bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of immune checkpoint gene CD155 Ala67Thr and CD226 Gly307Ser polymorphisms on small cell lung cancer clinical outcome
Authors: Lee Jang Hyuck , Yoo Seung Soo , Hong Mi Jeong , Choi Jin Eun , Kim Soyoun , Kang Hyo-Gyoung , Do Sook Kyung , Kim Ji Hyun , Baek Sun Ah , Lee Won Kee , Do Yoo Jae , Choi Sun Ha , Lee Yong Hoon , Seo Hyewon , Lee Jaehee , Lee Shin Yup , Cha Seung Ick , Kim Chang Ho , Park Jae Yong 
Published: January 2021

AbstractThis study was conducted to investigate the impact of genetic variants of immune checkpoint genes on the treatment outcome in small cell lung cancer (SCLC). In the present study, 261 platinum doublet-treated SCLC patients were enrolled. A total of 96 polymorphisms in 33 immune checkpoint-related genes were selected, and their association with chemotherapy response and survival outcomes were analyzed. Among the polymorphisms studied, CD155 rs1058402G > A (Ala67Thr, A67T) and CD226 rs763361C > T (Gly307Ser, G307S) were significantly associated with SCLC treatment outcome. The rs1058402G > A had a worse chemotherapy response and overall survival (under a dominant model, adjusted odds ratio [aOR] = 0.52, 95% confidence interval [CI] = 0.27–0.99, P = 0.05; adjusted hazard ratio [aHR] = 1.55, 95% CI = 1.12–2.14, P = 0.01, respectively). The rs763361C > T had better chemotherapy response and overall survival (under a dominant model, aOR = 2.03, 95% CI = 1.10–3.75, P = 0.02; aHR = 0.69, 95% CI = 0.51–0.94, P = 0.02, respectively). When the rs1058402GA/AA and rs763361CC genotypes were combined, the chemotherapy response and overall survival were significantly decreased as the number of bad genotypes increased (aOR = 0.52, 95% CI = 0.33–0.81, Ptrend = 0.004; aHR = 1.48, 95% CI = 1.19–1.84, Ptrend = 4 × 10−4, respectively). The 3-D structural model showed that CD155 A67T created a new hydrogen bond and structural change on CD155. These changes resulted in extending the distance and losing the hydrogen bonds between CD155 and CD226, thus weakening CD155/CD226 binding activity. In conclusion, CD155 rs1058402G > A and CD226 rs763361C > T may be useful for predicting the clinical outcomes of SCLC patients after chemotherapy.
A comparative study of evaluating missing value imputation methods in label-free proteomics
Authors: Jin Liang , Bi Yingtao , Hu Chenqi , Qu Jun , Shen Shichen , Wang Xue , Tian Yu 
Published: January 2021

AbstractThe presence of missing values (MVs) in label-free quantitative proteomics greatly reduces the completeness of data. Imputation has been widely utilized to handle MVs, and selection of the proper method is critical for the accuracy and reliability of imputation. Here we present a comparative study that evaluates the performance of seven popular imputation methods with a large-scale benchmark dataset and an immune cell dataset. Simulated MVs were incorporated into the complete part of each dataset with different combinations of MV rates and missing not at random (MNAR) rates. Normalized root mean square error (NRMSE) was applied to evaluate the accuracy of protein abundances and intergroup protein ratios after imputation. Detection of true positives (TPs) and false altered-protein discovery rate (FADR) between groups were also compared using the benchmark dataset. Furthermore, the accuracy of handling real MVs was assessed by comparing enriched pathways and signature genes of cell activation after imputing the immune cell dataset. We observed that the accuracy of imputation is primarily affected by the MNAR rate rather than the MV rate, and downstream analysis can be largely impacted by the selection of imputation methods. A random forest-based imputation method consistently outperformed other popular methods by achieving the lowest NRMSE, high amount of TPs with the average FADR < 5%, and the best detection of relevant pathways and signature genes, highlighting it as the most suitable method for label-free proteomics.
Field performance on grain yield and quality and genetic diversity of overwintering cultivated rice (Oryza sativa L.) in southwest China
Authors: Liang Yongshu , Nan Wenbin , Qin Xiaojian , Zhang Hanma 
Published: January 2021

