bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor Diagnosis of FFPE Sample by Target Genome Sequencing From Multiple Sequencing Platforms
Authors: Feng Baosheng , Lai Juan , Fan Xue , Guo Xin , Liu Yongfeng , Wang Miao , Wu Ping , Zhou Zhiliang , Yan Qin , Sun Lei 
Published: March 2022

Abstract
Technological innovation and increased affordability have contributed to the widespread adoption of target genome sequencing (TS) technologies in scientific research and clinical diagnostic applications. Cancer research consortia showed increasing acceptance of TS techniques to define the mutation landscape of multiple cancer types. These studies have primarily utilized Illumina’s sequencing instruments. In this study, we performed target genome sequencing of Reference OncoSpan FFPE (HD832) sample enriched by TSO500 panel using a new platform, GenoLab M, and compared it with NovaSeq 6000 and NextSeq 550 platforms. The data demonstrated that all three platforms showed high-quality scores, deep coverage, and high concordance for variant detection (94.8%). Besides, the GenoLab M platform displays high accuracy in tumor diagnosis of FFPE sample. Briefly, the GenoLab M platform shows comparable performances with NovaSeq 6000 and NextSeq 550, indicating its potential applicability in cancer TS at a lower cost.
Evaluation of anaemia in geriatric patients: a retrospective hospital based study from Northern Sri Lanka
Authors: Sujanitha Vathulan , Sooriyakumar Thaneswary , Kumarasiri Thusitha , Rajeshkannan Nadarajah , Tharmiga Sooriyakumaran 
Published: March 2022

Abstract
Background:Anaemia in elderly is a common medical problem but it is often not evaluated as a sole clinical entity and the importance of anaemia is often neglected. The gravity of anaemia in elders and its impact on other diseases is not well known in Sri Lanka.Methods:It is a cross sectional descriptive study where data was extracted retrospectively from the data base and clinical records of patients who were referred to haematology unit of Teaching Hospital Jaffna, Sri Lanka for the evaluation of anaemia during September 2020 to February 2021.Common type of anaemia, severity, aetiological classifications and association with other diseases were analysed.Results:A total of 1121 elderly patients of above 60 years were analysed during the study period. Main source of referral was from medical wards. Female to male ratio was 51.2:48.8. Majority of them belonged to the age group of 60-69 years. Two third of the patients had normocytic anaemia (70.3%) followed by microcytic and macrocytic anaemia (23.7%). Moderate degree of anaemia was seen commonly in the patient’s analysed but 28.3% found to have severe anaemia. Aetiological classification revealed anaemia of chronic diseases as the commonest type of anaemia in elderly accounting for 37% followed by multifactorial aetiology and iron deficiency anaemia. Common chronic diseases identified along with anaemia were diabetes, hypertension, ischaemic heart disease and chronic kidney disease.Conclusion:Normocytic anaemia is the commonest type of anaemia identified in this hospital based study and majority had a moderate degree of anaemia. Though the common aetiological cause identified is anaemia of chronic disease, there are significant percentage of multifactorial causes identified indicating a search of many possible causes are needed in elderly patients with anaemia. Identifying the prevalence of anaemia in all hospitalised elderly patients in the local setting, the causes and the impact on chronic and acute illnesses will immensely help in the management of elderly patients and to improve their quality of life.
Complete Genome Sequence and Iron-Sulfur Oxidation Characteristics of The Newly Isolated Acidithiobacillus Ferrooxidans YQ-N3
Authors: Li Wenbo , Feng Qiyan , Li Ze , Chen Di 
Published: March 2022

