bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioethanol Production From Leaves of Quercus Infectoria in Kurdistan Region
Authors: Tahir Bawar , Wang Xiaoqing , Zhong Yuan , Mezori Hassan , Liu Yan , Liao Wei 
Published: October 2020

Abstract
Quercus infectoria is one of the most abundant native oak species in the Kurdistan region of Iraq. This study focused on utilizing leaves of Quercus infectoria for ethanol production in the region. A typical three-step conversion process of acid pretreatment, enzymatic hydrolysis, and yeast fermentation was investigated to produce ethanol from the leaves. Under the selected acid pretreatment and enzymatic hydrolysis conditions, the glucose and xylose concentrations in the hydrolysates reached 11.4 g/L and 16.8 g/L, respectively, with the corresponding sugar conversions of 42.8% and 99.8%. A yeast strain, Kluyveromyces marxianus, was used to ferment mono-sugars in the hydrolysates for ethanol production. The ethanol production rate and conversion of K. marxianus in the fermentation were 0.17 g/L/h and 27%. The techno-economic analysis further concluded that a regional ethanol biorefinery can be established in the Zawita sub-district, Iraq to utilize Q. infectoria leaves to produce 200,000,000 kg ethanol/year with a positive energy balance of 745,052,623 MJ/year. The net annual revenue of the biorefinery is $123,692,804. The payback period of the biorefinery is 10 years.
Conducting Household Surveys on Reproductive Health in Urban Settings: Lessons From Karachi, Pakistan
Authors: Khan Mir Baz , Nausheen Sidrah , Hussain Imtiaz , Hackett Kristy , Kaneez Zahra , Feroze Khalid , Canning David , Shah Iqbal , Soofi Sajid Bashir 
Published: October 2020

Abstract
Background: Data collection is the most critical stage in any population health study and correctly implementing fieldwork enhances the quality of collected information. However, even the most carefully planned large-scale household surveys can encounter many context-specific issues. This paper reflected on our research team’s recent experiences of conducting surveys for a quasi-experimental evaluation of a reproductive health program in urban areas of Karachi, Pakistan. Methods: The study followed a three-stage random sampling design. Result: This paper has described the issues that were encountered around technical problems related to geographical information system (GIS) usage and computer assisted personal interviews (CAPI), household listing, interviewing respondents on sensitive topics and their expectations, and other field related concerns such as ensuring privacy etc. during the survey.Conclusion: The papers has also underscored on lessons learned from this process and presented some potential solutions for conducting future household surveys in similar urban environments.
A riskscore-based nomogram for the prediction of overall survival in cervical squamous cell carcinoma
Authors: Li Lingling , Zhang Sujie , Wang Lijie , Tao Haitao , Long Yaping , Gao Yiming , Hu Yi , Sun Yi 
Published: October 2020

Abstract
Background:Cervical cancer is still the major cause of cancer-related death among women. However, the prognosis of cervical cancer varies even in the same stage. Thus, exploring prognostic biomarkers that could reflect its biological heterogeneity may contribute to identify patients with a poor prognosis.Methods:Based on the ESTIMATE algorithm, we acquired the immune/stromal scores of cervical squamous cell carcinoma (CSCC) patients collected from The Cancer Genome Atlas (TCGA) dataset. Subsequently, we analyzed the DEGs between high- and low immune score groups using R package edgeR and performed K-M analysis to illustrate the relationship between differentially expressed genes (DEGs) and the overall survival to select survival-related DEGs. Then the LASSO regression model was constructed with the package “glmnet” in R to evaluate the riskscore of each patient. Finally, we developed a nomogram composing riskscore and clinicopathological characteristics to predict the overall survival (OS) of CSCC patients. The R software v3.6.1 was used for statistical analyses. All statistical tests were two-tailed.Results:We established a riskscore model composed of two genes including FOXP3 and ZAP70. The receiver operating characteristic (ROC) curve demonstrated a good potency of the riskscore model. Ultimately, we constructed a nomogram composing riskscore, age and stage to predict the overall survival (OS) of CSCC patients. The area under the ROC curve (AUC) of the nomogram for OS was 0.805, 0.723 and 0.748 for the first, third, and fifth years, respectively. The concordance index (C-index) was 0.746. The calibration curves also showed optimal accuracy of the nomogram for survival prediction. Conclusion:The nomogram based on riskscore could predict overall survival in CSCC and may benefit those patients through individualized immunotherapy.
Comprehensive Analysis of the Expression and Prognosis for E2Fs in Human Cervical Cancer
Authors: Zhu Shan , Yan Yiqi , Liu Tao , Wang Zijing , Jin Ya , Han Rui , Zhang Han , Xia Qingmei , HU Zhen , Li Nan 
Published: October 2020

