Miracle-dz/UniFAR-FTUs huggingface dataset:
Using existing questionnaires in latent class analysis: should we use summary scores or single items as input? A methodological study using a cohort of patients with low back pain

Background Latent class analysis (LCA) is increasingly being used in health research, but optimal approaches to handling complex clinical data are unclear. One issue is that commonly used questionnaires are multidimensional, but expressed as summary scores. Using the example of low back pain (LBP), the aim of this study was to explore and descriptively compare the application of LCA when using questionnaire summary scores and when using single items to subgrouping of patients based on multidimensional data. Materials and methods Baseline data from 928 LBP patients in an observational study were classified into four health domains (psychology, pain, activity, and participation) using the World Health Organization’s International Classification of Functioning, Disability, and Health framework. LCA was performed within each health domain using the strategies of summary-score and single-item analyses. The resulting subgroups were descriptively compared using statistical measures and clinical interpretability. Results For each health domain, the preferred model solution ranged from five to seven subgroups for the summary-score strategy and seven to eight subgroups for the single-item strategy. There was considerable overlap between the results of the two strategies, indicating that they were reflecting the same underlying data structure. However, in three of the four health domains, the single-item strategy resulted in a more nuanced description, in terms of more subgroups and more distinct clinical characteristics. Conclusion In these data, application of both the summary-score strategy and the single-item strategy in the LCA subgrouping resulted in clinically interpretable subgroups, but the single-item strategy generally revealed more distinguishing characteristics. These results 1) warrant further analyses in other data sets to determine the consistency of this finding, and 2) warrant investigation in longitudinal data to test whether the finer detail provided by the single-item strategy results in improved prediction of outcomes and treatment response.
Genetic Transformation of Neisseria gonorrhoeae to Streptomycin Resistance

Sparling, Philip F. (Communicable Disease Center, Atlanta, Ga.). Genetic transformation of Neisseria gonorrhoeae to streptomycin resistance. J. Bacteriol. 92:1364–1371. 1966. —Eight strains of Neisseria gonorrhoeae were transformed to streptomycin resistance by deoxyribonucleic acid (DNA) extracted from a streptomycin-resistant strain of N. gonorrhoeae. In all strains, competence was greatest in the naturally occurring, virulent clonal types 1 and 2, which gave transformation frequencies up to 1%. Clonal types 3 and 4, which arise on laboratory transfer and are avirulent, gave maximal transformation frequencies of 0.00005%. Competence was maximal in lag and early log phases of growth, but was maintained throughout the growth cycle. A complex broth was required for the physiological expression of competence. The kinetics of DNA uptake, dose-response curve of DNA versus transformants, time required for phenotypic expression, and other features were similar to those in other bacterial transformation systems.
Differential invariants for color images

We present a new method for matching points in stereoscopic, uncalibrated color images. Our approach consists of characterizing points of interest using differential invariants. We define additional invariants of first order, exploiting color information. We show that this contribution makes the characterization sufficient for first order. In addition, we make our description robust to usual transformations of image. We present a robust generalization of a gray level corner detector to the case of color images. We also propose a simple and efficient scheme for matching these points, using our characterization. Finally, we present matching results and the epipolar geometry obtained on complex scenes, which clearly show the pertinence of our approach. We are able to match points robustly and rapidly, using only first order derivatives.
Pellet: An OWL DL Reasoner

In order to gain experience with description logic reasoner, and to contribute to the OWL Candidate Recommendation process, a small team at MINDSWAP set out to implement a tableau reasoner for the Lite and DL dialects of OWL (corresponding roughly to the description logics SHIF(D) and SHION(D)). Our group found existing, available DL reasoners lacking for our purposes, because we needed an open-source tool that provides ABox reasoning, that does not make Unique Name assumption, supports entailment checks and works with XML Schema datatypes. Pellet has been developed to addresses these issues and has become both our test bed for experiments with DL and Semantic Web reasoning, as well as our standard reasoning component. While not (yet) in the performance range of Racer or Fact, it has many usability features that makes it a good choice for various lighter weight situations. Technically, Pellet is a sound and complete tableau reasoners for SHIN(D) and SHON(D) (with ABoxes), and a sound but incomplete tableau reasoner for SHION(D) (with ABoxes). Pellet has the usual suite of optimizations including lazy unfolding, absorption, dependency directed backjumping, and semantic branching. It incorporates datatype reasoning for the built-in primitive XML Schema datatypes. Pellet is implemented in pure Java and available as open source software.
Impact of a decade of successful antiretroviral therapy initiated at HIV-1 seroconversion on blood and rectal reservoirs

