bluuebunny/crossref_metadata_2025_split huggingface dataset:
AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation
Authors: Rawat Puneet , Prabakaran R , Kumar Sandeep , Gromiha M Michael 
Published: October 2019

Abstract

Motivation
Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases, biotechnology and biomaterial sciences. A majority of sequence-structural properties known for their mechanistic roles in protein aggregation do not correlate well with the aggregation kinetics. This limits the practical utility of predictive algorithms.

Results
We analyzed experimental data on 183 unique single point mutations that lead to change in aggregation rates for 23 polypeptides and proteins. Our initial mathematical model obtained a correlation coefficient of 0.43 between predicted and experimental change in aggregation rate upon mutation (P-value &lt;0.0001). However, when the dataset was classified based on protein length and conformation at the mutation sites, the average correlation coefficient almost doubled to 0.82 (range: 0.74–0.87; P-value &lt;0.0001). We observed that distinct sequence and structure-based properties determine protein aggregation kinetics in each class. In conclusion, the protein aggregation kinetics are impacted by local factors and not by global ones, such as overall three-dimensional protein fold, or mechanistic factors such as the presence of aggregation-prone regions.

Availability and implementation
The web server is available at http://www.iitm.ac.in/bioinfo/aggrerate-pred/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Towards a Political Economy of Charging Regimes: Fines, Fees and Force in Uk Immigration Control
Authors: Burnett Jon , Chebe Fidelis 
Published: October 2019

AbstractCharging regimes and the extraction of revenue are integral components of immigration control in the United Kingdom. However, while these have been analysed in their individual guises, to date, there has been little substantive analysis bringing these regimes together and locating them at the centre of its enquiry. Drawing on data obtained through the Freedom of Information Act 2000, this paper consequently examines the functions of charging regimes as a distinct form of statecraft, focussing its attention on UK Visas and Immigration fees and charges, carrier sanctions, charges related to accessing services and civil penalties administered though immigration enforcement. Analysing their historical roots and their contemporary prevalence, it suggests that they contribute to the political economy of financial power, which has significant implications for understandings of criminalization and immigration enforcement.
Development of a Multiresidue Method for Endocrine-Disrupting Pesticides by Solid Phase Extraction and Determination by UHPLC-MS/MS from Drinking Water Samples
Authors: Liu Shaoying , Huang Xihui , Hu Kejun , Jin Quan , Zhu Guonian 
Published: October 2019

Abstract
A rapid and efficient method based on solid phase extraction and liquid chromatography–tandem mass spectrometry was validated, allowing the determination of the endocrine-disrupting herbicides (acetochlor, alachlor, amitrole and atrazine), fungicides (carbendazim, triadimefon, penconazole and propiconazole), and insecticides (carbaryl and carbofuran) in drinking water. Low method detection limits (0.01–0.64 ng/L) and method quantification limits (0.03–2.13 ng/L) were obtained with satisfactory recoveries and precision for the endocrine-disrupting pesticides. The method was applied for real drinking water samples collected in the area of the city of Hangzhou (Zhejiang, China); the results showed that carbendazim, atrazine and acetochlor were detected in the drinking water samples and acetochlor was the most detected analyte.
The role of patient portals in enhancing self-care in patients with renal conditions
Authors: Hazara Adil M , Durrans Katherine , Bhandari Sunil 
Published: October 2019

AbstractWeb-based portals enable patients to access their electronic health records, including test results and clinical documents, from anywhere with Internet access. Some portals also serve as a means of two-way communication between patients and healthcare professionals and provide a platform for the recording of patient-entered data such as home blood pressure readings. Such systems are designed to encourage patient participation in the management of their condition, and ultimately to increase patient empowerment and self-management, which are associated with improved clinical outcomes. As an example of portal use in patients with renal conditions, we discuss the PatientView portal, which is offered free of cost to patients under the care of renal physicians in the UK. We present an account of its various features and briefly describe the user experience. Previous studies examining the impact of this portal on patient care have been very positive; it appears to be popular among users and overall levels of satisfaction with the service are high. As the use of patient portals increases, we discuss barriers to the more widespread use of portals. We offer suggestions on how the care of patients with renal conditions can be enhanced in the future by further developing the existing features, learning from experiences of other patient portals and providing better integration of portal use into the current model of care.
Differently sized cuckoos pose different threats to hosts
Authors: Yu Jiangping , E Mingju , Sun Wei , Liang Wei , Wang Haitao , Møller Anders Pape 
Published: October 2019

