LLukas22/scidocs huggingface dataset:
Warburg revisited: imaging tumour blood flow and metabolism

In the 1930s, Otto Warburg reported that anaerobic metabolism of glucose is a fundamental property of all tumours, even in the presence of an adequate oxygen supply. He also demonstrated a relationship between the degree of anaerobic metabolism and tumour growth rate. Today, this phenomenon forms the basis of tumour imaging with fluorodeoxyglucose positron emission tomography (FDG-PET). More recently, Folkman has demonstrated that malignant growth and survival are also dependent on tumour vascularity which is increasingly evaluated in vivo using techniques such as contrast enhanced computed tomography or magnetic resonance imaging (MRI). Although it is reasonable to hypothesise that the metabolic requirements of tumours are mirrored by alterations in tumour haemodynamics, the relationship between tumour blood flow and metabolism is in fact complex. A well-developed tumour vascular supply is required to ensure a sufficient delivery of glucose and oxygen to support the metabolism essential for tumour growth. However, an inadequate vascularisation of tumour will result in hypoxia, a factor that is known to stimulate anaerobic metabolism of glucose. Thus, the balance between tumour blood flow and metabolism will be an important indicator of the biological status of a tumour and hence the tumour's likely progression and response to treatment. This article reviews the molecular biology of tumour vascularisation and metabolism, relating these processes to currently available imaging techniques while summarising the imaging studies that have compared tumour blood flow and metabolism. The potential for vascular metabolic imaging to assess tumour aggression and sub-classify treatment response is highlighted.
The accuracy of cone-beam computed tomography in assessing maxillary molar furcation involvement.

AIM
The aim of this study was to investigate the accuracy of cone-beam computed tomography (CBCT) in assessing maxillary molar furcation involvement (FI).


MATERIALS AND METHODS
Fifteen patients with generalized chronic periodontitis after initial therapy were recruited. CBCT was performed in maxillary molars with probing pocket depths of ≥6 mm and advanced FI, and CBCT images were analysed. Furcation surgery was performed in 20 maxillary molars. Lastly, intra-surgical FI assessments were compared with CBCT-based data.


RESULTS
Intra-surgical findings confirmed 82.4% of the CBCT data, with a weighted kappa of 0.917. The agreement between both assessments was the highest in buccal furcation entrances, followed by distopalatal and mesiopalatal furcation entrances. Of the four parameters tested of detailed root anatomy and furcation morphology, the mean length of the root trunk and the width of the furcation entrance revealed by CBCT were consistent with their respective intra-surgical values (p > 0.05). Horizontal bone loss and vertical bone loss were underestimated by CBCT relative to their respective intra-surgical classifications (p ≤ 0.05).


CONCLUSIONS
Cone-beam computed tomography images demonstrate a high accuracy in assessing the loss of periodontal tissue of the FI and root morphologies in maxillary molars.
Antioxidant activity of some Moroccan marine microalgae: Pufa profiles, carotenoids and phenolic content.

In order to promote Moroccan natural resources, this study aims to evaluate the potential of microalgae isolated from Moroccan coastlines, as new source of natural antioxidants. Different extracts (ethanolic, ethanol/water and aqueous) obtained from 9 microalgae strains were screened for their in vitro antioxidant activity using DPPH free radical-scavenging assay. The highest antioxidant potentials were obtained in Dunalliela sp., Tetraselmis sp. and Nannochloropsis gaditana extracts. The obtained results indicate that ethanol extract of all microalgae strains exhibit higher antioxidant activity, when compared to water and ethanol/water extracts. Therefore, total phenolic and carotenoid content measurement were performed in active ethanol extracts. The PUFA profiles of ethanol extracts were also determined by GC/MS analysis. The studied microalgae strains displayed high PUFA content ranging from 12.9 to 76.9 %, total carotenoids content varied from 1.9 and 10.8mg/g of extract and total polyphenol content varied from 8.1 to 32.0mg Gallic acid Equivalent/g of extract weight. The correlation between the antioxidant capacities and the phenolic content and the carotenoids content were found to be insignificant, indicating that these compounds might not be major contributor to the antioxidant activity of these microalgae. The microalgae extracts exerting the high antioxidant activity are potential new source of natural antioxidants.
Attitudes toward borderline personality disorder: a survey of 706 mental health clinicians.

