bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of seismic reactions of an energy steam boiler
Authors: Yakovlev P V , Lebedev V A , Cqhurkin I S 
Published: November 2019

Abstract
Energy boilers for seismic impacts are different from other objects. Their individual characteristics are associated with the frame construction and the boilers used pipes of great length. The most important parameter used in the calculation of seismic effects is the damp-ratio. The damp-ratio is different for pipes and frame, and this creates difficulties in performing calculations. The paper proposed a method for taking into account the difference of the damp-ratio and estimated the calculation error in the case of the use of the damp-ratio for the frame when calculating the entire boiler without taking into account the features of pipe damping. According to the results of calculations, the elements with the greatest deformations and the elements with the highest stresses in the metal are identified in the boiler structure.
Potential for the wellbore zone development using the dynamic impact
Authors: Babichev I N , Fattakhov I G , Kuleshova L S , Zaripov L F , Morozov M A 
Published: November 2019

Abstract
To increase the effect of acid formation treatment (increase in production/injectivity, an overhaul period, reduction of costs of geological and technical works), the authors suggest using a dynamic impact on the wellbore zone (WZ) by using acid creating the rinsing effect with the help of swab equipment and an acid aggregate when waiting for the acid reaction. The article aims to analyze the potential for the application of dynamic impacts on the WZ. The differences of the technology from other impact methods were studied. The main parameters of the wells before and after the dynamic WZ treatment were determined using three indicators: a fluid flow rate, an oil flow rate and a water cut rate. The economic effect of the technology was compared with the effect of the clay-acid treatment (CAT) technology and complex vibrational depression chemical effects (CVDCE). The technology can be used at other NGDUs in order to improve the profitability of field development.
Effect of changes in the crank radius on the kinematics of the pumping unit when regulating the dynamic level of the fluid in the well
Authors: Gabzalilova A Kh , Soloviev N N , Garifullina Z A 
Published: November 2019

Abstract
The article deals with the effect of changes in the crank radius on the kinematics of the pumping unit when regulating the dynamic level of the fluid between the tubing strings and the casing in order to increase the well production rate or reduce the accident rate. To improve the quality of prediction, the movement of a polished rod over time is calculated using the Fourier variable separation method: the product of the rocker head of a pumping unit determined as movement of a slider crank mechanism along the straight line (as a circle chord), and the difference of this chord with a length of the circumference equivalent to the movement of the swivel joint of the balancer with a connecting rod. As a result, the accuracy of calculations is increased and the solution of the problem is simplified.
Prediction of production well flow rates using survey data
Authors: Mukhametshin V V , Kuleshova L S 
Published: November 2019

Abstract
The influence of geological and physical properties of the layers determined during geophysical studies on the maximum optimal flow rate of wells was studied for two groups of objects in terrigenous reservoirs of the Cretaceous age of Western Siberia. Multidimensional models were constructed. They allow for prediction of potential flow rates using indirect information when developing deposits in natural modes and using artificial waterflooding. An algorithm for substantiating selective and focal waterflooding, transfer of wells from other horizons and transfer of idle wells into the productive well stock was developed.
Modeling and mathematical evaluation of sidetracked wells operation in Tuymazy oil field
Authors: Petrova L V , Soloviev N N , Miller A F , Almukhametova E M 
Published: November 2019

Abstract
In order to extract residual oil in the Tuymazy Oil Field, sidetracks were drilled from wells that fell out of use to reservoir zones where oil reserves are not yet developed. Enhanced oil field’s recovery is an urgent problem, the solution of which will affect the efficiency of geological exploration production, oil production and the region’s economic potential.
An Ecological Momentary Assessment Study Investigating Self-efficacy and Outcome Expectancy as Mediators of Affective and Physiological Responses and Exercise Among Endometrial Cancer Survivors
Authors: Liao Yue , Song Jaejoon , Robertson Michael C , Cox-Martin Emily , Basen-Engquist Karen 
Published: November 2019

AbstractBackgroundPrevious studies have shown affective and physiological states in response to exercise as predictors of daily exercise, yet little is known about the mechanism underlying such effects.PurposeTo examine the mediating effects of self-efficacy and outcome expectancy on the relationships between affective and physiological responses to exercise and subsequent exercise levels in endometrial cancer survivors.MethodsEcological momentary assessment (EMA) surveys were delivered up to eight 5- to 7-day periods over 6 months. Participants (n = 100) rated their affective and physiological states before and after each exercise session (predictors) and recorded their self-efficacy and outcome expectancy each morning (mediators). Exercise (outcome) was based on self-reported EMA surveys and accelerometer measures. A 1-1-1 multilevel mediation model was used to disaggregate the within-subject (WS) and between-subject (BS) effects.ResultsAt the WS level, a more positive affective state after exercise was associated with higher self-efficacy and positive outcome expectation the next day, which in turn was associated with higher subsequent exercise levels (ps &lt; .05). At the BS level, participants who typically had more positive affective and experienced less intense physiological sensation after exercise had higher average self-efficacy, which was associated with higher average exercise levels (ps &lt; .05).ConclusionsIn endometrial cancer survivors, affective experience after exercise, daily self-efficacy and positive outcome expectation help explain the day-to-day differences in exercise levels within-person. Findings from this study highlight potentials for behavioral interventions that target affective experience after exercise and daily behavioral cognitions to promote physical activity in cancer survivors’ everyday lives.
Discussing age-related functional decline in family medicine: a qualitative study that explores both patient and physician perceptions
Authors: Viret Ophélie , Schwarz Joëlle , Senn Nicolas , Mueller Yolanda 
Published: November 2019

