Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive homogeneity-directed demosaicing algorithm

Most cost-effective digital camera uses a single image sensor, applying alternating patterns of red, green, and blue color filters to each pixel location. Demosaicing algorithm reconstructs a full three-color representation of color images from this sensor data. This paper identifies three inherent problems often associated with directional interpolation approach to demosaicing algorithms: misguidance color artifacts, interpolation color artifacts, and aliasing. The level of misguidance color artifacts present in two images can be compared using metric neighborhood modeling. The proposed demosaicing algorithm estimates missing pixels by interpolating in the direction with fewer color artifacts. The aliasing problem is addressed by applying filterbank techniques to directional interpolation. The interpolation artifacts are reduced using a nonlinear iterative procedure. Experimental results using digital images confirm the effectiveness of this approach.
Genome‐wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients

Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. We conducted a multi‐institutional genome‐wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma, including 523 patients of European ancestry and 109 from Brazil. We conducted a time‐to‐event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease. The results were combined across the European and Brazilian case sets using a random‐effects meta‐analysis. The strongest association after meta‐analysis was for rs3765555 at 9p24.1, which was inversely associated with overall survival (HR = 1.76; 95% CI 1.41–2.18, p = 4.84 × 10−7). After imputation across this region, the combined analysis identified two SNPs that reached genome‐wide significance. The strongest single association was with rs55933544 (HR = 1.9; 95% CI 1.5–2.4; p = 1.3 × 10−8), which localizes to the GLDC gene, adjacent to the IL33 gene and was consistent across both the European and Brazilian case sets. Using publicly available data, the risk allele was associated with lower expression of IL33 and low expression of IL33 was associated with poor survival in an independent set of patients with osteosarcoma. In conclusion, we have identified the GLDC/IL33 locus on chromosome 9p24.1 as associated with overall survival in patients with osteosarcoma. Further studies are needed to confirm this association and shed light on the biological underpinnings of this susceptibility locus.
Study and course of the psychological profile in 77 patients expressing panic disorder with agoraphobia after cognitive behaviour therapy with or without buspirone.

BACKGROUND The change of psychopathological dimensions during treatment of panic disorder is attracting increasing interest. METHODS A population of subjects experiencing panic disorder with agoraphobia is evaluated with the French version of the factor structure of the Symptom Checklist 90 R (SCL 90 R). Two groups of patients are compared: a group receiving cognitive behaviour therapy (CBT) combined with buspirone and a group receiving cognitive behaviour therapy combined with placebo. RESULTS Comparative analysis of pre- and post-test changes between both groups completing treatment showed that the combination cognitive behaviour therapy plus buspirone provided better results than those in patients who had received cognitive behaviour therapy plus placebo. This difference between treatments did not persist at the 1-year follow-up, since, while results had been effectively maintained in the CBT plus buspirone group, the CBT plus placebo group continued to improve significantly for the target dimensions of treatment. CONCLUSIONS Psychopathological dimensions on the SCL 90 R show that combination of buspirone and cognitive behaviour therapy accelerates the behaviour modification process only in the short term.
Structure, properties and treatments of carbon nanotube fibres

Carbon nanotubes (CNTs) possess exceptional mechanical, thermal and electrical properties along their main axis, superior to those of most materials. These can be exploited on a macroscopic scale by assembling the CNTs into a fibre with the nanotubes preferentially oriented parallel to each other and to the fibre axis. CNT fibres can be produced continuously, directly from the gas phase during CNT synthesis by chemical vapour deposition (CVD), and spun at rates of up to 70 m/min. Their combination of outstanding mechanical, electrical and thermal properties and low density (1 g/cm) makes CNT fibres a potential candidate for high-performance applications. The fibre specific strength and stiffness are typically 1 GPa/SG and 50 GPa/SG, respectively; however, at small gauge lengths (< 2mm) they also show values of 6 9 GPa/SG strength and 180 390 GPa/SG stiffness. The electrical conductivity of the CNT fibres is approximately 8 ×10 S/m and their thermal conductivity of the order of 50 W/mK. These properties derive from the long length, high alignment and efficient packing of the nanotubes in the fibre. Further improvements to the fibre structure and properties at long gauge lengths are possible through removal of impurities from the fibre by annealing.
Age differences in the motor control of speech: An fMRI study of healthy aging