Abstract
Background: Accumulating evidence was found that E2Fs are a family of transcription factors that are aberrantly expressed or multi-activated in malignant tumors and are found in a variety of tumorigenesis. However, the expression pattern and exact role of E2Fs in cervical cancer (CC) tumorigenesis and progression have not been elucidated.Methods: In the study arrangement, we examined the expression and prognostic value of E2Fs in CC patients using multiple databases, including ONCOMINE, GEPIA, cBioPortal, Metascape, and Kaplan-Meier mapper.Results: E2F1/2/3/8 is upregulated in CC patients, with E2F1 mRNA levels upregulated with better OS correlation. E2F3/8 has an even worse RFS difference and could presumably be used as a CC therapeutic target. Conclusion: These results suggest that E2F1/2/3/8 can exist as a marker for CC. However, more experimental results are needed to confirm this inference.
Competing Risk Analysis of Cardiovascular/Cerebrovascular Death in T1/2 Kidney Cancer: A SEER Database Analysis
Authors: Mo Xiaofei , Zhou Mingge , Yan Hui , Chen Xueqin , Wang Yuetao 
Published: October 2020

Abstract
Background: Kidney cancer (KC) is associated with cardiovascular regulation disorder, which easily leads to cardiovascular and cerebrovascular death (CCD), and CCD is one of the major causes of death in patients with KC, especially in T1/2 status. However, there are few studies treated CCD as an independent outcome and analyzed the risk factors related to this outcome. We aimed to evaluate the key factors associated with CCD or kidney cancer-specific death (KCD) in patients with T1/2 KC by competing risk analysis, and compared these two kinds of risk factors to offer some information for clinical management. Methods: A total of 45117 patients diagnosed with first primary KC in T1/2 status between 2004-2015 were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. According to their outcomes at the end of follow-up, all patients were divided into CCD group (n=3087), KCD group (n=3212), Other Events group (n=6312) and Alive group (n=32506). Patients’ clinical characteristics were estimated their association with CCD and KCD by Fine-Gray’s competing risk model. Factors significantly correlating with CCD or KCD were used to create forest plots to compare their differences.Results: The Fine-Gray’s competing risk analysis showed that age at diagnosis, race, marital status, tumor size, AJCC T stage, chemotherapy, kind of surgery of primary site and scope of lymph node were correlated significantly with CCD. Moreover, age at diagnosis, sex, marital status, tumor size, AJCC T/N status, radiation therapy, chemotherapy, kind of surgery of primary site and scope of lymph node were correlated significantly with KCD. Then the forest plots of these two kinds factors were established to compare their difference. It was found that age at diagnose, race, AJCC T/N status and therapy methods represented significantly different risks for patients with T1/2 KC developing to CCD or KCD.Conclusion: We firstly separated CCD and KCD as two independent outcomes to analysis the risk factors related them, and found that age at diagnose, race, AJCC T/N status and therapy methods differently affected patients with T1/2 KC developing to CCD or KCD.
Inverse Analysis to Reconstruct Hydraulic Conditions of Non-steady Turbidity Currents: Application to an Ancient Turbidite of the Kiyosumi Formation of the Awa Group, Boso Peninsula, Central Japan
Authors: Nakao Kento , Naruse Hajime , Tokuhashi Shuichi 
Published: October 2020

Abstract
This study proposes a new method of inverse analysis from ancient turbidites to the non-steady turbidity currents with consideration of multiple grain-size classes. The forward model employed in this study is based on the shallow water equation, and the initial condition of flows are assumed to be the lock-exchange type condition. To obtain a solution of the inverse problem, this study employed the genetic algorithm for finding the optimized initial conditions. The present method successfully estimated the true given initial conditions of the turbidity currents from the artificial data sets of deposits created by the calculation of the forward model. The author also applied the method to the turbidite bed in the Kiyosumi Formation. As a result of inverse analysis, the obtained solution fits well to the observed data of the individual turbidite, providing estimates of the flow velocity, the flow thickness and the sediment concentration of the turbidity current.

