bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data
Authors: Xu Xiaofeng , Bei Jinlong , Xuan Yibo , Chen Jiayuan , Chen Defu , Barker Stephen C. , Kelava Samuel , Zhang Xiaoai , Gao Shan , Chen Ze 
Published: September 2020

Abstract
Background
In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported.

Results
In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia.

Conclusions
To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.
Rapid identification of capsulated Acinetobacter baumannii using a density-dependent gradient test
Authors: Kon Hadas , Schwartz David , Temkin Elizabeth , Carmeli Yehuda , Lellouche Jonathan 
Published: September 2020

Abstract
Background
Gram-negative bacterial capsules are associated with production of carbohydrates, frequently resulting in a mucoid phenotype. Infections caused by capsulated or mucoid A. baumannii are associated with increased clinical severity. Therefore, it is clinically and epidemiologically important to identify capsulated A. baumannii. Here, we describe a density-dependent gradient test to distinguish between capsulated and thin/non-capsulated A. baumannii.

Results
Thirty-one of 57 A. baumannii isolates displayed a mucoid phenotype. The density-dependent gradient test was comprised of two phases, with silica concentrations of 30% (top phase) and 50% (bottom phase). Twenty-three isolates migrated to the bottom phase, indicating thin or non-capsulated strains, and 34 migrated to the top phase, suggesting strains suspected to be capsulated. There was agreement between the mucoid and the non-mucoid phenotypes and the density-dependent gradient test for all but three isolates. Total carbohydrates extracted from strains suspected to be capsulated were significantly higher. Transmission electron microscopy confirmed the presence of a capsule in the six representative strains suspected to be capsulated.

Conclusions
The density-dependent gradient test can be used to verify capsule presence in mucoid-appearing A. baumannii strains. Identifying capsulated strains can be useful for directing infection control measures to reduce the spread of hypervirulent strains.
Plant extinction excels plant speciation in the Anthropocene
Authors: Gao Jian-Guo , Liu Hui , Wang Ning , Yang Jing , Zhang Xiao-Ling 
Published: September 2020

Abstract
Background
In the past several millenniums, we have domesticated several crop species that are crucial for human civilization, which is a symbol of significant human influence on plant evolution. A pressing question to address is if plant diversity will increase or decrease in this warming world since contradictory pieces of evidence exit of accelerating plant speciation and plant extinction in the Anthropocene.

Results
Comparison may be made of the Anthropocene with the past geological times characterised by a warming climate, e.g., the Palaeocene-Eocene Thermal Maximum (PETM) 55.8 million years ago (Mya)—a period of “crocodiles in the Arctic”, during which plants saw accelerated speciation through autopolyploid speciation. Three accelerators of plant speciation were reasonably identified in the Anthropocene, including cities, polar regions and botanical gardens where new plant species might be accelerating formed through autopolyploid speciation and hybridization.

Conclusions
However, this kind of positive effect of climate warming on new plant species formation would be thoroughly offset by direct and indirect intensive human exploitation and human disturbances that cause habitat loss, deforestation, land use change, climate change, and pollution, thus leading to higher extinction risk than speciation in the Anthropocene. At last, four research directions are proposed to deepen our understanding of how plant traits affect speciation and extinction, why we need to make good use of polar regions to study the mechanisms of dispersion and invasion, how to maximize the conservation of plant genetics, species, and diverse landscapes and ecosystems and a holistic perspective on plant speciation and extinction is needed to integrate spatiotemporally.
A novel predictive model based on inflammatory markers to assess the prognosis of patients with HBV-related acute-on-chronic liver failure: a retrospective cohort study
Authors: Qiang Li , Qin Jiao , Sun Changfeng , Sheng Yunjian , Chen Wen , Qiu Bangdong , Chen Xin , Chen Yuanfang , Liu Fei , Wu Gang 
Published: September 2020

Abstract
Background
Systemic inflammatory response is closely related to the development and prognosis of liver failure. This study aimed to establish a new model combing the inflammatory markers including neutrophil/lymphocyte ratio (NLR) and red blood cell distribution width (RDW) with several hematological testing indicators to assess the prognosis of patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF).

