LLukas22/scidocs huggingface dataset:
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.
Reduction of wound angiogenesis in patients treated with BMS-275291, a broad spectrum matrix metalloproteinase inhibitor.

PURPOSE
The purpose of this study was to evaluate the feasibility of incorporating a novel wound angiogenesis assay into a Phase I study of BMS-275291, a broad-spectrum matrix metalloproteinase inhibitor, and to determine whether the wound angiogenesis assay was able to detect the inhibition of angiogenesis in patients treated with BMS-275291.


EXPERIMENTAL DESIGN
Before treatment began, a 4-mm skin biopsy was performed. The wound was imaged for 14 days. Treatment was started on day 0, and a separate 4-mm biopsy was performed 14 days later. The second wound was also imaged for 14 days. Wound angiogenesis was scored by two independent observers who were blinded to treatment status.


RESULTS
The median times in days (95% confidence interval) to reach the target average vascular score (AVS) of 1.5 and 2.0 based on the data of Observer 1 were 3.7 (2.2-6.9) and 8.0 (5.0-10.0) pretreatment whereas on-treatment the values were 4.9 (3.7-8.0) and 9.3 (7.0-11.5), respectively. The delay in the median time to reach an AVS of 1.5 was 1.2 days or a 32% reduction when comparing pretreatment with on-treatment (P = 0.06). For the target AVS of 2.0 the delay in the median time pretreatment versus on-treatment was 1.3 days or a 16% reduction (P = 0.04).


CONCLUSIONS
The wound angiogenesis assay used in this study was practical, well tolerated, and reproducible. Delays in wound angiogenesis because of BMS-275291 were detectable with this assay. This technique warrants additional investigation in clinical trials of other antiangiogenic agents.
The Online Parent Information and Support project, meeting parents' information and support needs for home-based management of childhood chronic kidney disease: research protocol.

AIM
This article is a report of a protocol for studying the development and evaluation of an online parent information and support package for home-based care of children with chronic kidney disease stages 3-5. The study is funded by a National Institute of Health Research, Research for Patient Benefit Grant awarded (December 2010). Approval to undetake the study was obtained from the Department of Health National Research Ethics Service (June 2011).


BACKGROUND
Children with chronic kidney disease require skilled, home-based care by parents, supported by professionals. Parents have identified a need for continuously available online resources to supplement professional support, and structured resources tailored to parents' needs are highlighted by policy makers as key to optimizing care; yet, online resource provision is patchy with little evidence base.


METHODS
Using mixed methods, we will (i) conduct parent/child/young person/professional/patient and parent volunteer focus groups to explore views on existing resources, (ii) collaboratively define gaps in provision, identify desirable components, develop/test resources and conduct a feasibility randomized controlled trial, and (iii) of usual professional support versus usual support supplemented by the package. Eighty parents of children with chronic kidney disease will be randomized. Primary outcomes will assess parents' self-efficacy and views of resources, using standardized measures at entry and 24 weeks, and semi-structured interviews at 24 weeks. We will finalize trial components for a later definitive trial.


DISCUSSION
By working collaboratively, we will derive a detailed insight into parents' information and support needs and experiences of using the package, and should see improved parental self-efficacy.
The Bimini Ghost Maps of William P. Cumming

Five manuscript maps of the early sixteenth century have been noted in the literature of the history of cartography for the place-name Bimini where Florida is today. An examination of the sources for these references reveals there are only two such maps. The other maps — bibliographical ghost maps — arose because of reliance upon secondary sources.
Attribute-Based Access Control

Attribute-based access control (ABAC) is a flexible approach that can implement AC policies limited only by the computational language and the richness of the available attributes, making it ideal for many distributed or rapidly changing environments.
Staffing, skill mix and the model of care.

AIMS AND OBJECTIVES
The study aimed to explore whether nurse staffing, experience and skill mix influenced the model of nursing care in medical-surgical wards.


BACKGROUND
Methods of allocating nurses to patients are typically divided into four types: primary nursing, patient allocation, task assignment and team nursing. Research findings are varied in regard to the relationship between these models of care and outcomes such as satisfaction and quality. Skill mix has been associated with various models, with implications for collegial support, teamwork and patient outcomes.


DESIGN
Secondary analysis of data collected on 80 randomly selected medical-surgical wards in 19 public hospitals in New South Wales, Australia during 2004-2005.


METHODS
Nurses (n = 2278, 80.9% response rate) were surveyed using The Nursing Care Delivery System and the Nursing Work Index-Revised. Staffing and skill mix was obtained from the ward roster and other data from the patient record. Models of care were examined in relation to these practice environment and organisational variables.


