bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning for screening and predicting the risk of anti-MDA5 antibody in juvenile dermatomyositis children
Authors: Xue Yuan , Zhang Junmei , Li Chao , Liu Xuanyi , Kuang Weiying , Deng Jianghong , Wang Jiang , Tan Xiaohua , Li Shipeng , Li Caifeng 
Published: January 2023

ObjectiveThe anti-MDA5 (anti-melanoma differentiation associated gene 5) antibody is often associated with a poor prognosis in juvenile dermatomyositis (JDM) patients. In many developing countries, there is limited ability to access myositis- specific antibodies due to financial and technological issues, especially in remote regions. This study was performed to develop a prediction model for screening anti-MDA5 antibodies in JDM patients with commonly available clinical findings.MethodsA cross-sectional study was undertaken with 152 patients enrolled from the inpatient wards of Beijing Children’s Hospital between June 2018 and September 2021. Stepwise logistic regression, least absolute shrinkage and selection operator (LASSO) regression, and the random forest (RF) method were used to fit the model. Model discrimination, calibration, and decision curve analysis were performed for validation.ResultsThe final prediction model included eight clinical variables (gender, fever, alopecia, periungual telangiectasia, digital ulcer, interstitial lung disease, arthritis/arthralgia, and Gottron sign) and four auxiliary results (WBC, CK, CKMB, and ALB). An anti-MDA5 antibody risk probability–predictive nomogram was established with an AUC of 0.975 predicted by the random forest algorithm. The model was internally validated by Harrell’s concordance index (0.904), the Brier score (0.052), and a 500 bootstrapped satisfactory calibration curve. According to the net benefit and predicted probability thresholds of decision curve analysis, the established model showed a significantly higher net benefit than the traditional logistic regression model.ConclusionWe developed a prediction model using routine clinical assessments to screen for JDM patients likely to be anti-MDA5 positive. This new tool may effectively predict the detection of anti-MDA5 in these patients using a non-invasive and efficient way.
Aerobic respiration, biochemical composition, and glycolytic responses to ultraviolet radiation in jellyfish Cassiopea sp
Authors: Aljbour Samir M. , Alves Ricardo N. , Agustí Susana 
Published: January 2023

The light-dependent zooxanthellate jellyfish Cassiopea sp. (the upside-down jellyfish) is invasive/exotic in many shallow and clear marine habitats, where the jellyfish might be exposed to high levels of ultraviolet radiation (UVR). Compared to other reef organisms, the sensitivity/resilience of the semi-transparent jellyfish to UVR exposure is overlooked. Therefore, we experimentally investigated the metabolic and physiological responses of Cassiopea sp. from the Red Sea to natural levels of underwater UVR following 16 days of exposure to three light treatments: 1) control group with only photosynthetically active radiation (PAR), 2) PAR+UV-B, and 3) PAR+UV-B+UV-A. While jellyfish body mass increased (by 40%) significantly in the control group, it did not increase in either of the UV treatments. However, both UV-exposed jellyfish had higher (98% to 120%) mitochondrial electron transport system (ETS) activity than the control group. Therefore, the results indicate elevated aerobic respiration rates in UV-exposed jellyfish (i.e., reflecting a higher energy cost of UVR exposure). Neither the lactate dehydrogenase (LDH) activity nor the available energy (Ea) exhibited different levels among UVR treatments compared to the control group. In contrast, pyruvate kinase activity was significantly lower (by 46%) in all UV-exposed jellyfish compared to the control group. Unchanged Ea and LDH activity combined with higher ETS activity indicates a high aerobic capacity of jellyfish, which might explain their ability to cope with UVR exposure-induced higher energy demands without inducing the onset of anaerobiosis. The results indicated that UV-A does not amplify or modulate jellyfish physiology and growth under UV-B exposure. In conclusion, the findings suggest that the jellyfish is more resilient (i.e., in terms of survival) to UVR than other cnidarians. This study on Cassiopea is the first to address its metabolic and physiological responses to UVR. Therefore, it could be used as a framework for further studies aiming to better understand jellyfish physiology.
Factors associated with worsened clinical symptoms of psoriasis and disease-related quality of life during the COVID-19 lockdown: A cross-sectional study
Authors: Burkauskas Julius , Slabadiene Margarita , Podlipskyte Aurelija , Steibliene Vesta 
Published: January 2023

