LLukas22/scidocs huggingface dataset:
Evidence for Two Morphotypes of Lake Charr, Salvelinus Namaycush, from Great Bear Lake, Northwest Territories, Canada

The lake charr, Salvelinus namaycush, is generally characterized as a morphologically stable specialized deepwater piscivore. Empirical observations suggested the existence of two or more morphotypes of lake charr in Great Bear Lake, NWT. I gathered morphological data over two seasons from a total of 72 individuals and used principal components analysis to summarize variation in the dataset. UPGMA classification showed that there were two groups in the dataset. I classified individuals into one of two morphotypes using discriminant function analysis. The two forms differed primarily in head proportions. I developed a function, usable in the field, that classifies 80% of all specimens correctly. This study represents one of the first documentations of sympatric morphotypes of lake charr outside the Laurentian Great Lakes and provides the basis for further investigation into origins of and genetic, morphological and ecological differences between the forms.
A strategy for preparing software organizations for statistical process control

Software organizations have increased their interest in software process improvement (SPI). Nowadays, there are several frameworks that support SPI implementation. Some of them, such as CMMI (Capability Maturity Model Integration), propose to implement SPI in levels. At high maturity levels, such as CMMI levels 4 and 5, SPI involves carrying out statistical process control (SPC), which requires measures and data suitable for this context. However, measurement problems have been pointed in the literature as one of the main obstacles for a successful implementation of SPC in SPI efforts. With this scenario in mind, we developed a strategy to help software organizations prepare themselves regarding measurement aspects in order to implement SPC. The strategy is made up of three components: a Reference Software Measurement Ontology, an Instrument for Evaluating the Suitability of a Measurement Repository for SPC, and a Body of Recommendations for Software Measurement Suitable for SPC. In this paper we present the strategy as a whole and describe each one of its components.
Photobiomodulation of the microbiome: implications for metabolic and inflammatory diseases.

The human microbiome is intimately associated with human health, with a role in obesity, metabolic diseases such as type 2 diabetes, and divergent diseases such as cardiovascular and neurodegenerative diseases. The microbiome can be changed by diet, probiotics, and faecal transplants, which has flow-on effects to health outcomes. Photobiomodulation has a therapeutic effect on inflammation and neurological disorders (amongst others) and has been reported to influence metabolic disorders and obesity. The aim of this study was to examine the possibility that PBM could influence the microbiome of mice. Mice had their abdomen irradiated with red (660 nm) or infrared (808 nm) low-level laser, either as single or multiple doses, over a 2-week period. Genomic DNA extracted from faecal pellets was pyrosequenced for the 16S rRNA gene. There was a significant (p < 0.05) difference in microbial diversity between PBM- and sham-treated mice. One genus of bacterium (Allobaculum) significantly increased (p < 0.001) after infrared (but not red light) PBM by day 14. Despite being a preliminary trial with small experimental numbers, we have demonstrated for the first time that PBM can alter microbiome diversity in healthy mice and increase numbers of Allobaculum, a bacterium associated with a healthy microbiome. This change is most probably a result of PBMt affecting the host, which in turn influenced the microbiome. If this is confirmed in humans, the possibility exists for PBMt to be used as an adjunct therapy in treatment of obesity and other lifestyle-related disorders, as well as cardiovascular and neurodegenerative diseases. The clinical implications of altering the microbiome using PBM warrants further investigation.
Modeling of low-density lipoprotein (LDL) transport in the artery—effects of hypertension