AbstractUnderstanding the field performance on grain yield and quality and the genetic diversity of overwintering (OW) cultivated rice (Oryza sativa L.) across main crop (MC) and ratooning crop (RC) is the premise to make strategies for the future OW rice variety improvement in rice production. The present field experiments were conducted in RC of 2016, in MC of both 2017 and 2018, and RC in 2019 to identify genotypes OW rice that perform stable in terms of grain yield and quality across different climate conditions. The grain yield plant-1 (GYP) and its components in six genotypes of OW rice exhibited significant difference across the 4 years (P ≤ 0.05), the maximum GYP in OW6 rice was harvested (60.28 g) in MC of 2017, but the minimum GYP in OW1 rice was harvested (33.01 g) in MC of 2018. Within six genotypes of OW rice, four grain shape traits displayed a relative small significant difference, four grain quality traits exhibited a relative small significant difference except for chalkiness rate (CR), there 226 pairs of significant PCC values between GYP and its components were calculated in all tested rice and varied from six in OW6 to eleven in OW1, there 130 pairs of significant PCC values among the four grain shape traits were calculated and ranged from twenty-one in OW1, 3, 5 to twenty-three in OW2, there 118 pairs of significant PCC values among the four grain quality traits were calculated and ranged from seventeen in OW2 to twenty-three in OW1. The numbers, directions, and size of PCC values for the grain yield and quality characters in all tested rice displayed a series of irregular variations. Six genotypes of OW rice were apparently distinguished by employing 196 pairs of simple-sequence repeats (SSRs) markers and exhibited abundant genetic diversity at the DNA level. Data from this study provide an extensive archive for the future exploration and innovation of overwintering cultivated rice variety.
The poor prognosis and influencing factors of high D-dimer levels for COVID-19 patients
Authors: He Xiaokang , Yao Fei , Chen Jie , Wang Yan , Fang Xiangming , Lin Xuan , Long Hui , Wang Qiang , Wu Qingming 
Published: January 2021

AbstractTo explore the value, and influencing factors, of D-dimer on the prognosis of patients with COVID-19. A total of 1,114 patients with confirmed COVID-19 who were admitted to three designated COVID-19 hospitals in Wuhan, China from January 18, 2020, to March 24, 2020, were included in this study. We examined the relationship between peripheral blood levels of D-dimer, and clinical classification and prognosis, as well as its related influencing factors. D-dimer levels were found to be related to the clinical classification and the prognosis of clinical outcome. D-dimer levels were more likely to be abnormal in severely and critically ill patients compared with mild and ordinary cases, while D-dimer levels of patients who had died were significantly higher than those of surviving patients according to the results of the first and last lab tests. The results from ROC analyses for mortality risk showed that the AUCs of D-dimer were 0.909, YI was 0.765 at the last lab test, and a D-dimer value of 2.025 mg/L was regarded to be the optimal probability cutoff for a prognosis of death. In addition, we found that patients with advanced age, male gender, dyspnea symptoms, and some underlying diseases have a higher D-dimer value (p < 0.05). In short, D-dimer is related to the clinical classification and can be used to evaluate the prognosis of COVID-19 patients. The D-dimer value of 2.025 mg/L was the optimal probability cutoff for judging an outcome of death. Advanced age, male gender, dyspnea symptoms, and some underlying diseases are influencing factors for D-dimer levels, which impacts the prognosis of patients.
Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies
Authors: Bordini Martina , Zappaterra Martina , Soglia Francesca , Petracci Massimiliano , Davoli Roberta 
Published: January 2021

AbstractIn recent years, the poultry industry has experienced an increased incidence of myopathies affecting breasts of fast-growing broilers, such as White Striping (WS) and Wooden Breast (WB) defects. To explore the molecular mechanisms and genes involved in WS and WB onset, we decided to perform a Weighted Gene Co-expression Network Analysis (WGCNA) using the gene expression profile and meat quality parameters of Pectoralis major muscles analysed in our previous study. Among the 212 modules identified by WGCNA, the red, darkred, midnightblue and paleturquoise4 modules were chosen for subsequent analysis. Functional analysis evidenced pathways involved in extracellular matrix (ECM) organization, collagen metabolism, cellular signaling and unfolded protein response. The hub gene analysis showed several genes coding for ECM components as the most interconnected nodes in the gene network (e.g. COL4A1, COL4A2, LAMA2, LAMA4, FBLN5 and FBN1). In this regard, this study suggests that alterations in ECM composition could somehow activate the cascade of biological reactions that result in the growth-related myopathies onset, and the involvement of Collagen IV alterations in activating the endoplasmic reticulum (ER) stress response may be hypothesized. Therefore, our findings provide further and innovative knowledge concerning the molecular mechanisms related to the breast abnormalities occurrence in modern broilers.
Serum immunoglobulin free light chains and their association with clinical phenotypes, serology and activity in patients with IgG4-related disease
Authors: Martín-Nares Eduardo , Saavedra-González Vanessa , Fagundo-Sierra Reynerio , Santinelli-Núñez Blanca Estela , Romero-Maceda Teresa , Calderón-Vasquez Karla , Hernandez-Molina Gabriela 
Published: January 2021