Persistent reservoirs remain the major obstacles to achieve an HIV-1 cure. Prolonged early antiretroviral therapy (ART) may reduce the extent of reservoirs and allow for virological control after ART discontinuation. We compared HIV-1 reservoirs in a cross-sectional study using polymerase chain reaction-based techniques in blood and tissue of early-treated seroconverters, late-treated patients, ART-naïve seroconverters, and long-term non-progressors (LTNPs) who have spontaneous virological control without treatment. A decade of early ART reduced the total and integrated HIV-1 DNA levels compared with later treatment initiation, but not reaching the low levels found in LTNPs. Total HIV-1 DNA in rectal biopsies did not differ between cohorts. Importantly, lower viral transcription (HIV-1 unspliced RNA) and enhanced immune preservation (CD4/CD8), reminiscent of LTNPs, were found in early compared to late-treated patients. This suggests that early treatment is associated with some immunovirological features of LTNPs that may improve the outcome of future interventions aimed at a functional cure. DOI: http://dx.doi. org/10.7554/eLife.09115. 001
Hiding Information in Completeness Holes: New Perspectives in Code Obfuscation and Watermarking

In this paper we show how abstract interpretation, and more specifically completeness, provides an adequate model for reasoning about code obfuscation and watermarking. The idea is that making a program obscure, or equivalently hiding information in it, corresponds to force an interpreter (the attacker) to become incomplete in its attempts to extract information about the program. Here abstract interpretation provides the model of the attacker (malicious host) and abstract interpretation transformers provide driving methods for understanding and designing new obfuscation and watermarking strategies: Obfuscation corresponds to make the malicious host incomplete and watermarking corresponds to hide secrets where incomplete attackers cannot extract them unless some secret key is given.
Stable Multilineage Chimerism without Graft versus Host Disease Following Nonmyeloablative Haploidentical Hematopoietic Cell Transplantation

Background. Hematopoietic cell transplantation may offer the only cure for patients with hematological diseases. The clinical application of this therapy has been limited by toxic conditioning and lack of matched donors. Haploidentical transplantation would serve to extend the potential donor pool; however, transplantation across major histocompatibility complex barriers is often associated with severe graft-versus-host disease. Here we evaluate a novel protocol to achieve engraftment across mismatch barriers without toxic conditioning or significant posttransplant complications. Methods. Nine major histocompatibility complex (MHC)-defined miniature swine received haploidentical hematopoietic cell transplantation following standard myeloablative conditioning. Nine additional animals received haploidentical hematopoietic cell transplantation following a minimally myelosuppressive regimen, consisting of 100 cGy total body irradiation, immunotoxin mediated T-cell depletion, and a short course of cyclosporine. Donor cell engraftment and peripheral chimerism was assessed by polymerase chain reaction and flow cytometry. Graft-versus-host disease was monitored by clinical grading and histology of skin biopsy specimens. Results. All animals conditioned for haploidentical hematopoietic cell transplantation using myeloablative conditioning were euthanized within 2 weeks due to engraftment failure or graft-versus-host disease. All animals conditioned with the nonmyeloablative regimen developed multilineage peripheral blood chimerism during the first 2 months following transplantation. Six animals evaluated beyond 100 days maintained multilineage chimerism in the peripheral blood and lymphoid tissues, showed evidence of progenitor cell engraftment in the bone marrow, and had minimal treatment-related complications. Conclusions. Here we report that stable multilineage chimerism and engraftment can be established across haploidentical major histocompatibility complex barriers with minimal treatment-related toxicity and without significant risk of graft-versus-host disease.
Experiences in the Adoption of Requirements Engineering Technologies

