of 0.836, and MF1 score of 0.818 on the SHHS1 test set, also with comparable performance to human scorers in scoring stage N1. Incorporating multiple cohort data improves its performance. Notably, the model maintains high performance when applied to unseen datasets and patients with neurological or psychiatric disorders.DiscussionThe proposed algorithm demonstrates strong performance and generalizablility, and its direct transferability is noteworthy among similar studies on automated sleep staging. It is publicly available, which is conducive to expanding access to sleep-related analysis, especially those associated with neurological or psychiatric disorders.