AbstractHole-nesting tits Parus spp. have been classified as “unsuitable” hosts for cuckoo parasitism because cuckoos cannot enter a cavity if the entrance is too small. However, Chinese tits could reject alien eggs and egg ejection rate increased with the local diversity of parasitic cuckoo species. Antiparasitic behavior among Chinese tits may have evolved due to greater size variation among sympatric cuckoo species. This raises the question of whether differently sized parasitic cuckoos pose different threats to Chinese tits. A green-backed tit Parus monticolus population that is sympatric with Asian emerald cuckoo Chrysococcyx maculatus (eme-cuckoo, small-sized parasite) and common cuckoo Cuculus canorus (com-cuckoo, large-sized parasite), and a cinereous tit P. cinereus population that is only sympatric with com-cuckoo were chosen as study organisms. We observed behavioral response and recorded alarm calls of the 2 tit species to eme-cuckoo, com-cuckoo, chipmunk Tamias sibiricus (a nest predator) and dove Streptopelia orientalis (a harmless control), and subsequently played back alarm calls to conspecific incubating females. In dummy experiments, both tit species performed intense response behavior to chipmunk, but rarely responded strongly to the 3 avian species. In playback experiments, both tit species responded strongly to conspecific chipmunk alarm calls, but rarely responded to dove alarm calls. The intensity of response of incubating female green-backed tits to eme-cuckoo and com-cuckoo alarm calls were similar to that of chipmunk alarm calls, while the intensity to eme-cuckoo alarm calls was higher than the intensity to dove alarm calls which was similar to that of com-cuckoo alarm calls. In contrast, few female cinereous tits responded to eme-cuckoo and com-cuckoo alarm calls. These findings indicated that the threat level of eme-cuckoo was slightly greater than that of com-cuckoo for sympatric green-backed tits, but not for allopatric cinereous tits.
Mechanisms of mitral regurgitation after percutaneous mitral valve repair with the MitraClip
Authors: Ikenaga Hiroki , Makar Moody , Rader Florian , Siegel Robert J , Kar Saibal , Makkar Raj R , Shiota Takahiro 
Published: October 2019

Abstract

Aims
We sought to find the morphological mechanisms of recurrent mitral regurgitation (MR) after MitraClip procedure using 3D transoesophageal echocardiography (TOE).

Methods and results
Of 478 consecutive patients treated with the initial MitraClip procedure, 41 patients who underwent repeat mitral valve (MV) transcatheter or surgical intervention for recurrent MR were retrospectively reviewed. Using 3D-TOE, we investigated morphological changes of MV leading to repeat MV intervention. Aetiology of MR at the index intervention was primary in 24 (59%) and secondary in 17 (41%) patients. In the primary MR group, worsening leaflet prolapse at the clip site caused recurrent MR in 12 (50%) patients, while 7 (29%) patients had a leaflet tear at the clip site. Acute single leaflet device detachment was seen in four patients and one patient had recurrent MR between the plug and the clip. In secondary MR, left ventricular (LV)/left atrial dilation caused recurrent MR in 13 (76%) patients. Significant increase in the LV end-diastolic volume and tenting height were observed from post-index procedure to repeat intervention (LV end-diastolic volume; from 205 to 237 ml, P &lt; 0.001, tenting height; from 0.8 to 1.3 cm, P &lt; 0.001). New emergent leaflet prolapse/flail was seen in 3 (18%) patients, suggesting iatrogenic MR.

Conclusion
Mechanisms of recurrent MR after MitraClip procedure varied and depended on the underlying MV pathology: in primary MR, worsening mitral leaflet prolapse and in secondary MR, progressive LV dilation with worsening tenting were the main causes of recurrent MR.
Computed tomography follow-up identifies radically treatable new primaries after resection for lung cancer
Authors: Mitchell Jenny , Benamore Rachel , Gleeson Fergus , Belcher Elizabeth 
Published: October 2019

Abstract

OBJECTIVES
The optimal imaging programme for the follow-up of patients who have undergone resection of primary lung cancer is yet to be determined. We investigated the incidence and patterns of new and recurrent malignancy after resection for early-stage lung cancer in patients enrolled into a computed tomography (CT) follow-up programme.

METHODS
We reviewed the outcomes of consecutive patients who underwent CT follow-up after resection of early-stage primary lung cancer at the Oxford University Hospitals NHS Foundation Trust, between 2013 and 2017.

