bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.)
Authors: Chiquito-Almanza Elizabeth , Gallegos Jorge Alberto Acosta , Anaya-López Jose Luis 
Published: May 2022

Abstract
The complete genome sequence of a novel polerovirus identified in chickpea (C. arietinum L.) is presented. Its sequence was assembled using small RNA sequencing and assembly, confirmed by RT-PCR, 5’ and 3’ RACE, and sequenced with the dideoxy-terminal method. According to the current ICTV taxonomic criterion, based on the differences in amino acid (aa) sequence identity greater than 10% in all gene products with other poleroviruses, the identified polerovirus corresponds to a new species, for which we propose the name Chickpea leafroll virus (CpLRV). The genome of CpLRV is 5,770 nucleotides (nt) long and it is organized into seven open reading frames (ORFs) designated as ORF0, ORF1, ORF2, ORF3a, ORF3, ORF4, and ORF5 that code for putative P0, P1, P1-P2, P3a, P3, P4, and P3-P5 proteins, respectively. The 5′ UTR consists of 27 nt starting with the conserved sequence 5′-ACAAAA-3′ typical of Polerovirus, while the 3′ UTR consisted of 229 nt. Phylogenetic analysis using the aa sequences of P0, P1, P1-P2, P3, P4, and P3-P5 show that CpLRV clustered with members of the genus Polerovirus and is closely related to Chickpea chlorotic stunt virus (CpCSV) and Faba bean polerovirus 1 (FBPV1). Recombination analysis supports that CpLRV is a recombinant from two unknown viruses that share the closest nucleotide identity with FBPV1 (72.3%) and Suakwa aphid-borne yellows virus (SAbYV) (53.4%), respectively. The putative recombination event was identified in the 5’ region of CpLRV, the region that encodes proteins P0, P1, and P1-P2. This is the first report of a polerovirus infecting chickpea in México.
Matrin-3 promotes hepatocellular carcinoma progression by regulating cell cycle
Authors: He Hengjing , Zeng Xingruo , Lei Yufei , Xiao Di , Wei Zimeng , Jamal Muhammad , Zhang Chengjie , Zhang Xiaoyu , Ding Qianshan , Tan Haiyan , Zhang Qiuping 
Published: May 2022

Abstract
PurposeThe overexpression of Matrin-3 (MATR3) is associated with tumor progression in several human tumors. However, the role of MATR3 in hepatocellular carcinoma (HCC) still remains unclear. In this study, we investigated the expression of MATR3 in HCC and elucidated the potential functions of MATR3 in HCC cells.MethodsThe differential expression of MATR3 and its association with HCC were analyzed using the UALCAN database, Human Protein Atlas (HPA) database, GSE datasets and gene expression profiling interaction analysis2 (GEPIA2) database. Furthermore, we performed the CCK-8 assays, colony formation assays and flow cytometry analysis in HCC cell lines after knocking down MATR3. The MATR3-interacting proteins were identified by co‐immunoprecipitation and mass spectrometry (Co-IP/MS). ResultsOverexpression of MATR3 protein and mRNA were observed in HCC. High MATR3 expression showed a prominent diagnostic value in HCC patients and significant correlations with clinical stages, tumor grades, nodal metastasis, TP53 mutant, poorer overall survival (OS) and disease-free survival (DFS). Moreover, downregulation of MATR3 inhibited proliferation and arrested cell cycle of HCC cells. Enrichment analysis results of MATR3-interacting proteins demonstrated that MATR3 might regulate cell cycle by interacting with DNA primase large subunit (PRIM2), chromobox protein homolog 5 (CBX5), and protein SEC13 homolog (SEC13).ConclusionMATR3 could be a diagnostic and prognostic marker in HCC patients. Furthermore, MATR3 enhanced tumor progression by regulating the cell cycle of HCC and could be a promising candidate for targeted therapy.
Biomechanical study of a new cannulated screw for Pauwels type III femoral neck fractures
Authors: Chen Zhigang , Chen Feiyang , Xu Xinbao , Zhang Wen , Jiang Dong , Zhang Feixiang , Chen Yinbing , Zhou Shiran , Lyu Shujun 
Published: May 2022

