LLukas22/scidocs huggingface dataset:
Phase I study of the histone deacetylase inhibitor entinostat in combination with 13-cis retinoic acid in patients with solid tumours

Background:Preclinical studies suggest that histone deacetylase (HDAC) inhibitors may restore tumour sensitivity to retinoids. The objective of this study was to determine the safety, tolerability, and the pharmacokinetic (PK)/pharmacodynamic (PD) profiles of the HDAC inhibitor entinostat in combination with 13-cis retinoic acid (CRA) in patients with solid tumours.Methods:Patients with advanced solid tumours were treated with entinostat orally once weekly and with CRA orally twice daily × 3 weeks every 4 weeks. The starting dose for entinostat was 4 mg m−2 with a fixed dose of CRA at 1 mg kg−1 per day. Entinostat dose was escalated by 1 mg m−2 increments. Pharmacokinetic concentrations of entinostat and CRA were determined by LC/MS/MS. Western blot analysis of peripheral blood mononuclear cells and tumour samples were performed to evaluate target inhibition.Results:A total of 19 patients were enroled. The maximum tolerated dose (MTD) was exceeded at the entinostat 5 mg m−2 dose level (G3 hyponatremia, neutropenia, and anaemia). Fatigue (G1 or G2) was a common side effect. Entinostat exhibited substantial variability in clearance (147%) and exposure. CRA trough concentrations were consistent with prior reports. No objective responses were observed, however, prolonged stable disease occurred in patients with prostate, pancreatic, and kidney cancer. Data further showed increased tumour histone acetylation and decreased phosphorylated ERK protein expression.Conclusion:The combination of entinostat with CRA was reasonably well tolerated. The recommended phase II doses are entinostat 4 mg m−2 once weekly and CRA 1 mg kg−1 per day. Although no tumour responses were seen, further evaluation of this combination is warranted.
Psychological benefits of virtual reality for patients in rehabilitation therapy.

CONTEXT
Whether virtual rehabilitation is beneficial has not been determined.


OBJECTIVE
To investigate the psychological benefits of virtual reality in rehabilitation.


DESIGN
An experimental group underwent therapy with a virtual-reality-based exercise bike, and a control group underwent the therapy without virtual-reality equipment.


SETTING
Hospital laboratory.


PATIENTS
30 patients suffering from spinal-cord injury.


INTERVENTION
A designed rehabilitation therapy.


MAIN OUTCOME MEASURES
Endurance, Borg's rating-of-perceived-exertion scale, the Activation-Deactivation Adjective Check List (AD-ACL), and the Simulator Sickness Questionnaire.


RESULTS
The differences between the experimental and control groups were significant for AD-ACL calmness and tension.


CONCLUSION
A virtual-reality-based rehabilitation program can ease patients' tension and induce calm.
Ontology-Based Architecture for Intelligent Transportation Systems Using a Traffic Sensor Network

Intelligent transportation systems are a set of technological solutions used to improve the performance and safety of road transportation. A crucial element for the success of these systems is the exchange of information, not only between vehicles, but also among other components in the road infrastructure through different applications. One of the most important information sources in this kind of systems is sensors. Sensors can be within vehicles or as part of the infrastructure, such as bridges, roads or traffic signs. Sensors can provide information related to weather conditions and traffic situation, which is useful to improve the driving process. To facilitate the exchange of information between the different applications that use sensor data, a common framework of knowledge is needed to allow interoperability. In this paper an ontology-driven architecture to improve the driving environment through a traffic sensor network is proposed. The system performs different tasks automatically to increase driver safety and comfort using the information provided by the sensors.
Combined exercise training in asymptomatic elderly with controlled hypertension: Effects on functional capacity and cardiac diastolic function

BACKGROUND
Aging is associated with changes in cardiac structure and function that are associated with left ventricular diastolic dysfunction. Whether diastolic functional alterations during senescence are manifestations of the intrinsic aging process or related to cardiac adaptations to a more sedentary lifestyle is still unsettled. This was a prospective study evaluating the effects of a 6-month combined exercise training period on functional capacity and diastolic function in sedentary elderly patients with controlled arterial hypertension.


MATERIAL/METHODS
Functional capacity was assessed by exercise stress test and muscle strength was evaluated by the one-repetition maximum test. Cardiac structures and function were analyzed by transthoracic echocardiography.


RESULTS
Fifteen patients, 68±8 years old, completed the training program. Exercise training significantly improved physical capacity (distance walked: 551±92 vs. 630±153 m, P<0.05; work load: 7.2±1.7 vs. 8.5±3.0 METs, P<0.05) and upper and lower extremity muscle strength (P<0.001). Arterial blood pressure significantly decreased after training (systolic blood pressure: 134±9 vs. 128±8 mmHg; diastolic blood pressure: 82±7 vs. 77±6 mmHg; P<0.05). Cardiac structures and left and right systolic and diastolic function did not change after combined training (P>0.05).