RESULTS
The models of nursing care most frequently reported by nurses in medical-surgical wards in this study were patient allocation (91%) and team nursing (80%). Primary nursing and task based models were unlikely to be practised. Skill mix, nurse experience, nursing workload and factors in the ward environment significantly influenced the model of care in use. Wards with a higher ratio of degree qualified, experienced registered nurses, working on their 'usual' ward were more likely to practice patient allocation while wards with greater variability in staffing levels and skill mix were more likely to practice team nursing.


CONCLUSIONS
Models of care are not prescriptive but are varied according to ward circumstances and staffing levels based on complex clinical decision making skills.


RELEVANCE TO CLINICAL PRACTICE
Variability in the models of care reported by ward nurses indicates that nurses adapt the model of nursing care on a daily or shift basis, according to patients' needs, skill mix and individual ward environments.
Itolizumab in combination with methotrexate modulates active rheumatoid arthritis: safety and efficacy from a phase 2, randomized, open-label, parallel-group, dose-ranging study

The objective of this study was to assess the safety and efficacy of itolizumab with methotrexate in active rheumatoid arthritis (RA) patients who had inadequate response to methotrexate. In this open-label, phase 2 study, 70 patients fulfilling American College of Rheumatology (ACR) criteria and negative for latent tuberculosis were randomized to four arms: 0.2, 0.4, or 0.8 mg/kg itolizumab weekly combined with oral methotrexate, and methotrexate alone (2:2:2:1). Patients were treated for 12 weeks, followed by 12 weeks of methotrexate alone during follow-up. Twelve weeks of itolizumab therapy was well tolerated. Forty-four patients reported adverse events (AEs); except for six severe AEs, all others were mild or moderate. Infusion-related reactions mainly occurred after the first infusion, and none were reported after the 11th infusion. No serum anti-itolizumab antibodies were detected. In the full analysis set, all itolizumab doses showed evidence of efficacy. At 12 weeks, 50 % of the patients achieved ACR20, and 58.3 % moderate or good 28-joint count Disease Activity Score (DAS-28) response; at week 24, these responses were seen in 22 and 31 patients. Significant improvements were seen in Short Form-36 Health Survey and Health Assessment Questionnaire Disability Index scores. Overall, itolizumab in combination with methotrexate was well tolerated and efficacious in RA for 12 weeks, with efficacy persisting for the entire 24-week evaluation period. (Clinical Trial Registry of India, http://ctri.nic.in/Clinicaltrials/login.php , CTRI/2008/091/000295).
Optimum BMI Cut Points to Screen Asian Americans for Type 2 Diabetes

OBJECTIVE
Asian Americans manifest type 2 diabetes at low BMI levels but may not undergo diagnostic testing for diabetes if the currently recommended BMI screening cut point of ≥25 kg/m(2) is followed. We aimed to ascertain an appropriate lower BMI cut point among Asian-American adults without a prior diabetes diagnosis.


RESEARCH DESIGN AND METHODS
We consolidated data from 1,663 participants, ages ≥45 years, without a prior diabetes diagnosis, from population- and community-based studies, including the Mediators of Atherosclerosis in South Asians Living in America study, the North Kohala Study, the Seattle Japanese American Community Diabetes Study, and the University of California San Diego Filipino Health Study. Clinical measures included a 2-h 75-g oral glucose tolerance test, BMI, and glycosylated hemoglobin (HbA1c).


RESULTS
Mean age was 59.7 years, mean BMI was 25.4 kg/m(2), 58% were women, and type 2 diabetes prevalence (American Diabetes Association 2010 criteria) was 16.9%. At BMI ≥25 kg/m(2), sensitivity (63.7%), specificity (52.8%), and Youden index (0.16) values were low; limiting screening to BMI ≥25 kg/m(2) would miss 36% of Asian Americans with type 2 diabetes. For screening purposes, higher sensitivity is desirable to minimize missing cases, especially if the diagnostic test is relatively simple and inexpensive. At BMI ≥23 kg/m(2), sensitivity (84.7%) was high in the total sample and by sex and Asian-American subgroup and would miss only ∼15% of Asian Americans with diabetes.


CONCLUSIONS
The BMI cut point for identifying Asian Americans who should be screened for undiagnosed type 2 diabetes should be <25 kg/m(2), and ≥23 kg/m(2) may be the most practical.
Financial Liberalization and Stability of the Financial System in Emerging Markets: The Institutional Dimension of Financial Crises

Emerging economies, which have implemented since the end of the 80's a process of financial liberalization, are confronted at the same time to banking crisis. The latter highlight the role played by the institutional framework in the process of financial liberalization. The objective of this paper is to go through the usual alternative too much/ too little market in order to explain that the success of any liberalization process relies on the complementarity between market and intermediation. The point is that the solution to financial instability is to be found within the institutional dynamics in which emerging economies may benefit from intermediation in order to enforce the market process.
Solving the Permutation Problem of Frequency-Domain BSS when Spatial Aliasing Occurs with Wide Sensor Spacing