AbstractThe clinical utility of serum immunoglobulin free light chains (sFLC) in IgG4-related disease (IgG4-RD) is unknown. Herein we evaluated their association with clinical phenotypes, serology and activity in patients with IgG4-RD. Cross-sectional study that included 45 patients with IgG4-RD, and as controls 25 with Sjögren’s syndrome (SS) and 15 with sarcoidosis. IgG4-RD patients were classified in clinical phenotypes: pancreato-hepato-biliary, retroperitoneum/aorta, head/neck-limited and Mikulicz/systemic; as well as proliferative vs. fibrotic phenotypes. We assessed the IgG4-RD Responder Index (IgG4-RD RI) at recruitment and measured IgG1, IgG4, κ and λ sFLC serum levels by turbidometry. sFLC levels were similar among IgG4-RD, SS and sarcoidosis groups. Regarding the IgG4-RD patients, the mean age was 49 years, 24 (53.3%) were men and 55.5% had activity. Eight (17.7%) belonged to pancreato-hepato-biliary, 6 (13.3%) to retroperitoneum/aorta, 14 (31.1%) to head/neck-limited, 16 (35.5%) to Mikulicz/systemic phenotypes, whereas 36 (80%) to proliferative and 9 (20%) to fibrotic phenotypes. High κ sFLC, λ sFLC and κ/λ ratio were present in 29 (64.4%), 13 (28.9%) and 13 (28.9%) of IgG4-RD patients, respectively. There were no differences in sFLC among IgG4-RD phenotypes. κ sFLC and κ/λ ratio correlated positively with the number of involved organs and IgG4-RD RI. Patients with renal involvement had higher κ sFLC and λ sFLC. The AUC for κ sFLC and λ sFLC, for renal involvement was 0.78 and 0.72, respectively. Active IgG4-RD had higher levels of κ sFLC and more frequently a high κ/λ ratio. The AUC for κ sFLC and κ/λ ratio for predicting active IgG4-RD was 0.67 and 0.70, respectively. sFLC correlated positively with IgG1 and IgG4 levels. sFLC may be useful as a biomarker of disease activity as well as multiorgan and renal involvement. In particular, a high κ/λ ratio may identify patients with active disease.
Preoperative CT-based detection of extrapancreatic perineural invasion in pancreatic cancer
Authors: Khristenko Ekaterina , Shrainer Igor , Setdikova Galia , Palkina Oxana , Sinitsyn Valentin , Lyadov Vladimir 
Published: January 2021

AbstractAccuracy for computed tomography (CT) diagnosis of extrapancreatic perineural invasion (EPNI) in pancreatic ductal adenocarcinoma (PDAC), which is a significant cause of recurrence, has not been established. The aim of the study was to evaluate the diagnostic accuracy of CT in detecting EPNI preoperatively in resectable PDAC of the pancreatic head. Retrospective study design was approved by institutional review board. Preoperative CT-series of 46 patients with resectable PDAC were evaluated by two independent observers. Plexus Pancreaticus Capitalis-II (PPC-II) was assessed as this area is more susceptible for EPNI. All patients underwent surgery with dedicated histopathology, which served as the reference standard. Histologically EPNI was confirmed in 63.1%. Sensitivity of MDCT was 93.1% (95% confidence interval (CI) 77.23% to 99.15%), specificity 64.7% (95% CI 38.33% to 85.79%) with area under the curve (AUC) 0.789 for the first observer. Positive predictive value (PPV) was 81.82% (95% CI 70.12% to 89.62%), negative predictive value (NPV—84.62% (95% CI 57.98% to 95.64%) with diagnostic accuracy of 82.61% (95% CI 68.58% to 92.18%). Interobserver agreement showed k-value of 0.893 ($${p} < 0.001$$

p
<
0.001

), which represents very good agreement between observers. Median actual survival in patients without EPNI was 30 months (95% CI 18.284–41.716), in patients with EPNI—13 months (95% CI 12.115–13.885). CT provides sufficient diagnostic information to detect PPC-II invasion in patients with resectable PDAC of the pancreatic head. Preoperative detection of EPNI might be an additional argument to perform neoadjuvant chemotherapy in patients with resectable PDAC. It should be included in preoperative evaluation form of CT-findings.
Identifying threshold sizes for enlarged abdominal lymph nodes in different age ranges from about 200,000 individual’s data
Authors: He Lili , Sun Yinghua , Huang Guoying 
Published: January 2021

