bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting survival-associated biomarkers from heterogeneous populations
Authors: Saegusa Takumi , Zhao Zhiwei , Ke Hongjie , Ye Zhenyao , Xu Zhongying , Chen Shuo , Ma Tianzhou 
Published: February 2021

AbstractDetection of prognostic factors associated with patients’ survival outcome helps gain insights into a disease and guide treatment decisions. The rapid advancement of high-throughput technologies has yielded plentiful genomic biomarkers as candidate prognostic factors, but most are of limited use in clinical application. As the price of the technology drops over time, many genomic studies are conducted to explore a common scientific question in different cohorts to identify more reproducible and credible biomarkers. However, new challenges arise from heterogeneity in study populations and designs when jointly analyzing the multiple studies. For example, patients from different cohorts show different demographic characteristics and risk profiles. Existing high-dimensional variable selection methods for survival analysis, however, are restricted to single study analysis. We propose a novel Cox model based two-stage variable selection method called “Cox-TOTEM” to detect survival-associated biomarkers common in multiple genomic studies. Simulations showed our method greatly improved the sensitivity of variable selection as compared to the separate applications of existing methods to each study, especially when the signals are weak or when the studies are heterogeneous. An application of our method to TCGA transcriptomic data identified essential survival associated genes related to the common disease mechanism of five Pan-Gynecologic cancers.
Role of PDZ-binding motif from West Nile virus NS5 protein on viral replication
Authors: Giraud Emilie , del Val Chloé Otero , Caillet-Saguy Célia , Zehrouni Nada , Khou Cécile , Caillet Joël , Jacob Yves , Pardigon Nathalie , Wolff Nicolas 
Published: February 2021

AbstractWest Nile virus (WNV) is a Flavivirus, which can cause febrile illness in humans that may progress to encephalitis. Like any other obligate intracellular pathogens, Flaviviruses hijack cellular protein functions as a strategy for sustaining their life cycle. Many cellular proteins display globular domain known as PDZ domain that interacts with PDZ-Binding Motifs (PBM) identified in many viral proteins. Thus, cellular PDZ-containing proteins are common targets during viral infection. The non-structural protein 5 (NS5) from WNV provides both RNA cap methyltransferase and RNA polymerase activities and is involved in viral replication but its interactions with host proteins remain poorly known. In this study, we demonstrate that the C-terminal PBM of WNV NS5 recognizes several human PDZ-containing proteins using both in vitro and in cellulo high-throughput methods. Furthermore, we constructed and assayed in cell culture WNV replicons where the PBM within NS5 was mutated. Our results demonstrate that the PBM of WNV NS5 is important in WNV replication. Moreover, we show that knockdown of the PDZ-containing proteins TJP1, PARD3, ARHGAP21 or SHANK2 results in the decrease of WNV replication in cells. Altogether, our data reveal that interactions between the PBM of NS5 and PDZ-containing proteins affect West Nile virus replication.
Application of combined model of stepwise regression analysis and artificial neural network in data calibration of miniature air quality detector
Authors: Liu Bing , Zhao Qingbo , Jin Yueqiang , Shen Jiayu , Li Chaoyang 
Published: February 2021

AbstractIn this paper, six types of air pollutant concentrations are taken as the research object, and the data monitored by the micro air quality detector are calibrated by the national control point measurement data. We use correlation analysis to find out the main factors affecting air quality, and then build a stepwise regression model for six types of pollutants based on 8 months of data. Taking the stepwise regression fitting value and the data monitored by the miniature air quality detector as input variables, combined with the multilayer perceptron neural network, the SRA-MLP model was obtained to correct the pollutant data. We compared the stepwise regression model, the standard multilayer perceptron neural network and the SRA-MLP model by three indicators. Whether it is root mean square error, average absolute error or average relative error, SRA-MLP model is the best model. Using the SRA-MLP model to correct the data can increase the accuracy of the self-built point data by 42.5% to 86.5%. The SRA-MLP model has excellent prediction effects on both the training set and the test set, indicating that it has good generalization ability. This model plays a positive role in scientific arrangement and promotion of miniature air quality detectors. It can be applied not only to air quality monitoring, but also to the monitoring of other environmental indicators.
Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt
Authors: Rampelli Simone , Turroni Silvia , Mallol Carolina , Hernandez Cristo , Galván Bertila , Sistiaga Ainara , Biagi Elena , Astolfi Annalisa , Brigidi Patrizia , Benazzi Stefano , Lewis Cecil M. , Warinner Christina , Hofman Courtney A. , Schnorr Stephanie L. , Candela Marco 
Published: February 2021

