LLukas22/scidocs huggingface dataset:
High-density lipoprotein cholesterol as a predictor of clinical outcomes in patients achieving low-density lipoprotein cholesterol targets with statins after percutaneous coronary intervention

BACKGROUND
A low level of high-density lipoprotein cholesterol (HDL-C) is strongly associated with cardiovascular events. However, the significance of HDL-C after statin therapy on the outcome of patients who have undergone percutaneous coronary intervention (PCI) with drug eluting stents (DES) is unclear.


OBJECTIVES
To investigate the significance of HDL-C after statin therapy on cardiovascular events in patients with coronary artery disease after DES implantation.


METHODS
Patients who underwent PCI with DES from January 2004 to December 2009 were prospectively enrolled. The follow-up lipid panel of 2693 patients (median lab follow-up duration 225 days) who had continued using statins after PCI and who attained low-density lipoprotein cholesterol (LDL-C) <100 mg/dl was analysed. Major adverse cardiac events (MACE), including all-cause death, non-fatal myocardial infarction, and target vessel revascularisation according to follow-up HDL-C level (40 mg/dl for men or 50 mg/dl for women) were compared with the use of propensity scores matching.


RESULTS
Median follow-up duration was 832 days. 1585 (58.9%) patients had low follow-up HDL-C and 1108 had high follow-up HDL-C. The low follow-up HDL-C group had significantly higher rates of MACE. Low follow-up HDL-C was a significant independent predictor of MACE (adjusted HR 1.404, 95% CI 1.111 to 1.774, p=0.004). In further analysis with propensity scores matching, overall findings were consistent.


CONCLUSIONS
Raising HDL-C levels may be a subsequent goal after achieving target LDL-C levels in patients with DES implantation.
Phase I/II docetaxel plus concurrent hyperfractionated radiotherapy in locally advanced unresectable head and neck cancer (TAX.ES1.102 study).

INTRODUCTION
Concurrent chemotherapy and radiotherapy is recommended for the treatment of locally advanced unresectable head and neck (H&N) cancer.


OBJECTIVE
The primary purpose of the Phase I part of the study was to determine the maximum tolerated dose (MTD), dose-limiting toxicity (DLT) and recommended dose (RD) of docetaxel with hyperfractionation radiotherapy. The primary objective of the Phase II part was to determine the response rate to the RD of treatment and, secondarily, to assess the toxicity of the schedule, time to progression, duration of response and overall survival (OS).


MATERIALS AND METHODS
Patients (n=9 in Phase I; n=19 in Phase II) had unresectable H&N cancer. The starting docetaxel dose was 20 mg/m(2) plus hyperfractionated radiotherapy. Ramping of docetaxel was 5 mg/m(2) if MTD was not reached.


RESULTS
MTD of docetaxel was 20 mg/m(2). Limiting toxicities were grade 4 pneumonia and grade 4 mucositis. The RD was 15 mg/m(2). Phase II initial response was 76% (CR=18%; PR=9%); updated response was 89% (CR=59%; PR=29%). The median progression-free survival was 7.8 months (95%CI: 0-22.3) and the median OS was 15.1 months (95%CI: 0-35.9). Grade 3-4 toxicities included mucositis (91%), pneumonia (27%) and fatigue (27%). There were 5 toxic deaths (2 from intestinal perforation, 3 from pneumonia).


CONCLUSIONS
Weekly docetaxel+hyperfractionation radiotherapy is active but with high toxicity rates and, hence, this treatment regimen would be difficult to justify.
Assembling short reads from jumping libraries with large insert sizes

MOTIVATION
Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.


RESULTS
We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.


AVAILABILITY AND IMPLEMENTATION
Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.


CONTACT
ap@bioinf.spbau.ru


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Lone atrial fibrillation as a positive predictor of left atrial volume reduction following ablation of atrial fibrillation.

