bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring biomarkers for prognosis and neoadjuvant chemosensitivity in rectal cancer: Multi-omics and ctDNA sequencing collaboration
Authors: Jiang Xiu-Feng , Zhang Bo-Miao , Du Fen-Qi , Guo Jun-Nan , Wang Dan , Li Yi-En , Deng Shen-Hui , Cui Bin-Bin , Liu Yan-Long 
Published: December 2022

IntroductionThis study aimed to identified the key genes and sequencing metrics for predicting prognosis and efficacy of neoadjuvant chemotherapy (nCT) in rectal cancer (RC) based on genomic DNA sequencing in samples with different origin and multi-omics association database.MethodsWe collected 16 RC patients and obtained DNA sequencing data from cancer tissues and plasma cell-free DNA before and after nCT. Various gene variations were analyzed, including single nucleotide variants (SNV), copy number variation (CNV), tumor mutation burden (TMB), copy number instability (CNI) and mutant-allele tumor heterogeneity (MATH). We also identified genes by which CNV level can differentiate the response to nCT. The Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database were used to further evaluate the specific role of therapeutic relevant genes and screen out the key genes in multi-omics levels. After the intersection of the screened genes from differential expression analysis, survival analysis and principal components analysis dimensionality reduction cluster analysis, the key genes were finally identified.ResultsThe genes CNV level of principal component genes in baseline blood and cancer tissues could significantly distinguish the two groups of patients. The CNV of HSP90AA1, EGFR, SRC, MTOR, etc. were relatively gained in the better group compared with the poor group in baseline blood. The CNI and TMB was significantly different between the two groups. The increased expression of HSP90AA1, EGFR, and SRC was associated with increased sensitivity to multiple chemotherapeutic drugs. The nCT predictive score obtained by therapeutic relevant genes could be a potential prognostic indicator, and the combination with TMB could further refine prognostic prediction for patients. After a series of analysis in multi-omics association database, EGFR and HSP90AA1 with significant differences in multiple aspects were identified as the key predictive genes related to prognosis and the sensitivity of nCT.DiscussionThis work revealed that effective combined application and analysis in multi-omics data are critical to search for predictive biomarkers. The key genes EGFR and HSP90AA1 could serve as an effective biomarker to predict prognose and neoadjuvant chemosensitivity.
Association of antithrombin with development of trauma-induced disseminated intravascular coagulation and outcomes
Authors: Wada Takeshi , Shiraishi Atsushi , Gando Satoshi , Kabata Daijiro , Yamakawa Kazuma , Fujishima Seitaro , Saitoh Daizoh , Kushimoto Shigeki , Ogura Hiroshi , Abe Toshikazu , Mayumi Toshihiko , Otomo Yasuhiro 
Published: December 2022

IntroductionTrauma activates the innate immune system to modulate hemostasis and minimize the damage caused by physiological bodily responses, including the activation of coagulation. Sufficiently severe trauma overwhelms physiological responses and elicits the systemic inflammatory response syndrome, which leads to the onset of disseminated intravascular coagulation (DIC), characterized by dysregulated inflammatory coagulofibrinolytic responses. Impaired anticoagulant mechanisms, including antithrombin, constitutes the pathology of DIC, while the dynamics of antithrombin and relevance to outcomes in trauma-induced coagulopathy have not been fully elucidated. This study investigated the associations of antithrombin activity with DIC onset and outcomes in severely injured patients.MethodsThis retrospective sub-analysis of a multicenter, prospective study included patients with an injury severity score ≥16. We characterized trauma patients with low antithrombin activity (antithrombin &lt;80% on hospital arrival, n = 75) in comparison with those who had normal antithrombin activity (antithrombin ≥80%, n = 200). Global markers of coagulation and fibrinolysis, molecular biomarkers for thrombin generation (soluble fibrin [SF]), and markers of anticoagulation (antithrombin) were evaluated to confirm the associations of antithrombin with DIC development and outcomes, including in-hospital mortality and the multiple organ dysfunction syndrome (MODS).ResultsPatients with low antithrombin activity had higher prevalence of shock, transfusion requirements, and in-hospital mortality. Higher DIC scores and more severe organ dysfunction were observed in the low AT group compared to that in the normal AT group. Antithrombin activity on arrival at the hospital was an independent predictor of the development of DIC in trauma patients, and levels of SF increased with lower antithrombin values (antithrombin activity &gt; 85%). Antithrombin activity at 3 h showed good predictive performance for in-hospital mortality, and a multivariable Cox proportional-hazard regression model with a cross-product term between the antithrombin and DIC showed that the in-hospital mortality in patients with DIC increased with decreased antithrombin activity. A multivariable logistic regression model showed that the odds for the development of MODS in patients with DIC increased with lower antithrombin values.ConclusionDecreased antithrombin activity in trauma-induced coagulopathy is associated with poor outcomes through worsening of DIC.
Humoral immune response following a third SARS-CoV-2 mRNA vaccine dose in solid organ transplant recipients compared with matched controls
Authors: Balsby Daniel , Nilsson Anna Christine , Petersen Inge , Lindvig Susan O. , Davidsen Jesper Rømhild , Abazi Rozeta , Poulsen Mikael K. , Holden Inge K. , Justesen Ulrik S. , Bistrup Claus , Johansen Isik Somuncu 
Published: December 2022