Methods
A derivation cohort with 421 patients and a validation cohort with 156 patients were recruited from three hospitals. Retrospectively collecting their clinical data and laboratory testing indicators. Medcalc-15.10 software was employed for data analyses.

Results
Multivariate analysis indicated that RDW, NLR, INR, TBIL and Cr were risk factors for 90-day mortality in patients with HBV-ACLF. The risk assessment model is COXRNTIC = 0.053 × RDW + 0.027 × NLR + 0.003 × TBIL+ 0.317 × INR + 0.003 × Cr (RNTIC) with a cut-off value of 3.08 (sensitivity: 77.89%, specificity: 86.04%). The area under the receiver operating characteristics curve (AUC) of the RNTIC was 0.873 [95% CI(0.837–0.903)], better than the predictive value of MELD score [0.732, 95% CI(0.687–0.774)], MELD-Na [0.714, 95% CI(0.668–0.757)], CTP[0.703, 95% CI(0.657–0.747)]. In the validation cohort, RNTIC also performed a better prediction value than MELD score, MELD-Na and CTP with the AUC of [0.845, 95% CI(0.778–0.898)], [0.768, 95% CI (0.694–0.832)], [0.759, 95% CI(0.684–0.824)] and [0.718, 95% CI(0.641–0.787)] respectively.

Conclusions
The inflammatory markers RDW and NLR could be used as independent predictors of 90-day mortality in patients with HBV-ACLF. Compared with MELD score, MELD-Na and CTP, RNTIC had a more powerful predictive value for prognosis of patients with HBV-ACLF.
A case report of wrist synovial infection due to Mycobacterium jacuzzii, Iran
Authors: Sakhaee Fatemeh , Masoumi Morteza , Vaziri Farzam , Siadat Seyed Davar , Fateh Abolfazl 
Published: September 2020

Abstract
Background
Mycobacterium jacuzzii (M. jacuzzii) was first isolated in 2003 by insertion of breast implants in Tel Aviv, Israel. In this case report, we describe our experience in detection of M. jacuzzii using phenotypic and genotypic test of wrist synovial sample.

Case presentation
A 73-year-old woman complained of pain and swelling in the right wrist for 4 months. Her body temperature was 37–38 °C, and symptoms, such as pain, swelling, and some movement limitation, were reported. Clinical laboratory parameters showed an elevated C-reactive protein (CRP) level, erythrocyte sedimentation rate (ESR), and white blood cells (WBC) count. The sequences of hsp65, rpoB, 16S rDNA, and sodA genes indicated very high homology to M. jacuzzii.

Conclusion
We report a case of synovial infection caused by M. jacuzzii in a patient with severe wrist pain in Iran, who was treated with amikacin, levofloxacin, and ethambutol. The outcomes of treatment after 8 months were positive, and no recurrence of infection was reported in the patient.
The diagnostic value of Superb Microvascular Imaging in identifying benign tumors of parotid gland
Authors: Zhao Lihui , Mao Yiran , Mu Jie , Zhao Jing , Li Fangxuan , Zhang Sheng , Xin Xiaojie 
Published: September 2020

Abstract
Background
We compared the ultrasound features, superb microvascular imaging (SMI) and micro vessel density (MVD) of pleomorphic adenoma (PA), Warthin’s tumor (WT) and basal cell adenoma (BCA) to explore the clinic value of SMI in differential diagnosis of benign tumors of parotid gland.

Methods
The vascular distributions and grade by color doppler flow imaging (CDFI) and SMI, as well as vascular index (VI) of 249 parotid gland masses from 217 patients were analyzed.

Results
The internal echogenicity of BCA are more homogeneous in comparing with WT and PA(P < 0.05). By SMI, the vascular distribution and vascular grade in PA were mainly peripheral (33.1%) and avascular (25.7%), Grade 1 (27.8%) and Grade 0 (25.7%). WT were mainly central (31.3%) and mixed distribution (34.9%), in Grade 3 (37.3%) and Grade 2 (36.2%). BCA was mainly peripheral (33.3%) and mixed distribution (33.3%), in Grade 2 (33.3%) and Grade 3 (33.3%). The overall detection rate of SMI for vascular Grade 2 and 3 was significantly higher than that of CDFI (P < 0.05). Both VI and MVD were lowest in PA, highest in WT (P < 0.001). The VI by SMI was correlated with MVD (P < 0.001). The correlation index between vascular distribution and grade by SMI and MVD were significantly higher than CDFI.