Abstract
Background
A new cannulated screw for the treatment of Pauwels type III femoral neck fracture (FNF) was developed and its biomechanical stability was analyzed by finite element analysis and mechanical tests to provide a new approach for the clinical treatment of Pauwels type III FNF.
Methods
A Pauwels III femoral neck fracture model with an angle of 70° was constructed using medical engineering software such as Mimics, Geomagic, and Hypermesh. Two parallel inverted triangular cannulated screw finite element models were established to simulate surgical fixation: three conventional cannulated screw models(CCS), and two upper cannulated screw + one new cannulated screw models(NCS). The biomechanical properties of the 2 fixation methods were compared and analyzed under the same loading and constraint conditions. An unstable femoral neck fracture model was made using a composite femur (Sawbone) at a Pauwels 70° angle. Reduction and fixation models of Pauwels III FNF were made according to CCS and NCS fixation methods. and the compression displacement of the femur was tested, then the load-displacement curve was used to calculate the stiffness and compare the advantages and disadvantages of the two internal fixation methods.
Results
In the computer-simulated reconstruction of the inverted triangular cannulated screw fixation model for Pauwels type III FNFs, the NCS model outperformed the CCS model in terms of strain and stress distribution. And the peak stress of the 2 groups appeared in the middle section of the screw closest to the femoral spur, close to the fracture line. In the experimental mechanical model of Pauwels type III FNF, under the same loading condition, the NCS group has smaller distance of femoral deformation and fracture end displacement than the CCS group, and from the perspective of stiffness, the former group had greater stiffness and smaller compression distance under the same vertical load.
Conclusions
The new cannulated screws provide good biomechanical stability for the treatment of Pauwels type III FNFs, which provides a new choice for the treatment of young patients with vertical fracture of femoral neck.
Transgenerational herbivory effects on performance of clonal offspring of the invasive plant Alternanthera philoxeroides
Authors: Fu Qiu-Yue , Yu Cheng-Ling , Dong Ran , Shi Juan , Luo Fang-Li , Gao Jun-Qin , Dong Bi-Cheng , Yu Fei-Hai 
Published: May 2022

Abstract
Interactions between alien plants and the newly emerging enemies in introduced ranges may determine plant invasion success. However, little is known about whether herbivory-induced responses are transmitted across vegetative generations of plants, and whether epigenetic changes are involved during this process. In a greenhouse experiment, we examined the effects of current, parental and/or grand-parental herbivory by the generalist herbivore Spodoptera litura on the growth, physiology, and biomass allocation, and the status of DNA methylation of the first-, second- and/or third-generation clonal offspring of the invasive plant Alternanthera philoxeroides, which were derived from two types of root fragments with different branching orders (i.e., the primary- or secondary-root fragments of taproots). Parental herbivory promoted the growth of the second-generation plants sprouted from the secondary-root fragments, but had a neutral or negative effect on the growth of the second-generation plants from the primary-root fragments. The growth of the third-generation plants was significantly reduced by current herbivory, but not affected by grand-parental herbivory. The first-generation plants exhibited a higher level of DNA methylation when they were grazed by herbivores than when they were not, while neither the second-generation nor the third-generation plants showed the herbivory-mediated changes in DNA methylation. Overall, the herbivory-induced growth response within one generation may represent rapid acclimatization of A. philoxeroides to the unpredictable generalist herbivores in the introduced ranges. Herbivory-induced trans-generational effects may be transient for clonal offspring of A. philoxeroides, which can be influenced by the branching order of taproots, but be less characterized by DNA methylation.
Cropland Displacement Drives Carbon Emission of Grain Transport in China
Authors: Zuo Chengchao , Wen Cheng , Clarke Graham , Turner Andy , You Liangzhi , Ke Xinli , Tang Lanping 
Published: May 2022