RESULTS
Four hundred and sixty-six consecutive patients underwent resection of primary lung cancer between 1 January 2013 and 31 March 2017. Three hundred and thirty-one patients (71.0%) were enrolled in CT follow-up. The median follow-up was 98 weeks (range 26–262). Sixty patients (18.2%) were diagnosed with programme-detected malignancy. Recurrence was diagnosed in 36 patients (10.9%), new primary lung cancer in 16 patients (4.8%) and non-lung primary tumours in 8 patients (2.4%). A routine CT scan identified the majority of new primary lung cancers (84.2%) and those with disease recurrence (85.7%). The majority of programme-detected malignancies were radically treatable (55%). The median survival of programme-detected cancers was 92.4 versus 23.0 weeks for patients with clinically detected tumours (P < 0.0001). Utilizing the CT scout image as a surrogate for chest X-ray, the sensitivity of this modality was 16.95% (8.44–28.97%) and specificity was 89.83% (79.17–96.18%). Negative likelihood ratio was 0.92 (0.8–1.07).

CONCLUSIONS
CT follow-up of surgically treated primary lung cancer patients identifies malignancy at a stage where radical treatment is possible in the majority of patients. Chest X-ray follow-up may not be of benefit following lung cancer resection.
Follow-up after biventricular repair of the hypoplastic left heart complex
Authors: IJsselhof Rinske J , Duchateau Saniyé D R , Schouten Rianne M , Freund Matthias W , Heuser Jörg , Fejzic Zina , Haas Felix , Schoof Paul H , Slieker Martijn G 
Published: October 2019

AbstractOBJECTIVESIn hypoplastic left heart complex patients, biventricular repair is preferred over staged-single ventricle palliation; however, there are too few studies to support either strategy. Therefore, we retrospectively characterized our patient cohort with hypoplastic left heart complex after biventricular repair to measure left-sided heart structures and assess our treatment strategy.METHODSPatients with hypoplastic left heart complex who had biventricular repair between 2004 and 2018 were retrospectively reviewed. Operative results were evaluated and echocardiographic mitral valve (MV) and aortic valve (AoV) dimensions, left ventricular length and left ventricular internal diastolic diameter (LVIDd) were measured preoperatively and during follow-up after 0.5, 1, 3, 5 and 10 years.RESULTSIn 32 patients, the median age at surgery was 10 (interquartile range 5.0) days. The median follow-up was 6.19 (interquartile range 6.04) years. During the 10-year follow-up, the mean Z-scores increased from −2.82 to −1.49 and from −2.29 to 0.62 for MV and AoV, respectively. Analysis of variance results with post hoc paired t-tests showed that growth of left-sided heart structures was accelerated in the first year after repair, but was not equal, with the MV lagging behind the AoV (P = 0.033), resulting in significantly smaller MV Z-scores compared with AoV Z-scores at 10-year follow-up (P < 0.001). There were 2 (6%) early deaths. The major adverse events occurred in 4 (13%) patients. The surgical or catheter-based reintervention was required in 14 (44%) patients.CONCLUSIONSThe growth rate of heart structures was most prominent during the first year after biventricular repair with lower growth rate of the MV compared with the AoV.
A risk model to predict 2-year survival after VATS lobectomy for non-small-cell lung cancer
Authors: Tan Hui Xian , Drake Benjamin Cooper , Chaudhuri Nilanjan , Kefaloyannis Manos , Milton Richard , Papagiannopoulos Kostas , Tcherveniakov Peter , Brunelli Alessandro 
Published: October 2019

Abstract

OBJECTIVES
We sought to identify the risk factors associated with mortality post-video-assisted thoracoscopic surgery (VATS) lobectomy over a 2-year period.

METHODS
Analysis was performed using a sample from an institutionally maintained database. All lobectomies for non-small-cell lung cancer from April 2014 to March 2018 started with VATS approach and with a complete follow-up were included (n = 732). Several clinical variables were screened using the Cox univariate analysis for their association with 2-year survival. Those with a P-value <0.1 were included in a Cox proportional hazard model.

RESULTS
After multivariable analysis, the following variables showed significant association with 2-year survival: age >75 [hazard ratio (HR) 1.527, P = 0.043], carbon monoxide lung diffusion capacity <70 (HR 1.474, P = 0.061), body mass index (BMI) <18.5 (HR 2.628, P = 0.012), American Society of Anesthesiologist Physical Status >2 (HR 1.518, P = 0.047), performance status >1 (HR 1.822, P = 0.032) and male gender (HR 2.700, P < 0.001). A score of 2 was assigned to the male gender and BMI <18.5, with all other variables assigned a score of 1. Each patient was scored and placed into their risk class. A Kaplan–Meier estimate for 2-year survival was calculated for each class. These were collapsed into the following 3 classes of risk based on their similar 2-year survival: class A (score 0) 97%, 95% CI 88–99, class B (score 1–3) 84%, 95% CI 80–88, class C (score > 3) 66%, 95% CI 57–74.

