bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case report: Severe disseminated infection caused by Strongyloides stercoralis in an immunocompromised patient by metagenomic next-generation sequencing
Authors: Xu Qinfu , Xi Xiaotong , Feng Dan , Sang Qian , Sheng Yanbing , Ding Ran , Xu Aiguo 
Published: April 2023

BackgroundStrongyloides stercoralis (S. stercoralis) is a nematode that is widely distributed in the tropical and subtropical regions of the world and which can cause severe disseminated infection in immunocompromised individuals. However, strongyloidiasis, the disease caused by S. stercoralis, is difficult to diagnose because of its non-specific clinical presentation and the inadequate performance of conventional diagnostic methods.Case descriptionWe report the case of a 75-year-old male patient with severe disseminated infection caused by S. stercoralis. The patient had a medical history of seasonal bronchitis and, as a consequence, had taken prednisone for many years. Initial clinical tests failed to detect any pathogens, but metagenomic next-generation sequencing (mNGS) resulted in the identification of S. stercoralis in the patient’s bronchoalveolar lavage fluid (BALF) and blood. Subsequently, routine testing repeatedly detected nematode larvae in the patient’s stool and sputum. Through a combination of mNGS results and clinical symptoms, the patient was finally diagnosed with severe disseminated infection caused by S. stercoralis.ConclusionThe clinical manifestations of disease caused by infection with S. stercoralis are not specific; therefore, early and accurate diagnosis is very important. mNGS can detect S. stercoralis even when it is present at only a low level. This case report supports the notion that mNGS is a valuable tool in the diagnosis of severe disseminated infections caused by S. stercoralis in immunocompromised patients.
Metabolic pathways that permit Mycobacterium avium subsp. hominissuis to transition to different environments encountered within the host during infection
Authors: Abukhalid Norah , Rojony Rajoana , Danelishvili Lia , Bermudez Luiz E. 
Published: April 2023

IntroductionM. avium subsp. hominissuis (M. avium) is an intracellular, facultative bacterium known to colonize and infect the human host through ingestion or respiratory inhalation. The majority of pulmonary infections occur in association with pre- existing lung diseases, such as bronchiectasis, cystic fibrosis, or chronic obstructive pulmonary disease. M. avium is also acquired by the gastrointestinal route in immunocompromised individuals such as human immunodeficiency virus HIV-1 patients leading to disseminated disease. A hallmark of M. avium pulmonary infections is the ability of pathogen to form biofilms. In addition, M. avium can reside within granulomas of low oxygen and limited nutrient conditions while establishing a persistent niche through metabolic adaptations.MethodsBacterial metabolic pathways used by M. avium within the host environment, however, are poorly understood. In this study, we analyzed M. avium proteome with a focus on core metabolic pathways expressed in the anaerobic, biofilm and aerobic conditions and that can be used by the pathogen to transition from one environment to another.ResultsOverall, 3,715 common proteins were identified between all studied conditions and proteins with increased synthesis over the of the level of expression in aerobic condition were selected for analysis of in specific metabolic pathways. The data obtained from the M. avium proteome of biofilm phenotype demonstrates in enrichment of metabolic pathways involved in the fatty acid metabolism and biosynthesis of aromatic amino acid and cofactors. Here, we also highlight the importance of chloroalkene degradation pathway and anaerobic fermentationthat enhance during the transition of M. avium from aerobic to anaerobic condition. It was also found that the production of fumarate and succinate by MAV_0927, a conserved hypothetical protein, is essential for M. avium survival and for withstanding the stress condition in biofilm. In addition, the participation of regulatory genes/proteins such as the TetR family MAV_5151 appear to be necessary for M. avium survival under biofilm and anaerobic conditions.ConclusionCollectively, our data reveal important core metabolic pathways that M. avium utilize under different stress conditions that allow the pathogen to survive in diverse host environments.
Characterization of anti-erythrocyte and anti-platelet antibodies in hemolytic anemia and thrombocytopenia induced by Plasmodium spp. and Babesiaspp. infection in mice
Authors: Zhou Mo , Xie Jun , Kawase Osamu , Nishikawa Yoshifumi , Ji Shengwei , Zhu Shanyuan , Cao Shinuo , Xuan Xuenan 
Published: April 2023