AbstractThe threshold size for enlarged abdominal lymph nodes (E-ALNs), a common pediatric disorder, has yet to be standardized. According to the maximum short-axis diameter, this study divided ALNs into Grade A (≥ 10 mm), Grade B (8–10 mm), Grade C (5–8 mm), and Grade D (< 5 mm, normal). To identify the threshold size for E-ALNs, the prevalence of each grade was compared between asymptomatic individuals and symptomatic (e.g., abdominal pain) individuals without other diseases (e.g., appendicitis) that could explain the symptoms for different ages using data from > 200,000 individuals. The results showed the following: (1) For ages 1–3 years, the recommended threshold size is 8 mm, as the differences in the prevalence between the two groups were nonsignificant for Grade C but significant (p < 0.05) for both Grades A and B. (2) For ages 3–14 years, the recommended threshold size is 5 mm, as the differences between the two groups were significant (p < 0.05) for Grades A, B, and C. (3) The prevalence of Grades A, B, and C was very low for ages 0–1 years and high for ages 1–6 years. (4) The prevalence for males was generally higher than that for females for Grades A and B.
White matter integrity in young medication-naïve bipolar II depressed adults
Authors: Mak Arthur Dun Ping , Leung Owen Ngo Wang , Chou Idy Wing Yi , Wong Sheila Lok Yiu , Chu Winnie Chiu-wing , Yeung David , So Suzanne Ho-wai , Ma Suk Ling , Lam Linda Chiu Wah , Leung Chi Ming , Lee Sing 
Published: January 2021

AbstractIt is unknown if young medication-naïve bipolar II (BPII) depressed patients have increased white matter (WM) disruptions. 27 each of young (average 23 years) and treatment-naïve BPII depressed, unipolar depressed (UD) patients and age–sex–education matched healthy controls (HC) underwent 3 T MRIs with diffusion tensor imaging. Diagnostic ratings included Structured Clinical Interview for DSM Disorders (SCID), Montgomery-Åsberg Depression Rating Scale (MADRS), Young Mania Rating Scale (YMRS) and Hamilton Anxiety Rating Scale (HAM-A). Patients were clinically depressed (MADRS-BPII: 26.15 [SD9.25], UD: 25.56 [5.24], p = 0.86). Compared to UD, BPII had increased family bipolarity (BPII 13.6% vs UD 2.5%, p = 0.01, φc = 0.28), hypomanic symptoms (YMRS-BPII: 4.22 [4.24], UD: 1.33 [2], p = 0.02, d = 0.87), lifetime number of depressive episodes (BPII: 2.37 [1.23], UD: 1.44 [0.75], p = 0.02, d = 0.91), lifetime and current-year number of episodes (lifetime BPII: 50.85 [95.47], UD: 1.7 [1.03]; current-year BPII: 9.93 [16.29], UD: 1.11 [0.32], ps = 0.04, ds = 0.73–0.77) and longer illness duration (BPII: 4.96 years [3.96], UD: 2.99 [3.33], p = 0.15, d = 0.54). BPII showed no increased WM disruptions vs UD or HC in any of the 15 a priori WM tracts. UD had lower right superior longitudinal fasciculus (SLF) (temporal) axial diffusivity (AD) (1.14 vs 1.17 (BPII), 1.16 (HC); F = 6.93, 95% CI of$${F}_{B}$$

F
B

: 0.00073, 5.22, ηp2 = 0.15). Principal component analysis followed by exploratory linear discriminant analysis showed that increased R-SLF (temporal) AD, YMRS and family bipolarity distinguished BPII from UD (81.5% sensitivity, 85.2% specificity) independent of episode number and frequency. Young, medication-naïve adults with BPII depression did not show the WM disruptions distinguishing more chronically ill BP patients from UD. These WM disruptions may therefore be partly attributable to illness chronicity. Longitudinal studies should examine the trajectory of WM changes in BPII and UD and predictive validity of these baseline clinical and imaging parameters.
A novel and sensitive real-time PCR system for universal detection of poxviruses
Authors: Luciani Léa , Inchauste Lucia , Ferraris Olivier , Charrel Rémi , Nougairède Antoine , Piorkowski Géraldine , Peyrefitte Christophe , Bertagnoli Stéphane , de Lamballerie Xavier , Priet Stéphane 
Published: January 2021