CONCLUSION
Our scoring system can serve as an adjunct to a clinician’s experience in risk-stratifying patients during multidisciplinary tumour board discussion and the shared decision-making process.
Uptake and detection rate of a stepwise cardiometabolic disease detection program in primary care—a cohort study
Authors: Stol Daphne M , Hollander Monika , Badenbroek Ilse F , Nielen Mark M J , Schellevis François G , de Wit Niek J 
Published: October 2019

Abstract

Background
Early detection and treatment of cardiometabolic diseases (CMD) in high-risk patients is a promising preventive strategy to anticipate the increasing burden of CMD. The Dutch guideline ‘the prevention consultation’ provides a framework for stepwise CMD risk assessment and detection in primary care. The aim of this study was to assess the outcome of this program in terms of newly diagnosed CMD.

Methods
A cohort study among 30 934 patients, aged 45–70 years without known CMD or CMD risk factors, who were invited for the CMD detection program within 37 general practices. Patients filled out a CMD risk score (step 1), were referred for additional risk profiling in case of high risk (step 2) and received lifestyle advice and (pharmacological) treatment if indicated (step 3). During 1-year follow-up newly diagnosed CMD, prescriptions and abnormal diagnostic tests were assessed.

Results
Twelve thousand seven hundred and thirty-eight patients filled out the risk score of which 865, 6665 and 5208 had a low, intermediate and high CMD risk, respectively. One thousand seven hundred and fifty-five high-risk patients consulted the general practitioner, in 346 of whom a new CMD was diagnosed. In an additional 422 patients a new prescription and/or abnormal diagnostic test were found.

Conclusions
Implementation of the CMD detection program resulted in a new CMD diagnosis in one-fifth of high-risk patients who attended the practice for completion of their risk profile. However, the potential yield of the program could be higher given the considerable number of additional risk factors—such as elevated glucose, blood pressure and cholesterol levels—found, requiring active follow-up and presumably treatment in the future.
Effect of temperature, pH, physical and chemical factors on germination rate of the chlamydospores of the nematophagous fungus Duddingtonia flagrans
Authors: Wang Bobo , Zhang Nan , Gong Peng-tao , Li Jianhua , Yang Ju , Zhang Xichen , Cai Kuizheng 
Published: October 2019

ABSTRACT
This study mainly investigated the effects of environmental factors on the germination/dormancy, sporulation and resistance of Duddingtonia flagrans chlamydospores. Results showed that the germination temperature of chlamydospores was &gt;10°C and ≤35°C. After the chlamydospores were treated at −20, −40 and −80°C for 12–24 h, they still had the ability to germinate. The chlamydospores germinated at pH 3–13 but did not germinate at pH 1–2 and pH 14. The chlamydospores could tolerate ultraviolet rays for 720 min, but visible light irradiation for 24 h significantly reduced their germination rate. The chlamydospores did not germinate under anaerobic conditions. After the chlamydospores were cultured on water agar (WA) containing 5, 10 and 20% NaCl, their germination rate was significantly inhibited. Once NaCl was removed, the chlamydospores almost completely recovered their germination ability. Among the nine kinds of additives used in the study, 0.3% arginine significantly promoted spore germination (P &lt; 0.05) but 1% trehalose and 1% glycerine significantly inhibited spore germination during incubation from 24 h to 48 h (P &lt; 0.05). This work indicated that D. flagrans chlamydospores are highly resistant to environmental variations and so could be used for biocontrol of animal parasites.
Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma
Authors: Liu Qi , Lin Deng , Li Mingkun , Gu Zhenglong , Zhao Yiqiang 
Published: October 2019

Abstract
Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.
Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen
Authors: Feurtey Alice , Stevens Danielle M , Stephan Wolfgang , Stukenbrock Eva H 
Published: October 2019

AbstractGenome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.
Soluble Blood Markers of Mucosal Healing in Inflammatory Bowel Disease: The Future of Noninvasive Monitoring
Authors: Nardone Olga Maria , Shivaji Uday Nagesh , Ferruzza Vittoria , Ghosh Subrata , Iacucci Marietta 
Published: October 2019

Abstract
The traditional management of inflammatory bowel disease (IBD) based on symptom control is not considered valid anymore by most specialists in this field, and a new paradigm called “treat to target” has been introduced. This is based on the assessment of disease activity using objective measures. The identification of noninvasive biomarkers is crucial to diagnosis and monitor IBD because frequent endoscopic examinations are costly and uncomfortable for the patient. In this review, we focus on blood markers that may be able to assess mucosal healing (MH) in IBD and recent advances in this area. Introduction of commercial panel to predict MH opens the way for further developments so that colonoscopy or fecal markers may be avoided in some patients. This may also permit frequent monitoring for therapeutic response and achieve MH. It is a challenging area of research to identify a panel of biomarkers that may reflect inflammation and healing to serve as a surrogate of MH.