IntroductionMalaria and Babesiosis are acute zoonotic disease that caused by infection with the parasite in the phylum Apicomplexa. Severe anemia and thrombocytopenia are the most common hematological complication of malaria and babesiosis. However, the mechanisms involved have not been elucidated, and only a few researches focus on the possible role of anti-erythrocyte and anti-platelet antibodies.MethodsIn this study, the Plasmodium yoelii, P. chabaudi, Babesia microti and B. rodhaini infected SCID and ICR mice. The parasitemia, survival rate, platelet count, anti-platelet antibodies, and the level of IFN-γ and interleukin (IL) -10 was tested after infection. Furthermore, the P. yoelii, P. chabaudi, B. rodhaini and B. microti infected ICR mice were treated with artesunate and diminaze, the development of the anti-erythrocyte and anti-platelet antibodies in chronic stage were examined. At last, the murine red blood cell and platelet membrane proteins probed with auto-antibodies induced by P. yoelii, P. chabaudi, B. rodhaini, and B. microti infection were characterized by proteomic analysis.Results and discussionThe high anti-platelet and anti-erythrocyte antibodies were detected in ICR mice after P. yoelii, P. chabaudi, B. rodhaini, and B. microti infection. Actin of murine erythrocyte and platelet is a common auto-antigen in Plasmodium and Babesia spp. infected mice. Our findings indicate that anti-erythrocyte and anti-platelet autoantibodies contribute to thrombocytopenia and anemia associated with Plasmodium spp. and Babesia spp. infection. This study will help to understand the mechanisms of malaria and babesiosis-related thrombocytopenia and hemolytic anemia.
The unembodied metaphor: comprehension and production of tactile metaphors without somatosensation
Authors: Phillips Jacob B. , Grenoble Lenore A. , Mason Peggy 
Published: April 2023

IntroductionProposals for embodied metaphor and embodied cognition have suggested abstract concepts are understood indirectly through the simulation of previous sensory experiences in a different domain. While exceptions have been observed for sensory deficits and impairments that are common, such as vision and audition, it is commonly assumed that somatosensation (proprioception, haptic touch, pain, pressure, temperature, etc.) is fundamental for the comprehension of production of sensory metaphors and much abstract thought in general. In this way, our past sensory experiences are critical to our understanding not just of the world around us but also of our sense of selves. This would suggest that Kim, who was born without somatosensation, would have difficulty understanding, using, or even thinking about many abstract concepts typically linked to different sensory experiences through metaphor, including a creation of a sense of self.MethodsTo examine her comprehension of sensory metaphors, Kim was asked to select the best sensory idiomatic expression given its context. Her friends and family as well as a representative sample of individuals online were recruited to complete the survey as controls. Additionally, we transcribed and analyzed six hours of unprompted speech to determine if Kim spontaneously uses somatosensory metaphors appropriately.ResultsResults from the idiomatic expression survey indicate that Kim performs as well as controls despite lacking any previous direct sensory experiences of these concepts. Analysis of the spontaneous speech highlights that Kim appropriately uses tactile expressions in both their concrete sensory and abstract metaphorical meanings.DiscussionTaken together, these two studies demonstrate that what is lost in sensory experiences can be made up in linguistic experiences, as Kim's understanding of tactile words was acquired in the complete absence of somatosensory experiences. This study demonstrates that individuals can comprehend and use tactile language and metaphor without recruiting past somatosensory experiences, and thus challenges a strong definition of embodied cognition which requires sensory simulations in language comprehension and abstract thought.
Straightforward data transfer in a blockwise dataflow for an analog RRAM-based CIM system
Authors: Liu Yuyi , Gao Bin , Yao Peng , Liu Qi , Zhang Qingtian , Wu Dong , Tang Jianshi , Qian He , Wu Huaqiang 
Published: April 2023