AbstractA comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such asBlautia,Dorea,Roseburia,Ruminococcus,FaecalibacteriumandBifidobacteriumalready populated the intestinal microbiome ofHomosince as far back as the last common ancestor between humans and Neanderthals.
Inducing nano-confined crystallization in PLLA and PET by elastic melt stretching
Authors: Razavi Masoud , Zhang Wenwen , Khonakdar Hossein Ali , Janke Andreas , Li Liangbin , Wang Shi-Qing 
Published: February 2021

Cold crystallization of pre-melt stretched PLLA and PET permits growth of nano-confined crystals with entanglement mesh size in undisrupted chain networking. Such PLLA and PET are ductile, transparent, rigid at the water-boiling temperature.
Estradiol-Responsive miR-365a-3p Interacts with Tissue Factor 3′UTR to Modulate Tissue Factor-Initiated Thrombin Generation
Authors: Tian Jiayin , Adams Murray J. , Tay Jasmine Wee Ting , James Ian , Powell Suzanne , Hughes Quintin W. , Gilmore Grace , Baker Ross I. , Tiao Jim Yu-Hsiang 
Published: February 2021

Abstract
Background High estradiol (E2) levels are linked to an increased risk of venous thromboembolism; however, the underlying molecular mechanism(s) remain poorly understood. We previously identified an E2-responsive microRNA (miR), miR-494–3p, that downregulates protein S expression, and posited additional coagulation factors, such as tissue factor, may be regulated in a similar manner via miRs.
Objectives To evaluate the coagulation capacity of cohorts with high physiological E2, and to further characterize novel E2-responsive miR and miR regulation on tissue factor in E2-related hypercoagulability.
Methods Ceveron Alpha thrombin generation assay (TGA) was used to assess plasma coagulation profile of three cohorts. The effect of physiological levels of E2, 10 nM, on miR expression in HuH-7 cells was compared using NanoString nCounter and validated with independent assays. The effect of tissue factor-interacting miR was confirmed by dual-luciferase reporter assays, immunoblotting, flow cytometry, biochemistry assays, and TGA.
Results Plasma samples from pregnant women and women on the contraceptive pill were confirmed to be hypercoagulable (compared with sex-matched controls). At equivalent and high physiological levels of E2, miR-365a-3p displayed concordant E2 downregulation in two independent miR quantification platforms, and tissue factor protein was upregulated by E2 treatment. Direct interaction between miR-365a-3p and F3-3′UTR was confirmed and overexpression of miR-365a-3p led to a decrease of (1) tissue factor mRNA transcripts, (2) protein levels, (3) activity, and (4) tissue factor-initiated thrombin generation.
Conclusion miR-365a-3p is a novel tissue factor regulator. High E2 concentrations induce a hypercoagulable state via a miR network specific for coagulation factors.
Milled Dry Ice as a C1 Source for the Carboxylation of Aryl Halides
Authors: Nicewicz David A. , O’Brien Connor J. 
Published: February 2021

AbstractThe use of carbon dioxide as a C1 chemical feedstock remains an active field of research. Here we showcase the use of milled dry ice as a method to promote the availability of CO2 in a reaction solution, permitting practical synthesis of arylcarboxylic acids. Notably, the use of milled dry ice produces marked increases in yields relative to those obtained with gaseous CO2, as previously reported in the literature.
Pedicle Screw Instrumentation of the Cervicothoracic Junction in the Sitting Position using CT-guided Navigation: Application and Technical Aspects
Authors: Hore Nirjhar , Lücking Hannes , Schmitt Hubert , Buchfelder Michael , Brandner Sebastian 
Published: February 2021