AIMS
We investigated predictors of left atrial volume reduction (LAVR) in patients with atrial fibrillation (AF) undergoing AF ablation.


METHODS AND RESULTS
Sixty patients with AF underwent pulmonary vein isolation (PVI) using a pulmonary vein ablation catheter (PVAC). All patients underwent cardiac imaging by computed tomography or magnetic resonance imaging to determine LAV 1 day before and 140 ± 9.5 days after PVI. Clinical follow-up and 72 h electrocardiogram Holter monitoring were performed 1, 3, and 6 months after ablation, and every 6 months thereafter. Significant LAVR (n = 60, 89.3 ± 3.9 vs. 79.5 ± 3.6 mL, P < 0.0001) was shown for the study group as a whole, caused particularly by the subgroup of patients with ablation success (n = 45, 85.2 ± 4.6 vs. 72.5 ± 3.7 mL, P < 0.0001). In addition, significant LAVR was shown for patients with lone AF (n = 25, 88.8 ± 6.8 vs. 72.7 ± 5.3 mL, P < 0.0001), but not for patients with AF and concomitant arterial hypertension (n = 32, 89 ± 4.8 vs. 86.7 ± 5 mL, P = 0.3), coronary artery disease (n = 12, 91.6 ± 7.8 vs. 89.1 ± 7.8 mL, P = 0.26), or left ventricular hypertrophy (n = 10, 86.3 ± 5.5 vs. 83.1 ± 5.3 mL, P = 0.27). Multivariate analysis revealed absence of arterial hypertension, lone AF, ablation success, and initial LA enlargement as independent predictors for significant LAVR following ablation (each P < 0.05).


CONCLUSION
Based on the subgroup of patients with lone AF, PVI leads to a significant LAVR 4 months after the procedure, especially in patients with clinical success in terms of AF freedom. Comorbidities such as arterial hypertension may prevent this reverse atrial remodelling, despite AF freedom. Clinical implications need to be further elucidated.
Quantum Computability

In this paper some theoretical and (potentially) practical aspects of quantum computing are considered. Using the tools of transcendental number theory it is demonstrated that quantum Turing machines (QTM) with rational amplitudes are sufficient to define the class of bounded error quantum polynomial time (BQP) introduced by Bernstein and Vazirani [Proc. 25th ACM Symposium on Theory of Computation, 1993, pp. 11–20, SIAM J. Comput., 26 (1997), pp. 1411–1473]. On the other hand, if quantum Turing machines are allowed unrestricted amplitudes (i.e., arbitrary complex amplitudes), then the corresponding BQP class has uncountable cardinality and contains sets of all Turing degrees. In contrast, allowing unrestricted amplitudes does not increase the power of computation for error-free quantum polynomial time (EQP). Moreover, with unrestricted amplitudes, BQP is not equal to EQP. The relationship between quantum complexity classes and classical complexity classes is also investigated. It is shown that when quantum Turing machines are restricted to have transition amplitudes which are algebraic numbers, BQP, EQP, and nondeterministic quantum polynomial time (NQP) are all contained in PP, hence in P#P and PSPACE. A potentially practical issue of designing “machine independent” quantum programs is also addressed. A single (“almost universal”) quantum algorithm based on Shor’s method for factoring integers is developed which would run correctly on almost all quantum computers, even if the underlying unitary transformations are unknown to the programmer and the device builder.
Krivine's intuitionistic proof of classical completeness (for countable languages)

Abstract In 1996, Krivine applied Friedman's A-translation in order to get an intuitionistic version of Godel completeness result for first-order classical logic and (at most) countable languages and models. Such a result is known to be intuitionistically underivable (see J. Philos. Logic 25 (1996) 559), but Krivine was able to derive intuitionistically a weak form of it, namely, he proved that every consistent classical theory has a model. In this paper, we want to analyze the ideas Krivine's remarkable result relies on, ideas which where somehow hidden by the heavy formal machinery used in the original proof. We show that the ideas in Krivine's proof can be used to intuitionistically derive some (suitable variants of) crucial mathematical results, which were supposed to be purely classical up to now: the Ultrafilter Theorem for countable Boolean algebras, and the maximal ideal theorem for countable rings.
K- NEAREST NEIGHBOR ALGORITHM FOR INSTANCE BASED LEARNING