Analog resistive random-access memory (RRAM)-based computation-in-memory (CIM) technology is promising for constructing artificial intelligence (AI) with high energy efficiency and excellent scalability. However, the large overhead of analog-to-digital converters (ADCs) is a key limitation. In this work, we propose a novel LINKAGE architecture that eliminates PE-level ADCs and leverages an analog data transfer module to implement inter-array data processing. A blockwise dataflow is further proposed to accelerate convolutional neural networks (CNNs) to speed up compute-intensive layers and solve the unbalanced pipeline problem. To obtain accurate and reliable benchmark results, key component modules, such as straightforward link (SFL) modules and Tile-level ADCs, are designed in standard 28 nm CMOS technology. The evaluation shows that LINKAGE outperforms the conventional ADC/DAC-based architecture with a 2.07×∼11.22× improvement in throughput, 2.45×∼7.00× in energy efficiency, and 22%–51% reduction in the area overhead while maintaining accuracy. Our LINKAGE architecture can achieve 22.9∼24.4 TOPS/W energy efficiency (4b-IN/4b-W) and 1.82 ∼4.53 TOPS throughput with the blockwise method. This work demonstrates a new method for significantly improving the energy efficiency of CIM chips, which can be applied to general CNNs/FCNNs.
Establishment and validation of nomograms to predict survival probability of advanced malignant pleural mesothelioma based on the SEER database and a Chinese medical institution
Authors: Zhang Xuemei , Chang Lele , Zhu Yingying , Mao Yuxin , Zhang Tao , Zhang Qian , Wang Chunbo 
Published: April 2023

ObjectiveThe purpose of this study was to build nomograms for predicting the survival of individual advanced pleural mesothelioma (MPM) patients using the Surveillance, Epidemiology, and End Results (SEER) database.MethodsThe 1251 patients enrolled from the SEER database were randomized (in a 7:3 ratio) to a training cohort and an internal validation cohort. Eighty patients were enrolled from the Harbin Medical University Cancer Hospital as the external validation cohort. Nomograms were constructed from variables screened by univariate or multivariate Cox regression analyses and evaluated by consistency indices (C-index), calibration plots, and receiver operating characteristic (ROC) curves. Patients from the SEER database who received chemotherapy alone and chemoradiotherapy were statistically paired using propensity score matching of the two groups and performed subgroup analysis in the screened variables.ResultsThe nomograms are well-structured and well-validated prognostic maps constructed from four variables: gender, histology, AJCC stage, and treatment. All individuals were allocated into high-risk versus low-risk groups based on the median risk score of the training cohort, with the high-risk group having worse OS and CSS in all three cohorts (P&lt;0.05). The outcomes of the subgroup analysis indicated that the advanced MPM patients receiving chemotherapy with or without local radiotherapy do not affect OS or CSS.ConclusionThe accurate nomograms to predict the survival of patients with advanced MPM were built and validated based on an analysis of the SEER database with an external validation cohort. The study suggests that the additional local radiotherapy to chemotherapy does not increase the survival benefit of patients.
Dietary flaxseed oil and vitamin E improve semen quality via propionic acid metabolism
Authors: Yuan Chongshan , Zhang Kaiyan , Wang Zhe , Ma Xin , Liu Hongyu , Zhao Jing , Lu Wenfa , Wang Jun 
Published: April 2023