BackgroundSolid organ transplant (SOT) recipients have shown suboptimal antibody response following COVID-19 vaccination. Several risk factors for the diminished response have been identified including immunosuppression and older age, but the influence of different comorbidities is not fully elucidated.MethodThis case-control study consisted of 420 Danish adult SOT recipients and 840 sex- and age-matched controls, all vaccinated with a third homologous dose of either BNT162b2 (Pfizer–BioNTech) or mRNA-1273 (Moderna) vaccine. The primary outcome was differences in humoral immune response. The secondary outcome was breakthrough infections. Additionally, we looked for factors that could predict possible differences between the two groups.ResultsResponse rate increased from 186/382 (49%) to 275/358 (77%) in SOT recipients and remained on 781/790 (99%) to 601/609 (99%) in controls following a third vaccine dose. SOT recipients had significantly lower median antibody concentrations after third dose compared to controls (332.6 BAU/ml vs 46,470.0 BAU/ml, p &lt;0.001). Lowest median antibody concentrations were seen in SOT recipients with liver disease (10.3 BAU/ml, IQR 7.1-319) and diabetes (275.3 BAU/ml, IQR 7.3-957.4). Breakthrough infections occurred similarly frequent, 150 (40%) among cases and 301 (39%) among controls (p = 0.80).ConclusionA third COVID-19 vaccine dose resulted in a significant increase in humoral immunogenicity in SOT recipients and maintained high response rate in controls. Furthermore, SOT recipients were less likely to produce antibodies with overall lower antibody concentrations and humoral immunity was highly influenced by the presence of liver disease and diabetes. The prevalence of breakthrough infections was similar in the two groups.
Association of complement components with the risk and severity of NAFLD: A systematic review and meta-analysis
Authors: Zhao Jianbo , Wu Yafei , Lu Peng , Wu Xiaoqin , Han Junming , Shi Yingzhou , Liu Yue , Cheng Yiping , Gao Ling , Zhao Jiajun , Wang Zhen , Fan Xiude 
Published: December 2022