It has been known since as early as the 1950s that addressing requirements issues improves the chance of systems development success. In fact, whole software development standards (such as MIL-STD-2167, MIL-STD-2167A, MIL-STD-498, and IEEE/EIA 12207) were designed to enforce this behavior for software-intensive systems. Relatively recently (sidebar) a new field of study, requirements engineering, has begun to systematically and scientifically address barriers to the successful use of requirements in systems development . Since 1992, the Software Technology Support Center (STSC) has been helping organizations adopt new technologies. This article defines requirements engineering (RE) from the viewpoint of technology adoption, discusses which RE technologies are most critical to mission success and why and which are most difficult to adopt, and outlines successful adoption approaches.
Self-testing of FPGA delay faults in the system environment

We propose a procedure for self-testing of an FPGA programmed to implement a user-defined function. The procedure is intended to improve the detectability of FPGA delay faults. This improvement is obtained by modifying the functions of LUTs in the section under test, so that each LUT implements a XOR function. We show that, despite many potential problems, the proposed modification can significantly enhance the susceptibility of FPGA delay faults to random testing.
IMPACT OF CYP2C9 GENOTYPE ON PHARMACOKINETICS: ARE ALL CYCLOOXYGENASE INHIBITORS THE SAME?

The market withdrawals of rofecoxib (Vioxx) and valdecoxib (Bextra) have focused considerable attention on the side effect profiles of cyclooxygenase (COX) inhibitors. As a result, attempts will be made to identify risk factors in the hope that physicians might be able to ensure patient safety. At first glance, CYP2C9 genotype might be considered a risk factor because many COX inhibitors are CYP2C9 substrates in vitro. This observation has led some to hypothesize that a reduction in clearance, in subjects expressing variant forms of the enzyme (e.g., CYP2C9*1/*3 or CYP2C9*3/*3 genotype), will lead to increased exposure and a greater risk of cardiovascular or gastrointestinal side effects. For any drug, however, one has to consider all clearance pathways. Therefore, a number of COX inhibitors were surveyed and it was determined that CYP2C9 plays a relatively minor role in the overall clearance (≤20% of the dose) of sulindac, naproxen, ketoprofen, diclofenac, rofecoxib, and etoricoxib. CYP2C9 genotype would have no clinically meaningful impact on the pharmacokinetics of these drugs. In contrast, CYP2C9 genotype is expected to impact the clearance of ibuprofen, indomethacin, flurbiprofen, celecoxib, valdecoxib, lornoxicam, tenoxicam, meloxicam, and piroxicam. However, even when CYP2C9 is a major determinant of clearance, it is necessary to consider CYP2C8 genotype (e.g., ibuprofen) and, possibly, CYP3A4 activity (e.g., celecoxib, valdecoxib, and meloxicam) also.
DNA polymerases as useful reagents for biotechnology – the history of developmental research in the field

DNA polymerase is a ubiquitous enzyme that synthesizes complementary DNA strands according to the template DNA in living cells. Multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, labeling, mutagenesis, and other purposes. The fundamental ability of DNA polymerases to synthesize a deoxyribonucleotide chain is conserved. However, the more specific properties, including processivity, fidelity (synthesis accuracy), and substrate nucleotide selectivity, differ among the enzymes. The distinctive properties of each DNA polymerase may lead to the potential development of unique reagents, and therefore searching for novel DNA polymerase has been one of the major focuses in this research field. In addition, protein engineering techniques to create mutant or artificial DNA polymerases have been successfully developing powerful DNA polymerases, suitable for specific purposes among the many kinds of DNA manipulations. Thermostable DNA polymerases are especially important for PCR-related techniques in molecular biology. In this review, we summarize the history of the research on developing thermostable DNA polymerases as reagents for genetic manipulation and discuss the future of this research field.
Heterogeneous BISR-approach using system level synthesis flexibility