A robust four-layer model is presented to describe the LDL transport in the arterial wall coupled with the transport in the lumen. The endothelium, intima, internal elastic lamina (IEL) and media are all treated as macroscopically homogeneous porous media and the volume-averaged porous media equations are employed to model various layers, with Staverman filtration and osmotic reflection coefficients introduced to account for selective permeability of each porous layer to certain solutes. The physiological parameters within the various layers are obtained from literature. The set of governing equations for fluid flow and mass transport is descretized using a finite element scheme based on the Galerkin method of weighted residuals. Filtration velocity and LDL concentration profiles are developed at different locations for various clinical conditions. The results are consistent with previous numerical and experimental studies. Effects of hypertension and boundary conditions are discussed based upon the present model. Furthermore, the effects of pulsatile flows on LDL transport in the arterial wall are studied in some detail. Compared to previous transport models, the newly developed model is found to be a more robust tool for investigation of LDL accumulation within different arterial wall layers for various clinical conditions. This will be helpful in understanding the role of transmural transport processes in the initiation and development of atherosclerosis. 2005 Elsevier Ltd. All rights reserved.
Assessment of left heart and pulmonary circulation flow dynamics by a new pulsed mock circulatory system

We developed a new mock circulatory system that is able to accurately simulate the human blood circulation from the pulmonary valve to the peripheral systemic capillaries. Two independent hydraulic activations are used to activate an anatomical-shaped left atrial and a left ventricular silicon molds. Using a lumped model, we deduced the optimal voltage signals to control the pumps. We used harmonic analysis to validate the experimental pulmonary and systemic circulation models. Because realistic volumes are generated for the cavities and the resulting pressures were also coherent, the left atrium and left ventricle pressure–volume loops were concordant with those obtained in vivo. Finally we explored left atrium flow pattern using 2C3D?T PIV measurements. This gave a first overview of the complex 3D flow dynamics inside realistic left atrium geometry. Abbreviations MCS Mock circulatory system LA Left atrium LV Left ventricle PA Pulmonary arteries AO Aorta PIV Particle image velocimetry xx LV, LA Vxx(t) Volume of the cavity in ml VaxxðtÞ Volume of the residual air inside the activation box in ml VacxxðtÞ Volume of the activation fluid in ml QacxxðtÞ Activation flow in l/min QaxxðtÞ Residual air flow that is the variation of the air volume due to compressibility in l/min Qav(t) Aortic valve flow in l/min Qmv(t) Mitral valve flow in l/min Qpv(t) Pulmonary venous flow in l/min Pxx(t) Pressure in the cavity in mmHg PaxxðtÞ Pressure in the residual air compliance in mmHg UcxxðtÞ Reference voltage signal that actuates the gear pump in V hxxðtÞ Open loop transfer function of the pump Caxx ;Eaxx Residual air compliance (Caxx ) and elastance (Eaxx1⁄4 1=Caxx ) in ml/mmHg and mmHg/ml, respectively
AMR Parsing as Graph Prediction with Latent Alignment

Abstract meaning representations (AMRs) are broad-coverage sentence-level semantic representations. AMRs represent sentences as rooted labeled directed acyclicmeaning representations (AMRs) are broad-coverage sentence-level semantic representations. AMRs represent sentences as rooted labeled directed acyclic graphs. AMR parsing is challenging partly due to the lack of annotated alignments between nodes in the graphs and words in the corresponding sentences. We introduce a neural parser which treats alignments as latent variables within a joint probabilistic model of concepts, relations and alignments. As exact inference requires marginalizing over alignments and is infeasible, we use the variational autoencoding framework and a continuous relaxation of the discrete alignments. We show that joint modeling is preferable to using a pipeline of align and parse. The parser achieves the best reported results on the standard benchmark (73.6% on LDC2016E25).
Investigating queries and search failures in academic search