BackgroundIt is generally believed that complement system is strongly associated with the risk of nonalcoholic fatty liver disease (NAFLD). However, complement system contains a variety of complement components, and the relationship between complement components and the risk and severity of NAFLD is inconsistent. The aim of this meta-analysis was to evaluate the association of complement components with the risk and severity of NAFLD.MethodsWe searched PubMed, Embase, Cochrane Library, Google Scholar, Scopus, and ZhiWang Chinese databases from inception to May 2022 for observational studies reporting the risk of NAFLD with complement components. Random-effects meta-analysis was used to obtain pooled estimates of the effect due to heterogeneity.ResultsWe identified 18 studies with a total of 18560 included subjects. According to recent studies, levels of complement component 3 (C3) (mean difference (MD): 0.43, 95% confidence interval (CI) 0.26-0.60), complement component 4 (C4) (MD: 0.04, 95% CI 0.02-0.07), complement component 5(C5) (MD: 34.03, 95% CI 30.80-37.27), complement factor B (CFB) (MD: 0.22, 95% CI 0.13-0.31) and acylation stimulating protein (ASP) (standard mean difference (SMD): 5.17, 95% CI 2.57-7.77) in patients with NAFLD were significantly higher than those in the control group. However, no statistical significance was obtained in complement factor D (CFD) levels between NAFLD and non-NAFLD (MD=156.51, 95% CI -59.38-372.40). Moreover, the levels of C3, C5, CFB, and ASP in patients with moderate and severe NAFLD were significantly higher than those in patients with mild NAFLD. Except for C4 and CFD, the included studies did not explore the changes in the severity of NAFLD according to the concentration of C4 and CFD.ConclusionsThis meta-analysis demonstrates that an increase in complement components including C3, C5, CFB, and ASP is associated with an increased risk and severity of NAFLD, indicating that they may be good biomarkers and targets for the diagnosis and treatment of NAFLD.Systematic review registrationPROSPERO [https://www.crd.york.ac.uk/PROSPERO/], identifier CRD42022348650.
Molecular and anatomical roadmap of stroke pathology in immunodeficient mice
Authors: Weber Rebecca Z. , Mulders Geertje , Perron Patrick , Tackenberg Christian , Rust Ruslan 
Published: December 2022

BackgroundStroke remains a leading cause of disability and death worldwide. It has become apparent that inflammation and immune mediators have a pre-dominant role in initial tissue damage and long-term recovery. Still, different immunosuppressed mouse models are necessary in stroke research e.g., to evaluate therapies using human cell grafts. Despite mounting evidence delineating the importance of inflammation in the stroke pathology, it is poorly described to what extent immune deficiency influences overall stroke outcome.MethodsHere, we assessed the stroke pathology of popular genetic immunodeficient mouse models, i.e., NOD scid gamma (NSG) and recombination activating gene 2 (Rag2–/–) mice as well as pharmacologically immunosuppressed mice and compared them to immune competent, wildtype (WT) C57BL/6J mice three weeks after injury. We performed histology, gene expression, blood serum and behavioural analysis to identify the impact of immunosuppression on stroke progression.ResultsWe detected changes in microglia activation/macrophage infiltration, scar-forming and vascular repair in immune-suppressed mice three weeks after injury. Transcriptomic analysis of stroked tissue revealed the strongest deviation from WT was observed in NSG mice affecting immunological and angiogenic pathways. Pharmacological immunosuppression resulted in the least variation in gene expression compared with the WT. These anatomical and genetic changes did not affect functional recovery in a time course of three weeks. To determine whether timing of immunosuppression is critical, we compared mice with acute and delayed pharmacological immunosuppression after stroke. Mice with delayed immunosuppression (7d) showed increased inflammatory and scarring responses compared to animals acutely treated with tacrolimus, thus more closely resembling WT pathology. Transplantation of human cells in the brains of immunosuppressed mice led to prolonged cell survival in all immunosuppressed mouse models, which was most consistent in NSG and Rag2–/– mice.ConclusionsWe detected distinct anatomical and molecular changes in the stroke pathology between individual immunosuppressed mouse models that should be considered when selecting an appropriate mouse model for stroke research.
Diagnostic accuracy of loop-mediated isothermal amplification for pulmonary tuberculosis in China
Authors: Lin Jing-Jing , Xi Xiu-Hong , Xia Lu , Tan Yao-Ju , Chen Yu , Di Hong-Qin , Chen Zhen-Hua , Yu Ting , Wei Jian-Hao , Fang Peng , Lin Xiao-Ma , Su Bi-Yi , Yan Ming-Zhe , Yu Yong-Min , Okada Kosuke , Noguchi Norihisa , Annaka Toshimitsu , Liu Xu-Hui , Lu Shui-Hua 
Published: December 2022