Abstract
Rapid urbanization has driven a greater need for grain transportation as more grain is consumed in the urban area by the increasing urban population, and croplands have been displaced and are in general further from urban areas due to the urban expansion. The increased transport of grain and other food, which is expected to continue alongside urbanization throughout the world, lead to higher energy consumption and higher carbon emissions associated with that transport. Here we show a model-based approach to estimate the carbon emissions associated with the changing grain transport in China between 1990 and 2015. We found that carbon emission associated with grain transport in China more than doubled from 4.46 million-ton in 1990 to 10.73 million-ton in 2015. The cropland displacement contributed more than 60% of the increase in carbon emission of grain transport between 1990 and 2015, and the change of dietary structure and population growth contributed 31.7% and 16.6%, respectively. We also found that the development of transport infrastructures, such as newly built highways and railways in western China, helped offset 0.54 million-ton of carbon emissions associated with grain transport. These findings contribute to a better understanding of the life cycle environmental impact within the food supply chain. The methodology proposed in this study could be applicable to a wide range of other food products that involve trans-regional production and consumption, both in China and other countries.
Air plethysmography characteristic of the pathological segmental hypervolemia of the calf in patients with CVD clinical classes (CEAP)
Authors: Sannikov A. B. , Shaydakov E. V. 
Published: May 2022

Introduction. The involvement of pathological segmental venous hypervolemia of the lower leg in patients with varicose veins in the formation of chronic venous insufficiency (CVI) is an established fact, however, objective criteria for this pathohemodynamic phenomenon have not been definitively determined today.The purpose of the study. Determination by air plethysmography (APG) of the degree of functional disorders in the limb and establishment of significant criteria characterizing pathological segmental hypervolemia of the lower leg in patients with CVD of various clinical classes according to CEAP.Materials and methods. For the period from 2002 to 2019, 380 healthy individuals with no symptoms of chronic venous diseases and 896 patients with CVD were examined with the use of APG, with their distribution in accordance with the CEAR international classification as follows: C0–C1, C2–C3, C4–C6 clinical classes. To assess the intensity of venous blood flow, the following values were calculated: the maximum capacity of the leg veins (Venous Capacity – VC), the volume of their evacuation (Evacuation Volume – EV) for a set time, the maximum venous outflow (Maximum Venous Outflow – MVO), the ratio of these values on both limbs (Venous Capacity Index – VC1, Evacuation Volume Index – EVI, Maximum Venous Outflow Index – MVOI).Results. The most statistically significant and conjugate correlation data were obtained (expectation, mean square deviation, standard error of expectation, median and coefficient of variation) during the analysis in groups according to the characteristic VCI.Discussion. The obtained results allowed us to assert that APG is an informative functional method for diagnosing hemodynamic disorders in patients with lower limb CVD.Conclusion. The established criteria of the venous capacity index will allow in practice to give an objective characterization of the degree of change in hemodynamic disorders in patients with CVD before and after the treatment undertaken.
Some features of compression therapy for varicose veins of the lower extremities of clinical class C2 according to CEAP
Authors: Bogachev V. Yu. , Boldin B. V. , Turkin P. Yu. , Klyuchevskaya M. N. 
Published: May 2022

Introduction.The main method of varicose vein disease treatment is surgical intervention. At the same time, there is a rather large group of patients who postpone surgical treatment indefinitely. In this situation, conservative measures come to the fore, the key one among which is compression therapy.Aim.Study of the immediate effect of compression therapy on venous outflow from the lower extremities in patients with varicose veins and the medium-term results of medical knitwear classes 1 and 2.Materials and methods.The study enrolled 64 patients (mean age 28.3 ± 2.2 years, mean BMI 25.3 ± 4.1) with large saphenous vein reflux to the upper third of the tibia. Blood flow return time and pump force were measured while walking without and with zero, class 1, and class 2 compression knitted garments on.Results and discussion.On photoplethysmography return times without and with zero compression were 18.4 ± 2.2 s and 18.9 ± 1.4 s (p = 0.62), tibial venous pump strength was 3.6 ± 0.3% and 3.4 ± 0.2% (p = 0.57). Wearing a class 1 knitwear significantly increased return time and lower leg muscle venous pump strength to 21.6 ± 1.9 sec and 6.2 ± 1.8% (p < 0.001). Grade 2 knitwear increased return blood-flow time and tibia musculo-venous pump strength to 28.2 ± 2.6 sec and 12.3 ± 1.6%, which was significantly higher (p < 0.001). Global quality of life index according to CIVIQ-14 at baseline and follow-up was 44.3 ± 4.6 and 17.8 ± 3.6 points respectively (p < 0.001) in the class 1 group. Compression Class II had a mean value of 45.1 ± 3.9 and 18.1 ± 4.3 (p < 0.001).Conclusion.In summary, the RAL class 2 standard compression knitted fabric shows better immediate correction of lower leg muscle venous pump function in patients with primary varicose veins compared to the class 1 compression knitted fabric. In the mid-term followup there were no differences in the elimination of initial venous specific symptoms and in the improvement of the global quality of life index between class I and class II knitwear.
Influence of treatment methods on quality of life of patients with hemorrhoidal disease
Authors: Zagriadskiǐ E. A. , Bogomazov A. M. , Golovko E. B. , Abritsova M. V. 
Published: May 2022

