LLukas22/scidocs huggingface dataset:
Functional analysis of MADS-box genes controlling ovule development in Arabidopsis using the ethanol-inducible alc gene-expression system

In Arabidopsis, different combinations of ABC organ identity proteins interact in the presence of SEPALLATA (SEP) proteins to regulate floral organ differentiation. Ectopic expression of SEP3 in combination with class A and B or B and C genes is sufficient to homeotically convert vegetative leaves into petal-like organs and bracts into stamen-like structures, respectively. Recently, it has been shown that the three MADS-box genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1) and SHP2 act redundantly to control ovule identity. Protein interaction assays performed in yeast in combination with genetic studies demonstrated that these MADS-box factors only interact in the presence of SEP proteins to form complexes that determine ovule differentiation. Here, we address the question whether the ectopic co-expression of ovule identity proteins is sufficient to induce the homeotic conversion of vegetative leaves into carpel-like structures bearing ovules. We present the phenotypic characterization of Arabidopsis plants that ectopically express ovule identity factors under the regulation of the ethanol inducible gene expression system. These experiments indicate that the ectopic co-expression of SEP3 and SHP1 and/or STK is probably not sufficient to homeotically transform vegetative tissues into carpels with ovules. However, comparing the phenotypes obtained by ectopic expression of STK and/or SHP1 with or without SEP3 shows that co-expression of factors that are able to form complexes in yeast cause more extreme homeotic transformations, confirming the functional role of these complexes in vivo.
Association of polymorphisms in genes regulating the corticotropin-releasing factor system with antidepressant treatment response.

CONTEXT
The corticotropin-releasing factor (CRF, or corticotropin-releasing hormone) and arginine vasopressin systems have been implicated in the pathophysiology of anxiety and depressive disorders and response to antidepressant treatment.


OBJECTIVE
To study the association of genetic variants in 10 genes that regulate the CRF and arginine vasopressin systems with treatment response to citalopram in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) sample (N = 1768).


DESIGN
Pharmacogenetic association study derived from the STAR*D study, a multicenter, prospective, open, 12-week effectiveness trial.


SETTING
Outpatient primary care and psychiatric clinics. Patients Individuals with nonpsychotic major depressive disorder for whom DNA was available who were subsequently treated with citalopram hydrobromide for 4 to 12 weeks. Intervention Flexible doses of citalopram. Main Outcome Measure Association of genetic polymorphisms in genes encoding the CRF system with response and remission to citalopram treatment at exit visit.


RESULTS
One single-nucleotide polymorphism (SNP) (rs10473984) within the CRHBP locus showed a significant association with both remission (P = 6.0 x 10(-6); corrected, P = .0026) and reduction in depressive symptoms (P = 7.0 x 10(-7); corrected, P = .00031) in response to citalopram. The T allele of this SNP was associated with poorer treatment outcome in 2 of the 3 ethnic subsamples (African American and Hispanic), despite large differences in minor allele frequency. This association was more pronounced in patients with features of anxious depression (P = .008). The nonresponse allele was shown to be associated with overall higher plasma corticotropin levels and more pronounced dexamethasone suppression of corticotropin.


CONCLUSIONS
These data indicate that a genetic variant within the CRHBP locus affects response to citalopram in African American and Hispanic patients, suggesting a role for this gene and for the CRF system in antidepressant treatment response.
Comparison of the Hardware Performance of the AES Candidates Using Reconfigurable Hardware

The results of implementations of all five AES finalists using Xilinx Field Programmable Gate Arrays are presented and analyzed. Performance of four alternative hardware architectures is discussed and compared. The AES candidates are divided into three classes depending on their hardware performance characteristics. Recommendation regarding the optimum choice of the algorithms for AES is provided.
Ramadan fastings effect on plasma leptin, adiponectin concentrations, and body composition in trained young men.

PURPOSE
To evaluate the effect of Ramadan fasting on parameters of insulin resistance in trained athletes at rest and after aerobic exercise.


