bluuebunny/crossref_metadata_2025_split huggingface dataset:
Another de novo mutation in the SOD1 gene: the first Turkish patient with SOD1-His47Arg, a case report
Authors: Bayraktar Elif , Çiftçi Vildan , Uysal Hilmi , Başak A. Nazlı 
Published: August 2023

Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease of motor neurons. Most ALS cases are considered sporadic due to the presence of a combination of environmental and complex genetic risk factors, while approximately 10% of cases have a family history. Pathogenic variants in the SOD1 gene are the second most frequent causative factor of genetics-based ALS worldwide, after C9ORF72 hexanucleotide repeat expansion. The De novo occurrence of pathogenic mutations in ALS-associated genes and its effect on disease progression have been studied previously, especially in the FUS gene. Recent studies have shown that a very small portion of SOD1 cases occurred de novo. Here, we present the first de novo case of the SOD1 His47Arg mutation in a young female patient with mild symptoms and, currently, a slow progression for 7 years.
Construction of a genetic map and QTL mapping of seed size traits in soybean
Authors: Jiang Aohua , Liu Jiaqi , Gao Weiran , Ma Ronghan , Tan Pingting , Liu Fang , Zhang Jian 
Published: August 2023

Soybean seed size and seed shape traits are closely related to plant yield and appearance quality. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiang Chun 2 and JiYu 166 were selected as the mapping population to construct a molecular genetic linkage map, and the phenotypic data of hundred-grain weight, seed length, seed width, and seed length-to-width ratio of soybean under three generations of F2 single plants and F2:3 and F2:4 lines were combined to detect the QTL (quantitative trait loci) for the corresponding traits by ICIM mapping. A soybean genetic map containing 455 markers with an average distance of 6.15 cM and a total length of 2799.2 cM was obtained. Forty-nine QTLs related to the hundred-grain weight, seed length, seed width, and seed length-to-width ratio of soybean were obtained under three environmental conditions. A total of 10 QTLs were detected in more than two environments with a phenotypic variation of over 10%. Twelve QTL clusters were identified on chromosomes 1, 2, 5, 6, 8, 13, 18, and 19, with the majority of the overlapping intervals for hundred-grain weight and seed width. These results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean seed weight and seed shape. Eighteen candidate genes that may be involved in the regulation of soybean seed size were screened by gene functional annotation and GO enrichment analysis.
Dynamics of IgG antibody response against Plasmodium antigens among Nigerian infants and young children
Authors: Leonard Colleen M. , Uhomoibhi Perpetua , Abubakar Ado , Ogunniyi Abiodun , Mba Nwando , Greby Stacie M. , Okoye McPaul I. , Iriemenam Nnaemeka C. , Ihekweazu Chikwe , Steinhardt Laura , Rogier Eric ,   NMS4 Technical Working Group
Published: August 2023

BackgroundPlasmodium falciparum malaria is a leading cause of child mortality in Nigeria. Neonates are born with maternal antibodies from placental transfer which may protect against malaria infection in the first months of life. The IgG dynamics of the transition from passively transferred antimalarial antibodies to actively acquired IgG from natural exposure have not been well elucidated.MethodsBlood samples collected during a 2018 Nigeria nationwide HIV/AIDS household survey were available for 9,443 children under 5 years of age, with a subset of infants under 2 months of age having maternal samples available (n=41). Samples were assayed for the P. falciparum HRP2 antigen and anti-malarial IgG antibodies. LOESS regression examined the dynamics in IgG response in the first 5 years of life. Correlation with maternal IgG levels was assessed for mother/child pairs.ResultsConsistent decreases were observed in median IgG levels against all Plasmodium spp. antigen targets for the first months of life. At a population level, P. falciparum apical membrane antigen-1 (AMA1) and merozoite surface protein-1 19kD (PfMSP1) IgG decreased during the first 12 months of life before reaching a nadir, whereas IgGs to other targets only declined for the first 4 months of life. Seropositivity showed a similar decline with the lowest seropositivity against AMA1 and PfMSP1 at 10-12 months, though remaining above 50% during the first 2 years of life in higher transmission areas. No protective association was observed between IgG positivity and P. falciparum infection in infants. Maternal antibody levels showed a strong positive correlation with infant antibody levels for all P. falciparum antigens from birth to 2 months of age, but this correlation was lost by 6 months of age.DiscussionMaternally transferred anti-malarial IgG antibodies rapidly decline during the first 6 months of life, with variations among specific antigens and malaria transmission intensity. From 3-23 months of age, there was a wide range in IgG levels for the blood-stage antigens indicating high individual variation in antibody production as children are infected with malaria. Non-falciparum species-specific antigens showed similar patterns in waning immunity and correlation with paired mother’s IgG levels compared to P. falciparum antigens.
The m6A-related gene signature stratifies poor prognosis patients and characterizes immunosuppressive microenvironment in hepatocellular carcinoma
Authors: Ma Ensi , Li Jianhua , Shen Conghuan , Gu Yange , Zhang Xinju , Li Li , Zhao Jing , Wang Zhengxin 
Published: August 2023