Healthy aging is associated with a decline in cognitive, executive, and motor processes that are concomitant with changes in brain activation patterns, particularly at high complexity levels. While speech production relies on all these processes, and is known to decline with age, the mechanisms that underlie these changes remain poorly understood, despite the importance of communication on everyday life. In this cross‐sectional group study, we investigated age differences in the neuromotor control of speech production by combining behavioral and functional magnetic resonance imaging (fMRI) data. Twenty‐seven healthy adults underwent fMRI while performing a speech production task consisting in the articulation of nonwords of different sequential and motor complexity. Results demonstrate strong age differences in movement time (MT), with longer and more variable MT in older adults. The fMRI results revealed extensive age differences in the relationship between BOLD signal and MT, within and outside the sensorimotor system. Moreover, age differences were also found in relation to sequential complexity within the motor and attentional systems, reflecting both compensatory and de‐differentiation mechanisms. At very high complexity level (high motor complexity and high sequence complexity), age differences were found in both MT data and BOLD response, which increased in several sensorimotor and executive control areas. Together, these results suggest that aging of motor and executive control mechanisms may contribute to age differences in speech production. These findings highlight the importance of studying functionally relevant behavior such as speech to understand the mechanisms of human brain aging. Hum Brain Mapp 38:2751–2771, 2017. © 2017 Wiley Periodicals, Inc.
Crosstalk between apoptosis and autophagy in prostate epithelial cells under androgen deprivation

The present study investigated the molecular mechanism of apoptosis and autophagy in prostate epithelial cells under androgen deprivation (AD). BPH-1 cells were divided into four groups as follows: Control (Cont), AD, autophagy inhibition (AI) and AD + AI groups. Cells in the four groups were treated accordingly, and the level of apoptosis was subsequently measured via flow cytometry. The expression of the microtubule-associated proteins 1A/1B light chain 3 (LC3), caspase-3, poly (ADP-ribose) polymerase 1 (PARP-1) and Beclin-1 proteins of BPH-1 cells was detected at different time points following culture in androgen-deprived medium. Western blotting revealed that the basal levels of the LC3-II protein were detected at 0 h. At 4 h, LC3-II was significantly increased compared with 0 h (P<0.05). Beginning at 20 h, the expression level of the LC3-II protein decreased significantly (P<0.05). Western blotting revealed that beginning at 24 h, the expression level of the PARP-1 protein decreased significantly (P<0.001) and the cleavage fragments of the PARP-1 protein appeared. These results further imply that autophagy serves a cell protective function by mutual inhibition with apoptosis in BPH-1 cells in the removal of androgen conditions. Furthermore, the fragments of the cleaved Beclin-1 protein appeared as 35 and 37 kDa bands. Flow cytometry analysis demonstrated that the rate of cell apoptosis in the AD, AI and AD + AI groups was significantly increased compared with the Cont group (P<0.01). Compared with the AD or the AI groups individually, the rate of cell apoptosis in the AD + AI group was significantly increased (P<0.001). These findings suggest that in the early stage of AD, autophagy has a compensatory function in the cell, whereas in the whole process, autophagy and apoptosis share a mutual antagonism. The Beclin-1-C protein fragment contributed positive feedback to the process of apoptosis, which may be a potential mechanism of AD therapy. Therefore, AD and AI exhibit a synergistic effect to further improve the level of apoptosis.
A genetic stochastic process model for genome‐wide joint analysis of biomarker dynamics and disease susceptibility with longitudinal data

Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post‐GWAS (where GWAS is genome‐wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene‐environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases. This model is characterized by more profound biological interpretation and takes into account the dynamics of biomarkers during follow‐up when investigating the hazards of a disease. We illustrate the rationale and evaluate the performance of the proposed model through two GWAS. One is to detect single nucleotide polymorphisms (SNPs) having interaction effects on type 2 diabetes (T2D) with body mass index (BMI) and the other is to detect SNPs affecting the optimal BMI level for protecting from T2D. We identified multiple SNPs that showed interaction effects with BMI on T2D, including a novel SNP rs11757677 in the CDKAL1 gene (P = 5.77 × 10−7). We also found a SNP rs1551133 located on 2q14.2 that reversed the effect of BMI on T2D (P = 6.70 × 10−7). In conclusion, the proposed GSPM provides a promising and useful tool in GWAS of longitudinal data for interrogating pleiotropic and interaction effects to gain more insights into the relationship between genes, quantitative biomarkers, and risks of complex diseases.
Compressing Java class files

Java class files are often distributed as jar files, which are collections of individually compressed class files (and possibility other files). Jar files are typically about 1/2 the size of the original class files due to compression. I have developed a wire-code format for collections of Java class files. This format is typically 1/2 to 1/5 of the size of the corresponding compressed jar file (1/4 to 1/10 the size of the original class files).
Quantitative iTRAQ‐based proteomic analysis of rice grains to assess high night temperature stress

Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat‐tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat‐tolerant and ‐sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database. These proteins were then classified into seven functional subgroups, which include signal transduction, transcript regulation, oxidation, defense response, transport, energy metabolism, and biosynthesis. Further analysis indicated that HNT stress could disrupt the redox equilibrium of plant cells, which in turn triggers the calcium‐dependent protein kinase and COP9 signalosome, thereby regulating downstream genes/proteins that are involved in the HNT response. The candidate proteins may provide genetic resources for the improvement of heat‐tolerant characteristics in rice, and the proposed model for signal transduction and transcriptional regulation may facilitate in the elucidation of the molecular mechanism underlying the response to HNT stress in rice.
Unsupervised Classification of Polarimetric SAR Images via Riemannian Sparse Coding

Unsupervised classification plays an important role in understanding polarimetric synthetic aperture radar (PolSAR) images. One of the typical representations of PolSAR data is in the form of Hermitian positive definite (HPD) covariance matrices. Most algorithms for unsupervised classification using this representation either use statistical distribution models or adopt polarimetric target decompositions. In this paper, we propose an unsupervised classification method by introducing a sparsity-based similarity measure on HPD matrices. Specifically, we first use a novel Riemannian sparse coding scheme for representing each HPD covariance matrix as sparse linear combinations of other HPD matrices, where the sparse reconstruction loss is defined by the Riemannian geodesic distance between HPD matrices. The coefficient vectors generated by this step reflect the neighborhood structure of HPD matrices embedded in the Euclidean space and hence can be used to define a similarity measure. We apply the scheme for PolSAR data, in which we first oversegment the images into superpixels, followed by representing each superpixel by an HPD matrix. These HPD matrices are then sparse coded, and the resulting sparse coefficient vectors are then clustered by spectral clustering using the neighborhood matrix generated by our similarity measure. The experimental results on different fully PolSAR images demonstrate the superior performance of the proposed classification approach against the state-of-the-art approaches.
Lipid Based Vesicular Drug Delivery Systems

Vesicular drug delivery system can be defined as highly ordered assemblies consisting of one or more concentric bilayers formed as a result of self-assembling of amphiphilic building blocks in presence of water. Vesicular drug delivery systems are particularly important for targeted delivery of drugs because of their ability to localize the activity of drug at the site or organ of action thereby lowering its concentration at the other sites in body. Vesicular drug delivery system sustains drug action at a predetermined rate, relatively constant (zero order kinetics), efficient drug level in the body, and simultaneously minimizes the undesirable side effects. It can also localize drug action in the diseased tissue or organ by targeted drug delivery using carriers or chemical derivatization. Different types of pharmaceutical carriers such as polymeric micelles, particulate systems, and macro- and micromolecules are presented in the form of novel drug delivery system for targeted delivery of drugs. Particulate type carrier also known as colloidal carrier system, includes lipid particles, micro- and nanoparticles, micro- and nanospheres, polymeric micelles and vesicular systems like liposomes, sphingosomes, niosomes, transfersomes, aquasomes, ufasomes, and so forth.
Sub-Millisecond Measurements of Thermal Conductivity and Thermal Diffusivity Using Micrometer-Sized Hot Strips