METHODS
Nine male rugby players (age 19 +/- 2 yr, height 1.78 +/- 0.74 m) were tested 3 times: 1 week before observance of Ramadan (C), at the end of the first week (R1), and during the fourth week (R2). They performed a progressive cycle-ergometer test at each visit. Data collected at rest and at the end of aerobic exercise included simple anthropometry (body mass, body-mass index, body fat, fat-free mass), biochemical parameters (serum glucose, cholesterol, HDL cholesterol, triglycerides, creatinine, and serum proteins), and selected hormone concentrations (plasma insulin, leptin, and adiponectin).


RESULTS
Ramadan fasting was associated with a reduction of body mass and body fat (R2 vs. C, p < .01) without significant change in leptin or adiponectin levels.


CONCLUSION
Lipolysis might have occurred because of increased plasma triglycerides and HDL cholesterol concentrations.
HIGH PRESSURE CO2 CORROSION ELECTROCHEMISTRY AND THE EFFECT OF ACETIC ACID

The carbon dioxide corrosion electrochemistry of mild steel has been studied in the presence of high CO2 partial pressures and acetic acid (HAc). Potentiodynamic sweeps, linear polarization resistance (LPR) and weight loss (WL) experiments have been conducted to investigate the effects of flow velocity, CO2 partial pressure, and acetic acid concentration on the corrosion rate of mild steel. Electrochemical impedance spectroscopy measurements have also been conducted to help elucidate the corrosion mechanisms under the test conditions.
The MD 6 hash function A proposal to NIST for SHA-3

This report describes and analyzes the MD6 hash function and is part of our submission package for MD6 as an entry in the NIST SHA-3 hash function competition. Significant features of MD6 include: • Accepts input messages of any length up to 2 − 1 bits, and produces message digests of any desired size from 1 to 512 bits, inclusive, including the SHA-3 required sizes of 224, 256, 384, and 512 bits. • Security—MD6 is by design very conservative. We aim for provable security whenever possible; we provide reduction proofs for the security of the MD6 mode of operation, and prove that standard differential attacks against the compression function are less efficient than birthday attacks for finding collisions. We also show that when used as a MAC within NIST recommendedations, the keyed version of MD6 is not vulnerable to linear cryptanalysis. The compression function and the mode of operation are each shown to be indifferentiable from a random oracle under reasonable assumptions. • MD6 has good efficiency: 22.4–44.1M bytes/second on a 2.4GHz Core 2 Duo laptop with 32-bit code compiled with Microsoft Visual Studio 2005 for digest sizes in the range 160–512 bits. When compiled for 64-bit operation, it runs at 61.8–120.8M bytes/second, compiled with MS VS, running on a 3.0GHz E6850 Core Duo processor. • MD6 works extremely well for multicore and parallel processors; we have demonstrated hash rates of over 1GB/second on one 16-core system, and over 427MB/sec on an 8-core system, both for 256-bit digests. We have also demonstrated MD6 hashing rates of 375 MB/second on a typical desktop GPU (graphics processing unit) card. We also show that MD6 runs very well on special-purpose hardware. • MD6 uses a single compression function, no matter what the desired digest size, to map input data blocks of 4096 bits to output blocks of 1024 bits— a fourfold reduction. (The number of rounds does, however, increase for larger digest sizes.) The compression function has auxiliary inputs: a “key” (K), a “number of rounds” (r), a “control word” (V ), and a “unique ID” word (U). • The standard mode of operation is tree-based: the data enters at the leaves of a 4-ary tree, and the hash value is computed at the root. See Figure 2.1. This standard mode of operation is highly parallelizable. 1http://www.csrc.nist.gov/pki/HashWorkshop/index.html
Analysis of composition of microbiomes: a novel method for studying microbial composition

BACKGROUND
Understanding the factors regulating our microbiota is important but requires appropriate statistical methodology. When comparing two or more populations most existing approaches either discount the underlying compositional structure in the microbiome data or use probability models such as the multinomial and Dirichlet-multinomial distributions, which may impose a correlation structure not suitable for microbiome data.