BackgroundN6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of RNA, which can affect RNA metabolism and protein translation. The m6A modification plays a critical role in cancer development, including hepatocellular carcinoma (HCC). Despite several m6A-related signatures in HCC, most of them lack the necessary validation and the reliability is still elusive.MethodsDifferentially expressed genes (DEGs) in the Cancer Genome Atlas were comprehensively analyzed to identify m6A signature associated with HCC prognosis. Gene set enrichment analysis, tumor mutation burden (TMB), immune infiltration, and therapeutic response were evaluated. Importantly, mass spectrometry proteomics and multiplex immunofluorescence assays were performed for validation.ResultsThe m6A-related protein-coding gene signature was established, which can divide HCC into high-/low-risk subgroups with markedly different overall survival (OS) and clinical stages. Furthermore, we validated its reliability and robustness in our 101 independent HCC specimens using proteomic detection and confirmed that our signature readily identified high-risk HCC patients with 3-year survival rates of 44.1% vs. 71.8% in the low-risk group. Functional analysis indicated that the high-risk group might stimulate the cell cycle and activate oncogenic pathways such as MAPK, mTOR, and VEGF, whereas the low-risk group mainly regulated amino acid, fatty acid, and drug metabolism. Additionally, the high-risk group had more TMB, upregulated immune checkpoint molecule expression, including PD-1, CTLA4, TIM3, and LAG3, and preferentially formed an immunosuppressive microenvironment. Accordingly, potential therapeutic responses showed that high-risk patients were potentially sensitive to inhibitors targeting the cell cycle and MAPK signaling, with patients possibly benefiting from immunotherapy. Moreover, multiplex immunofluorescence assays indicated that high-risk HCC samples displayed distinct immunosuppressive features, with abundant M2-polarized macrophages and T-regulatory cell infiltration.ConclusionThe m6A signature had a prominent capacity to evaluate OS and characterize the tumor immune microenvironment of HCC, which may serve as a useful approach for risk stratification management and provide a valuable clue to choosing rational therapeutic strategies.
Population connectivity and dynamics in early-life stages of Atlantic fish communities
Authors: Pereira Gabellini Aurelia , Mariani Patrizio , Christensen Asbjørn 
Published: August 2023

IntroductionMany hypotheses have been suggested to explain recruitment variability in fish populations. These can generally be divided into three groups, either related to: larval food limitation, predation, or transport. Transport mechanisms are central for reproduction in pelagic species and three physical processes, concentration, enrichment, and retention are commonly referred as the fundamental “ocean triads” sustaining larval survival and thus success of reproductive effort. The aim of this study is to investigate linkages between primary production and transport processes of eggs and larvae for the most important commercial fish species in the Atlantic Ocean.MethodsWe simulated eggs and larvae dispersion using an individualbased model and integrating information on the fish ecology of the major fish stocks. Our work included a review on spawning ground locations, spawning time, eggs and larvae duration. Simulations were performed over a 10-year time period for 113 stocks (17 species) in order to assess variability in dispersion and common trends and factors affecting transport.ResultsThe level of primary production from initial to final position, i.e. from spawning to larval settlement, increased for some stocks (n=31), for others it declined (n=64), and for a smaller group (n=18) there was no substantial changes in level of primary production.DiscussionThis result implies that larval transport will not necessarily introduce larvae into areas of enhanced food availability expressed by the primary production at the site. These findings thus suggest marked differences in how physical and biological processes interact in the early life of major fish groups in the Atlantic Ocean. The results provide a further insight into fish larval drift and the potential role of primary production in emergence of spawning strategies.
Is acupuncture safe in the ICU? A systematic review and meta-analysis
Authors: Ben-Arie Eyal , Lottering Bernice Jeanne , Chen Fang-Pey , Ho Wen-Chao , Lee Yu-Chen , Inprasit Chanya , Kao Pei-Yu 
Published: August 2023