Instance Based Learning (IBL) results in classifying a new instance by examining and comparing it to the rest of the instances in the dataset. An example of this type of learning is the K-Nearest Neighbor algorithm which is based on examining an average Euclidian distance of the nearest k neighbors' parameters given a certain situation.
Developmental biology: This worm is not for turning

Molecular investigations of the origin of the dorso-ventral axis in an obscure marine invertebrate illuminate one of the longest-running debates in evolutionary biology — that over the origin of vertebrates.
Maternal Factors Associated with Fetal Growth and Birthweight Are Independent Determinants of Placental Weight and Exhibit Differential Effects by Fetal Sex

INTRODUCTION
Maternal nutritional and metabolic factors influence the developmental environment of the fetus. Virtually any nutritional factor in the maternal blood has to pass the placental membranes to reach the fetal blood. Placental weight is a commonly used measure to summarize placental growth and function. Placental weight is an independent determinant of fetal growth and birthweight and modifies the associations between maternal metabolic factors and fetal growth. We hypothesized that maternal factors known to be related to fetal growth, newborn size and body composition are determinants of placental weight and that effects of maternal metabolic factors on placental weight differ between the genders.


METHODS
The STORK study is a prospective longitudinal study including 1031 healthy pregnant women of Scandinavian heritage with singleton pregnancies. Maternal determinants (parity, body mass index, gestational weight gain and fasting plasma glucose) of placental weight were explored by linear regression models, stratified by fetal sex.


RESULTS
Parity, maternal BMI, gestational weight gain and fasting glucose had positive effects on placental weight. There was a sex specific effect in these associations. Fasting glucose was significantly associated with placental weight in females but not in males.


CONCLUSION
Maternal factors known to influence fetal growth, birthweight and neonatal body composition are determinants of placental weight. The effect of maternal factors on placental weight is influenced by sex as illustrated in the relation between maternal glucose and placental weight.
The Habits of Highly Effective Researchers: An Empirical Study

Interest in the habits of influential individuals cuts across domains. As researchers, we are intrigued why few attain significant eminence in their fields, whereas many operate in obscurity. An empirical examination of this question has been made possible by the recent availability of large scale publication data. In this paper, we use information from the AMiner Paper Citation and Author Collaboration Networks to discern factors that relate to the impact of influential researchers across five domains in the computing discipline. We propose and apply a novel algorithm to identify influential vertices in co-authorship networks built from total corpora of 1,00,000+ papers and 72,000+ authors over a span of more than 50 years. The results from our study indicate that the impact of these influential researchers relate to a variety of factors. Surprisingly, we find evidence across the domains that higher impact is associated with lower levels of collaboration, and authority.
Brief report: Cognitive emotion regulation strategies and psychological adjustment in adolescents with a chronic disease.

Objective of the study was to examine how cognitive emotion regulation strategies were related to psychological maladjustment in adolescents with a chronic disease. The sample consisted of adolescents with a diagnosis of Juvenile Idiopathic Arthritis (JIA). A self-report questionnaire was used to assess Internalizing problems and Quality of Life. The specific cognitive emotion regulation strategies that were used in response to the disease were measured by the Cognitive Emotion Regulation Questionnaire (CERQ). Correlations and Multiple regression analyses showed that Rumination and Catastrophizing were the most important 'predictors' of psychological maladjustment in adolescents with JIA, suggesting that they should be considered as maladaptive cognitive emotion regulation strategies in response to a chronic disease such as JIA. Challenging these maladaptive cognitive emotion regulation strategies may therefore play an important role in intervention strategies.
Goal setting using telemedicine in rural underserved older adults with diabetes: experiences from the informatics for diabetes education and telemedicine project.