CONCLUSIONS
Combined and supervised training for a 6-month period increases physical capacity and muscle strength in elderly patients with controlled arterial hypertension without changing resting left ventricular diastolic function.
Does treatment of ruptured intracranial aneurysms within 24 hours improve clinical outcome?

BACKGROUND AND PURPOSE
The purpose of this study was to analyze whether treating ruptured intracranial aneurysms within 24 hours of subarachnoid hemorrhage improves clinical outcome.


METHODS
An 11-year database of consecutive ruptured intracranial aneurysms treated with endovascular coiling or craniotomy and clipping was analyzed. Outcome was measured by the modified Rankin Scale at 6 months. Our policy is to treat all cases within 24 hours of subarachnoid hemorrhage. Treatment delays are due to nonclinical logistical factors.


RESULTS
Two hundred thirty cases were coiled or clipped within 24 hours of subarachnoid hemorrhage and 229 at >24 hours. No difference in age, gender, smoking, family history of subarachnoid hemorrhage, aneurysm size, or aneurysm location was found between the groups. Poor World Federation of Neurological Surgeons clinical grade patients were overrepresented in the ultra-early group. Increasing age and higher World Federation of Neurological Surgeons clinical grade were predictors of poor outcome. Eight point zero percent (16 of 199) of cases treated within 24 hours of SAH (ultra-early) were dependent or dead at 6 months compared with 14.4% (30 of 209) of those treated at >24 hours post-SAH (delayed; (χ2, P0.044) [corrected]. A total of 3.5% of cases coiled within 24 hours were dependent or dead at 6 months compared with 12.5% of cases coiled at 1 to 3 days, an 82% relative risk reduction and a 10.2% absolute risk reduction (χ2, P=0.040). These groups did not differ in age, World Federation of Neurological Surgeons clinical grade, aneurysm size, or aneurysm location.


CONCLUSIONS
Treatment of ruptured aneurysms within 24 hours is associated with improved clinical outcomes compared with treatment at >24 hours. The benefit is more pronounced for coiling than clipping.
Toll-like receptor 2 is highly expressed in lesions of acne inversa and colocalizes with C-type lectin receptor.

BACKGROUND
Acne inversa (hidradenitis suppurativa) is a chronic inflammatory and cicatricial disorder that affects skin areas rich in apocrine glands and terminal hairs, such as perineum and axillae. The exact pathogenesis of the disease is not well understood and the mechanisms by which bacterial superinfection contributes to the disease progression are not clear. Toll-like receptors (TLRs) expressed by inflammatory cells play a crucial role in the innate immune response to bacteria.


OBJECTIVES
We sought to investigate the role of TLR2 in the pathogenesis of acne inversa.


METHODS
We investigated the expression of TLR2 using real-time polymerase chain reaction analysis and immunohistochemical stainings of tissue samples from patients with acne inversa. Furthermore, we phenotypically characterized the infiltrating cells and their expression of TLR2.


RESULTS
Compared with normal skin, a highly increased in situ expression of TLR2 in acne inversa skin lesions was found at both the mRNA and the protein level. The most abundant cells in the dermal infiltrate of acne inversa were CD68+ macrophages, CD209+ dendritic cells (DCs) and CD3+ T cells. CD19+ B cells and CD56+ natural killer cells were found only in small numbers. Double staining with fluorescence-labelled antibodies showed that TLR2 was expressed by infiltrating macrophages (CD68+) and DCs (CD209+). Flow cytometric analysis of isolated infiltrating cells further confirmed surface expression of TLR2 by macrophages and DCs.


CONCLUSIONS
These data indicate that the enhanced expression of TLR2 by infiltrating macrophages and DCs may contribute to the pathogenesis of inflammatory lesions of acne inversa.
Design and stability analysis of a lane following controller

This paper considers the design and stability analysis of a steering controller. The objective of the controller is to steer a ground vehicle along a reference line located in the middle of the lane to be followed. We define an arbitrary look-ahead point located on the local longitudinal axis of the vehicle. The distance between the look-ahead point and the reference line is called the look-ahead offset. During perfect lane tracking, the ratio of the steer angle to the look-ahead offset is independent of the curve radius under reasonable approximations. That ratio is computed in terms of the vehicle speed and various vehicle parameters. Then, a constant controller is designed to achieve that ratio at steady state. The controller is a continuous function of the vehicle speed. The only information processed by the controller is the look-ahead offset, which can be measured using a radarbased or a vision-based sensor. Using Routh–Hurwitz analysis, we analytically prove that the closed-loop system is stable. Given any range of longitudinal speeds, there exists a sufficiently large look-ahead distance ensuring the closed-loop stability for all speeds in that speed range. For a particular set of parameter variations, it is also shown that choosing the look-ahead distance large enough guarantees the robustness of closed-loop stability. Various simulation results demonstrating the performance of the controller are included.
Performance evaluation and tuning for MapReduce computing in Hadoop distributed file system