Background and purposeThe safety of interventions for critically ill patients is a crucial issue. In recent years, several studies have treated critically ill patients with acupuncture. However, the safety of acupuncture in this setting remains to be systematically measured.MethodsIn May 2022, the electronic databases of PubMed and the Cochrane Library were searched for studies comparing acupuncture interventions to control interventions in critically ill patients. Study outcomes examined the incidence of severe adverse events (AEs), minor AEs, adverse reactions, ICU stays, and 28-day mortality.ResultsA total of 31 articles were analyzed, and no serious AEs related to acupuncture treatment were identified. No significant differences were found between the groups in the meta-analysis of minor AEs (risk ratio [RR] 5.69 [0.34, 96.60], P = 0.23, I2 = 76%). A reduced risk in the incidence of adverse reactions following acupuncture intervention was evidenced (RR 0.33 [0.22, 0.50], P = 0.00001, I2 = 44%). The patients in the acupuncture arm spent significantly less time in the intensive care unit (ICU) (Mean difference −1.45 [−11.94, −10.97], P = 0.00001, I2 = 56%) and also exhibited lower 28-day mortality rates (odds ratio 0.61 [0.48, 0.78], P = 0.0001, I2 = 0%).ConclusionThere is no evidence to indicate a higher risk of severe or minor AEs in patients who receive acupuncture. Acupuncture demonstrated favorable results in both ICU stay and 28-day mortality measurements, in addition to presenting with fewer adverse reactions compared to routine ICU care. However, the low certainty of the evidence resulting from a high risk of bias in the included studies merits substantial consideration, and further research is still warranted.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=142131, identifier: CRD42020142131.
Association of serum lipids with inflammatory bowel disease: a systematic review and meta-analysis
Authors: Chen Hongxin , Li Weiyang , Hu Jingyi , Xu Feng , Lu Yizhou , Zhu Lei , Shen Hong 
Published: August 2023

BackgroundSerum lipid levels seem to be abnormal in Inflammatory bowel disease (IBD). However, the specific manifestation of abnormal serum lipid levels in IBD are heterogeneous among studies and have not been sufficiently determined yet.MethodsPubMed, EMBASE, and Cochrane Library databases were searched. Serum lipid levels were compared between IBD patients and Health individuals, Crohn’s (CD) and ulcerative colitis (UC), active and inactive, mild and non-mild patients, respectively. Meta-analyses were performed by using a random-effect model. Weight mean difference (WMD) with 95% confidence intervals (CIs) were calculated.ResultsOverall, 53 studies were included. Compared with healthy controls, IBD patients had significantly lower TC (WMD = −0.506, 95%CI = −0.674 to −0.338, p &lt; 0.001), HDL-c (WMD = −0.122, 95%CI = −0.205 to −0.039, p = 0.004), and LDL-c (WMD = −0.371, 95%CI = −0.547 to −0.194, p &lt; 0.001) levels. CD groups had a significantly lower TC (WMD = −0.349, 95%CI = −0.528 to −0.170, p &lt; 0.0001) level as compared to UC groups. Active IBD and non-mild UC groups had significantly lower TC (WMD = −0.454, 95%CI = −0.722 to −0.187, p = 0.001) (WMD =0.462, 95%CI = 0.176 to 0.748, p = 0.002) and LDL-c (WMD = −0.225, 95%CI = −0.445 to −0.005, p = 0.045) (WMD =0.346, 95%CI = 0.084–0.609, p = 0.010) levels as compared to inactive IBD and mild UC groups, respectively.ConclusionThe overall level of serum lipids in IBD patients is lower than that of healthy individuals and is negatively associated with disease severity.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier: CRD42022383885.
Survival implications vs. complications: unraveling the impact of vitamin D adjunctive use in critically ill patients with COVID-19—A multicenter cohort study
Authors: Al Sulaiman Khalid , Korayem Ghazwa B. , Aljuhani Ohoud , Altebainawi Ali F. , Shawaqfeh Mohammad S. , Alarfaj Sumaiah J. , Alharbi Reham A. , Ageeli Mawaddah M. , Alissa Abdulrahman , Vishwakarma Ramesh , Ibrahim Alnada , Alenazi Abeer A. , Alghnam Suliman , Alshehri Nadiyah , Alshammari Maqbulah M. , Alhubaishi Alaa , Aldhaeefi Mohammed , Alamri Faisal F. , Syed Yadullah , Khan Raymond , Alalawi Mai , Alanazi Khalaf A. , Alresayes Faisal S. , Albarqi Khalid J. , Al Ghamdi Ghassan 
Published: August 2023