Abstract
Acidithiobacillus ferrooxidans (A. ferrooxidans) is a chemoautotroph that can simultaneously oxidize Fe2+, S, and reduced sulfur compounds. Therefore, this bacterium plays a key role in the natural cycles of Fe and S. In this study, a novel A. ferrooxidans strain was isolated from sediments of a river polluted by the acid mine drainage (AMD) of an abandoned mine in Shanxi, China, after which it was characterized via whole-genome sequencing. Furthermore, its functional genes related to iron and sulfur metabolism and response to environmental stress were analyzed, and its capacity to oxidize FeSO4·7H2O, S0, and FeS2 as an energy source was preliminarily discussed. The whole-genome sequencing results revealed that A. ferrooxidans YQ-N3 has a 3,217,720 bp genome, which is comprised of one circular chromosome and five circular plasmids (Plasmid A, Plasmid B, Plasmid C, Plasmid D, Plasmid E). Among these, Plasmid E had not been previously described in this species, and its genome contains various functional genes related to iron and sulfur, drug resistance, and heavy metal resistance. A. ferrooxidans YQ-N3 can increase the oxidation rate of Fe2+ and S0 and enhance the hydrophilicity of S0. Moreover, this strain can accelerate FeS2 oxidation and the formation of secondary minerals. The present study demonstrated that the newly isolated A. ferrooxidans YQ-N3 could bio-oxidize iron and sulfur under acidic conditions, which was supported by our genome analysis results. Collectively, our findings provide important insights into the role and potential of A. ferrooxidans in biogeochemistry and industrial applications.
Global Longitudinal Strain for Detection of Cardiac Iron Overload in Patients with Thalassemia: A Meta-analysis of Observational Studies with Individual-Level Participant Data
Authors: Attar Armin , Hosseinpour Alireza , Hosseinpour Hamidreza , Rezaeian Nahid , Abtahi Firoozeh , Mehdizadeh Fereshte , Parsaee Mozhgan , Akiash Nehzat , Behjati Mohaddeseh , Meloni Antonella , Pepe Alessia 
Published: March 2022

Abstract
Background
Although cardiac magnetic resonance (CMR) is the most reliable tool for assessment of CIO in patients with thalassemia, it is not always readily available. Recent studies have explored the potential of GLS as an alternative for diagnosis of CIO. We aimed to investigate the efficacy of global longitudinal strain (GLS) for detection of cardiac iron level (CIO).
Methods
We searched SCOPUS, MEDLINE, and Embase to identify the studies which used GLS for assessment of CIO. We searched for individual participant data (IPD) in eligible studies to perform ROC curve analysis. CMR with a T2* cut-off value of 20ms was considered as the gold standard. A meta-analysis was performed and the risk of bias was assessed using the JBI Checklist.
Results
A total of 14 studies with 789 thalassemia patients (310 and 430 with and without CIO respectively and 49 with undetermined condition) were considered eligible for meta-analysis. IPDs of 405 participants were available. GLS was significantly lower in patients with CIO (-17.5 ± 2.7%) compared to those without CIO (-19.9 ± 2.3%; WMD = 1.6%, 95% CI= [0.76–2.4], p = 0.001, I2 = 77.1%) and to normal population (-20.61 ± 2.26%; WMD = 2.2%, 95% CI= [0.91–3.5], p = 0.001, I2 = 83.9%). A GLS<-19.5% could predict CIO with 92.8% sensitivity and 34.63% specificity (AUC = 0.659, 95% CI= [0.6–0.72], p-value < 0.0001). A GLS value≤-5.74% has 100% positive predictive and ≥-24.5% has 100% negative predictive values for detection of CIO.
Conclusions
According to our study, GLS is a strong predictor of CIO and when CMR is not available, it may be a useful screening method for identification of CIO in thalassemia patients.
Clinical Relevance of Incomplete Device Endothelialization After Left Atrial Appendage Closure
Authors: Xu Jing , Chen Chuan Zhi , Xing Jun , Wang Liang , Tao Yi Rao , Yang Bing , Zhang Qi , Shen Yun Li , Hu Jian Qiang 
Published: March 2022

Abstract
Purpose
This study aimed to assess the incidence, potential risk factors and clinical impact of incomplete device endothelialization (IDE) after left atrial appendage closure (LAAC).
Methods
A total of 101 consecutive patients with nonvalvular atrial fibrillation (AF) who underwent successful LAAC and received antithrombotic treatment using a standard regimen were prospectively followed up to 6 months after the procedure. The status of device endothelialization and device-related thrombus (DRT) were evaluated using cardiac computed tomography (CT). Major adverse cardio-cerebral events (MACCE) including all-cause death, heart failure(HF) hospitalization, acute ischemic stroke, transient ischemic attack(TIA), peripheral vascular embolism, and major bleeding were recorded.
Results
IDE was detected in 65 (64.4%) patients. Patients with IDE or complete device endothelialization (CDE) did not significantly differ with respect to baseline clinical characteristics and interventional procedure features. Multivariate analysis model revealed that persistent AF, left atrial appendage ostial diameter and left atrial size were independent risk factors for IDE. During 6-month follow-up, the incidence of DRT was 4.6% in patients with IDE and 2.8% in those with CDE, respectively (p > 0.05), and the overall rate of MACCE was non-significantly higher in the IDE group (7.7% vs. 2.8%, p = 0.32).
Conclusions
IDE is common after LAAC, especially in patients with persistent AF, higher left atrial appendage ostial diameter and left atrial size. IDE confers an increased risk for DRT, but may be not necessarily associated with thromboembolic events and poor clinical outcome, providing careful monitoring and continued antithrombotic therapy are given.
Exploring the Implementation of Teaching and Learning English Speaking Skills in Ethiopian EFL Classes: The Case of selected Five Woredas Secondary Schools in Kafa Zone
Authors: Bulbula Dereje Asfaw , Fayisa Obsa Neme , Bulti Tesfa Alemu , Modofa Mulualem Getachew , Abajobir Fedila Abazinab , Areda Damtew Bulbula , Sada Eyasu Yaya 
Published: March 2022