Introduction. The effectiveness of the treatment of hemorrhoidal disease is based on the frequency of recurrence of hemorrhoid symptoms, the development of early and late postoperative complications, as well as the degree of patient satisfaction with the results of treatment. However, such an indicator as quality of life, which reflects the health of the patient, is not taken into account.Aim. Obtaining data on the influence of the method and type of treatment on the quality of life of patients suffering from acute or chronic hemorrhoids.Materials and methods. The analysis of the influence of the treatment method on the quality of life of patients suffering from acute or chronic hemorrhoids was carried out. The analysis included 1032 patients with stage I–IV hemorrhoids. The age of the patients was 44.8 ± 13.0 (18–94) years. The study included 509 (49.3%) men and 523 (50.7%) women.Results. Quality of life indicators before treatment in all groups are within the reference values, which is associated with adaptation of patients to the disease. After treatment, quality of life indicators naturally increase. However, in patients after hemorrhoidectomy, regardless of the nature of the technique, quality of life indicators are significantly lower than in patients of groups 1 and 2.Conclusions. Quality of life indicators in all groups before treatment are within the reference values and do not have statistically significant differences in the considered indicators. After the treatment, there is a statistically significant increase in the quality of life indicators in all scales. After hemorrhoidectomy, regardless of the nature of the technique, quality of life indicators are significantly lower than in patients of groups 1 and 2, which is associated with surgical trauma. Since the groups of patients are heterogeneous in terms of the stages of the disease, it can be assumed that for each stage of hemorrhoids, there is a subjective perception of the disease, which can be reflected in the quality of life indicators, which requires additional analysis of the results obtained.
Experience of homeopathic ointment during the non-surgical treatment for acute hemorrhoids in the outpatient settings
Authors: Belik B. M. , Kovalev A. N. 
Published: May 2022

Introduction. The use of traditional anti-inflammatory and local anesthetic preparations during the non-surgical treatment of acute hemorrhoids is liable to cause the progression of serious side effects in patients.Purpose of the study. To evaluate the clinical efficacy of homeopathic ointment as the topical preparation in the complex treatment of patients with acute hemorrhoids on the outpatient settings.Materials and methods. The comparative analysis of the results of the non-surgical treatment was conducted and applied to 48 patients with acute hemorrhoids of 1–3 degrees, who were divided into two groups. In 23 patients (control group), traditional non-surgical treatment was conducted without the use of topical preparations. In 25 patients (the main group), traditional preparation therapy was supplemented with local treatment using homeopathic ointment.Results. In the patients of the main group, a faster regression of pain syndrome and other manifestations of the disease (itching, burning and discomfort in the anal canal, perianal edema) was noted in the dynamics of treatment, and higher values of quality of life parameters were recorded than in patients of the control group. In the main group, good and satisfactory treatment results were obtained in 23 (92.0%) patients, unsatisfactory – in 2 (8.0%) patients. In the control group, good and satisfactory treatment results were observed in 18 (78.3%) patients, unsatisfactory results – in 5 (21.7%) patients.Discussion. The maximum therapeutic effect with topical application of ointment was observed in patients with acute hemorrhoids of 2–3 degrees, the disease in which proceeded with a pronounced inflammatory-allergic component.Conclusion. Our results allow us to consider homeopathic ointment as an alternative topical preparation in the non-surgical treatment of acute hemorrhoids in outpatient settings in patients with serious contraindications to the use of traditional topical preparations.
Use of Multiple Correspondence Analysis and K-means to Explore Associations Between Risk Factors and Likelihood of Colorectal Cancer: Cross-sectional Study
Authors: Florensa Dídac , Mateo-Fornés Jordi , Solsona Francesc , Pedrol Aige Teresa , Mesas Julió Miquel , Piñol Ramon , Godoy Pere 
Published: May 2022