Conclusion
SMI can provide low-velocity blood flow information, which is helpful for the differential diagnosis of common benign tumors of parotid gland, and is expected to be more widely used.
Cognitive remediation following electroconvulsive therapy in patients with treatment resistant depression: randomized controlled trial of an intervention for relapse prevention – study protocol
Authors: Van de Velde Nele , Kappen Mitchel , Koster Ernst H. W. , Hoorelbeke Kristof , Tandt Hannelore , Verslype Pieter , Baeken Chris , De Raedt Rudi , Lemmens Gilbert , Vanderhasselt Marie-Anne 
Published: September 2020

Abstract
Background
Major depressive episode (MDE) is worldwide one of the most prevalent and disabling mental health conditions. In cases of persistent non-response to treatment, electroconvulsive therapy (ECT) is a safe and effective treatment strategy with high response rates. Unfortunately, longitudinal data show low sustained response rates with 6-month relapse rates as high as 50% using existing relapse prevention strategies. Cognitive side effects of ECT, even though transient, might trigger mechanisms that increase relapse in patients who initially responded to ECT. Among these side effects, reduced cognitive control is an important neurobiological driven vulnerability factor for depression. As such, cognitive control training (CCT) holds promise as a non-pharmacological strategy to improve long-term effects of ECT (i.e., increase remission, and reduce depression relapse).

Method/design
Eighty-eight patients aged between 18 and 70 years with MDE who start CCT will be included in this randomized controlled trial (RCT). Following (partial) response to ECT treatment (at least a 25% reduction of clinical symptoms), patients will be randomly assigned to a computer based CCT or active placebo control. A first aim of this RCT is to assess the effects of CCT compared to an active placebo condition on depression symptomatology, cognitive complaints, and quality of life. Secondly, we will monitor patients every 2 weeks for a period of 6 months following CCT/active placebo, allowing the detection of potential relapse of depression. Thirdly, we will assess patient evaluation of the addition of cognitive remediation to ECT using qualitative interview methods (satisfaction, acceptability and appropriateness). Finally, in order to further advance our understanding of the mechanisms underlying effects of CCT, exploratory analyses will be conducted using video footage collected during the CCT/active control phase of the study.

Discussion
Cognitive remediation will be performed following response to ECT, and an extensive follow-up period will be employed. Positive findings would not only benefit patients by decreasing relapse, but also by increasing acceptability of ECT, reducing the burden of cognitive side-effects.

Trial registration
The study is registered with ClinicalTrials.gov. Study ID: NCT04383509
Trial registration date: 12.05.2020.
Households experiencing catastrophic costs due to tuberculosis in Uganda: magnitude and cost drivers
Authors: Muttamba Winters , Tumwebaze Racheal , Mugenyi Levicatus , Batte Charles , Sekibira Rogers , Nkolo Abel , Katamba Achilles , Kasasa Simon , Majwala Robert Kaos , Turyahabwe Stavia , Mugabe Frank , Mugagga Kaggwa , Lochoro Peter , Dejene Seyoum , Birabwa Estella , Marra Claudio , Baena Ines Garcia , Kirenga Bruce 
Published: September 2020

Abstract
Background
Tuberculosis (TB) patients in Uganda incur large costs related to the illness, and while seeking and receiving health care. Such costs create access and adherence barriers which affect health outcomes and increase transmission of disease. The study ascertained the proportion of Ugandan TB affected households incurring catastrophic costs and the main cost drivers.

Methods
A cross-sectional survey with retrospective data collection and projections was conducted in 2017. A total of 1178 drug resistant (DR) TB (44) and drug sensitive (DS) TB patients (1134), 2 weeks into intensive or continuation phase of treatment were consecutively enrolled across 67 randomly selected TB treatment facilities.