OBJECTIVE
We sought to determine attitudes toward patients with borderline personality disorder (BPD) among mental health clinicians at nine academic centers in the United States.


METHODS
A self-report questionnaire was distributed to 706 mental health clinicians, including psychiatrists, psychiatry residents, social workers, nurses, and psychologists.


RESULTS
The study showed that most clinicians consider BPD a valid diagnosis, although nearly half reported that they preferred to avoid these patients. The clinician's occupational subgroup was significantly related to attitude. Staff nurses had the lowest self-ratings on overall caring attitudes, while social workers had the highest. Social workers and psychiatrists had the highest ratings on treatment optimism. Social workers and psychologists were most optimistic about psychotherapy effectiveness, while psychiatrists were most optimistic about medication effectiveness. Staff nurses had the lowest self-ratings on empathy toward patients with BPD and treatment optimism.DiscussionNegative attitudes persist among clinicians toward BPD, but differ among occupational subgroups. Overall, caring attitudes, empathy, and treatment optimism were all higher among care providers who had cared for a greater number of BPD patients in the past 12 months.


CONCLUSION
These findings hold important implications for clinician education and coordination of care for patients with BPD.
Exploring the medication duration based on the effect of traditional Chinese medicine on postoperative stage I-III colorectal patients: a retrospective cohort study

PURPOSE
To clarify the effect of tradional Chinese medicine (TCM) on different stage patients and to explore medication duration based on survival analysis.


RESULTS
523 and 294 patients were respectively in the TCM group and the control group. For all patients, 6-year disease-free survival (DFS) was 57.6% after TCM and 46.6% after non-TCM (p = 0.0006). 6-year DFS for patients with stage I disease in the TCM group was 79.5% compared with 89.1% in the control group (p = 0.65). For patients with stage II disease, 6-year DFS was 63.1% in the TCM group compared with 50.2% in the control group (p = 0.054), and for patients with stage III disease, it was 43.3% in the TCM group compared with 22.0% in the control group (p = 0.0000).


MATERIALS AND METHODS
Data for patients with stage I-III disease between 2004 and 2013 were retrieved for this study, who underwent TCM after surgery were in the TCM group and the others were in the control group. Clinic appointments or phone were used to collect data by research assistants. Survival data were collected on Nov 2015 from the database, which is continuously updated by the researchers.


CONCLUSIONS
TCM is associated with significantly improved disease-free survival, in particular for patients with stage III disease. Among of these, TCM is not necessary for patients with stage I disease, and postoperative patients with stage II disease should be recommended to take 2 years of TCM. For patients with stage III disease, adherence to medication of TCM during the 6-year follow-up is worthy of being recommended.
Drug-induced adverse events prediction with the LINCS L1000 data

MOTIVATION
Adverse drug reactions (ADRs) are a central consideration during drug development. Here we present a machine learning classifier to prioritize ADRs for approved drugs and pre-clinical small-molecule compounds by combining chemical structure (CS) and gene expression (GE) features. The GE data is from the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 dataset that measured changes in GE before and after treatment of human cells with over 20 000 small-molecule compounds including most of the FDA-approved drugs. Using various benchmarking methods, we show that the integration of GE data with the CS of the drugs can significantly improve the predictability of ADRs. Moreover, transforming GE features to enrichment vectors of biological terms further improves the predictive capability of the classifiers. The most predictive biological-term features can assist in understanding the drug mechanisms of action. Finally, we applied the classifier to all  >20 000 small-molecules profiled, and developed a web portal for browsing and searching predictive small-molecule/ADR connections.