Background
Previous works have shown that risk factors are associated with an increased likelihood of colorectal cancer.

Objective
The purpose of this study was to detect these associations in the region of Lleida (Catalonia) by using multiple correspondence analysis (MCA) and k-means.

Methods
This cross-sectional study was made up of 1083 colorectal cancer episodes between 2012 and 2015, extracted from the population-based cancer registry for the province of Lleida (Spain), the Primary Care Centers database, and the Catalan Health Service Register. The data set included risk factors such as smoking and BMI as well as sociodemographic information and tumor details. The relations between the risk factors and patient characteristics were identified using MCA and k-means.

Results
The combination of these techniques helps to detect clusters of patients with similar risk factors. Risk of death is associated with being elderly and obesity or being overweight. Stage III cancer is associated with people aged ≥65 years and rural/semiurban populations, while younger people were associated with stage 0.

Conclusions
MCA and k-means were significantly useful for detecting associations between risk factors and patient characteristics. These techniques have proven to be effective tools for analyzing the incidence of some factors in colorectal cancer. The outcomes obtained help corroborate suspected trends and stimulate the use of these techniques for finding the association of risk factors with the incidence of other cancers.
Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality
Authors: Menke Joe , Eckmann Peter , Ozyurt Ibrahim Burak , Roelandse Martijn , Anderson Nathan , Grethe Jeffrey , Gamst Anthony , Bandrowski Anita 
Published: May 2022

Background
Improving rigor and transparency measures should lead to improvements in reproducibility across the scientific literature; however, the assessment of measures of transparency tends to be very difficult if performed manually.

Objective
This study addresses the enhancement of the Rigor and Transparency Index (RTI, version 2.0), which attempts to automatically assess the rigor and transparency of journals, institutions, and countries using manuscripts scored on criteria found in reproducibility guidelines (eg, Materials Design, Analysis, and Reporting checklist criteria).

Methods
The RTI tracks 27 entity types using natural language processing techniques such as Bidirectional Long Short-term Memory Conditional Random Field–based models and regular expressions; this allowed us to assess over 2 million papers accessed through PubMed Central.

Results
Between 1997 and 2020 (where data were readily available in our data set), rigor and transparency measures showed general improvement (RTI 2.29 to 4.13), suggesting that authors are taking the need for improved reporting seriously. The top-scoring journals in 2020 were the Journal of Neurochemistry (6.23), British Journal of Pharmacology (6.07), and Nature Neuroscience (5.93). We extracted the institution and country of origin from the author affiliations to expand our analysis beyond journals. Among institutions publishing >1000 papers in 2020 (in the PubMed Central open access set), Capital Medical University (4.75), Yonsei University (4.58), and University of Copenhagen (4.53) were the top performers in terms of RTI. In country-level performance, we found that Ethiopia and Norway consistently topped the RTI charts of countries with 100 or more papers per year. In addition, we tested our assumption that the RTI may serve as a reliable proxy for scientific replicability (ie, a high RTI represents papers containing sufficient information for replication efforts). Using work by the Reproducibility Project: Cancer Biology, we determined that replication papers (RTI 7.61, SD 0.78) scored significantly higher (P<.001) than the original papers (RTI 3.39, SD 1.12), which according to the project required additional information from authors to begin replication efforts.

Conclusions
These results align with our view that RTI may serve as a reliable proxy for scientific replicability. Unfortunately, RTI measures for journals, institutions, and countries fall short of the replicated paper average. If we consider the RTI of these replication studies as a target for future manuscripts, more work will be needed to ensure that the average manuscript contains sufficient information for replication attempts.