This paper proposes a method to facilitate the identification process for a set of configuration parameters to achieve the optimal performance with respect to a benchmark program in HDFS in an automated manner. Performance optimization of Hadoop processes is a tedious yet challenging problem due to the complexity of the systems organization with an extensive list of configuration parameters to be considered. An Automated Benchmarking Configuration Method (ABCM) is developed in this work to facilitate the identification process for the set of configuration parameters that minimizes the execution time of a benchmark, namely TestDFSIO Write and Read in particular. A two-phased configuration parameters selection process with a simple sampling technique is proposed in order to mediate the exponential computation time otherwise. By using the proposed technique, we have automatically found the sets of top five selected optimal configuration parameters that reduced the average execution time by 32% compared to the execution time with the default set of Hadoop configuration parameters.
Handwritten Digit Recognition Using Multiple Feature Extraction Techniques and Classifier Ensemble

It is herein proposed a handwritten digit recognition system which uses multiple feature extraction methods and classifier ensemble. The combination of the feature extraction methods is motivated by the observation that different feature extraction algorithms have a better discriminative power for some types of digits. Six features sets were extracted, two proposed by the authors and four published in previous works. It is shown that combining these feature sets is sufficient to achieve high recognition rates. Several combination schemes were tested, showing good results. A scheme using neural networks as a combiner achieved a recognition rate of 99.68%, the highest one on the MNIST database. Keywords-Handwritten recognition, Feature Extraction, Classifier Ensemble, Neural Networks.
Digital heritage application as an edutainment tool

With the fast-growing technological advancements in Virtual Reality (VR) technology and easier access to more affordable computer graphics hardware, it has become possible to create a diverse range of VR applications that are not only geared towards scientific research and medical training applications but also for "edutainment" purposes for the general public. "Edutainment" is an upcoming field that combines education with entertainment aspects thus enhancing the learning environment to be much more engaging and fun-filled. In this paper, we describe a project on a Digital Heritage application aimed to serve as an edutainment tool. The visitors are able to virtually "enter and explore" the reconstructed heritage environment and learn more on the presented content through virtual experiences. We have incorporated a Virtual Tour Guide that presents the cultural and historical content through nonlinear digital storytelling techniques for the dynamic content creation to fit the changing profiles and needs of the visiting audience.
Relationship between PCO2 and unfavorable outcome in infants with moderate-to-severe hypoxic ischemic encephalopathy

Background:Abnormal PCO2 is common in infants with hypoxic ischemic encephalopathy (HIE). The objective was to determine whether hypocapnia was independently associated with unfavorable outcome (death or severe neurodevelopmental disability at 18 mo) in infants with moderate-to-severe HIE.Methods:This was a post hoc analysis of the CoolCap Study in which infants were randomized to head cooling or standard care. Blood gases were measured at prespecified times after randomization. PCO2 and follow-up data were available for 196 of 234 infants. Analyses were performed to investigate the relationship between hypocapnia in the first 72 h after randomization and unfavorable outcome.Results:After adjusting for pH, amplitude-integrated electroencephalogram background and seizures, birth weight, Apgar score at 5 min, cooling status, and Sarnat stage, PCO2 was inversely associated with unfavorable outcome (P < 0.001). The probability of unfavorable outcome was 0.20 ± 0.1 (point estimate ± SE), 0.53 ± 0.23 and 0.89 ± 0.16 for a PCO2 of 40, 30, and 20 mm Hg respectively and was greater in infants with severe HIE than with moderate HIE.Conclusions:Hypocapnia in infants with moderate-to-severe HIE was independently associated with unfavorable outcome. Future studies of controlled normocapnia will be important.
Roots of a compact Lie group

This expository article introduces the topic of roots in a compact Lie group. Compared to the many other treatments of this standard topic, I intended for mine to be relatively elementary, example-driven, and free of unnecessary abstractions. Some familiarity with matrix groups and with maximal tori is assumed. 
This article is self-contained, but is also intended to serve as a supplemental 10th chapter of an eventual new edition of my textbook, ``Matrix Groups for Undergraduates.''
Graph Classification