The flow thickness and velocity when the turbidity current reached at the downstream end of the study area were reconstructed to be 334.6 m, 0.98 m/s respectively at the location of the downstream end. Result of our analysis is the first example of reconstructing a reasonable conditions of the turbidity current from an ancient turbidite observed in the field, and the method is expected to be applied in various regions in the future.
Novel Epigenetic Clock for Fetal Brain Development Predicts Fetal Epigenetic Age for iPSCs and iPSC-Derived Neurons.
Authors: Steg Leonard C , Shireby Gemma L , Imm Jennifer , Davies Jonathan P , Flynn Robert , Namboori Seema C , Bhinge Akshay , Jeffries Aaron R , Burrage Joe , Neilson Grant W.A. , Walker Emma M , Perfect Leo W , Price Jack , Bray Nicholas L , Cope Emma L , Jones Kimberly M , Allen Nicholas D , Pishva Ehsan , Mill Jonathan , Lunnon Katie , Hannon Eilis 
Published: October 2020

Abstract
Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the early stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age, and is has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons, here, we establish the fetal brain clock (FBC), a bespoke epigenetic clock trained in prenatal neurodevelopmental samples. Our data show that the FBC outperforms other established epigenetic clocks in predicting the age of fetal brain samples. We then applied the FBC to DNA methylation data of cellular datasets that have profiled iPSCs and iPSC-derived neuronal precursor cells and neurons and find that these cell types are characterized by a fetal epigenetic age. Furthermore, while differentiation from iPSCs to neurons significantly increases the epigenetic age, iPSC-neurons are still predicted as having fetal epigenetic age. Together our findings reiterate the need for better understanding of the limitations of existing epigenetic clocks for answering biological research questions and highlight a potential limitation of iPSC-neurons as a cellular model for the research of age-related diseases as they might not fully recapitulate an aged phenotype.
Magnetic Resonance Imaging and Neurological Findings in Dogs with Disc-Associated Cervical Spondylomyelopathy (63 cases)
Authors: Bonelli Marília de Albuquerque , Costa Luciana Bignardi de Soares Brisola Casimiro da , Costa Ronaldo Casimiro da 
Published: October 2020

Abstract
Background: Canine cervical spondylomyelopathy can be separated into osseous and disc-associated (DA-CSM) forms. Our aim was to describe the magnetic resonance imaging (using a high-field scanner) and neurological findings in dogs with DA-CSM and investigate a relationship between these findings.Results: Sixty-three dogs were included: 60/63 (95%) were large breeds, with Doberman Pinschers and males over-represented (70%). Mean and median age at the time of diagnosis was 7.25 and 7.2 years (range 0.41 – 12 years). Chronic signs were noted in 52/63 (83%) dogs, with proprioceptive ataxia the most common. Main site of spinal cord compression was commonly C6-C7 or C5-C6. Thirty-six (57%) dogs had various sites of spinal cord compression. Most dogs younger than 6 years of age had a single affected. Foraminal stenosis was present in 51/63 dogs (81%). T2-weighted hyperintensity was present in 40/63 dogs (63%). Eighty-eight percent of the articular processes showed degenerative changes, which correlated strongly with intervertebral disc degeneration. Ligamentum flavum hypertrophy was seen in 38% of dogs. No correlation was observed between neurologic signs and number of affected sites. A moderate positive correlation was observed between severity of spinal cord compression and neurologic grade (r 0.48; p<0.001).Conclusions: DA-CSM was predominantly observed in older, male Dobermans, with chronic neurologic signs, with compressive lesions located in the caudal cervical vertebral region. Although less common, DA-CSM was also seen in dogs 3 years of age or younger (8%). Single compressive lesions were more common in dogs younger than 6 years of age. Most dogs had concomitant changes (e.g.: ligamentum flavum hypertrophy and foraminal stenosis) that may affect neurologic signs. Most dogs with ligamentum flavum hypertrophy were 6 years or older. A correlation was observed between severity of spinal cord compression and neurologic grade; dogs with more severe spinal cord compression were more likely to have a higher neurologic grade. Dogs with more sites of spinal cord compression did not have more severe neurologic involvement. A very high percentage of dogs had articular process degenerative changes. Possible biomechanical or genetic relationships between degenerative changes in articular processes, ligamentum flavum, and intervertebral discs warrants further investigation.
Biomechanics of Artificial Pedicle Fixation in a 3d-printed Prosthesis After Total en Bloc Spondylectomy: A Finite Element Analysis
Authors: Wang Xiao Dong , Hanpeng Xu , Han Ye , Wu Jincheng , Song Yang , Jiang Yuanyuan , Wang Jianzhong , Miao Jun 
Published: October 2020