IntroductionFlaxseed oil (FO) and vitamin E (VE) both have antioxidant effects on sperm. The present study investigated the effects of dietary supplementation with FO and/or VE on semen quality.Methods16 fertile Simmental bulls were selected and randomly divided into 4 groups (n = 4): the control group (control diet), FO group (control diet containing 24 g/kg FO), VE group (control diet containing 150 mg/kg VE) and FOVE group (control diet containing 150 mg/kg VE and 24 g/kg FO), and the trial lasted 10 weeks.ResultsThe results showed that the addition of FO independently can increase sperm motion parameters, the levels of catalase (CAT), glutathione peroxidase (GSH-Px), testosterone (T) and estradiol (E2), while reduce oxidative stress in seminal plasma (P &lt; 0.05). Supplement of VE independently can increased the motility, motility parameters, CAT and superoxide dismutase (SOD) levels, and reduce oxidative stress in seminal plasma (P &lt; 0.05). There was an interaction effect of FO × VE on motility and reactive oxygen species (ROS), while GSH-Px and ROS were affected by week × VE 2-way interaction, levels of T and E2 were also affected by the dietary FO × week interaction (P &lt; 0.05). The triple interaction effects of FO, VE and week were significant for malondialdehyde (MDA) (P &lt; 0.05). Compared with the control group, sperm from the FOVE group had a significantly higher in vitro fertilization (IVF) rate, and subsequent embryos had increased developmental ability with reduced ROS levels at the eight-cell stage, then increased adenosine triphosphate (ATP) content and gene expression levels of CAT, CDX2, Nanog, and SOD at the blastocyst stage (P &lt; 0.05). Metabolomic and transcriptomic results indicated that dietary supplementation of FO and VE increased the expression of the metabolite aconitic acid, as well as the expression of ABAT and AHDHA genes.ConclusionWith in-silico analysis, it can be concluded that the effects of dietary FO and VE on improving semen quality and embryo development may be related to increased aconitic acid via the ABAT and AHDHA genes involved in the propionic acid metabolism pathway.
Diversified crop rotations and organic amendments as strategies for increasing soil carbon storage and stabilisation in UK arable systems
Authors: Zani Caio F. , Manning David A. C. , Abbott Geoffrey D. , Taylor James A. , Cooper Julia , Lopez-Capel Elisa 
Published: April 2023

Adaptations in crop rotation with the inclusion of temporary grass-clover leys and organic amendments, have been promoted as effective ways to improve soil carbon (C) sequestration and mitigate climate change in agricultural systems. However, there are still a lot of uncertainties related to i) the combined effects of different crop rotations and different fertilisation sources, e.g., organic amendments, on soil C stocks; and ii) their potential effect on C stabilisation. The objective of this study was to evaluate the effect of different arable crop rotations with varying degrees of diversity in crop type and lengths of grass-clover ley periods and fertilisation sources on soil C stocks and C stabilisation down to 0.60 m soil depth. This was investigated in a long-term factorial field experiment-combining different crop rotation (cereal-intensive conventionalvs.diversified legume-intensive organic) with different lengths of grass-clover ley periods (2vs.3 years), fertilisation sources (mineralvs.compost), and years (samples taken at the beginning and at the last year of one complete cycle of rotation; 8 years apart)-to explore their individual and interactive effect on soil C stock and C stabilisation at two soil depths (0–0.30 and 0.30–0.60 m). Soil C stabilisation was assessed using a unique combination of three different techniques: physical fractionation for separation of C associated to organic and mineral fractions, thermal analysis combined with differential scanning calorimetry and a quadrupole mass spectrometry (TG-DSC-QMS) for physical-chemical aspects, and pyrolysis coupled with gas chromatography-mass spectrometry (Py-GC/MS) for molecular structural information. The findings showed higher soil C stocks under the diversified organic rotation with 3 years of grass-clover ley period at both soil depths, regardless of the fertilisation source or sampling year. However, the organic rotation seemed to deliver stable soil C stocks only in the subsoil layer. Compost fertilisation, in turn, increased topsoil C stocks between the two sample dates under both rotations, and it appears to be stable. These results suggested that combining a diversified organic rotation with 3 years grass-clover ley with compost fertilisation could be one way for agricultural systems to deliver stable soil C sequestration.
Lifetime violence and suicidal ideation among young women (18–24 years) in Uganda: Results from a population-based survey
Authors: Kisaakye Peter , Kafuko Agatha , Bukuluki Paul 
Published: April 2023