OBJECTIVE
To develop a methodology that accounts for compositional constraints to reduce false discoveries in detecting differentially abundant taxa at an ecosystem level, while maintaining high statistical power.


METHODS
We introduced a novel statistical framework called analysis of composition of microbiomes (ANCOM). ANCOM accounts for the underlying structure in the data and can be used for comparing the composition of microbiomes in two or more populations. ANCOM makes no distributional assumptions and can be implemented in a linear model framework to adjust for covariates as well as model longitudinal data. ANCOM also scales well to compare samples involving thousands of taxa.


RESULTS
We compared the performance of ANCOM to the standard t-test and a recently published methodology called Zero Inflated Gaussian (ZIG) methodology (1) for drawing inferences on the mean taxa abundance in two or more populations. ANCOM controlled the false discovery rate (FDR) at the desired nominal level while also improving power, whereas the t-test and ZIG had inflated FDRs, in some instances as high as 68% for the t-test and 60% for ZIG. We illustrate the performance of ANCOM using two publicly available microbial datasets in the human gut, demonstrating its general applicability to testing hypotheses about compositional differences in microbial communities.


CONCLUSION
Accounting for compositionality using log-ratio analysis results in significantly improved inference in microbiota survey data.
ATM Security Using Fingerprint Biometric Identifer: An Investigative Study

The growth in electronic transactions has resulted in a greater demand for fast and accurate user identification and authentication. Access codes for buildings, banks accounts and computer systems often use personal identification numbers (PIN's) for identification and security clearances. Conventional method of identification based on possession of ID cards or exclusive knowledge like a social security number or a password are not all together reliable. An embedded fingerprint biometric authentication scheme for automated teller machine (ATM) banking systems is proposed in this paper. In this scheme, a fingerprint biometric technique is fused with the ATM for person authentication to ameliorate the security level. KeywordsATM; PIN; Fingerprint; security; biometric.
Development and validation of novel biomarker assays for osteoarthritis

BACKGROUND
Osteoarthritis (OA) is the most common chronic joint disease usually diagnosed at relatively advanced stages when there is irreparable damage to the joint(s). Recently, we have identified two novel biomarkers C3f and V65 which appear to be OA-specific and therefore potential markers of early disease. We report the development of immunoassays for quantitative measure of these two novel biomarkers.


METHOD
Monoclonal and polyclonal antibodies were generated by immunising mouse and rabbits respectively with peptide-carrier conjugates of C3f and V65. Affinity purified antibodies were used for immunoassays development and assays validated using serum from OA patients and controls.


RESULTS
The ELISAs developed showed spiked recovery of up to 96% for C3f and V65 peptides depending on serum dilutions with a coefficient of variation (CV) <10%. The intra- and inter-assay CVs for C3f and V65 were 1.3-10.8% and 4.2-10.3% respectively. Both assays were insensitive for measurements of the peptides in patients and the use of different signal amplification systems did not increase assay sensitivity.


CONCLUSION
We have developed two immunoassays for measurements of C3f and V65 peptides biomarkers discovered by our earlier proteomic study. These assays could detect the endogenous peptides in serum samples from patients and controls but lacked sensitivity for accurate measurements of the peptides in patients. Our study highlights the difficulties and challenges of validating biomarker from proteomic studies and demonstrates how to overcome some of the technical challenges associated with developing immunoassays for small peptides.
Clinical research Heart failure / cardiomyopathy Characteristics , outcomes , and predictors of 1-year mortality in patients hospitalized for acute heart failure