Abstract

Background
evaluating a patient’s functional status and screening for geriatric syndromes by general practitioners (GPs) are increasingly encouraged. This study aimed to explore how older people and GPs define and perceive autonomy and functional decline, patients’ propensity to discuss age-related issues and integration of such topics into routine medical consultations.

Methods
this qualitative study was conducted in Western Switzerland with older people followed in primary care practices and who participated in a trial assessing the effectiveness of a screening and management tool for geriatric syndromes to prevent functional decline. We interviewed 15 participants (patients ≥75 years old) and five GPs about their screening experience. We used semi-structured grids for data collection and an inductive thematic approach for data analysis.

Results
participants gave several definitions of autonomy, directly depending on their health status and functional limitations. Implementing various coping strategies, participants also expressed contrasted feelings related to functional decline such as fear, inability to accept and resilience. Functional decline was often perceived as normal ageing; participants were therefore not prompt at discussing age-related issues with their GP. However, screening was perceived positively by both participants and GPs, making addressing sensitive issues and detecting new problems possible.

Conclusions
a geriatric syndrome-screening intervention was well accepted by both patients and physicians. This type of initiative may be an opportunity to address various age-related issues and to inform patients of existing solutions.
Development of an electronic trigger tool at a children’s hospital within an academic medical center
Authors: Fortenberry Megan , Odinet Johlee , Shah Pooja , McKinzie Cameron , Murphy Kristin , Faircloth Cassidy Beach , Falato Christopher , Pappas Ashley 
Published: November 2019

Abstract

Purpose
To evaluate the validity and reliability of select recommended triggers, defined as flags found on review of the medical record that prompt further investigation to determine the presence or absence of an adverse drug event (ADE), selected from a list initially constructed based on severity, frequency, and detectability of triggers within a pediatric population.

Methods
This was a single-center, retrospective cohort analysis of pediatric patients admitted to University of North Carolina (UNC) Children’s Hospital who received trigger-associated medications between January 2015 and December 2016. Patient-care areas of the emergency department, operating rooms, and post-anesthesia care units were excluded. Trigger-detection encounters were evaluated by two reviewers using pre-established, consensus ADE criteria as determined by a panel of pediatric and medication safety specialists at UNC Medical Center. Events were categorized according to medication-related trigger and analyzed using descriptive statistics.

Results
A total of 3,836 positive triggers were included in this study. For the aggregate 12-part trigger tool package, 1,055 positive ADEs were identified, leading to a positive predictive value (PPV) of 27.5%. A 50% increase from baseline serum creatinine, resulting from co-administration of 2 or more nephrotoxic medications accounted for a total of 3,698/3,836 (96.4%). Incomplete documentation was the leading cause for event exclusion, 8/27 (30%). The triggers with the highest PPV included protamine 4/4 (100%), flumazenil 1/1 (100%), and vancomycin-related events 51/67 (76.1%), respectively. Phenytoin level >30 µg/mL or free level >2.5 µg/mL resulted in the lowest PPV, 1/12 (8.3%).

Conclusion
This study lays the foundation for further studies to develop a robust pediatric trigger tool that may involve developing multi-element triggers, determining sensitivity and specificity of triggers, or mobilizing the trigger tool to an automated system. Trigger tools can be individualized to meet each institutions’ needs and unique patient population.
Canagliflozin-induced Fanconi syndrome in a patient with previously unrecognized type 1 diabetes
Authors: Khan Naseer , Tso Katie , Broussard Joan , Dziuba Monica 
Published: November 2019

Abstract

Purpose
Canagliflozin is a sodium-glucose cotransporter-2 (SGLT2) inhibitor which received U.S. Food and Drug Administration approval in 2013 for the treatment of type 2 diabetes mellitus. Fanconi syndrome is a rare acquired disorder which typically occurs in adults as an adverse effect of medications. The literature includes few case reports of Fanconi syndrome caused by the use of canagliflozin. Here, we present a case of Fanconi syndrome in a patient with type 1 diabetes previously miscategorized as type 2 diabetes.