IntroductionViolence is a major global public health issue that threatens the physical and mental health of victims. Of particular concern is the increasing evidence which suggests that violence is strongly associated with suicidal behavior including ideation.MethodsThis study uses data from the 2015 Violence Against Children Survey (VACS). This study seeks to highlight the relationship between lifetime violence and suicidal ideation using a nationally representative sample of 1,795 young women (18–24 years) in Uganda.ResultsResults indicate that respondents who experienced lifetime sexual violence (aOR = 1.726; 95%CI = 1.304–2.287), physical violence (aOR = 1.930; 95%CI = 1.293–2.882) or emotional violence (aOR = 2.623; 95%CI = 1.988–3.459) were more likely to experience suicidal ideation. Respondents who were not married (aOR = 1.607; 95%CI = 1.040–2.484), not having too much trust with community members (aOR = 1.542; 95%CI = 1.024–2.320) or not having a close relationship with biological parents (aOR = 1.614; 95%CI = 1.230–2.119) were more likely to experience suicidal ideation. Respondents who did not engage in work in the past 12 months prior to the survey (aOR = 0.629; 95%CI = 0.433–0.913) were less likely to experience suicidal ideation.ConclusionThe results can be used to inform policy and programming and for integration of mental health and psychosocial support in programming for prevention and response to violence against young women.
The TNF-α rs361525 and IFN-γ rs2430561 polymorphisms are associated with liver cirrhosis risk: a comprehensive meta-analysis
Authors: Zheng Minghui , Li Jing , Fang Weizhen , Luo Ling , Ding Rui , Zeng Hua , Luo Hong , Lin Xianghua , Duan Chaohui 
Published: April 2023

BackgroundInflammation serves as an essential driver of liver cirrhosis (LC) incidence. Accordingly, a meta-analysis was carried out to explore the association between specific polymorphisms in the interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) genes and the incidence of LC based on comparisons of genotype and allele frequencies.ObjectivesTo study the relationship between TNF-α rs361525 and IFN-γ rs2430561 polymorphisms and the risk of LC.MethodsA database search was performed for all studies published as of September 10, 2022. The strength of risk relationships was assessed based on odds ratios (ORs) with 95% confidence intervals (CIs).ResultsPooled analyses were conducted for one common TNF-α polymorphism (rs361525) as well as one common IFN-γ polymorphism (rs2430561). Both of these SNPs were identified as LC-related risk factors. Specifically, rs361525 was related to LC incidence in both alcoholic liver cirrhosis (OR: 1.86, 95%CI: 1.03-3.34) and hepatitis B virus (HBV)-related cirrhosis cases (OR: 1.44, 95%CI: 1.00-2.06) when using an allelic contrast model. Moreover, rs2430561 was significantly related to LC in an Asian population (OR: 1.45, 95%CI: 1.13-1.86) and in the context of HBV-related cirrhosis (OR: 1.48, 95%CI: 1.13-1.93) when using an allelic contrast model.ConclusionThese findings indicate that rs361525 and rs2430561 represent LC-related risk factors, although additional large-scale clinical and case-control studies will be vital to confirm these results.
Identification of immune-associated genes in diagnosing osteoarthritis with metabolic syndrome by integrated bioinformatics analysis and machine learning
Authors: Li Junchen , Wang Genghong , Xv Xilin , Li Zhigang , Shen Yiwei , Zhang Cheng , Zhang Xiaofeng 
Published: April 2023

BackgroundIn the pathogenesis of osteoarthritis (OA) and metabolic syndrome (MetS), the immune system plays a particularly important role. The purpose of this study was to find key diagnostic candidate genes in OA patients who also had metabolic syndrome.MethodsWe searched the Gene Expression Omnibus (GEO) database for three OA and one MetS dataset. Limma, weighted gene co-expression network analysis (WGCNA), and machine learning algorithms were used to identify and analyze the immune genes associated with OA and MetS. They were evaluated using nomograms and receiver operating characteristic (ROC) curves, and finally, immune cells dysregulated in OA were investigated using immune infiltration analysis.ResultsAfter Limma analysis, the integrated OA dataset yielded 2263 DEGs, and the MetS dataset yielded the most relevant module containing 691 genes after WGCNA, with a total of 82 intersections between the two. The immune-related genes were mostly enriched in the enrichment analysis, and the immune infiltration analysis revealed an imbalance in multiple immune cells. Further machine learning screening yielded eight core genes that were evaluated by nomogram and diagnostic value and found to have a high diagnostic value (area under the curve from 0.82 to 0.96).ConclusionEight immune-related core genes were identified (FZD7, IRAK3, KDELR3, PHC2, RHOB, RNF170, SOX13, and ZKSCAN4), and a nomogram for the diagnosis of OA and MetS was established. This research could lead to the identification of potential peripheral blood diagnostic candidate genes for MetS patients who also suffer from OA.