Abstract
Background We evaluate the feasibility and potential advantages of spinal CT navigation in the placement of pedicle screws at the cervicothoracic junction in the sitting position to counteract the anatomy-related limitations of 2D fluoroscopy.
Methods We retrospectively analyze the data from 15 patients who underwent CT-based navigation-guided placement of a total of 36 pedicle screws at the cervicothoracic junction in the sitting position.
Results CT-based spinal navigation is a useful method in increasing accuracy of pedicle screw instrumentation in the sitting position, successfully counteracting the anatomy-related limitations of 2D fluoroscopy at the cervicothoracic junction.
Conclusion CT-based navigation-guided placement of pedicle screws at the cervicothoracic junction in the sitting position proved to be an accurate, safe, and user-friendly method.
Preoperative and Postoperative Opioid Dependence in Patients Undergoing Anterior Cervical Diskectomy and Fusion for Degenerative Spinal Disorders
Authors: Dietz Nicholas , Sharma Mayur , Alhourani Ahmad , Ugiliweneza Beatrice , Nuno Miriam , Drazin Doniel , Wang Dengzhi , Boakye Maxwell 
Published: February 2021

Abstract
Background Anterior cervical diskectomy and fusion (ACDF) is a procedure for effectively relieving radiculopathy. Opioids are commonly overprescribed in postsurgical settings and prescriptions vary widely among providers. We identify trends in opioid dependence before and after ACDF.
Methods We used the Truven Health MarketScan data to identify adult patients undergoing ACDF for degenerative cervical spine conditions between 2009 and 2015. Patients were segregated in four cohorts of preoperative and postoperative opioid nondependence (ND) or dependence (D) with 15 months of postoperative follow-up.
Results A total of 25,403 patients with median age of 52 years (18–92) who underwent ACDF met the inclusion criteria. Breakdown of the four cohorts was as follows: prior nondependent who remain nondependent (NDND): 62.76% (n = 15,944); prior nondependent who become dependent (NDD): 4.6% (n = 1,168); prior dependent who become nondependent (DND): 14.03% (n = 3,564); and prior dependent who remain dependent (DD): 18.61% (n = 4,727). Opioid dependence decreased 9.43% postoperatively. Overall payments and 30-day readmissions increased 1.96 and 1.79 times for opioid dependent versus nondependent cohorts, respectively. Adjusted payments at 3 to 15 months were significantly increased for dependent cohorts with 3.56-fold increase for the DD cohort when compared with the NDND cohort. Length of stay, complications, medication refills, outpatient measures, and hospital admissions were also higher in those groups with postoperative opioid dependence when compared with those who were not opioid dependent.
Conclusions Opioid dependence after ACDF is associated with increased hospital readmissions, complication rates at 30 days, and payments within 3 months and 3 to 15 months postdischarge. Overall opioid dependence was decreased after ACDF procedure, however, a smaller number of opioid-dependent and opioid-naive patients became dependent postoperatively and should be followed carefully.
Outcome Features Analysis in Intramedullary Tumors of the Cervicomedullary Junction: A Surgical Series
Authors: Brunetto Giacoma Maria Floriana , Tariciotti Leonardo , Landi Alessandro , Gregori Fabrizio , Santoro Francesca , Frati Alessandro , Delfini Roberto , Santoro Antonio 
Published: February 2021