BackgroundDespite insufficient evidence, vitamin D has been used as adjunctive therapy in critically ill patients with COVID-19. This study evaluates the effectiveness and safety of vitamin D as an adjunctive therapy in critically ill COVID-19 patients.MethodsA multicenter retrospective cohort study that included all adult COVID-19 patients admitted to the intensive care units (ICUs) between March 2020 and July 2021. Patients were categorized into two groups based on their vitamin D use throughout their ICU stay (control vs. vitamin D). The primary endpoint was in-hospital mortality. Secondary outcomes were the length of stay (LOS), mechanical ventilation (MV) duration, and ICU-acquired complications. Propensity score (PS) matching (1:1) was used based on the predefined criteria. Multivariable logistic, Cox proportional hazards, and negative binomial regression analyses were employed as appropriate.ResultsA total of 1,435 patients were included in the study. Vitamin D was initiated in 177 patients (12.3%), whereas 1,258 patients did not receive it. A total of 288 patients were matched (1:1) using PS. The in-hospital mortality showed no difference between patients who received vitamin D and the control group (HR 1.22, 95% CI 0.87–1.71; p = 0.26). However, MV duration and ICU LOS were longer in the vitamin D group (beta coefficient 0.24 (95% CI 0.00–0.47), p = 0.05 and beta coefficient 0.16 (95% CI −0.01 to 0.33), p = 0.07, respectively). As an exploratory outcome, patients who received vitamin D were more likely to develop major bleeding than those who did not [OR 3.48 (95% CI 1.10, 10.94), p = 0.03].ConclusionThe use of vitamin D as adjunctive therapy in COVID-19 critically ill patients was not associated with survival benefits but was linked with longer MV duration, ICU LOS, and higher odds of major bleeding.
Multi-omics analysis reveals the prognostic and tumor micro-environmental value of lumican in multiple cancer types
Authors: Guo Zehuai , Li Zeyun , Chen Ming , Qi Xiangjun , Sun Zhe , Wu Siqi , Hou Xuenan , Qiu Mengli , Cao Yang 
Published: August 2023

Background: Lumican (LUM), a proteoglycan of the extracellular matrix, has been reported to be involved in the regulation of immune escape processes, but the data supporting this phenomenon are not sufficient. In this study, we aimed to explore the links among LUM expression, survival, tumor microenvironment (TME), and immunotherapy in 33 cancer types.Methods: Data from several databases, such as UCSC Xena, GTEx, UALCAN, HPA, GEPIA2, TISIDB, PrognoScan, TIMER2, and GEO, as well as published studies, were used to determine the relationship between LUM expression and clinical features, TME, heterogeneity, and tumor stemness.Results: The expression of LUM was statistically different in most tumors versus normal tissues, both at the RNA and protein expression levels. High expression of LUM was typically associated with a poor prognosis in tumors. Additionally, immune scores, six immune cells, four immunosuppressive cells, cancer-associated fibroblasts (CAFs)-associated and immunosuppressive factors, tumor mutation burden (TMB), microsatellite instability (MSI), DNAss, and RNAss were all significantly associated with LUM. Among them, LUM expression displayed a significant positive correlation with CAFs and their factors, and exhibited immunosuppressive effects in six independent immunotherapy cohorts.Conclusion: Multi-omics analysis suggests that LUM may have been a prognostic marker, contributed to immunosuppression in the TME, and decreased the effectiveness of immune checkpoint inhibitors.
Neuroimaging anomalies in asymptomatic middle cerebral artery steno-occlusive disease with normal-appearing white matter
Authors: Huang Zhaodi , Xia Xiaona , Guan Shuai , Gong Gaolang , Luo Yishan , Shi Lin , Zhang Juntao , Meng Xiangshui 
Published: August 2023