Abstract
Communication capacity (Speaking skill) in English in language education is a difficult task that needs effective guidance and sustainable practice. Therefore, this study aimed at exploring the Implementation of Teaching and Learning English Speaking Skills in Ethiopian EFL Classes. The design of the study was descriptive survey. The participants were 523 students included using simple random sampling technique and 30 EFL teachers using availability sampling technique. To collect data, questionnaire for students and Focus Group Discussions for teachers were used. Mixed method data analysis was used. The result showed that EFL teachers were not using different techniques of teaching English speaking skill, and they were not making sustainable follow up on how learners perform. They also apply teacher centered method than learner’s method. Learners faced challenges from mother tongue influence, lack of confidence, and fear of making a mistake. EFL teachers were also challenged by student related problem like disinterested to be involved in the actual teaching and learning actively, uncomfortably of the school compound, absence of well- equipped English mini-media and bulkiness of the textbook. Thus, EFL teachers should use various techniques, school administration should avail the resource and students should be participatory in their learning.
Measuring alexisomia and its relation to alexithymia using the Body Awareness Questionnaire
Authors: Carre Arnaud , Shankland Rebecca , Guillaume Philippe , Duclos Jeanne , Pellissier Sonia , Flaudias Valentin 
Published: March 2022

Abstract
Background: Awareness of one’s own states is a particularly important part of cognition and emotion regulation. Difficulties in this domain is seen as the roots of several types of disorders. Impairments in perceiving emotional states has been widely documented, leading to show alexithymia - the difficulty in identifying, conceiving and communicating one's states - as a central mechanism of somatic and mental disorders. Recently, the concept of alexisomia has been used to refer to lack of awareness and expression of somatic sensations. Developing self-reported questionnaires to evaluate alexisomia represents a challenge for clinical psychology and medicine. In this context, we suggested to adapt the Body Awareness Questionnaire (BAQ, Shields et al., 1989) in France to assess alexisomia in relation to alexithymia. Methods: For this study, 610 participants completed questionnaires measuring alexithymia and alexisomia. Results: Confirmatory factor analyses showed that the BAQ can be envisaged through 4 factors as well as a unidimensional model to refer to alexisomia. We also found that body awareness was negatively related to scores of alexithymia. Conclusion: Results are discussed in light of the construct of alexisomia and its clinical implications in somatic as well as mental disorders. We suggest that alexisomia is a key concept, in the same way as alexithymia, to design treatment and prevention programs.
Effect of Competitive Binding of Long Non-coding RNA CCDC26 with miR-340 on the Chemosensitivity of HCC Cells to Cisplatin
Authors: LI Cai , YE Qi-Fa 
Published: March 2022