Abstract
Background: This study compared the biomechanics of artificial pedicle fixation in spine reconstruction with a 3-dimensional (3D)-printed prosthesis after total en bloc spondylectomy (TES) by finite element analysis.Methods: A thoracolumbar (T10–L2) finite element model was developed and validated. Two models of T12 TES were established in combination with different fixation methods: Model A consisted of long-segment posterior fixation (T10/11, L1/2) + 3D-printed prosthesis; and Model B consisted of Model A + two artificial pedicle fixation screws. The models were evaluated with an applied of 7.5 N·m and axial force of 200 N. We recorded and analyzed the following: 1) stiffness of the two fixation systems; 2) hardware stress in the two fixation systems; and 3) stress on the endplate adjacent to the 3D-printed prosthesis.Results: The fixation strength of Model B was enhanced by the screws in the artificial pedicle, which was mainly manifested as an improvement in rotational stability. The stress transmission of the artificial pedicle fixation screws reduced the stress on the posterior rods and endplate adjacent to the 3D-printed prosthesis in all directions of motion, especially in rotation.Conclusions: After TES, the posterior long-segment fixation combined with the anterior 3D printed prosthesis could maintain postoperative spinal stability, but adding artificial pedicle fixation increased the stability of the fixation system and reduced the risk of prosthesis subsidence and instrumentation failure.
Can the Bone Mineral Density of the Non-fractured Contralateral Hip Predict Medial Migration of Helical Blade-type Lag Screws in Osteoporotic Hip Fractures?
Authors: Jo Suenghwan , Lee Hyun Jun , Lee Sang Hong , Ryu Je Hong , Kim Ba Rom , Lim Dong Seop , Kim Soo Ah 
Published: October 2020

Abstract
Background: In this study, we performed a biomechanical tests on the osteoporotic femoral heads to validate whether the bone mineral density (BMD) measured at the non-fractured contralateral hip can predict the BMD and potential medial migration of helical blade-type lag screws on the fractured femoral head.Methods: Twenty-four osteoporotic femoral heads were retrieved from patients with femoral neck fracture undergoing hip arthroplasty. The patients had their BMD measured from the contralateral hip using dual-energy X-ray absorptiometry prior to surgery. The BMD of the retrieved femoral heads was measured using micro-computed tomography. The mechanical properties for the medial migration of lag screw were measured by performing an uniaxial compression test on the femoral head using a helical blade-type lag screw. Statistical analysis was performed to determine the correlation among the BMDs of the non-fractured contralateral hip and the retrieved femoral head and the mechanical properties of the fractured femoral head.Results: The mean BMD of the contralateral hip was 0.60±0.14 g/cm2 in the neck region and 0.63±0.15 g/cm2 in the total proximal femur. The mean BMD of the fractured femoral head was 463.3±48.05 mg HA/cm3. The mechanical properties of the fractured femoral head were measured to be 0.92 kN for the maximum compressive load and 14.50±5.48 kN for the accumulated compression load. In the analysis of the correlation among the parameters, we found no correlation between the BMD of the non-fractured contralateral hip and the mechanical properties of the fractured femoral head. In addition, we observed no correlation between the BMD of the fractured femoral head and that of the contralateral hip.Conclusions: Our results indicate that the BMD of the contralateral hip does not reflect the BMD or the mechanical properties of the fractured femoral head. Therefore, helical blade-type lag screw migration may not be predicted from the BMD of the non-fractured contralateral hip.
Identification of Candidate Genes Associated with Steroid-Induced Osteonecrosis of The Femoral Head by Bioinformatics Based on GEO Database
Authors: Cheng Shile , Nie Zhigang , Peng Hao 
Published: October 2020