Aims Acute heart failure (AHF) is associated with poor prognosis and requires recurrent hospitalizations. However, studies on AHF characteristics, treatment, and prognostic factors are few. Our aim was to investigate the characteristics, treatment, and 1-year prognosis of AHF and identify prognostic factors in different clinical groups. Methods and results We conducted a prospective multicentre study with 620 patients hospitalized due to AHF; mean age 75.1 (10.4) years, 50% male. Half of the patients had new-onset heart failure. Acute congestion (63.5%) and pulmonary oedema (26.3%) were the most common clinical presentations. Left ventricular ejection fraction (LVEF) was reported in two-thirds of patients. Half of these had preserved systolic function (LVEF 45%). At discharge, 86% of patients had beta-blockers and 76% either ACE-inhibitors or angiotensin receptor blockers in use. The 12-month all-cause mortality was 27.4%. We identified several clinical and biochemical prognostic risk factors in univariate analysis. Independent predictors of 1-year mortality were older age, male gender, lower systolic blood pressure (SBP) on admission, C-reactive protein, and serum creatinine .120 mmol/L. Conclusion We present the characteristics and prognosis of an unselected population of AHF patients. One-year mortality is high, and independent clinical risk factors include age, male gender, lower SBP on admission, C-reactive protein, and renal dysfunction.
Bootstrap Model Selection in Generalized Linear Models

Model selection is a central component of data analysis Though there are a variety of methods for likelihood based estimation methods there are relatively few for non likelihood based generalized linear models GLM such as in the quasi likelihood and generalized es timating equation GEE approaches In this paper we develop basic and bias corrected bootstrap approaches to estimate the predictive mean squared error PMSE of a model and use the PMSE for model selection Simulation studies show that the bias corrected boot strap estimate works well when quasi likelihood or GEE is used to t either overdispersed or correlated response GLMs For correlated response data when the marginal distribution assumption is almost correct Akaike s Information Criterion AIC and Bayesian Infor mation Criterion BIC calculated under the working independence model also perform well For illustration the methods are applied to data sets from evolutionary biology and teratology
Problem Based Learning, curriculum development and change process at Faculty of Medicine, Makerere University, Uganda.

INTRODUCTION
The faculty of Medicine, (FOM) Makerere University Kampala was started in 1924 and has been running a traditional curriculum for 79 years. A few years back it embarked on changing its curriculum from traditional to Problem Based Learning (PBL) and Community Based Education and Service (COBES) as well as early clinical exposure. This curriculum has been implemented since the academic year 2003/2004. The study was done to describe the steps taken to change and implement the curriculum at the Faculty of Medicine, Makerere University Kampala.


OBJECTIVE
To describe the steps taken to change and implement the new curriculum at the Faculty of Medicine.


METHODS
The stages taken during the process were described and analysed.


RESULTS
The following stages were recognized characterization of Uganda's health status, analysis of government policy, analysis of old curriculum, needs assessment, adoption of new model (SPICES), workshop/retreats for faculty sensitization, incremental development of programs by faculty, implementation of new curriculum.


CONCLUSION
The FOM has successfully embarked on curriculum change. This has not been without challenges. However, challenges have been taken on and handled as they arose and this has led to the implementation of new curriculum. Problem based learning can be adopted even in a low resourced country like Uganda.
The relationship between the big five personality traits and academic motivation

Understanding the relationship between personality characteristics and academic motivation may be central to developing more effective teaching strategies. The current research examined the relationship between the Big Five personality traits and individual differences in college students academic motivation. Individuals (172 undergraduates) were asked to complete the NEO Five Factor Inventory (Costa & McCrae, 1992) and the Academic Motivations Inventory (AMI; Moen & Doyle, 1977). Results revealed a complex pattern of significant relationships between the Big Five traits and the 16 subscales of the AMI. Stepwise (forward) multiple regressions further clarified the relationships between personality and three core factors of the AMI (engagement, achievement, and avoidance). Specifically, engagement was best explained by Openness to experience and Extraversion. Achievement was best explained by Conscientiousness, Neuroticism, and Openness to experience. Finally, avoidance was best explained by Neuroticism, Extraversion, and by an inverse relationship with Conscientiousness and Openness to experience. Results are interpreted in terms of creating an appropriate fit between teaching modalities and individual differences in students academic motivation due to personality traits. Directions for future research and educational practice are considered. 2005 Elsevier Ltd. All rights reserved.
The design of compassionate care.