We propose a novel methodology for designing fault-tolerant real-time system to achieve optimal productivity on a single-chip multiprocessor platform using the heterogeneous built-in-self-repair (BISR) based graceful degradation and yield enhancement technique as an embedded optimization engine which exploits task-level scheduling and algorithm selection flexibility. We also developed a hardware fault model for modern superscalar processors and multi-processors which enables an efficient treatment of the synthesis and compilation goals.
Impact of Post‐Lithography Polymer Residue on the Electrical Characteristics of MoS2 and WSe2 Field Effect Transistors

The residue of common photo‐ and electron‐beam resists, such as poly(methyl methacrylate) (PMMA), is often present on the surface of 2D crystals after device fabrication. The residue degrades device properties by decreasing carrier mobility and creating unwanted doping. Here, MoS2 and WSe2 field effect transistors (FETs) with residue are cleaned by contact mode atomic force microscopy (AFM) and the impact of the residue on: 1) the intrinsic electrical properties, and 2) the effectiveness of electric double layer (EDL) gating are measured. After cleaning, AFM measurements confirm that the surface roughness decreases to its intrinsic state (i.e., ≈0.23 nm for exfoliated MoS2 and WSe2) and Raman spectroscopy shows that the characteristic peak intensities (E2g and A1g) increase. PMMA residue causes p‐type doping corresponding to a charge density of ≈7 × 1011 cm−2 on back‐gated MoS2 and WSe2 FETs. For FETs gated with polyethylene oxide (PEO)76:CsClO4, removing the residue increases the charge density by 4.5 × 1012 cm−2, and the maximum drain current by 247% (statistically significant, p < 0.05). Removing the residue likely allows the ions to be positioned closer to the channel surface, which is essential for achieving the best possible electrostatic gate control in ion‐gated devices.
Geographic Variation in Cancer Incidence among Children and Adolescents in Taiwan (1995–2009)

Background Evidence from our recent study suggested that the overall trend for cancer incidence in children and adolescents has been increasing in Taiwan. Methods To analyze geographic variations in this trend, cancer frequencies and incidence rates of disease groups were quantified according to geographic areas among 12,633 patients aged <20 years during 1995–2009 by using the population-based Taiwan Cancer Registry. Three geographic levels were defined, namely county or city, region (Northern, Central, Southern, and Eastern Taiwan), and local administrative area (special municipality, provincial city, county-administered city, township, and aboriginal area). Results Of the regions, Northern Taiwan had the highest incidence rate at 139.6 per million person-years, followed by Central (132.8), Southern (131.8), and Eastern (128.4) Taiwan. Significantly higher standardized rate ratios (SRRs) were observed in Northern Taiwan (SRR = 1.06, 95% confidence interval [CI] = 1.02–1.10) and at the township level (SRR = 1.07, 95% CI = 1.03–1.11). Of the cities or counties, New Taipei City yielded the highest SRR (1.08), followed by Taipei City (SRR = 1.07). A comparison of the rates in the four regions and the remainder of Taiwan according to cancer type revealed that only the rate of neuroblastomas in Eastern Taiwan was significantly low. Trend analysis showed that the most significant increase in incidence rate was observed at the township level, with an annual percent change of 1.8% during the 15-year study period. Conclusions The high rate of childhood cancer in Northern Taiwan and at the township level deserves further attention. The potential impacts of environmental factors on the upward trend of childhood cancer incidence rate in townships warrant further investigation.
Overlay energy circle formation for cloud data centers with renewable energy futures contracts