Abstract
Object The aim of this study is to investigate the impact of surgery for different cervicomedullary lesions on symptomatic pattern expression and postoperative outcome. We focused on specific outcome features of the early and late postoperative assessments. The former relies on surgery-related transient and permanent morbidity and feasibility of radicality in eloquent areas, whereas the latter on long-term course in lower grade tumors and benign tumorlike lesions (cavernomas, etc.).
Material and Methods We retrospectively analyzed 28 cases of intramedullary tumors of the cervicomedullary junction surgically treated at our institution between 1990 and 2018. All cases were stratified for gender, histology, macroscopic appearance, location, surgical approach, and presence of a plane of dissection (POD). Mean follow-up was 5.6 years and it was performed via periodic magnetic resonance imaging (MRI) and functional assessments (Karnofsky Performance Scale [KPS] and modified McCormick [MC] grading system).
Results In all, 78.5% were low-grade tumors (or benign lesions) and 21.5% were high-grade tumors. Sixty-one percent underwent median suboccipital approach, 18% a posterolateral approach, and 21% a posterior cervical approach. Gross total resection was achieved in 54% of cases, near-total resection (>90%) in 14%, and subtotal resection (50–90%) in 32% of cases. Early postoperative morbidity was 25%, but late functional evaluation in 79% of the patients showed KPS > 70 and MC grade I; only 21% of cases showed KPS < 70 and MC grades II and III at late follow-up. Mean overall survival was 7 years in low-grade tumors or cavernomas and 11.7 months in high-grade tumors. Progression-free survival at the end of follow-up was 71% (evaluated mainly on low-grade tumors).
Conclusions The surgical goal should be to achieve maximal cytoreduction and minimal postoperative neurologic damage. Functional outcome is influenced by the presence of a POD, radicality, histology, preoperative status, and employment of advanced neuroimaging planning and intraoperative monitoring.
Surgical Procedure in the Treatment of Organized Chronic Subdural Hematoma: A Single-Center Experience
Authors: Chen Keng , Wang Kun , Chen Danzhi , Niu Huanjiang , Yang Shuxu , Wang Yirong 
Published: February 2021

Abstract
Background Organized chronic subdural hematoma (CSDH) is a special type of CSDH. However, the optimal surgical procedure has not been established. We present our experience here to discuss the surgical procedure in treatment of organized CSDH.
Methods Thirty-three patients with organized CSDH were admitted between January 1, 2008 and January 1, 2018. Age, gender, clinical symptoms, imaging data, type of surgical procedure, Barthel index (BI), and postoperative complications were collected and retrospectively analyzed. The BI was assessed both pre and postoperatively (1 week and 1 month after surgery).
Results Overall, 14 patients underwent large craniotomy and 19 patients underwent small craniotomy. No significant differences in gender, age, initial clinical symptoms, and preoperative BI were found between the groups (p > 0.05). Among the 14 patients who underwent large craniotomy, 2 patients developed epilepsy after the operation, while 1 patient had postoperative aphasia. None of the patients had recurrence in 6 months postoperatively. Among the 19 patients who underwent small craniotomy, 1 patient developed an acute subdural hematoma and 1 patient developed aphasia. No obvious complications were found in the remaining 18 patients and none of the 19 patients had recurrence in 6 months postoperatively. BI scores of the small craniotomy group were significantly better than those of the large craniotomy group at 1 week postoperatively (p < 0.05). However, there was no significant difference in the 1-month results (p > 0.05).
Conclusion According to our single-center experience, a small craniotomy for treating organized CSDH can be considered as an alternative to a larger craniotomy.
Comparación entre las secuencias axiales densidad de protones y T2 en lesiones medulares cervicales de pacientes con esclerosis múltiple
Authors: Herazo-Bustos Cherina , Tramontini Jens Carolina , Mora Salazar Juan Andrés , Taborda Karen Nieto , Navas Carlos 
Published: February 2021

Resumen
Introducción Las secuencias ponderaras en T2 con tiempo de eco largo son tradicionalmente usadas para la evaluación de las lesiones de la médula espinal en esclerosis múltiple (EM). Existen otras secuencias, como la densidad de protones (primer eco T2), que pueden ser útiles en el plano axial pero que no se han estudiado lo suficiente.
Objetivos Establecer la concordancia entre la densidad de protones (DP) y las secuencias axiales ponderadas en T2 en las lesiones de la médula espinal cervical en pacientes con EM.
Métodos Se trata de un estudio de concordancia entre secuencias DP y T2 axiales en magneto de 1,5 Tesla en sujetos colombianos. Las imágenes fueron revisadas por dos radiólogos, que determinaron el número de lesiones, así como la intensidad de señal —mediante la relación contraste— ruido (RCR). La comparación se realizó con el coeficiente de correlación y concordancia de Lin.
Resultados Se evaluaron 56 pacientes, 30,36% hombres y 69,64% mujeres. Se encontraron diferentes números de lesiones entre las secuencias axiales DP vs T2 (210 vs 144), coeficiente de concordancia entre el número de lesiones 0,72 (IC95%: 0,6–0,82, error estándar 0,05, desviación estándar 1,37) y en la conspicuidad —RCR— 0,62 (IC95%: 0,48–0,75, SE 0,05, DE 12,25).
Conclusión No encontramos concordancia en la evaluación del número o intensidad de la señal entre secuencias axiales DP y T2. Aunque las secuencias ponderadas en T2 son las más utilizadas, investigaciones recientes han demostrado falta de concordancia e incluso superioridad de las secuencias DP en otros planos, lo que sugiere que es necesario realizar estudios para evaluar la efectividad de las secuencias DP en el plano axial.
Video-Assisted Thoracoscopic Segmentectomy for Deep and Peripheral Small Lung Cancer
Authors: Takamori Satoshi , Oizumi Hiroyuki , Suzuki Jun , Suzuki Katsuyuki , Kabasawa Takanobu 
Published: February 2021