Summary
A 32-year-old woman with a 6-year history of type 2 diabetes was started on canagliflozin. Within 2 months of therapy initiation, she began to develop symptoms of high anion gap metabolic acidosis. Further laboratory test results showed severe life-threatening hypophosphatemia. Further investigation by nephrology revealed the presence of Fanconi syndrome. During the admission, she was found to have clinical and laboratory features of type 1 (insulin-dependent) diabetes. After discontinuation of canagliflozin, she was treated with intravenous (i.v.) fluids for hydration, subcutaneous insulin, and i.v. potassium phosphate. She recovered from all metabolic acidosis and electrolyte abnormalities.

Conclusion
Fanconi syndrome is a rare, exogenously acquired disorder in adults that often develops as an adverse effect of medication therapy. Our patient presented with Fanconi syndrome as a complication of canagliflozin use for the treatment of presumed type 2 diabetes. She was then started on subcutaneous insulin monotherapy for the treatment of type 1 diabetes mellitus.
NCutYX: a package for clustering analysis of multilayer omics data
Authors: Teran Hidalgo Sebastian J , Wu Mengyun , Ma Shuangge 
Published: November 2019

Abstract

Summary
Multilayer omics profiling has become a major venue for understanding complex diseases. We develop NCutYX, an R package for clustering analysis of multilayer omics data. The package and methods jointly analyze multiple layers of omics measurements and effectively accommodate their regulations. They systematically conduct a series of analysis based on the normalized cut technique, including the clusterings of subjects and omics measurements and biclustering. The package can be valuable for its timely context, novel methods and comprehensiveness.

Availability and implementation
https://cran.r-project.org/web/packages/NCutYX/.

Supplementary information
Supplementary data are available at Bioinformatics online.
DigestiFlow: from BCL to FASTQ with ease
Authors: Holtgrewe Manuel , Messerschmidt Clemens , Nieminen Mikko , Beule Dieter 
Published: November 2019

Abstract

Summary
Management of raw-sequencing data and its pre-processing (conversion into sequences and demultiplexing) remains a challenging topic for groups running sequencing devices. They face many challenges in such efforts and solutions ranging from manual management of spreadsheets to very complex and customized laboratory information management systems handling much more than just sequencing raw data. In this article, we describe the software package DigestiFlow that focuses on the management of Illumina flow cell sample sheets and raw data. It allows for automated extraction of information from flow cell data and management of sample sheets. Furthermore, it allows for the automated and reproducible conversion of Illumina base calls to sequences and the demultiplexing thereof using bcl2fastq and Picard Tools, followed by quality control report generation.

Availability and implementation
The software is available under the MIT license at https://github.com/bihealth/digestiflow-server. The client software components are available via Bioconda.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English
Authors: Perez Naiara , Accuosto Pablo , Bravo Àlex , Cuadros Montse , Martínez-Garcia Eva , Saggion Horacio , Rigau German 
Published: November 2019

Abstract

Motivation
Biomedical literature is one of the most relevant sources of information for knowledge mining in the field of Bioinformatics. In spite of English being the most widely addressed language in the field; in recent years, there has been a growing interest from the natural language processing community in dealing with languages other than English. However, the availability of language resources and tools for appropriate treatment of non-English texts is lacking behind. Our research is concerned with the semantic annotation of biomedical texts in the Spanish language, which can be considered an under-resourced language where biomedical text processing is concerned.

Results
We have carried out experiments to assess the effectiveness of several methods for the automatic annotation of biomedical texts in Spanish. One approach is based on the linguistic analysis of Spanish texts and their annotation using an information retrieval and concept disambiguation approach. A second method takes advantage of a Spanish–English machine translation process to annotate English documents and transfer annotations back to Spanish. A third method takes advantage of the combination of both procedures. Our evaluation shows that a combined system has competitive advantages over the two individual procedures.

Availability and implementation
UMLSMapper (https://snlt.vicomtech.org/umlsmapper) and the annotation transfer tool (http://scientmin.taln.upf.edu/anntransfer/) are freely available for research purposes as web services and/or demos.