Supervised learning on graphs is a central subject in graph data processing. In graph classification and regression, we assume that the target values of a certain number of graphs or a certain part of a graph are available as a training dataset, and our goal is to derive the target values of other graphs or the remaining part of the graph. In drug discovery applications, for example, a graph and its target value correspond to a chemical compound and its chemical activity. In this chapter, we review state-of-the-art methods of graph classification. In particular, we focus on two representative methods, graph kernels and graph boosting, and we present other methods in relation to the two methods. We describe the strengths and weaknesses of different graph classification methods and recent efforts to overcome the challenges.
Thermal reliability & IMC behavior of low cost alternative Au-Ag-Pd wire bonds to Al metallization

To reduce material cost of Au bonding wire, Au-Ag alloy wire had been tried to use in electronic device, in alternative for Au wire. Nevertheless, Au-Ag alloy wire had not been applied to device due to failure problem during high humidity reliability test, like PCT(Pressure Cooker Test) for a while. Recently, as the technology adding Pd element to conventional Au-Ag was developed, corrosive failure problem at interface between wire ball and Al pad (metallization) was solved in PCT. Finally, mass production of Au-Ag-Pd wire starts to grow up. The study on reliability and behavior of intermetallic compounds(IMC) have not been performed in terms of thermal Aging or HTST(High Temperature Storage Life Test) yet. This study investigates IMC & voids behavior between Au-Ag-Pd wire and Al metallization under thermal aged condition (175'C). The chemical compositions of gold wires tested are 99.99% Au, Au-30wt.%Ag and Au-30wt.%Ag-5.5%wt.Pd, respectively. The wires are bonded on Al metallization by using thermosonic bonder, IMC behavior was characterized by FIB(Focused ion beam), TEM (Transmission Electron Microscope), EDS (Energy Dispersive X-ray Spectrometer) The findings reveal that, interfacial reliability between Au-Ag-Pd wire and Al metallization is considerably improved, compared with 4N Au or Au-30%Ag, Growth of IMCs as well as the voids formation are significantly suppressed.
An empirical investigation of the factors that influence Internet user's ability to correctly identify a phishing website

Purpose – The aim of this study is to report on the results of an empirical investigation of the various factors which have significant impacts on the Internet user’s ability to correctly identify a phishing website. Design/methodology/approach – The research participants were Internet users who have had at least some experience of financial transactions over the Internet. This study conducted a quantitative research with the help of a structured survey questionnaire along with three experimental tasks. A total of 621 valid samples were collected and the multiple regression analysis technique was used to deduce the answers to the research question. Findings – The results show that the model is useful and has explanatory power. And adjusted R computed as 0.927, means that 92.7 per cent of the variations in the Internet user’s ability to identify phishing website can be explained by the predictors selected for the model. Research limitations/implications – Future research should account for the Internet user’s general security practices and behaviour, attitude towards online financial activity, risk-taking ability or risk behaviour and their potential effects on Internet users’ ability to identify a phishing website. Practical implications – The implications of this study provide the foundation for future research on the areas that intend to explain the Internet user’s necessity to take protection or avoid risky behaviour while performing financial transaction over the Internet. Originality/value – This study provides the body of knowledge with an empirical analysis of impact of various factors on an Internet user’s ability to identify phishing websites. The results of this study can help practitioners create a more successful research model and help researchers better understand user behaviour on the Internet.
Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae).

Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

MOTIVATION
Accurately predicting protein secondary structure and relative solvent accessibility is important for the study of protein evolution, structure and function and as a component of protein 3D structure prediction pipelines. Most predictors use a combination of machine learning and profiles, and thus must be retrained and assessed periodically as the number of available protein sequences and structures continues to grow.


RESULTS
We present newly trained modular versions of the SSpro and ACCpro predictors of secondary structure and relative solvent accessibility together with their multi-class variants SSpro8 and ACCpro20. We introduce a sharp distinction between the use of sequence similarity alone, typically in the form of sequence profiles at the input level, and the additional use of sequence-based structural similarity, which uses similarity to sequences in the Protein Data Bank to infer annotations at the output level, and study their relative contributions to modern predictors. Using sequence similarity alone, SSpro's accuracy is between 79 and 80% (79% for ACCpro) and no other predictor seems to exceed 82%. However, when sequence-based structural similarity is added, the accuracy of SSpro rises to 92.9% (90% for ACCpro). Thus, by combining both approaches, these problems appear now to be essentially solved, as an accuracy of 100% cannot be expected for several well-known reasons. These results point also to several open technical challenges, including (i) achieving on the order of ≥ 80% accuracy, without using any similarity with known proteins and (ii) achieving on the order of ≥ 85% accuracy, using sequence similarity alone.


AVAILABILITY AND IMPLEMENTATION
SSpro, SSpro8, ACCpro and ACCpro20 programs, data and web servers are available through the SCRATCH suite of protein structure predictors at http://scratch.proteomics.ics.uci.edu.