This paper describes a method for solving the permutation problem of frequency-domain blind source separation (BSS). The method analyzes the mixing system information estimated with independent component analysis (ICA). When we use widely spaced sensors or increase the sampling rate, spatial aliasing may occur for high frequencies due to the possibility of multiple cycles in the sensor spacing. In such cases, the estimated information would imply multiple possibilities for a source location. This causes some difficulty when analyzing the information. We propose a new method designed to overcome this difficulty. This method first estimates the model parameters for the mixing system at low frequencies where spatial aliasing does not occur, and then refines the estimations by using data at all frequencies. This refinement leads to precise parameter estimation and therefore precise permutation alignment. Experimental results show the effectiveness of the new method
More Dengue, More Questions

engue is epidemic or endemic in virtually every country in the tropics; it is even cited in the Guinness World Records, 2002, as the world's most important viral hemorrhagic fever and the most geographically widespread of the arthropodborne viruses. As illustrated in this issue of Emerging Infectious Diseases, dengue epidemics are expanding rapidly, as is the literature on the subject. That dengue was transmitted in the United States for nearly 1 year in 2001 (1) should serve as a wake up call to Americans, most of whom are ignorant of the threat of this disease. Both the major dengue vectors, Aedes aegypti and Ae. albopictus, are widely distributed in the continental United States. This emerging disease continues to baffle and challenge epidemiologists and clinicians. Despite endemicity of 3 or more different dengue viruses, why does severe dengue occur in some populations and not in others? Why are children principally affected in some areas and adults in oth-ers? How can severe dengue reliably be recognized early enough to permit appropriate therapy to be applied? Recent studies point in the direction of answers to these questions. During an infection with any of the 4 dengue viruses, the principal threat to human health resides in the ability of the infecting virus to produce an acute febrile syndrome characterized by clinically significant vascular permeabil-ity, dengue hemorrhagic fever (DHF). However, because at onset vascular permeability exhibits only subtle changes, how can a diagnosis be made early enough to begin life-saving intravenous treatment? In persons with light skin color, the standard syphygmomanometer cuff tourniquet test has been widely used to screen children in outpatient settings; a positive test result is an early warning of incipient DHF. Because of genetic diversity among humans, the tourniquet test as a screening tool requires widespread evaluation and validation. In a prospective study of 1,136 Vietnamese children with serologically confirmed overt dengue infections, the tourniquet test had a sensitivity of 41.6%, a specificity of 94.4%, a positive pre-dictive value of 98.3%, and a negative predictive value of 17.3% (2). A positive result should prompt close observation , but a negative result does not exclude an ongoing dengue infection. A more robust screening test could result from the studies of Wills et al., who measured the size and charge characteristics of proteins leaking through the endothelial sieve in DHF patients (3). Such changes are caused, presumably, by a cytokine cascade, as yet …
Learning Visual Models from Shape Contours Using Multiscale Convex/Concave Structure Matching

A novel approach is proposed for learning a visual model from real shape samples of the same class. The visual model means a prototype shape that contains the salient shape features of the class. Conventional methods cannot form visual models because they are based on the generalization of structural descriptions with symbolic representations. Our approach can directly acquire a visual model by generalizing the multiscale convedconcave structure of a class of shapes, that is, the approach is based on the concept that shape generalization is shape simplification wherein perceptually relevant features are retained. The simplification does not mean the approximation of shapes but rather the extraction of the optimum scale convedconcave structure common to shape samples of the class. The common structure is obtained by applying our multiscale convex/concave structure-matching method to all shape pairs among given shape samples of the class and by integrating the matching results. The matching method, which is newly proposed in this paper, is applicable to heavily deformed shapes and is effectively implemented with dynamic programming techniques. Our approach can acquire a visual model from a few samples without any a priori knowledge of the class. The obtained model is very useful for shape recognition. Therefore, a flexible shape recognition system having a learning function can be constructed. The results of applying the proposed method to synthetic and real shapes show that the method is useful for learning and shape recognition. Index Tenns-Dynamicprogramming,multiscale convedconcave structure, shape generalization, shape learning, shape matching, visual model generation.
Phase I trial of nelarabine in indolent leukemias.

PURPOSE
To test whether nelarabine is an effective agent for indolent leukemias and to evaluate whether there is a relationship between cellular pharmacokinetics of the analog triphosphate and clinical responses.


PATIENTS AND METHODS
Thirty-five patients with relapsed/refractory leukemias (n = 24, B-cell chronic lymphocytic leukemia and n = 11, T-cell prolymphocytic leukemia) were entered onto three different protocols. For schedule A, patient received nelarabine daily for 5 days, whereas for schedule B, nelarabine was administered on days 1, 3, and 5. Schedule C was similar to schedule B except that fludarabine was also infused. Plasma and cellular pharmacokinetics were studied during the first cycle.