AVAILABILITY AND IMPLEMENTATION
The interface for the adverse event predictions for the  >20 000 LINCS compounds is available at http://maayanlab.net/SEP-L1000/ CONTACT: avi.maayan@mssm.edu


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Improving outcomes for diverse populations disproportionately affected by diabetes: final results of Project IMPACT: Diabetes.

OBJECTIVE
To improve key indicators of diabetes care by expanding a proven community-based model of care throughout high-risk areas in the United States.


DESIGN
Observational, multisite, pre-post comparison study.


SETTING
Federally qualified health centers, free clinics, employer worksites, community pharmacies, departments of health, physician offices, and other care facilities in 25 communities in 17 states from June 2011 through January 2013.


PARTICIPANTS
1,836 patients disproportionately affected by diabetes representing diverse ethnicities, insurance statuses, and social and economic backgrounds.


INTERVENTION
Pharmacists were integrated into local, interdisciplinary diabetes care teams and provided customized diabetes education and medication consultations to patients.


MAIN OUTCOME MEASURES
Clinical measures included glycosylated hemoglobin (A1C), body mass index, systolic and diastolic blood pressures, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides, and total cholesterol. Process measures included smoking status, eye examination status, foot examination status, and influenza vaccine status.


RESULTS
Pharmacist patient care services for those underserved or disproportionately affected by diabetes resulted in a statistically significant and clinically relevant decrease in mean A1C levels (-0.8%). Other outcome indicators were below target levels at baseline and decreased significantly but not by clinically relevant amounts (LDL-C, -7.1 mg/dL; triglycerides, -23.7 mg/dL, and total cholesterol, -8.8 mg/dL). The mean increase in HDL-C (+0.6 mg/dL) was not statistically significant or clinically relevant. Among evaluable patients who were not at target for process measures at baseline, 51.7% of 453 patients received eye examinations, 72.0% of 271 patients received foot examinations, 41.7% of 307 patients received influenza vaccinations, and 9.3% patients of 270 quit smoking during the project. Of the communities involved in the study, 92% intend to sustain pharmacists' services.


CONCLUSION
Project


IMPACT
Diabetes results show significant improvement in patients' clinical outcomes and demonstrate that all patients, even those with tremendous barriers to appropriate diabetes care, benefit from patient-centered, interdisciplinary health care teams that include pharmacists.
Text Mining in Biomedical Domain with Emphasis on Document Clustering

OBJECTIVES
With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents.


METHODS
This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain.


RESULTS
Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail.


CONCLUSIONS
Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise.
Ensemble Empirical Mode Decomposition: a Noise-Assisted Data Analysis Method

A new Ensemble Empirical Mode Decomposition (EEMD) is presented. This new approach consists of sifting an ensemble of white noise-added signal (data) and treats the mean as the final true result. Finite, not infinitesimal, amplitude white noise is necessary to force the ensemble to exhaust all possible solutions in the sifting process, thus making the different scale signals to collate in the proper intrinsic mode functions (IMF) dictated by the dyadic filter banks. As EEMD is a time–space analysis method, the added white noise is averaged out with sufficient number of trials; the only persistent part that survives the averaging process is the component of the signal (original data), which is then treated as the true and more physical meaningful answer. The effect of the added white noise is to provide a uniform reference frame in the time–frequency space; therefore, the added noise collates the portion of the signal of comparable scale in one IMF. With this ensemble mean, one can separate scales naturally without any a priori subjective criterion selection as in the intermittence test for the original EMD algorithm. This new approach utilizes the full advantage of the statistical characteristics of white noise to perturb the signal in its true solution neighborhood, and to cancel itself out after serving its purpose; therefore, it represents a substantial improvement over the original EMD and is a truly noise-assisted data analysis (NADA) method.
Pro-inflammatory effects of e-cigarette vapour condensate on human alveolar macrophages

OBJECTIVE
Vaping may increase the cytotoxic effects of e-cigarette liquid (ECL). We compared the effect of unvaped ECL to e-cigarette vapour condensate (ECVC) on alveolar macrophage (AM) function.