ObjectiveIn this cross-sectional study, we aimed to evaluate the factors associated with psoriasis symptom worsening and impaired quality of life (QoL) in individuals with psoriasis during the COVID-19 pandemic lockdown.MethodsDuring the second COVID-19 national lockdown (January–April 2021) in Lithuania, individuals diagnosed with psoriasis were invited to fill in an anonymous online survey including sociodemographic and life-style factors, psoriasis-related clinical symptoms, the Dermatology Life Quality Index (DLQI) and the Patients' Health Questionnaire (PHQ).ResultsA total of 297 respondents completed the survey. The majority of them (52.5%) reported worsened clinical symptoms of psoriasis during the COVID-19 lockdown period. In total, 43.1% of responders reported significant depressive symptoms (PHQ-9 ≥ 10) and 23.6% reported impaired disease-related QoL (DLQI &gt; 10). The strongest predictor of psoriasis symptoms worsening was the need for changes in psoriasis treatment, with an odds ratio (OR) of 2.73 (95% CI 1.37–5.44, p = 0.004) and decreased income (OR = 2.33, 95% CI 1.30–4.17, p = 0.004). The strongest predictor of impaired QoL was male sex (OR = 3.35, 95% CI 1.70–6.59, p &lt; 0.001). Contribution of specific depressive symptoms was evident for both models.ConclusionWorsening of psoriasis symptoms during the COVID-19 lockdown was associated with decreased income, psoriasis treatment changes and depression symptoms. Impaired QoL was associated with male sex, symptom worsening and depression. Specific depression symptoms may have contributed to more symptom worsening and impaired QoL than the depressive symptomatology as a whole.
Ultrasonographic findings in long COVID: A cross-sectional study of 312 patients
Authors: Imamura Marta , Uchyiama Sabrina Saemy Tome , Naves Gabriella Souza , Abicalaf Cláudia Andréia Rabay Pimentel , Mirisola Aline Rossetti , Santos Artur César Aquino dos , Battistella Linamara Rizzo ,   HCFMUSP COVID-19 Study Group
Published: January 2023

BackgroundFatigue and muscle weakness are common complaints in COVID-19 survivors. However, little is still known about the skeletal muscle qualitative and quantitative characteristics after hospitalization due to moderate and severe COVID-19.ObjectivesTo assess rectus femoris and vastus intermedius muscle thickness (MT) and rectus femoris echo intensity (EI) and to establish its association with demographic, clinical, functional, and inflammatory parameters in long COVID patients after hospital discharge.MethodsCross-sectional study with 312 COVID-19 patients (53.53% male; age: 54.59 ± 13.50 years), with a laboratory-confirmed diagnosis of COVID-19. Patients were assessed 3–11 months after hospital discharge. We evaluated MT of the right rectus femoris and vastus intermedius and EI of the right rectus femoris using a portable ultrasound system, 6–13 MHz, broadband linear transducer. We corrected EI using the subcutaneous fat thickness. Ultrasonographic parameters were tested in association with demographic (sex and age); functional (Handgrip strength measurement, Timed Up and Go, 1 min Sit-to-Stand test, EuroQoL-5 Dimensions-5 Levels, World Health Organization Disability Assessment Schedule (WHODAS 2.0), Post-COVID-19 Functional Status, Functional Assessment of Chronic Illness Therapy—Fatigue (FACIT), Medical Research Council (MRC) sum score, Borg Dyspnea Scale, MRC Dyspnea score, Visual Analogue Scale (VAS), Epworth Sleepiness Scale, Insomnia Severity Index, Functional Independence Measurement (FIM), and Functional Oral Intake Scale); clinical (length of hospital stay, intubation, and presence of comorbidities such as systemic hypertension, diabetes, obesity, chronic obstructive pulmonary disease, asthma), and inflammatory data assessed by the C-reactive protein and D-dimer serum concentrations.ResultsRectus femoris MT was associated with age, handgrip strength, Epworth Sleepiness Scale, and subcutaneous fat thickness (r2 = 27.51%; p &lt; 0.0001). Vastus intermedius MT was associated with age, pain intensity, handgrip strength, Epworth Sleepiness scale, FIM, and time since hospital discharge (r2 = 21.12%; p &lt; 0.0001). Rectus femoris EI was significantly associated with the male sex, TUG, Epworth Sleepiness Scale, and C-Reactive Protein levels (r2 = 44.39%; p &lt; 0.0001). Mean MT of rectus femoris and vastus intermedius are significantly different (p &lt; 0.001).ConclusionAfter hospital discharge, long COVID patients present qualitative and quantitative skeletal muscle characteristics associated with a combination of demographic, clinical, and functional parameters.
Moderate level platelet count might be a good prognostic indicator for intra-abdominal infection in acute pancreatitis: A retrospective cohort study of 1,363 patients
Authors: Sun Wenwu , Huang Jun , Ni Tongtian , Wen Yi , Menglu Gui , Yongguo Wang , Yanbin Zhao , Sheng Huiqiu , Chen Ying , Ma Li , Zhao Bing , Mao Enqiang 
Published: January 2023