Results
Of the 1178 respondents, 62.7% were male, 44.7% were aged 15–34 years and 55.5% were HIV positive. For each TB episode, patients on average incurred costs of USD 396 for a DS-TB episode and USD 3722 for a Multi drug resistant tuberculosis (MDR TB) episode. Up to 48.5% of households borrowed, used savings or sold assets to defray these costs. More than half (53.1%) of TB affected households experienced TB-related costs above 20% of their annual household expenditure, with the main cost drivers being non-medical expenditure such as travel, nutritional supplements and food.

Conclusion
Despite free health care in public health facilities, over half of Ugandan TB affected households experience catastrophic costs. Roll out of social protection interventions like TB assistance programs, insurance schemes, and enforcement of legislation related to social protection through multi-sectoral action plans with central NTP involvement would palliate these costs.
Pneumoperitoneum-induced pneumothorax during laparoscopic living donor hepatectomy: a case report
Authors: Chae Min Suk , Kwak Jueun , Roh Kyungmoon , Kim Minhee , Park Sungeun , Choi Ho Joong , Park Jaesik , Shim Jung-Woo , Lee Hyung Mook , Kim Yong-Suk , Moon Young Eun , Hong Sang Hyun 
Published: September 2020

Abstract
Background
We present a living donor case with an unexpected large-volume pneumothorax diagnosed using lung ultrasound during a laparoscopic hepatectomy for liver transplantation (LT).

Case presentation
A 38-year-old healthy female living donor underwent elective laparoscopic right hepatectomy. The preoperative chest radiography (CXR) and computed tomography images were normal. The surgery was uneventfully performed with tolerable CO2 insufflation and the head-up position. SpO2 decreased and airway peak pressure increased abruptly after beginning the surgery. There were no improvements in the SpO2 or airway pressure despite adjusting the endotracheal tube. Eventually, lung ultrasound was performed to rule out a pneumothorax, and we verified the stratosphere sign as a marker for the pneumothorax. The surgeon was asked to temporarily hold the surgery and cease with the pneumoperitoneum. Portable CXR verified a large right pneumothorax with a small degree of left lung collapse; thus, a chest tube was inserted on the right side. The hemodynamic parameters fully recovered and were stable, and the surgery continued laparoscopically. The surgeon explored the diaphragm and surrounding structures to detect any defects or injuries, but there were no abnormal findings. The postoperative course was uneventful, and a follow-up CXR revealed complete resolution of the two-sided pneumothorax.

Conclusion
This living donor case suggests that a pneumothorax can occur during laparoscopic hepatectomy due to the escape of intraperitoneal CO2 gas into the pleural cavity. Because missing the chance to identify a pneumothorax early significantly decreases the safety for living donors, point-of-care lung ultrasound may help attending physicians reach the final diagnosis of an intraoperative pneumothorax more rapidly and to plan the treatment more effectively.
Health-related quality of life became worse in short-term during treatment in head and neck cancer patients: a prospective study
Authors: do Nascimento Santos Lima Emanuelle , Ferreira Isabela Borges , Lajolo Paula Philbert , Paiva Carlos Eduardo , de Paiva Maia Yara Cristina , das Graças Pena Geórgia 
Published: September 2020

Abstract
Background
Quality of life (QoL) is influenced in head and neck cancer (HNC) patients by a set of factors related to diagnosis, treatment and tumor impacts. The aim of this study was to evaluate the Quality of Life (QoL) changes in Head and Neck cancer (HNC) patients during treatment (radiotherapy and/or chemoradiotherapy).

Methods
QoL was evaluated prospectively in 63 HNC patients during radiotherapy and/or chemoradiotherapy at three moments: before or at beginning (T0), in the middle (T1 ~ four weeks) and immediately at the end (T2 ~ eight weeks) of treatment. The differences between the scores at different time points was verified using Friedman’s non-parametric test. Negative changes between time points were evaluated, with differences (delta) of ±10 points being considered to be clinically significant.