BackgroundAsymptomatic chronic cerebrovascular steno-occlusive disease is common, but the cognitive function and alterations in the brain’s structural and functional profiles have not been well studied. This study aimed to reveal whether and how patients with asymptomatic middle cerebral artery (MCA) steno-occlusive disease and normal-appearing white matter differ in brain structural and functional profiles from normal controls and their correlations with cognitive function.MethodsIn all, 26 patients with asymptomatic MCA steno-occlusive disease and 22 healthy controls were compared for neurobehavioral assessments, brain volume, cortical thickness, fiber connectivity density (FiCD) value, and resting-state functional connectivity (FC) using multimodal MRI. We also investigated the associations between abnormal cortical thicknesses, FiCD values, and functional connectivities with the neurobehavioral assessments.ResultsPatients performed worse on memory tasks (Auditory Verbal Learning Test-Huashan version) compared with healthy controls. Patients were divided into two groups: the right group (patients with right MCA steno-occlusive disease) and the left group (patients with left MCA steno-occlusive disease). The left group showed significant cortical thinning in the left superior parietal lobule, while the right group showed significant cortical thinning in the right superior parietal lobule and caudal portion of the right middle frontal gyrus. Increased FiCD values in the superior frontal region of the left hemisphere were observed in the left group. In addition, a set of interhemispheric and intrahemispheric FC showed a significant decrease or increase in both the left and right groups. Many functional connectivity profiles were positively correlated with cognitive scores. No correlation was found between cortical thickness, FiCD values, and cognitive scores.ConclusionEven if the patients with MCA steno-occlusive disease were asymptomatic and had normal-appearing white matter, their cognitive function and structural and functional profiles had changed, especially the FC. Alterations in FC may be an important mechanism underlying the neurodegenerative process in patients with asymptomatic MCA steno-occlusive disease before structural changes occur, so FC assessment may promote the detection of network alterations, which may be used as a biomarker of disease progression and therapeutic efficacy evaluation in these patients.
Extensive spinal epidural abscess due to Streptococcus intermedius: a case report treated conservatively and literature review
Authors: Liu Dianqi , Lu Weijie , Huang Wenbin , Zhai Wenrun , Ling Qinjie 
Published: August 2023

PurposeTo describe the clinical significance of prompt, adequate, and targeted intravenous antibiotic (IV antibiotic) therapy in the successful management of spinal epidural abscess (SEA) associated with Streptococcus intermedius (S. intermedius) infection.Case descriptionSEA is a rare, but catastrophic infection that may result in a high risk of permanent neurological disability. A 52-year-old Chinese female patient was presented to the emergency department due to 2 years of low back pain and 3 days of decreased muscle strength in the extremities. The blood culture confirmed the presence of S. intermedius infection, and gadolinium-enhanced magnetic resonance imaging (MRI) demonstrated widespread epidural abscesses in the cervical, thoracic, and lumbar spine canal. Empirical IV antibiotic therapy with vancomycin was promptly initiated, with meropenem and moxifloxacin added subsequently based on blood culture results. After 5 days of IV antibiotic treatment, the patient’s blood culture became negative. 6 weeks later, a follow-up MRI showed a decrease in the size of the abscess. The patient’s muscle strength was mostly restored after 2 months of IV antibiotic treatment.ConclusionRepeat examinations or gadolinium-enhanced MRI should be considered when initial MRI findings are not diagnostic of SEA. For extensive SEA caused by Streptococcus intermedius infection, surgery may be non-essential, and the judicious antibiotic selection and adequate treatment duration are pivotal for successful conservative management. Furthermore, for patients who are not amenable to surgery, a comprehensive evaluation of their condition and meticulous implementation of a precise pharmacological regimen holds noteworthy clinical significance.