BackgroundEarly recognition of the risk factors is important for acute pancreatitis management. The aim of this study is to investigate the relationship between platelet count and clinical outcomes in patients with acute pancreatitis.MethodsThe data are collected from a university-affiliated hospital between January 2013 and December 2020. A generalized additive model and a two-piecewise linear regression model are used to estimate the association between platelet count and the risks of intra-abdominal infection, surgical intervention, in-hospital mortality, and length of hospital stay.ResultsAmong the 1,363 patients, 99 (7.3%) patients suffered intra-abdominal infection, 190 (13.9%) patients underwent surgical intervention, and 38 (2.8%) patients died in the hospital. The median length of hospital stay is 21 days. Generalized additive model and two-piecewise linear regression analysis show that the risk of intra-abdominal infection decreases as the platelet count increases to 160 × 109/L (OR: 0.991, 95% CI: 0.984–0.998, p = 0.015) and then increases as the platelet count levels up (OR: 1.007, 95% CI: 1.004–1.010, p &lt; 0.001). The trend is similar to the risk of surgical intervention and length of hospital stay. Even though there seems a declining trend in mortality, no significant association is found after adjustment for potential confounders. Further analysis shows that changes in platelet count within the first 3 days after admission have no obvious association with clinical outcomes.ConclusionA platelet count of approximately 160 × 109/L on admission is associated with the lowest risk of intra-abdominal infection, surgical intervention, and shortest hospital stay in patients with acute pancreatitis.
Peripapillary and macular microvasculature in neovascular age-related macular degeneration in long-term and recently started anti-VEGF therapy versus healthy controls
Authors: Türksever Cengiz , Hoffmann Laura , Hatz Katja 
Published: January 2023

AimTo investigate the peripapillary and macular microvasculature in neovascular age-related macular degeneration (nAMD) in recently started versus long-term anti-vascular endothelial growth factor (VEGF) therapy and healthy controls.MethodsEyes with nAMD treated in a treat-and-extend regimen were assigned to group 1 (&lt;5 injections) or 2 (≥20 injections) whereas group 3 constituted the healthy age-matched controls. Blood flow signals were acquired using PLEX® Elite 9000 swept-source optical coherence tomography angiography (OCTA) of the macular and peripapillary regions. Mean ganglion cell complex (GCC) thickness values were quantified using spectral-domain optical coherence tomography (SD-OCT).ResultsIncluding 80 eyes whereof 40 controls, macular superficial perfusion density was significantly reduced in group 1 and 2 compared to controls (p &lt; 0.001; p = 0.010) without a difference between groups 1 and 2. Peripapillary perfusion parameters did not correlate with post-operative intraocular pressure (IOP) or number of anti-VEGF injections. Mean peripapillary flux index was significantly lower in group 2 than in controls (p = 0.023) and significantly decreased in the nasal quadrants for both AMD groups compared to group 3 (p = 0.013; p &lt; 0.001). Mean peripapillary perfusion density was significantly reduced in both AMD groups compared to controls (0.515 ± 0.02 versus 0.556 ± 0.03, p &lt; 0.0001).ConclusionFrequency of anti-VEGF treatment in nAMD and post-operative IOP showed no correlation with peripapillary perfusion parameters, but anti-VEGF treated nAMD patients exhibited partly altered peripapillary perfusion compared to healthy controls. Reduced macular perfusion density of the inner retina in anti-VEGF treated nAMD compared to healthy controls might be discussed as an anti-VEGF treatment effect or a characteristic of nAMD.
Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas
Authors: Pu Junyu , Li Zhongyi , Tang Hongqin , Zhou Guopeng , Wei Caihui , Dong Wenbin , Jin Zhenjiang , He Tieguang 
Published: January 2023

Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN60: green manure couple with 60% nitrogen fertilizer, MN80: green manure couple with 80% nitrogen fertilizer; and MN100: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN100treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20–40% for rice production.Graphical Abstract
Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing
Authors: Jiang Fan , Li Qiang , Wang Sen , Shen Ting , Wang Hengchao , Wang Anqi , Xu Dong , Yuan Lihua , Lei Lihong , Chen Rong , Yang Boyuan , Deng Yu , Fan Wei 
Published: January 2023

BackgroundAnaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced.ResultsIn this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes.ConclusionHigh-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.
Effects of non-invasive brain stimulation on walking and balance ability in Parkinson’s patients: A systematic review and meta-analysis
Authors: Zhang Xinxin , Jing Feiyue , Liu Yu’ang , Tang Jinyong , Hua Xianfeng , Zhu Jialin , Tuo Haowen , Lin Qihan , Gao Pincao , Liu Weiguo 
Published: January 2023