OBJECTIVE
To describe the use of telemedicine for setting goals for behavior change and examine the success in achieving these goals in rural underserved older adults with diabetes.


MATERIALS AND METHODS
Medicare beneficiaries with diabetes living in rural upstate New York who were enrolled in the telemedicine intervention of the Informatics for Diabetes Education and Telemedicine (IDEATel) project (n = 610) participated in home televisits with nurse and dietitian educators every 4-6 weeks for 2-6 years. Behavior change goals related to nutrition, physical activity, monitoring, diabetes health maintenance, and/or use of the home telemedicine unit were established at the conclusion of each televisit and assessed at the next visit.


RESULTS
Collaborative goal setting was employed during 18,355 televisits (mean of 33 goal-setting televisits/participant). The most common goals were related to monitoring, followed by diabetes health maintenance, nutrition, exercise, and use of the telemedicine equipment. Overall, 68% of behavioral goals were rated as "improved" or "met." The greatest success was achieved for goals related to proper insulin injection technique and daily foot care. These elderly participants had the most difficulty achieving goals related to use of the computer. No gender differences in goal achievement were observed.


CONCLUSION
Televisits can be successfully used to collaboratively establish behavior change goals to help improve diabetes self-management in underserved elderly rural adults.
Grammar inference algorithms and applications in software engineering

Many problems exist whose solutions take the form of patterns that may be expressed using grammars (e.g., speech recognition, text processing, genetic sequencing). Construction of these grammars is usually carried out by computer scientists working with domain experts. In the case when there is a lack of domain experts, grammar inference can be applied. In this paper, two grammar inference algorithms are briefly described and their application to software engineering is presented.
Visualizing Big Data with augmented and virtual reality: challenges and research agenda

This paper provides a multi-disciplinary overview of the research issues and achievements in the field of Big Data and its visualization techniques and tools. The main aim is to summarize challenges in visualization methods for existing Big Data, as well as to offer novel solutions for issues related to the current state of Big Data Visualization. This paper provides a classification of existing data types, analytical methods, visualization techniques and tools, with a particular emphasis placed on surveying the evolution of visualization methodology over the past years. Based on the results, we reveal disadvantages of existing visualization methods. Despite the technological development of the modern world, human involvement (interaction), judgment and logical thinking are necessary while working with Big Data. Therefore, the role of human perceptional limitations involving large amounts of information is evaluated. Based on the results, a non-traditional approach is proposed: we discuss how the capabilities of Augmented Reality and Virtual Reality could be applied to the field of Big Data Visualization. We discuss the promising utility of Mixed Reality technology integration with applications in Big Data Visualization. Placing the most essential data in the central area of the human visual field in Mixed Reality would allow one to obtain the presented information in a short period of time without significant data losses due to human perceptual issues. Furthermore, we discuss the impacts of new technologies, such as Virtual Reality displays and Augmented Reality helmets on the Big Data visualization as well as to the classification of the main challenges of integrating the technology.
Drawings of graphs on surfaces with few crossings

We give drawings of a complete graphK n withO(n 4 log2 g/g) many crossings on an orientable or nonorientable surface of genusg ≥ 2. We use these drawings ofK n and give a polynomial-time algorithm for drawing any graph withn vertices andm edges withO(m 2 log2 g/g) many crossings on an orientable or nonorientable surface of genusg ≥ 2. Moreover, we derive lower bounds on the crossing number of any graph on a surface of genusg ≥ 0. The number of crossings in the drawings produced by our algorithm are within a multiplicative factor ofO(log2 g) from the lower bound (and hence from the optimal) for any graph withm ≥ 8n andn 2/m ≤g ≤m/64.
Organisation of maternity care and choices of mode of birth: a worldwide view.