AIMS AND OBJECTIVES
To investigate the tension between individual and organisational responses to contemporary demands for compassionate interactions in health care.


BACKGROUND
Health care is often said to need more compassion among its practitioners. However, this represents a rather simplistic view of the issue, situating the problem with individual practitioners rather than focusing on the overall design of care and healthcare organisations, which have often adopted a production-line approach.


DESIGN
This is a position paper informed by a narrative literature review.


METHODS
A search of the PubMed, Science Direct and CINAHL databases for the terms compassion, care and design was conducted in the research literature published from 2000 through to mid-2013.


RESULTS
There is a relatively large literature on compassion in health care, where authors discuss the value of imbuing a variety of aspects of health services with compassion including nurses, other practitioners and, ultimately, among patients. This contrasts with the rather limited attention that compassionate practice has received in healthcare curricula and the lack of attention to how compassion is informed by organisational structures and processes. We discuss how making the clinic more welcoming for patients and promoting bidirectional compassion and compassion formation in nursing education can be part of an overall approach to the design of compassionate care.


CONCLUSIONS
We discuss a number of ways in which compassion can be enhanced through training, educational and organisational design, through exploiting the potential of brief opportunities for communication and through initiatives involving patients and service users, as well as practitioners and service leaders.


RELEVANCE TO CLINICAL PRACTICE
The development of contemporary healthcare systems could usefully address the overall design of compassionate care rather than blame individual practitioners for a lack of compassion.
Predicting room occupancy with a single passive infrared (PIR) sensor through behavior extraction

Passive infrared sensors have widespread use in many applications, including motion detectors for alarms, lighting systems and hand dryers. Combinations of multiple PIR sensors have also been used to count the number of humans passing through doorways. In this paper, we demonstrate the potential of the PIR sensor as a tool for occupancy estimation inside of a monitored environment. Our approach shows how flexible nonparametric machine learning algorithms extract useful information about the occupancy from a single PIR sensor. The approach allows us to understand and make use of the motion patterns generated by people within the monitored environment. The proposed counting system uses information about those patterns to provide an accurate estimate of room occupancy which can be updated every 30 seconds. The system was successfully tested on data from more than 50 real office meetings consisting of at most 14 room occupants.
Not for Profit

In this book Nussbaum makes a strong case for the importance of the liberal arts in education. If the economic pressure of globalization is not kept under control, the end result might be an erosion of our democracies. The book is more a manifesto (178 pages) and not an empirical study. Quantitative data have been omitted.
Use of multiple social media platforms and symptoms of depression and anxiety: A nationally-representative study among U.S. young adults

Introduction: While increased time spent on social media (TSSM) has been associated with depression and anxiety, the independent role of using multiple social media (SM) platforms is unclear. Methods: We surveyed a nationally-representative sample of 1787 U.S. young adults ages 19e32. Depression and anxiety symptoms were measured using the Patient-Reported Outcomes Measurement Information System (PROMIS). We assessed use of multiple SM platforms with an adapted Pew Internet Research scale. We used ordered logistic regression models to assess associations between use of multiple SM platforms and mental health outcomes while controlling for eight covariates, including overall TSSM. Results: Compared to those who used 0e2 social media platforms, participants who used 7e11 social media platforms had substantially higher odds of having increased levels of both depression (Adjusted Odds Ratio [AOR] 1⁄4 3.0, 95% CI 1⁄4 1.9e4.8) and anxiety symptoms (AOR 1⁄4 3.2, 95% CI 1⁄4 2.0e5.1). Associations were linear (p < 0.001 for all) and robust to all sensitivity analyses. Conclusions: Use of multiple SM platforms is independently associated with symptoms of depression and anxiety, even when controlling for overall TSSM. These associations are strong enough that it may be valuable for clinicians to ask individuals with depression and anxiety about multiple platform use and to counsel regarding this potential contributing factor. © 2016 Published by Elsevier Ltd.