ObjectivesTo evaluate the diagnostic accuracy of Loop-Mediated Isothermal Amplification Platform (LAMP) in detecting pulmonary tuberculosis (PTB).MethodsThis multicenter prospective study was conducted at six sites in China from June, 2018 to December, 2019. Patients with suspected PTB were consecutively recruited and respiratory samples were collected from all patients. LAMP, Xpert MTB/RIF assay (Xpert), fluorescence smear microscopy, and BACTEC MGIT 960 liquid culture (Mtb culture) were performed for each sample. Diagnostic accuracy indices were calculated against Mtb culture results.ResultsA total of 845 participants were enrolled, but only 799 were included in the analysis. The sensitivities of LAMP, Xpert, and smear microscopy were 78.6% (239/304), 82.2% (250/304), and 63.8% (194/304), respectively, and their specificities were 88.7% (439/495), 86.1% (426/495), and 94.9% (470/495), respectively. The LAMP assay showed substantial agreement with other tests (kappa 0.64–0.79).ConclusionThe LAMP assay performs as well as Xpert MTB/RIF assay and Mtb culture in tertiary-care hospitals. It can be used as an alternative test for detecting PTB with the advantages of being fast, inexpensive, and easy to operate.
Competing with each other: Fish isotopic niche in two resource availability contexts
Authors: Pelage Latifa , Lucena-Frédou Flávia , Eduardo Leandro Nole , Le Loc’h François , Bertrand Arnaud , Lira Alex Souza , Frédou Thierry 
Published: December 2022

IntroductionCompetition embodies species struggle for space and food and is, therefore, a critical evolutionary mechanism influencing species spatiotemporal patterns and persistence. One of the main drivers of competition is resource availability. In marine ecosystems, resource availability is determined, among other things, by habitat structural complexity, as it increases biodiversity and species abundance. In this context, our study aims at understanding how the differences in substrate complexity affect potential trophic competition between demersal fishes in Northeast Brazil.MethodsWe selected two zones contrasted in terms of substrates, one dominated by sand (zone A) and the other by complex substrates such as reefs and calcareous algae (zone B). We used Stable Isotope Analysis (SIA) to quantify intraspecific and interspecific interactions of demersal fishes in both zones. We compared the competitive interactions between zones using social network analysis (SNA), a suitable method to quantitatively study a set of interactions.ResultsIn the sand-dominated zone, demersal fish showed greater interspecific competition and occupied a larger isotopic niche suggesting that a resource-limited context led to diet diversification in the community. Some species expanded their niche through diet plasticity, while others showed higher intraspecific competition than in Zone B to cope with the greater interspecific competition.DiscussionCombining SNA and SIA provided a new method to investigate competition. This study potentially gives a perspective on the future ecological response of the demersal fishes at the community and species level. With habitat degradation and climate change, the complex substrates in zone B will probably disappear gradually, transforming this zone into an ecosystem akin to zone A. This would be detrimental to species more vulnerable to interspecific competition, particularly those targeted by fisheries.
An assessment of burden of hospital-acquired pneumonia among abdominal surgical patients in tertiary university hospital in Serbia: A matched nested case-control study
Authors: Taušan Ðorde , Rančić Nemanja , Kostić Zoran , Ljubenović Nenad , Rakonjac Bojan , Šuljagić Vesna 
Published: December 2022

BackgroundIn the population of abdominal surgical patients hospital-acquired pneumonia (HAP) significantly increases morbidity and mortality.Patients and methodsThrough regular hospital surveillance of patients who received abdominal operations, we identified postoperative HAP from 2007 to 2019. In an initial nested case-control study, every surgical patient with HAP was compared with three control patients without HAP. Control patients were matched to the cases by age, gender, the American Society of Anesthesiologists score, and type of surgical operation. Also, the patients with HAP, who died were compared with those who survived.ResultsMultivariate logistic regression analysis (MLRA) revealed that other postoperative infections, length of intensive care unit stay, use of H2RA, use of PPI/ H2RA, multiple transfusion, and use of vancomycin in surgical prophylaxis were independent RFs for occurrence of HAP. Also, MLRA identified that age, lenght of hospital stay, use of mechanical ventilation and ceftriaxone in HAP therapy were indepedenttly associated with poor outcome of HAP. All Acinetobacter baumannii isolates were resistant to aminoglycoside antimicrobial agents and showed carbapenem resistance. The most frequently used antibiotics in patients with HAP and without HAP were vancomycin and metronidazole, respectively.ConclusionOur study provided an insight into the burden of HAP in abdominal surgical patients, and highlighted several priority areas and targets for quality improvement.
A pilot study on the efficacy of topical lotion containing anti-acne postbiotic in subjects with mild -to -moderate acne
Authors: Cui Hongchang , Guo Chaoqun , Wang Qian , Feng Congrui , Duan Zhi 
Published: December 2022