Supplementary information
Supplementary data are available at Bioinformatics online.
Homozygous GRN mutations: new phenotypes and new insights into pathological and molecular mechanisms
Authors: Huin Vincent , Barbier Mathieu , Bottani Armand , Lobrinus Johannes Alexander , Clot Fabienne , Lamari Foudil , Chat Laureen , Rucheton Benoît , Fluchère Frédérique , Auvin Stéphane , Myers Peter , Gelot Antoinette , Camuzat Agnès , Caillaud Catherine , Jornéa Ludmila , Forlani Sylvie , Saracino Dario , Duyckaerts Charles , Brice Alexis , Durr Alexandra , Le Ber Isabelle 
Published: November 2019

AbstractHomozygous mutations in the progranulin gene (GRN) are associated with neuronal ceroid lipofuscinosis 11 (CLN11), a rare lysosomal-storage disorder characterized by cerebellar ataxia, seizures, retinitis pigmentosa, and cognitive disorders, usually beginning between 13 and 25 years of age. This is a rare condition, previously reported in only four families. In contrast, heterozygous GRN mutations are a major cause of frontotemporal dementia associated with neuronal cytoplasmic TDP-43 inclusions. We identified homozygous GRN mutations in six new patients. The phenotypic spectrum is much broader than previously reported, with two remarkably distinct presentations, depending on the age of onset. A childhood/juvenile form is characterized by classical CLN11 symptoms at an early age at onset. Unexpectedly, other homozygous patients presented a distinct delayed phenotype of frontotemporal dementia and parkinsonism after 50 years; none had epilepsy or cerebellar ataxia. Another major finding of this study is that all GRN mutations may not have the same impact on progranulin protein synthesis. A hypomorphic effect of some mutations is supported by the presence of residual levels of plasma progranulin and low levels of normal transcript detected in one case with a homozygous splice-site mutation and late onset frontotemporal dementia. This is a new critical finding that must be considered in therapeutic trials based on replacement strategies. The first neuropathological study in a homozygous carrier provides new insights into the pathological mechanisms of the disease. Hallmarks of neuronal ceroid lipofuscinosis were present. The absence of TDP-43 cytoplasmic inclusions markedly differs from observations of heterozygous mutations, suggesting a pathological shift between lysosomal and TDP-43 pathologies depending on the mono or bi-allelic status. An intriguing observation was the loss of normal TDP-43 staining in the nucleus of some neurons, which could be the first stage of the TDP-43 pathological process preceding the formation of typical cytoplasmic inclusions. Finally, this study has important implications for genetic counselling and molecular diagnosis. Semi-dominant inheritance of GRN mutations implies that specific genetic counselling should be delivered to children and parents of CLN11 patients, as they are heterozygous carriers with a high risk of developing dementia. More broadly, this study illustrates the fact that genetic variants can lead to different phenotypes according to their mono- or bi-allelic state, which is a challenge for genetic diagnosis.
Human Transmission of Blastocystis by Fecal Microbiota Transplantation Without Development of Gastrointestinal Symptoms in Recipients
Authors: Terveer Elisabeth M , van Gool Tom , Ooijevaar Rogier E , Sanders Ingrid M J G , Boeije-Koppenol Eline , Keller Josbert J , Bart Aldert , Kuijper Ed J ,   Netherlands Donor Feces Bank (NDFB) Study Group, Terveer Elisabeth M , Vendrik Karuna E W , Ooijevaar Rogier , Emilie van Lingen , Boeije-Koppenol Eline , van Prehn Joffrey , van Beurden Yvette , Bauer Martijn P , van Nood Els , Goorhuis Abraham , Seegers Jos F M L , Dijkgraaf Marcel G W , Mulder Chris J J , Vandenbroucke-Grauls Christina M J E , Verspaget Hein W , Kuijper Ed J , Keller Josbert J 
Published: November 2019

Abstract

Background
Patients with multiple recurrent Clostridioides difficile infections (rCDI) are treated with fecal microbiota transplantation (FMT), using feces provided by healthy donors. Blastocystis colonization of donors is considered an exclusion criterion, whereas its pathogenicity is still under debate.

Methods
The introduction of molecular screening for Blastocystis sp. at our stool bank identified 2 donors with prior negative microscopies but positive polymerase chain reactions (PCRs). Potential transmission of Blastocystis sp. to patients was assessed on 16 fecal patient samples, pre- and post-FMT, by PCR and subtype (ST) analyses. In addition, clinical outcomes for the treatment of rCDI (n = 31), as well as the development of gastrointestinal symptoms, were assessed.

Results
There was 1 donor who carried Blastocystis ST1, and the other contained ST3. All patients tested negative for Blastocystis prior to FMT. With a median diagnosis at 20.5 days after FMT, 8 of 16 (50%) patients developed intestinal colonization with Blastocystis, with identical ST sequences as their respective donors. Blastocystis-containing fecal suspensions were used to treat 31 rCDI patients, with an FMT success rate of 84%. This success rate was not statistically different from patients transferred with Blastocystis sp.–negative donor feces (93%, 76/82). Patients transferred with Blastocystis sp.–positive donor feces did not report any significant differences in bowel complaints in the first week, after 3 weeks, or in the months following FMT.

Conclusions
We demonstrated the first transmission of Blastocystis ST1 and ST3 from donors to patients by FMT. This did not result in gastrointestinal symptomatology or have any significant effect on rCDI treatment outcomes.