Academic search concerns the retrieval and profiling of information objects in the domain of academic research. In this paper we reveal important observations of academic search queries, and provide an algorithmic solution to address a type of failure during search sessions: null queries. We start by providing a general characterization of academic search queries, by analyzing a large-scale transaction log of a leading academic search engine. Unlike previous small-scale analyses of academic search queries, we find important differences with query characteristics known from web search. E.g., in academic search there is a substantially bigger proportion of entity queries, and a heavier tail in query length distribution. We then focus on search failures and, in particular, on null queries that lead to an empty search engine result page, on null sessions that contain such null queries, and on users who are prone to issue null queries. In academic search approximately 1 in 10 queries is a null query, and 25% of the sessions contain a null query. They appear in different types of search sessions, and prevent users from achieving their search goal. To address the high rate of null queries in academic search, we consider the task of providing query suggestions. Specifically we focus on a highly frequent query type: non-boolean informational queries. To this end we need to overcome query sparsity and make effective use of session information. We find that using entities helps to surface more relevant query suggestions in the face of query sparsity. We also find that query suggestions should be conditioned on the type of session in which they are offered to be more effective. After casting the session classification problem as a multi-label classification problem, we generate session-conditional query suggestions based on predicted session type. We find that this session-conditional method leads to significant improvements over a generic query suggestion method. Personalization yields very little further improvements over session-conditional query suggestions. © 2017 Elsevier Ltd. All rights reserved.
Predictive factors of telemedicine service acceptance and behavioral intention of physicians

PURPOSE
Despite the proliferation of telemedicine technology, telemedicine service acceptance has been slow in actual healthcare settings. The purpose of this research is to develop a theoretical model for explaining the predictive factors influencing physicians' willingness to use telemedicine technology to provide healthcare services.


METHODS
We developed the Telemedicine Service Acceptance model based on the technology acceptance model (TAM) with the inclusion of three predictive constructs from the previously published telemedicine literature: (1) accessibility of medical records and of patients as clinical factors, (2) self-efficacy as an individual factor and (3) perceived incentives as regulatory factors. A survey was conducted, and structural equation modeling was applied to evaluate the empirical validity of the model and causal relationships within the model using the data collected from 183 physicians.


RESULTS
Our results confirmed the validity of the original TAM constructs: the perceived usefulness of telemedicine directly impacted the behavioral intention to use it, and the perceived ease of use directly impacted both the perceived usefulness and the behavioral intention to use it. In addition, new predictive constructs were found to have ramifications on TAM variables: the accessibility of medical records and of patients directly impacted the perceived usefulness of telemedicine, self-efficacy had a significant positive effect on both the perceived ease of use and the perceived usefulness of telemedicine, and perceived incentives were found to be important with respect to the intention to use telemedicine technology.


CONCLUSIONS
This study demonstrated that the Telemedicine Service Acceptance model was feasible and could explain the acceptance of telemedicine services by physicians. These results identified important factors for increasing the involvement of physicians in telemedicine practice.
Association Between KCNQ1 Genetic Variants and Type 2 Diabetes in the Uyghur Population.

OBJECTIVE
To investigate the association between KCNQ1 gene polymorphisms and type 2 diabetes (T2D) in an admixed ethnic minority, Uyghur population, living in the Northwest region of China.


MATERIALS AND METHODS
We genotyped three tagging single-nucleotide polymorphisms rs2283171, rs11023485, and rs2283208 of the KCNQ1 gene in 1006 T2D participants and 1004 controls and conducted association analysis.


RESULTS
The frequencies of the AG and GG genotypes and the G allele of rs2283171 were higher in the control group (51.4%, 22%, and 47.7%, respectively) than in the case group (49%, 17.6%, and 42.1%, respectively). The minor G allele decreased the risk of T2D with a per-allele odds ratio of 0.79 (95% CI: 0.70-0.90) for the additive genetic model in univariate analysis (p = 0.0001). After adjustment for the covariates of age, gender, smoking, alcohol use, systolic blood pressure (SBP), diastolic blood pressure (DBP), body mass index (BMI), triglyceride (TG), and total cholesterol (TC), the diabetic protective effect of the rs2283171-G allele remained. No difference was observed in the frequency distributions of the rs11023485 and rs2283208 genotypes between the two groups.


CONCLUSION
We identified a novel association between rs2283171 of KCNQ1 and T2D in the Uyghur population. Further association and functional studies are required to identify the causal functional variant that is in linkage disequilibrium with this polymorphism.
Mealtime behavior and diabetes-specific parent functioning in young children with type 1 diabetes.