Abstract
BACKGROUNDː Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive bone disorder and its characterized by femoral head collapse and hip joint dysfunction and the biomarkers of SONFH remain unclear. The purposes of this study are to identify the significant biological function and pathway involved in SONFH, and further to search the underlying mechanism of this pathway in SONFH. METHODSː The GSE123568 dataset obtained from the Gene Expression Omnibus (GEO) database and normalized using Robust Multiarray Averaging (RMA) methods. And the Gene set enrichment analysis (GSEA), Ingenuity pathway analysis (IPA), VarElect online tool, MalaCards database, miRWalk online tool, DIANA too, and Cytoscape were integrated for bioinformatics analyses.RESULTSː 6 biological processes and 4 KEGG pathways were enriched by GSEA, and 68 candidate genes were involved in these pathways. Besides, the canonical pathway and molecule function analysis by IPA, the results revealed that 10 canonical pathways and 12 candidate genes were identified, and 20 modules and 101 candidate genes were enriched by molecule function analysis. The above candidate genes were combined and filtered using the VarElect online tool. The filtered candidate genes were overlapped with another cluster of candidate genes from the MalaCards database to identify hub genes ACP5, TNF, MMP8. Based on the hub genes, the miRNAs were screened and overlapped to predict the lncRNAs. Total 7 miRNAs of ACP5, TNF, MMP8 were targeted 956 candidate lncRNAs.CONCLUSIONSː In summary, this study identified the hub candidate genes and pathways associated with SONFH progress, and constructed the ceRNA network based on the hub candidate genes. Our findings might provide the potential biomarkers of SONFH diagnosis and treatment.
Degeneration of the Lumbar Paravertebral Muscle in Patients With Dynamic Sagittal Imbalance, A Retrospective Cohort Study
Authors: Ru Nan , Li Yang , Cui Xingang , Sun Jianmin , Wang Guodong 
Published: October 2020

Abstract
Study Design: A retrospective cohort study.Background: Sagittal imbalance of the spine is a comprehensive concept ..In appearance, it is often manifested as body leaning forward instability; whereas on standing full-spine lateral digital radiographs, it shows an increased sagittal vertical axis (SVA) .Clinically, we found that some patients showed normal sagittal balance at initiation, but hunched or leaned forward after a period of walk or activity. This condition is called dynamic sagittal imbalance(DSI). There is no systematic study to explore the paravertebral muscles changes of dynamic sagittal imbalance.Method: The study group comprised 31 DSI patients and 42 control patients. All subjects underwent radiologic whole spine X-ray examination and lumbar MRI( Magnetic Resonance Imaging) scanning. Spinal-pelvic parameters at initiation such as sagittal vertical axis (SVA), thoracic kyphosis (TK), thoracolumbar kyphosis (TLK), lumbar lordosis (LL), sacral slope (SS), pelvic tilt (PT) and pelvic incidence (PI) was measured. The cross-sectional areas CSA of the erector spinae (ES), multiﬁdus (MF), and vertebral body area were measured at L2/L3 and L4/L5. The fat infiltration (FI) and relative cross-sectional area (RCSA)of muscle of these above muscles were quantitatively measured though Image J softwore.Result : Compared with the control group, the DSI group had a smaller lumbar lordosis, more severe fat infiltration and lower relative functional cross-sectional area(RFCSA) of paravertebral muscle (erector spinae and multifidus) . In DSI group, the point-in-time of occurrence of dynamic sagittal imbalance was statistically correlated with degeneration of paravertbral muscles at L4/L5 level, whereas no correlation between the two above at L2/L3 level.Conclusion: In conclusion, DSI an normal SVA (SVA＜40mm) at initiation, and prominent increase in SVA after activity with thunks marked inclined. Paravertebral muscle degeneration plays an important role in the DSI process, Patients in the DSI group had more severe paravertebral muscle degeneration compared with patients in control group. There was a significant correlation between the severity of DSI symptoms and the degeneration of lower lumbar paravertebral muscles. These findings may help spinal surgeons better understand sagittal balance of spine.