Abstract
Background We investigate the effect of long non-coding RNA (lncRNA) CCDC26 on the chemosensitivity of HCC cells to cisplatin and the underlying mechanisms. Methods Firstly, the expression of CCDC26 in HCC tissues was detected. After siRNA interference of CCDC26, the HCC cells QGY8105 and HCC9204 were selected as the objects of study to detect the changes in their chemosensitivity to cisplatin through the terminal-deoxynucleotidyl transferase mediated nick end labeling (TUNEL) and IC50 assays. Additionally, the RT-PCR assay, RNA hybrid software analysis, and luciferase reporter assay were performed to screen and verify the miRNAs that showed endogenous competitive relationship with CCDC26. Finally, miRNA was co-transfected with CCDC26, so as to explore whether the competitive binding of CCDC26 with miRNA changed the sensitivities of QGY8105 and HCC9204 cells to cisplatin. t-test or analysis of variance was adopted to compare data between groups based on the data property.. Results CCDC26 expression in HCC tissues was higher than that in normal tissues. Under the action of cisplatin, the IC50 value in si-CCDC26 group was lower than that in si-NC group, while the percentage of TUNEL-positive cells was higher than that in si-NC group, and the differences were statistically significant. RT-PCR results indicated that, miR-340 expression in si-CCDC26 group was up-regulated relative to that in si-NC group; meanwhile, RNA hybrid analysis and luciferase verification results demonstrated that there was base complementation between CCDC26 and the “seed” region of miR-340. Thereafter, miR-340 was co-transfected with CCDC26 into HCC9204 cells, and it was discovered that, the IC50 value in miR-340 + CCDC26-wild type group increased compared with those in miR-340 + NC and miR-340 + CCDC26-mutant groups. Meanwhile, the percentage of TUNEL-positive cells was reduced, and the differences were of statistical significance. Conclusions LncRNA CCDC26 can reduce the chemosensitivity of HCC cells to cisplatin through the endogenous competitive binding with miR-340.
Prevention of Glucocorticoid-induced Osteoporosis in Elderly Patients With Immune Thrombocytopenia: a Single-institute Retrospective Study
Authors: Yamasaki Satoshi , Kamezaki Kenjiro , Ito Yoshikiyo , Horiuchi Takahiko 
Published: March 2022

Abstract
Introduction: Prednisolone, used as a standard initial treatment for immune thrombocytopenia (ITP), is an important risk factor for osteoporosis. To investigate the prevention of glucocorticoid-induced osteoporosis (GIO) in elderly ITP patients, associations between GIO prevention and score changes of a dual-energy X-ray absorptiometry (DXA) scan, FRAX®, and the Garvan tool during initial loading of prednisolone were examined.Methods: In our institute, 22 ITP patients aged >70 years received 0.5–1.0 mg/kg prednisolone for 2–3 weeks as the initial ITP treatment between 2014 and 2021. The femoral neck bone mineral density (BMD) measured by DXA scan was entered into FRAX® to define the risk-adapted approach to bisphosphonate during the initial loading of prednisolone. Additional active vitamin D with bisphosphonate was prescribed for women. Results: During the initial loading of prednisolone in ITP patients aged >70 years, seven patients achieved a complete response. Fifteen patients with a platelet count <30 × 109/L received thrombopoietin receptor agonist at the tapering phases of prednisolone. Bisphosphonate was performed according to <−1.0 femoral neck BMD T-score measured by DXA scan. Worse scores of FRAX® and the Garvan tool were associated with use of bisphosphonate for short-term fracture prevention in primary GIO; however, there were no incidents of fracture and no significant differences in probabilities determined by FRAX® and the Garvan tool. Conclusions: During the initial loading of prednisolone, prescribing bisphosphonate might prevent the reduction of BMD, but additional prescription of active vitamin D for women is still controversial.
Improvement of myelopoiesis in a cyclophosphamide-induced myelodepression model by administration of a Newly Synthesized Pyrazolo- Piperidine β-Cyclodextrine complex compound
Authors: Daulet Guldana , Baktybayeva Layilya , Belyaev Nikolai , Koshetova Zhanargul , Ostapchuk Yekaterina , Perfilyeva Yuliya , Kali Aikyn , Abdolla Nurshat , Tleulieva Raikhan , Ten Assel , Yu Valentina , Zazybin Alexey 
Published: March 2022