OBJECTIVE
Management of meals and mealtime behavior is often challenging for parents of young children with Type 1 diabetes. Parent functioning related to diabetes care may directly affect mealtime behaviors and glycemic control. This study evaluated associations among diabetes-specific parent functioning, parent and child mealtime behaviors, and glycemic control.


METHOD
Parents of young children with Type 1 diabetes (n = 134) completed self-report measures assessing diabetes-specific functioning (hypoglycemia fear, diabetes self-efficacy, diabetes-related quality of life) and child and parent mealtime behaviors. Hemoglobin A1c and percentage of blood glucose values out of range (<70 mg/dL or >200 mg/dL) over a 30-day period were abstracted from medical charts as indicators of glycemic control. Structural equation modeling was utilized to evaluate predictors and related outcomes of child and parent mealtime behavior.


RESULTS
The proposed model fit the data very well. More frequent problematic child mealtime behaviors were associated with poorer glycemic control; however, more frequent problematic parent mealtime behaviors were marginally associated with better glycemic control. Poorer diabetes-specific parent functioning was associated with more frequent problematic child and parent mealtime behaviors.


CONCLUSIONS
Problematic child mealtime behaviors, such as disruptive behavior, present a significant risk for poorer glycemic control. Parents may engage in ineffective mealtime management strategies in an effort to meet glycemic recommendations and avoid hyperglycemia and hypoglycemia. Future research will help to determine whether parents may benefit from specific, developmentally appropriate behavioral strategies to manage meals and snacks and promote optimal diabetes management.
On Interpreting Keynes: A Study in Reconciliation.

There is discontent with how the textbooks have come to reinterpret Keynes but there is little communication between the most prominent schools of criticism. This book argues that this lack of dialogue is mistaken and damaging. A synthesis is possible as many of the arguments between them can be traced to simple misunderstadings and differences of emphasis.
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

SUMMARY
BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks of conservation sequence length, similarity, and the presence of insertions and N/C-terminal extensions.


AVAILABILITY
From http://www-igbmc. u-strasbg.fr/BioInfo/BAliBASE/index.html
The role of high-resolution endoscopy and narrow-band imaging in the evaluation of upper GI neoplasia in familial adenomatous polyposis.

BACKGROUND
The Spigelman classification stratifies cancer risk in familial adenomatous polyposis (FAP) patients with duodenal adenomatosis. High-resolution endoscopy (HRE) and narrow-band imaging (NBI) may identify lesions at high risk.


OBJECTIVE
To compare HRE and NBI for the detection of duodenal and gastric polyps and to characterize duodenal adenomas harboring advanced histology with HRE and NBI.


DESIGN
Prospective, nonrandomized, comparative study. Retrospective image evaluation study.


SETTING
Tertiary-care center.


PATIENTS
Thirty-seven FAP patients undergoing surveillance upper endoscopies.


INTERVENTION
HRE endoscopy was followed by NBI. The number of gastric polyps and Spigelman staging were compared. Duodenal polyp images were systematically reviewed in a learning and validation phase.


MAIN OUTCOME MEASUREMENTS
Number of gastric and duodenal polyps detected by HRE and NBI and prevalence of specific endoscopic features in duodenal adenomas with advanced histology.


RESULTS
NBI did not identify additional gastric polyps but detected more duodenal adenomas in 16 examinations, resulting in upgrades of the Spigelman stage in 2 cases (4.4%). Pictures of 168 duodenal adenomas (44% advanced histology) were assessed. In the learning phase, 3 endoscopic features were associated with advanced histology: white color, enlarged villi, and size ≥1 cm. Only size ≥1 cm was confirmed in the validation phase (odds ratio 3.0; 95% confidence interval, 1.2-7.4).


LIMITATIONS
Nonrandomized study, scant number of high-grade dysplasia adenomas.


CONCLUSION
Inspection with NBI did not lead to a clinically relevant upgrade in the Spigelman classification and did not improve the detection of gastric polyps in comparison with HRE. The only endoscopic feature that predicted advanced histology of a duodenal adenoma was size ≥1 cm.
Evidence of atrial functional mitral regurgitation due to atrial fibrillation: reversal with arrhythmia control.