ObjectiveTo investigate and contrast the effects of non-invasive brain stimulation (NIBS), including repeated transcranial magnetic stimulation (rTMS) and transcranial direct current stimulation (tDCS), on walking and balance ability in patients with Parkinson’s disease (PD).MethodsThe PubMed, Embase, Medline, Cochrane, CNKI, and Chinese WanFang databases were searched up to June 2022. Quality assessment was performed using the Cochrane Collaboration’s risk-of-bias guidelines, and the standardized mean differences (SMD) or mean differences (MD) for each outcome were calculated.ResultsAmong 32 eligible studies, including 1,586 participants were analyzed in this meta-analysis. The results of the meta-analysis showed that NIBS was effective in improving UPDRS-III scores (MD = −2.07; 95% CI, −2.62 to −1.53; P &lt; 0.00001; I2 = 6%) and variables associated with the ability of walk such as step width (SMD = 0.35; 95% CI, 0.16–0.55; P = 0.0005; I2 = 38%), cadence (SMD = 0.3; 95% CI, 0.05 to 0.55; P = 0.02; I2 = 25%), and 6MWT (MD = 62.86; 95% CI, 39.43–86.29; P &lt; 0.00001; I2 = 0%). In subgroup analyses across intervention types, UPDRS-III scores (rTMS: MD = −2.54; 95% CI, −3.16 to −1.92; P &lt; 0.00001; I2 = 0%; tDCS: MD = −1.20; 95% CI, −1.99 to −0.40; P = 0.003; I2 = 0%) and TUGT time (rTMS: MD = −4.11; 95% CI, −4.74 to −3.47; P &lt; 0.00001; I2 = 0%; tDCS: MD = −0.84; 95% CI, −1.48 to −0.21; P = 0.009; I2 = 0%) significantly improved. Moreover, our results also showed that compared to tDCS, rTMS was more significant in improving UPDRS-III scores and TUGT time (p &lt; 0.05).ConclusionNIBS benefits some walking ability variables but not balance ability in 36 patients with PD. The rTMS significantly improved UPDRS-III scores and TUGT time compared to tDCS. Further studies are needed to determine the optimal protocol and to illuminate effects based on the ideal target brain regions, stimulation intensity, timing, and type of intervention.Systematic review registrationhttp://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022350782.
Effect of exercise on cognitive function and synaptic plasticity in Alzheimer's disease models: A systematic review and meta-analysis
Authors: Guo Linlin , Yang Xinxin , Zhang Yuanyuan , Xu Xinyi , Li Yan 
Published: January 2023

IntroductionCognitive decline is a central manifestation of Alzheimer's disease (AD), and its process is inseparable from changes in synaptic plasticity. The aim of this review was to summarize and evaluate the effectiveness of exercise on cognitive function and synaptic plasticity in AD animal models.Materials and methodsEligible studies were searched from PubMed, MEDLINE, EMBASE, Web of Science, and Cochrane Library from April to May 2022. The risk of bias was evaluated by Systematic Review Centre for Laboratory Animal Experimentation (SYRCLE). The Morris water maze (MWM) test and synaptic plasticity were considered outcome measures. Data were analyzed using random-effects meta-analyses using the software Stata. Heterogeneity was examined by using I2 test. Sensitivity analysis and publication bias were also assessed.ResultsA total of 20 randomized controlled studies were eligible for study inclusion. Compared with controls, exercise decreased escape latency (SMD = −0.86, 95% CI: −1.21 to −0.50, P &lt; 0.001), increased platform crossover numbers (SMD = 1.34, 95% CI: 0.57–2.11, P = 0.001) and time in the target quadrant (SMD = 1.65, 95% CI: 0.95–2.36, P &lt; 0.001) and the expression of PSD95 (SMD = 0.73, 95% CI: 0.25–1.21, P = 0.003) in AD animals. The results of the subgroup analysis showed that exercise before AD had a greater effect on escape latency (SMD = −0.88, 95% CI: −1.25 to −0.52, P &lt; 0.001), platform crossover numbers (SMD = 1.71, 95% CI: 1.23–2.18, P &lt; 0.001), time in the target quadrant (SMD = 2.03, 95% CI: 1.19–2.87, P &lt; 0.001) and the expression of PSD95 (SMD = 0.94, 95% CI: 0.19–1.69, P = 0.014) than exercise after AD. The results of the subgroup analysis also showed that treadmill running might be an appropriate exercise type.ConclusionOur findings suggested that exercise had a potential effect on improving cognitive function and synaptic plasticity. It can play a better neuroprotective role before AD.Systematic review registrationPROSPERO, identifier: CRD42022328438.