IntroductionAcne can compromise facial esthetics and become a mental burden, especially when it occurs in puberty. Skincare cosmetics with anti-acne efficiency is more convenient than other treatment modalities, such as dietary supplements, in certain circumstances. The purpose of this study was to investigate the efficacy of an anti-acne lotion in alleviating acne.MethodsIn our study, an anti-acne lotion containing ferment lysate produced by Lactiplantibacillus plantarum VHProbi® E15 were applied to subjects with mild -to -moderate acne over 4 weeks. The efficacy was evaluated based on instrumental measurements using Visia®-CR and CK-MPA® system.Results and discussionThe anti-acne lotion exhibited favorable safety, meeting the stringent criteria for the detection of microbes, heavy metals, toxicity, and irritation. After 2 weeks of treatment, a statistically significant improvement in acne lesions was observed compared to baseline (P &lt; 0.01), and this continued to the end of the study. After 4 weeks of treatment, the transepidermal water loss (P &lt; 0.05) and sebum production (P &lt; 0.05) were significantly decreased in subjects compared to baseline. In addition, the pore/area of interest (AOI) and stratum corneum hydration displayed slightly positive changes throughout treatment. Thus, we conclude that applying topical anti-acne lotion may be safe and confer effective benefits in people with mild -to -moderate acne and represents a promising therapeutic option for acne.
fNIRS-based brain functional response to robot-assisted training for upper-limb in stroke patients with hemiplegia
Authors: Huo Congcong , Sun Zhifang , Xu Gongcheng , Li Xinglou , Xie Hui , Song Ying , Li Zengyong , Wang Yonghui 
Published: December 2022

BackgroundRobot-assisted therapy (RAT) has received considerable attention in stroke motor rehabilitation. Characteristics of brain functional response associated with RAT would provide a theoretical basis for choosing the appropriate protocol for a patient. However, the cortical response induced by RAT remains to be fully elucidated due to the lack of dynamic brain functional assessment tools.ObjectiveTo guide the implementation of clinical therapy, this study focused on the brain functional responses induced by RAT in patients with different degrees of motor impairment.MethodsA total of 32 stroke patients were classified into a low score group (severe impairment, n = 16) and a high score group (moderate impairment, n = 16) according to the motor function of the upper limb and then underwent RAT training in assistive mode with simultaneous cerebral haemodynamic measurement by functional near-infrared spectroscopy (fNIRS). Functional connectivity (FC) and the hemisphere autonomy index (HAI) were calculated based on the wavelet phase coherence among fNIRS signals covering bilateral prefrontal, motor and occipital areas.ResultsSpecific cortical network response related to RAT was observed in patients with unilateral moderate-to-severe motor deficits in the subacute stage. Compared with patients with moderate dysfunction, patients with severe impairment showed a wide range of significant FC responses in the bilateral hemispheres induced by RAT with the assistive mode, especially task-related involvement of ipsilesional supplementary motor areas.ConclusionUnder assisted mode, RAT-related extensive cortical response in patients with severe dysfunction might contribute to brain functional organization during motor performance, which is considered the basic neural substrate of motor-related processes. In contrast, the limited cortical response related to RAT in patients with moderate dysfunction may indicate that the training intensity needs to be adjusted in time according to the brain functional state. fNIRS-based assessment of brain functional response assumes great importance for the customization of an appropriate protocol training in the clinical practice.