METHODS
AMs were treated with ECVC and nicotine-free ECVC (nfECVC). AM viability, apoptosis, necrosis, cytokine, chemokine and protease release, reactive oxygen species (ROS) release and bacterial phagocytosis were assessed.


RESULTS
Macrophage culture with ECL or ECVC resulted in a dose-dependent reduction in cell viability. ECVC was cytotoxic at lower concentrations than ECL and resulted in increased apoptosis and necrosis. nfECVC resulted in less cytotoxicity and apoptosis. Exposure of AMs to a sub-lethal 0.5% ECVC/nfECVC increased ROS production approximately 50-fold and significantly inhibited phagocytosis. Pan and class one isoform phosphoinositide 3 kinase inhibitors partially inhibited the effects of ECVC/nfECVC on macrophage viability and apoptosis. Secretion of interleukin 6, tumour necrosis factor α, CXCL-8, monocyte chemoattractant protein 1 and matrix metalloproteinase 9 was significantly increased following ECVC challenge. Treatment with the anti-oxidant N-acetyl-cysteine (NAC) ameliorated the cytotoxic effects of ECVC/nfECVC to levels not significantly different from baseline and restored phagocytic function.


CONCLUSIONS
ECVC is significantly more toxic to AMs than non-vaped ECL. Excessive production of ROS, inflammatory cytokines and chemokines induced by e-cigarette vapour may induce an inflammatory state in AMs within the lung that is partly dependent on nicotine. Inhibition of phagocytosis also suggests users may suffer from impaired bacterial clearance. While further research is needed to fully understand the effects of e-cigarette exposure in humans in vivo, we caution against the widely held opinion that e-cigarettes are safe.
Use of the SINBAD classification system and score in comparing outcome of foot ulcer management on three continents.

OBJECTIVE
To compare populations with and outcomes of diabetic foot ulcers managed in the U.K., Germany, Tanzania, and Pakistan and to explore the use of a new score of ulcer type in comparing outcomes among different countries.


RESEARCH DESIGN AND METHODS
Data from a series of 449 patients with diabetic foot ulcers managed in the U.K. were used to evaluate the new simplified system of classification and to derive an aggregate score. The use of the score was then explored using data from series managed in Germany (n = 239), Tanzania (n = 479), and Pakistan (n = 173).


RESULTS
A highly significant difference was found in time to healing between ulcers of increasing score in the U.K. series (Kruskal-Wallis test; P = 0). When data from all centers were examined, a step-up in days to healing was noted for those with scores of >or=3 (out of 6). Examination of baseline variables contributing to outcome revealed the following differences among centers: ischemia, ulcer area, and depth contributing to outcome in the U.K.; ischemia, area, depth, and infection in Germany; depth, infection, and neuropathy in Tanzania; and depth alone in Pakistan.


CONCLUSIONS
Any system of classification designed for general implementation must encompass all the variables that contribute to outcome in different communities. Adoption of a simple score based on these variables, the Site, Ischemia, Neuropathy, Bacterial Infection, and Depth (SINBAD) score, may prove useful in predicting ulcer outcome and enabling comparison among different centers.
Randomized controlled effectiveness trial of executive function intervention for children on the autism spectrum.

BACKGROUND
Unstuck and On Target (UOT) is an executive function (EF) intervention for children with autism spectrum disorders (ASD) targeting insistence on sameness, flexibility, goal-setting, and planning through a cognitive-behavioral program of self-regulatory scripts, guided/faded practice, and visual/verbal cueing. UOT is contextually-based because it is implemented in school and at home, the contexts in which a child uses EF skills.