Results
The total mean age was 59.1 ± 9.5y, and 82.5% were male. The oral cavity and larynx were more frequent tumors. The functional score for ‘role’ was decreased at time points T1 and T2 as compared to T0, while an improvement in scores was observed for cognitive function. Several physical symptoms also worsened over time, such as: fatigue, nausea and vomiting, dry mouth and sticky saliva, swallowing and skin symptoms, senses and teeth problems. A high frequency of altered and clinically meaningful values were observed for most of domains, ranging from 6 to 74%.

Conclusions
The QoL became worse at approximately one month after treatment beginning in HNC patients, and this remained until the end of therapy. Protocols directing to early nutritional counseling and management of symptoms of nutritional impact are important to improve clinical outcomes. This is part of preventive actions aiming to make the exhausting treatment process less traumatic and easier to complete.
Prevalence of venous obstructions in (recurrent) venous thromboembolism: a case-control study
Authors: Notten Pascale , Strijkers Rob H. W. , Toonder Irwin , ten Cate Hugo , ten Cate-Hoek Arina J. 
Published: September 2020

Abstract
Background
The role of venous obstructions as a risk factor for recurrent venous thromboembolism has never been evaluated. This study aimed to determine whether there is a difference in prevalence of venous obstructions between patients with and without recurrent venous thromboembolism. Furthermore, its influence on the development of post-thrombotic syndrome and patient-reported quality of life was assessed.

Methods
This matched nested case-control study included 32 patients with recurrent venous thromboembolism (26 recurrent deep-vein thrombosis and 6 pulmonary embolism) from an existing prospective cohort of deep-vein thrombosis patients and compared them to 24 age and sex matched deep-vein thrombosis patients without recurrent venous thromboembolism. All participants received standard post-thrombotic management and underwent an additional extensive duplex ultrasonography. Post-thrombotic syndrome was assessed by the Villalta-scale and quality of life was measured using the SF36v2 and VEINES-QOL/Sym-questionnaires.

Results
Venous obstruction was found in 6 patients (18.8%) with recurrent venous thromboembolism compared to 5 patients (20.8%) without recurrent venous thromboembolism (Odds ratio 0.88, 95%CI 0.23–3.30, p = 1.000). After a median follow-up of 60.0 months (IQR 41.3–103.5) the mean Villalta-score was 5.55 ± 3.02 versus 5.26 ± 2.63 (p = 0.909) and post-thrombotic syndrome developed in 20 (62.5%) versus 14 (58.3%) patients, respectively (Odds ratio 1.19, 95%CI 0.40–3.51, p = 0.752). If venous obstruction was present, it was mainly located in the common iliac vein (n = 7, 63.6%). In patients with an objectified venous obstruction the mean Villalta-score was 5.11 ± 2.80 versus 5.49 ± 2.87 in patients without venous obstruction (p = 0.639). Post-thrombotic syndrome developed in 6 (54.5%) versus 28 (62.2%) patients, respectively (Odds ratio 1.37, 95%CI 0.36–5.20, p = 0.736). No significant differences were seen regarding patient-reported quality of life between either groups.

Conclusions
In this exploratory case-control study patients with recurrent venous thromboembolism did not have a higher prevalence of venous obstruction compared to patients without recurrent venous thromboembolism. The presence of recurrent venous thromboembolism or venous obstruction had no impact on the development of post-thrombotic syndrome or the patient-reported quality of life.
Discrete fractional order two-point boundary value problem with some relevant physical applications
Authors: Selvam A. George Maria , Alzabut Jehad , Dhineshbabu R. , Rashid S. , Rehman M. 
Published: September 2020

AbstractThe results reported in this paper are concerned with the existence and uniqueness of solutions of discrete fractional order two-point boundary value problem. The results are developed by employing the properties of Caputo and Riemann–Liouville fractional difference operators, the contraction mapping principle and the Brouwer fixed point theorem. Furthermore, the conditions for Hyers–Ulam stability and Hyers–Ulam–Rassias stability of the proposed discrete fractional boundary value problem are established. The applicability of the theoretical findings has been demonstrated with relevant practical examples. The analysis of the considered mathematical models is illustrated by figures and presented in tabular forms. The results are compared and the occurrence of overlapping/non-overlapping has been discussed.