Cloud data centers are significant players in the electricity market due to their high energy consumption. It is highly desired to operate cloud data centers on only renewable energy such as solar, wind or tidal to reduce their cost and emissions. In the literature, utilization of renewable energy is maximized through workload migration towards data centers that are forecasted to have surplus renewable energy which is also known as “follow the sun chase the wind” approach. In practice, it is rather difficult and unrealistic to shift workloads based on instantaneous output of renewable generation. Generally forecast tools are used which can only provide a rough estimate of the generation capacity. In this paper, we use a more realistic approach and propose an overlay architecture to form energy circles of cloud data centers depending on their load and renewable energy futures contracts. A futures contract is an electricity purchase agreement between the data center operator and the renewable energy generator to purchase electricity in the future with today's price. Futures contracts are electricity market mechanisms that reduce the cost related risks for both parties and are seen as tools to scale-up renewable generation. On the other hand, fluctuating loads of cloud data centers may leave some contract capacity left unused or exceed the capacity. In this case, electricity will be purchased at current market price from the renewable generator or the utility grid where in both cases the electricity bill will increase. Hence, a mechanism to utilize the unused capacity in the contracts of peer data centers and shifting workloads towards available capacity can reduce bills as well as increase the utilization of renewable energy. Our proposed energy circles approach aims to group cloud data centers to achieve those goals.
Mammalian ASIC2a and ASIC3 Subunits Co-assemble into Heteromeric Proton-gated Channels Sensitive to Gd3+ *

Proton receptors of the acid-sensing ion channel (ASIC) family are expressed in sensory neurons and thus could play a critical role in the detection of noxious acidosis. To investigate the subunit composition of native ASICs in peripheral and central neurons, we co-injected human as well as rodent ASIC2a and ASIC3 subunits inXenopus oocytes. The amplitudes of acid-induced biphasic responses mediated by co-expressed ASIC2a and ASIC3 subunits were much larger (as much as 20-fold) than the currents mediated by the respective homomers, clearly indicating functional association. The reversal potential of the ASIC2a+3 current (≥+20 mV) reflected a cationic current mainly selective for sodium. The sensitivity to pH or amiloride of single versus co-expressed ASIC subunits was not significantly different; however, gadolinium ions inhibited ASIC3 and ASIC2a+3 responses with much higher potency (IC50 ∼40 μm) than the ASIC2a response (IC50 ≥1 mm). Biochemical interaction between ASIC2a and ASIC3 subunits was demonstrated by co-purification from transfected human embryonic kidney (HEK293) cells and Xenopus oocytes. Ourin situ hybridization data showed that rat ASIC2a and ASIC3 transcripts are co-localized centrally, whereas reverse transcription-polymerase chain reaction data led us to detect co-expression of human ASIC2a and ASIC3 subunits in trigeminal sensory ganglia, brain, and testis where they might co-assemble into a novel subtype of proton-gated channels sensitive to gadolinium.
Efficient Algorithms for Power Maximization in the Vector Model for Wireless Energy Transfer

Rapid technological advances in the domain of Wireless Power Transfer (WPT) pave the way for novel methods for power management in systems of wireless devices and recent research works have already started considering algorithmic solutions for tackling emerging problems. However, those works are limited by the system modelling, and more specifically the one-dimensional abstraction suggested by Friis formula for the power received by one antenna under idealized conditions given another antenna some distance away. Different to those works, we use a model which arises naturally from fundamental properties of the superposition of energy fields. This model has been shown to be more realistic than other one-dimensional models that have been used in the past and can capture superadditive and cancellation effects. Under this model, we define two new interesting problems for configuring the wireless power transmitters so as to maximize the total power in the system and we prove that the first problem can be solved in polynomial time. We present a distributed solution that runs in pseudo-polynomial time and uses various knowledge levels and we provide theoretical performance guarantees. Finally, we design three heuristics for the second problem and evaluate them experimentally.
Contactless power supply and charging system

The disclosed apparatus and a non-contact power charging system. Using at least one magnetic field resonance non-contact power charging device includes an AC power source; at least one circuit; charging surface; and at least one indicator for indicating the charging priority relative to the charging surface according to magnetic field strength. In comparison to an external device indicated by the indicator is disposed close to having a lower charging priority charging surface areas, will be indicated by the indicator more quickly charging apparatus having a high priority is placed near the surface of the charging zone. Charging surface may be indicated by different materials, patterns, shapes or offsets charging indication on the priority zone. Further, the contactless power supply may have more than one zone of high charging priority.