OBJECTIVES
The purpose of this study was to determine whether atrial fibrillation (AF) might cause significant mitral regurgitation (MR), and to see whether this MR improves with restoration of sinus rhythm.


BACKGROUND
MR can be classified by leaflet pathology (organic/primary and functional/secondary) and by leaflet motion (normal, excessive, restrictive). The existence of secondary, normal leaflet motion MR remains controversial.


METHODS
We performed a retrospective cohort study. Patients undergoing first AF ablation at our institution (n = 828) were screened. Included patients had echocardiograms at the time of ablation and at 1-year clinical follow-up. The MR cohort (n = 53) had at least moderate MR. A reference cohort (n = 53) was randomly selected from those patients (n = 660) with mild or less MR. Baseline echocardiographic and clinical characteristics were compared, and the effect of restoration of sinus rhythm was assessed by follow-up echocardiograms.


RESULTS
MR patients were older than controls and more often had persistent AF (62% vs. 23%, p < 0.0001). MR patients had larger left atria (volume index: 32 cm(3)/m(2) vs. 26 cm(3)/m(2), p = 0.008) and annular size (3.49 cm vs. 3.23 cm, p = 0.001), but similar left ventricular size and ejection fraction. Annular size, age and persistent AF were independently associated with MR. On follow-up echocardiogram, patients in continuous sinus rhythm had greater reductions in left atrial size and annular dimension, and lower rates of significant MR (24% vs. 82%, p = 0.005) compared with those in whom sinus rhythm was not restored.


CONCLUSIONS
AF can result in "atrial functional MR" that improves if sinus rhythm is restored.
The Potential of Mobile Apps for Improving Asthma Self-Management: A Review of Publicly Available and Well-Adopted Asthma Apps

BACKGROUND
Effective disease self-management lowers asthma's burden of disease for both individual patients and health care systems. In principle, mobile health (mHealth) apps could enable effective asthma self-management interventions that improve a patient's quality of life while simultaneously reducing the overall treatment costs for health care systems. However, prior reviews in this field have found that mHealth apps for asthma lack clinical evaluation and are often not based on medical guidelines. Yet, beyond the missing evidence for clinical efficacy, little is known about the potential apps might have for improving asthma self-management.


OBJECTIVE
The aim of this study was to assess the potential of publicly available and well-adopted mHealth apps for improving asthma self-management.


METHODS
The Apple App store and Google Play store were systematically searched for asthma apps. In total, 523 apps were identified, of which 38 apps matched the selection criteria to be included in the review. Four requirements of app potential were investigated: app functions, potential to change behavior (by means of a behavior change technique taxonomy), potential to promote app use (by means of a gamification components taxonomy), and app quality (by means of the Mobile Application Rating Scale [MARS]).


RESULTS
The most commonly implemented functions in the 38 reviewed asthma apps were tracking (30/38, 79%) and information (26/38, 68%) functions, followed by assessment (20/38, 53%) and notification (18/38, 47%) functions. On average, the reviewed apps applied 7.12 of 26 available behavior change techniques (standard deviation [SD]=4.46) and 4.89 of 31 available gamification components (SD=4.21). Average app quality was acceptable (mean=3.17/5, SD=0.58), whereas subjective app quality lied between poor and acceptable (mean=2.65/5, SD=0.87). Additionally, the sum scores of all review frameworks were significantly correlated (lowest correlation: r36=.33, P=.04 between number of functions and gamification components; highest correlation: r36=.80, P<.001 between number of behavior change techniques and gamification components), which suggests that an app's potential tends to be consistent across review frameworks.


CONCLUSIONS
Several apps were identified that performed consistently well across all applied review frameworks, thus indicating the potential mHealth apps offer for improving asthma self-management. However, many apps suffer from low quality. Therefore, app reviews should be considered as a decision support tool before deciding which app to integrate into a patient's asthma self-management. Furthermore, several research-practice gaps were identified that app developers should consider addressing in future asthma apps.