METHODS
To evaluate the effectiveness of UOT compared with a social skills intervention (SS), 3rd-5th graders with ASD (mean IQ = 108; UOT n = 47; SS n = 20) received interventions delivered by school staff in small group sessions. Students were matched for gender, age, race, IQ, ASD symptomotolgy, medication status, and parents' education. Interventions were matched for 'dose' of intervention and training. Measures of pre-post change included classroom observations, parent/teacher report, and direct child measures of problem-solving, EF, and social skills. Schools were randomized and evaluators, but not parents or teachers, were blinded to intervention type.


RESULTS
Interventions were administered with high fidelity. Children in both groups improved with intervention, but mean change scores from pre- to postintervention indicated significantly greater improvements for UOT than SS groups in: problem-solving, flexibility, and planning/organizing. Also, classroom observations revealed that participants in UOT made greater improvements than SS participants in their ability to follow rules, make transitions, and be flexible. Children in both groups made equivalent improvements in social skills.


CONCLUSIONS
These data support the effectiveness of the first contextually-based EF intervention for children with ASD. UOT improved classroom behavior, flexibility, and problem-solving in children with ASD. Individuals with variable background/training in ASD successfully implemented UOT in mainstream educational settings.
False Positives, False Negatives, and False Analyses: a Rejoinder to " Machine Bias: There's Software Used across the Country to Predict Future Criminals. and It's Biased against Blacks. "

Skeem for their thoughtful comments and suggestions.
Heart rate, pacing, and outcome in the Dual Chamber and VVI Implantable Defibrillator (DAVID) trials.

BACKGROUND
Slower heart rates are believed to confer a better prognosis in heart disease. The Dual Chamber and VVI Implantable Defibrillator (DAVID) Trial found that patients with ventricular dysfunction and isolated sinus bradycardia (rate <60 with normal PR interval) had an unusually low incidence of heart failure (HF) hospitalization and mortality when paced infrequently.


OBJECTIVES
The purpose of this study was to prospectively test our hypotheses that a similar benefit from bradycardia would be conferred in DAVID II as in DAVID but that this would be nullified by the faster heart rate achieved during atrial pacing in DAVID II.


METHODS
Effects of atrial versus minimal ventricular pacing on outcome in defibrillator recipients with isolated bradycardia in DAVID II were prospectively evaluated.


RESULTS
Ninety-eight DAVID II patients with isolated bradycardia were similar to 502 patients without it but had less baseline HF. HF medications were used comparably in both groups at baseline and throughout the study. Overall, patients with isolated bradycardia were less likely to die or be hospitalized for HF than others (12.2% vs. 26%; P = .01). There was no evidence that atrial pacing diminished this association. Adjusted for covariates, particularly baseline HF and its treatment, isolated bradycardia patients had substantially reduced risk for HF/death (P = .018) with or without atrial pacing (relative risk 0.47 and 0.71, respectively).


CONCLUSIONS
Isolated bradycardia identifies patients at lower risk for HF and mortality, an association that is not necessarily negated by accelerating heart rate with atrial pacing. This apparent conundrum challenges the use of heart rate as a therapeutic target in patients with ventricular dysfunction.


TRIAL REGISTRATION
http://www.clinicaltrials.gov NCT00187187.
Noise characterization of multiport amplifiers

This paper addresses the issue of the definition and measurement of the noise figure and parameters to characterize multiport devices, particularly differential amplifiers. A parameterization in terms of the noise matrix appears to be the most practical. The noise figure for a given output port is defined and related to the noise matrix and scattering parameters of the device, as well as the correlations between different input noise waves. The degradation of the signal-to-noise ratio is obtained from a special choice of the input correlation function. Two examples are considered in detail: a three-port differential amplifier and a four-port mixed-mode amplifier, both with reflectionless terminations. The noise figures, effective input temperatures, and gains are related to the results of a series of hot–cold measurements, as in the familiar two-port case.
Analysis of Bitcoin Pooled Mining Reward Systems

In this paper we describe the various scoring systems used to calculate rewards of participants in Bitcoin pooled mining, explain the problems each were designed to solve and analyze their respective advantages and disadvantages.