Abstract
According to WHO, the acquired secondary form of hematopoietic-depressive states increases the risk of death in people with cancer, infectious, and hormonal diseases. The choice of drugs that stimulate the proliferative activity of bone marrow cells is limited. The stimulus to the search for hematopoietic-stimulating compounds among pyridine derivatives was the manifestation of the activity of the cerebroprotective drug Mexidol (2-ethyl-6-methyl-3-hydroxypyridine succinate) to restore the granulocytes and B-lymphocytes homeostasis in clinical practice. The hematopoietic-stimulating activity of the newly synthesized compound Complex of 5-benzyl-7-(o-fluorobenzylidene)-2,3-bis(o-fluorophenyl)-3,3a,4,5,6,7-hexahydro-2H-pyrazolo [4,3-c]pyridine complex with β-cyclodextrin (BIV) was studied on a model of cyclophosphamide-induced myelodepression in C57BL6/J mouse line. The BIV compound demonstrated a stimulating effect on the process of restoring the level of Ly-6G+ Ly-6C+ granulocytes, monocytes/macrophages, CD19+ B-lymphocytes in the bone marrow, exceeding the activity of the reference drug Methyluracil. The BIV compound did not affect on the proliferative activity of c-kit (CD117+)-expressing cells, CD3e+ pre-T-lymphocytic cells and Ter-119+ erythroid cells in the bone marrow. The total number of bone marrow myelokaryocytes in the experimental groups was significantly higher than in the intact group. The pronounced hematopoietic-stimulating effect of the BIV compound gives in the future the prospect of development as a drug used for the treatment of B-lymphocytic and granulocytic-macrophage hematopoietic-depressive states.
A Novel External Immobilization Method to Establish a Rat Model of Knee Extension Contracture
Authors: Zhou Yun , Zhou Chen Xu , Wang Feng , Hua Wang , Fang Qiao Zhou , Xiong Kai Ge , Zhang Quan Bing 
Published: March 2022

Abstract
Background: The study aimed to elucidate the formation process and therapeutic strategies of knee extension contracture, we developed a novel rat model using an aluminum external fixator.Methods: Sixty male SD rats with mature bones were divided into the control group (n=6) and groups that had the left knee immobilized with an aluminum external fixator for 1, 2, and 3 days, and 1, 2, 3, 4, 6, and 8 weeks (n=6 in each group). The passive extension range of motion, histology, and expression of fibrosis-related proteins were compared between the control group and the immobilization groups.Results: Myogenic contracture progressed very quickly during the initial 2 weeks of immobilization; after 2 weeks, the contracture gradually changed from myogenic to arthrogenic. The arthrogenic contracture progressed slowly during the first week, rapidly progressed until the third week, and then showed a steady progression. Histological analysis confirmed that the anterior joint capsule of the extended fixed knee became increasingly thicker over time. Correspondingly, the level of TGFβ-1 in the anterior joint capsule also increased with the immobilization time. Over time, the cross-sectional area of muscle fibers gradually decreased, while the amount of intermuscular collagen and TGFβ-1 increased. Unexpectedly, the amount of intermuscular collagen and TGFβ-1 decreased during the late stage of immobilization (6–8 weeks).Conclusion: Myogenic contracture is stabilized after 2 weeks of immobilization, while arthrogenic contracture is stabilized after 3 weeks of immobilization. This novel rat model may be a useful tool to study the etiology of joint contracture and establish new therapeutic approaches.
The COVID-19 Omicron wave in the framework of a new mathematical modeling in few European countriesand the right time for lifting restrictions
Authors: Petkov Pavel 
Published: March 2022

Abstract
The COVID-19 Omicron wave in Romania, Bulgaria and Germany is considered within a new approach [6] for modeling Epidemics and a short comparison is made of similar applicationto few strongly affected countries in the beginning of 2022: the USA, the UK and France.The main novelty of that approach is the tracking of successive generations of infected people instead of treating in time the evolution of several large compartments within which the total population is partitioned (susceptible, infected, recovered,...). Because of the much strongest transmission of Omicron, its wave starts to dominate the Pandemic after some moment in time, and then the simplest version of the model [6] can be employed (without consecutive waves, no incoming from outside infected individuals e.t.c.) The daily observed new infection cases are described in a reasonable way after normalization. The position of the calculated Pandemic peaks in time in Romania and Bulgaria indicates a transition from the second to to the third generation of infected people. For comparison, in the USA, UK and France the transition is from the third to the fourth generation.The parameters derived by reproducing the data in the three countries considered are consistent with those derived earlier for the USA, the UK and France (i.e. infection and recovery rates). Due to the high contagiousness of Omicron, a very large part of the population will be gone through a contact with the virus in a relatively small period of time (3-4 months). This part is comparable to the total number of infections which occurred for two years, since the beginning of the Pandemic by end of 2019.Therefore, one may hope that some temporary acquired immunity will be reached. Adding the effects of vaccination, one may hope with moderate optimism that it will be possible to control/stop the COVID-19 Pandemic soon. However, lifting restrictions should be done carefully and country specifically, and of course at the right time, as illustrated by the examples of the UK and Germany.The present work represents exclusively a mathematical modeling of the Pandemic and does not deal with any other aspect of health, social or economic character as well with throwing away any possibility for unexpected developments. Yet we hope that the present results will be of some help.