RESULTS
Responses were achieved in 20%, 15%, and 63% of patients receiving schedule A, B, and C, respectively. Histologic category, number of prior therapies, and fludarabine refractoriness did not influence the response rate. The most common nonhematologic toxicity was peripheral neuropathy. Grade 4 neutropenia and thrombocytopenia complicated 23% and 26% of courses respectively, and were significantly more frequent among patients with pre-existing marrow failure. Pharmacokinetics of plasma nelarabine and arabinosylguanine (ara-G) and of cellular ara-G triphosphate (ara-GTP) were similar in the two groups of diagnoses, and the elimination of ara-GTP from leukemia cells was slow (median, > 24 hours). The median peak intracellular concentrations of ara-GTP were significantly different (P = .0003) between responders (440 micromol/L; range, 35 to 1,438 micromol/L; n = 10) and nonresponders (50 micromol/L; range, 22 to 178 micromol/L; n = 15).


CONCLUSION
Nelarabine is an effective regimen against indolent leukemias, and combining it with fludarabine was most promising. Determination of tumor cell ara-GTP levels may provide a predictive test for response to nelarabine.
Diabetes Research in Iran: a Scientometric Analysis of Publications Output

INTRODUCTION
In the developing countries, diabetes mellitus as a chronic diseases, have replaced infectious diseases as the main causes of morbidity and mortality. International Diabetes Federation (IDF) recently estimates 382 million people have diabetes globally and more than 34.6 million people in the Middle East Region and this number will increase to 67.9 million by 2035. The aim of this study was to analyze Iran's research performance on diabetes in national and international context.


METHODS
This Scientometric analysis is based on the Iranian publication data in diabetes research retrieved from the Scopus citation database till the end of 2014. The string used to retrieve the data was developed using "diabetes" keyword in title, abstract and keywords, and finally Iran in the affiliation field was our main string.


RESULTS
Iran's cumulative publication output in diabetes research consisted of 4425 papers from 1968 to 2014, with an average number of 96.2 papers per year and an annual average growth rate of 25.5%. Iran ranked 25th place with 4425 papers among top 25 countries with a global share of 0.72 %. Average of Iran's publication output was 6.19 citations per paper. The average citation per paper for Iranian publications in diabetes research increased from 1.63 during 1968-1999 to 10.42 for 2014.


CONCLUSIONS
Although diabetic population of Iran is increasing, number of diabetes research is not remarkable. International Diabetes Federation suggested increased funding for research in diabetes in Iran for cost-effective diabetes prevention and treatment. In addition to universal and comprehensive services for diabetes care and treatment provided by Iranian health care system, Iranian policy makers should invest more on diabetes research.
A patient decision aid for antidepressant use in pregnancy: study protocol for a randomized controlled trial

BACKGROUND
Many women with depression experience significant difficulty making a decision about whether or not to use antidepressant medication in pregnancy. Patient decision aids (PDAs) are tools that assist patients in making complex health decisions. PDAs can reduce decision-making difficulty and lead to better treatment outcomes. We describe the methods for a pilot randomized controlled trial of an interactive web-based PDA for women who are having difficulty deciding about antidepressant drug use in pregnancy.


METHODS/DESIGN
This is a pilot randomized controlled trial that aims to assess the feasibility of a larger, multi-center efficacy study. The PDA aims to help a woman: (1) understand why an antidepressant is being recommended, (2) be knowledgeable about potential benefits and risks of treatment and non-treatment with antidepressants, and (3) be clear about which benefits and risks are most important to her, with the goal of improving confidence in her decision-making. We include women aged 18 years or older who are: (1) planning a pregnancy or are pregnant (gestational age less than 30 weeks), (2) diagnosed with major depressive disorder, (3) deciding whether or not to use a selective serotonin reuptake inhibitor (SSRI) or serotonin norepinephrine reuptake inhibitor (SNRI) antidepressant in pregnancy, and (4) having at least moderate decision-making difficulty as per a Decisional Conflict Scale (DCS) Score ≥25. Participants are randomized to receive the PDA or an informational resource sheet via a secure website, and have access to the stated allocation until their final study follow-up. The primary outcomes of the pilot study are feasibility of recruitment and retention, acceptability of the intervention, and adherence to the trial protocol. The primary efficacy outcome is DCS score at 4 weeks post randomization, with secondary outcomes including depressive and anxiety symptoms.


DISCUSSION
Our PDA represents a key opportunity to optimize the decision-making process for women around antidepressants in pregnancy, leading to effective decision-making and optimizing improved maternal and child outcomes related to depression in pregnancy. The electronic nature of the PDA will facilitate keeping it up-to-date, and allow for widespread dissemination after efficacy is demonstrated.


TRIAL REGISTRATION
This trial is registered on ClinicalTrials.Gov under the identifier NCT02308592 (first registered: 2 December 2014).