Drawing on the findings from a Cochrane systematic review of midwife-led care vs. other models of maternity care, this article discusses maternity organisation of care, women's choice of mode of birth and a global trend in reducing normality of childbirth. The review included 11 trials involving 12,276 women. The results showed that women who received models of midwife led care were less likely to experience fetal loss before 24 weeks' gestation, less likely to have regional analgesia, less likely to have instrumental birth, less likely to have an episiotomy (with no significant differences in perineal lacerations), and were more likely to be attended at birth by a known midwife, more likely to have a spontaneous vaginal birth, initiate breast feeding and more stated to feel in control. In addition, their babies were more likely to have a shorter length of hospital stay. No statistically significant differences were observed in fetal loss/neonatal death of at least 24 weeks or in overall fetal/neonatal death between women who were allocated to the midwifery led care and those in the medical led care. In light of these findings, the interrelationship between social organisation of maternity care, philosophy of care and choice is explored using case examples with high and low rates of caesarean section rates. A worldwide overview of vaginal birth and caesarean section rates as indicators of normality (and lack of it) is also presented. Questions are raised with regard to the fast growing rate of caesarean section rates particularly among middle income countries. The rate of caesarean section is twice as much in private settings compared to public hospitals in these countries. In conclusion, the importance of sharing good practice among countries with particular attention to social location of midwifery, mobilisation of consumer groups as well as education of maternity health-care professionals and women, in facilitation of an effective 'informed choice', is highlighted. Areas for further global research on factors, which may influence women's choice of mode of birth are debated.
On the chemistry of ion exchange in monomolecular layers of lipids.

Abstract The main purpose of this work has been to study further the association of cations and anions with cell membrane lipids, in particular with phosphatidylcholine. The adsorption of Ca 2+ or SO 4 2− to phosphatidylcholine monolayers (measured with isotopes) shows that there is no uptake of these ions under various experimental conditions including different bulk pH values and concentrations. The presence or absence of charges in monomolecular films of lipids can be inferred by utilizing a method of analysis proposed here; it depends on the study of the cation and anion exchange properties of each functional group found in lipids. To mimic the structure of the polar head of phosphatidylserine and phosphatidylcholine, surface-active molecules with phosphoric, carboxyl and trimethylammonium groups were combined in various proportions and used to form a mixed monolayer. The uptake of Ca 2+ or SO 4 2− by mixed monolayers of octadecyltrimethylammonium and octadecyl phosphate (both groups present in phosphatidylcholine) indicate that when the molar fraction of octadecyltrimethylammonium is about 0.4 the mixed monolayers behaves as neutral.
Ephedra: a c to java migration environment

The Internet has grown in popularity in recent years, and thus it has gained importance for many current businesses. They need to offer their products and services through their Web sites. To present not only static content but also interactive services, the logic behind these services needs to be programmed. Various approaches for programming Web services exist. The Java programming language can be used to implement Web services that run both on Internet clients and servers, either exclusively or in interaction with each other. The Java programming language is standardised across computing platforms and has matured over the past few years, and is therefore a popular choice for the implementation of Web services. The amount of available and well-tested Java source code is still small compared to other programming languages. Rather than taking the risks and costs of redeveloping program libraries, it is often preferable to move the core logic of existing solutions to Java and then integrate it into Java programs that present the services in a Web interface. In this Ph.D. dissertation, we survey and evaluate a selection of current approaches to the migration of source code to Java. To narrow the scope of the dissertation to a reasonable limit, we focus on the C and C++ programming languages as the source languages. Many mature programs and program libraries exist in these languages. The survey of current migration approaches reveals a number of their restrictions and disadvantages in the context of moving program libraries to Java and integrating them with Java programs. Using the experiences from this survey, we established a number of goals for an improved migration approach and developed the Ephedra approach by closely following these goals. To show the practicality of this approach, we implemented an automated tool that performs the migration according to the Ephedra approach and evaluated