Abstract
Background We aimed to retrospectively compare the long-term prognosis and recurrence after segmentectomy between nonsmall cell lung cancer (NSCLC) patients with deep and peripheral lesions.
Methods Data were extracted for 85 lobectomy-tolerable NSCLC patients with tumors measuring ≤2 cm, who underwent video-assisted thoracoscopic segmentectomy with curative intent during January 2006 to December 2014. Tumor location was determined by the surgeon using thin-slice (1 mm) and three-dimensional computed tomography. Overall and recurrence-free survival was compared between patients with peripheral and deep lesions using univariate and multivariate Cox proportional hazard models. The indications for segmentectomy included NSCLC measuring ≤2 cm and consolidation/tumor ratio ≤20%, solid NSCLC ≤1 cm, and indeterminate nodule ≤1.5 cm.
Results No recurrence of peripheral and deep lesions was noted. The 5-year overall survival was 96.4% for all patients, and 100 and 95.3% for patients with deep and peripheral lesions, respectively. There was no significant difference between the overall survival rates associated with the deep and peripheral lesions (95% confidence interval [CI], 89.5–98.8, nonsignificant, 86.4–98.4, respectively; p = 0.189). In a multivariate analysis, the American Society of Anesthesiologists score (hazard ratio [HR], 13.30; 95% CI, 1.31–210.36; p = 0.028) and histology (HR, 0.03; 95% CI, 0.00–0.32; p = 0.037) were independent prognostic factors for overall survival; tumor location was not a prognostic factor.
Conclusions When video-assisted thoracoscopic segmentectomy with curative intent was performed with sufficient surgical margins, the location of small NSCLC did not affect recurrence risk and prognosis. Video-assisted thoracoscopic segmentectomy for small NSCLC is acceptable, regardless of the tumor location.
Transoral Endoscopic Localization of the Parapharyngeal Internal Carotid Artery
Authors: Zhang Guoliang , Zhao Xia , Sun Guangbin , Gao Nan , Yu Pengcheng , Chen Zhongchun 
Published: February 2021

Abstract
Objectives To define transoral endoscopic surgical landmarks for the parapharyngeal segment of the internal carotid artery (ppICA) using cadaveric dissection.
Methods Ten fresh cadaveric heads were dissected to demonstrate the parapharyngeal space anatomy and course of the ppICA as seen in a transoral approach. Anatomical measurements of the distance between the ppICA and bony landmarks were recorded and analyzed.
Results The stylohyoid ligament, styloglossus, and stylopharyngeus could be considered to be the safe anterior boundary of the ppICA in the transoral approach; among them, the styloid ligament was the most rigid tissue. Dissection between the stylopharyngeus muscle and superior pharyngeal constrictor muscle provides direct access to the ppICA. At the level of the skull base, the distance from the root of the styloid process to the lateral margin of the external aperture of the carotid canal on the left side and on the right side was 8.57 ± 1.97 and 8.80 ± 1.21 mm, respectively. At the level of the maxillary tuberosity, the distance from the ppICA to the maxillary tuberosity on the left side and on the right side was 31.48 ± 2.24 and 31.01 ± 2.88 mm, respectively.
Conclusion The endoscopic-assisted transoral approach can facilitate exposure of the ppICA. The root of the styloid process, styloid ligament, and maxillary tuberosity are critical landmarks in the identification of the ppICA in the transoral approach.