AbstractSuccess in smallpox eradication was enabled by the absence of non-human reservoir for smallpox virus. However, other poxviruses with a wider host spectrum can infect humans and represent a potential health threat to humans, highlighted by a progressively increasing number of infections by (re)emerging poxviruses, requiring new improved diagnostic and epidemiological tools. We describe here a real-time PCR assay targeting a highly conserved region of the poxvirus genome, thus allowing a pan-Poxvirus detection (Chordopoxvirinae and Entomopoxvirinae). This system is specific (99.8% for vertebrate samples and 99.7% for arthropods samples), sensitive (100% for vertebrate samples and 86.3% for arthropods samples) and presents low limit of detection (< 1000 DNA copies/reaction). In addition, this system could be also valuable for virus discovery and epidemiological projects.
Integrin α2β1 plays an important role in the interaction between human articular cartilage-derived chondrocytes and atelocollagen gel
Authors: Kanamoto Takashi , Hikida Minami , Sato Seira , Oyama Shohei , Tachi Yoshihito , Kuroda Sanae , Mazuka Takeo , Ebina Kosuke , Nakai Tsuyoshi , Nakata Ken 
Published: January 2021

AbstractAlthough atelocollagen gel is used as a scaffold for culturing human articular cartilage-derived chondrocytes, little is known about cell–gel interactions. In this study, we investigated the mechanism via which atelocollagen gel affects human articular cartilage-derived chondrocytes. Two types of three-dimensional cultures of human articular cartilage-derived chondrocytes (i.e., with and without atelocollagen gel) were compared. While the amount of atelocollagen gel in culture gradually decreased with time, it promoted the expression of matrix metalloproteinases (MMPs) during the early stages of culture. Genome-wide differential gene expression analysis revealed that cell membrane- and extracellular matrix-related genes were highly ranked among up- and down-regulated groups in cells cultured in the presence of atelocollagen gel. Among the integrin family of genes, the expression of integrin subunit alpha 2 and integrin subunit alpha 10 was significantly increased in the presence of atelocollagen gel. Blocking α2β1 integrin with the specific inhibitor BTT 3033 had a significant effect on cell proliferation, MMP expression, and cell shape, as well as on the response to mechanical stimulation. Taken together, our findings indicate that the α2β1 integrin pathway plays an important role in the interaction of atelocollagen gel with human articular cartilage-derived chondrocytes and may be a potential therapeutic target for articular cartilage disorders.
Decreased serum betatrophin may correlate with the improvement of obstructive sleep apnea after Roux-en-Y Gastric Bypass surgery
Authors: Song Zhiyuan , Guo Kaifeng , Huang Weijun , Xu Huajun , Liu Yupu , Guan Jian , Yin Shankai , Yu Haoyong , Yi Hongliang , Zou Jianyin 
Published: January 2021

AbstractObesity is strongly correlated with obstructive sleep apnea (OSA), and bariatric surgery can effectively treat obesity and alleviate OSA. However, the contributing factors are still unclear. We aimed to explore the relationship between betatrophin and OSA in patients undergoing Roux-en-Y gastric bypass (RYGB) surgery. Our study consisted of thirty-seven individuals with OSA and type 2 diabetes (16 males, 21 females) undergoing RYGB surgery. The polysomnography test, anthropometric results, serum betatrophin, and abdominal magnetic resonance images were evaluated both before and 1 year after RYGB surgery. Factors that may correlate with the alleviation of OSA were investigated. In our study, RYGB surgery significantly decreased apnea hypopnea index (AHI) and serum betatrophin concentration (p < 0.001). The abdominal visceral fat area, subcutaneous fat area and HOMA-IR were also significantly decreased (p < 0.001). The preoperative AHI, postoperative AHI and the change in AHI were significantly correlated with the preoperative betatrophin, postoperative betatrophin and the change in betatrophin, respectively (p < 0.05). These correlations were still significant after adjustment for other risk factors. The change in betatrophin was also independently associated with the change in minimum oxygen saturation (p < 0.001). Our data might indicate that serum betatrophin was significantly independently correlated with the improvement of OSA after bariatric surgery.