A new measurement technique based on the transient hot strip technique has recently been developed for studying anisotropic thermal transport properties of thin crystalline films. A micrometer-sized hot strip sensor is evaporated on the surface of the crystalline film sample, which has been deposited on a substrate wafer of limited thickness. From a pulsed transient recording, using sub-millisecond square-shaped pulses, a thermal probing depth that is less than the film thickness is assured. In the ongoing work of verifying the technique, we show results from measurements on z-cut crystal quartz and fused silica, using thermal probing depths of only 30 μm, which closely conform to bulk values found in the literature.
Holographic scattering in phenanthrenequinone-doped poly(methyl methacrylate) bulk photopolymers

This paper presented an experimental study of holographic scattering caused by noise gratings recorded in the PQ-PMMA photopolymers. Dependence of the thickness and temperature on the holographic scattering losses was evaluated. It is found that the scattering losses increased as the thickness and temperature. According to the relationship between the polymerization rate and exposure, the optimal material parameters thickness 2mm and the temperature 20-30°C were obtained for avoiding the buildup of strong noise gratings.
Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts

Simple Summary Marine mammals stranding on coastal beaches is not unusual. However, there appears to be no single cause for this, with several causes being probable, such as starvation, contact with humans (for example boat strike or entanglement with fishing gear), disease, and parasitism. We evaluated marine mammal stranding off the Washington and Oregon coasts and looked at offshore earthquakes as a possible contributing factor. Our analysis showed that offshore earthquakes did not make marine mammals more likely to strand. We also analysed a subset of data from the north of Washington State and found that non-adult animals made up a large proportion of stranded animals, and for dead animals the commonest cause of death was disease, traumatic injury, or starvation. Abstract The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or juveniles, and in the case of dead stranded mammals, the commonest cause of death was trauma, disease, and emaciation.
Efficient and Security Enhanced Anonymous Authentication with Key Agreement Scheme in Wireless Sensor Networks

At present, users can utilize an authenticated key agreement protocol in a Wireless Sensor Network (WSN) to securely obtain desired information, and numerous studies have investigated authentication techniques to construct efficient, robust WSNs. Chang et al. recently presented an authenticated key agreement mechanism for WSNs and claimed that their authentication mechanism can both prevent various types of attacks, as well as preserve security properties. However, we have discovered that Chang et al’s method possesses some security weaknesses. First, their mechanism cannot guarantee protection against a password guessing attack, user impersonation attack or session key compromise. Second, the mechanism results in a high load on the gateway node because the gateway node should always maintain the verifier tables. Third, there is no session key verification process in the authentication phase. To this end, we describe how the previously-stated weaknesses occur and propose a security-enhanced version for WSNs. We present a detailed analysis of the security and performance of our authenticated key agreement mechanism, which not only enhances security compared to that of related schemes, but also takes efficiency into consideration.
A case study in SIMD text processing with parallel bit streams: UTF-8 to UTF-16 transcoding

High performance SIMD text processing using the method of parallel bit streams is introduced with a case study of UTF-8 to UTF-16 transcoding. A forward transform converts byte-oriented character stream data into eight parallel bit streams. Decoding, validation and computation of UTF-8 indexed UTF-16 bit streams are performed using bit-parallel logic and shifting operations. Conversion from UTF-8 indexing to UTF-16 indexing is performed using parallel bit deletion. The inverse transform is applied to yield high and low UTF-16 byte streams which are then merged. Combined with optimization techniques for blocks of ASCII data, speed-ups of 3 to 25 times are achieved on commodity processors compared with optimized byte-at-a-time code. Further applications of the method of parallel bit streams to bulk text processing applications are briefly discussed along with future prospects for the combination of intraregister and intrachip parallelism on multicore processors.
Effectiveness of a Culturally Tailored Diabetes Self-Management Program for Chinese Americans

Purpose The purpose of the study was to test the feasibility and efficacy of a diabetes self-management and education program for Chinese Americans in a support group format. The rationale for the study was to create culturally appropriate diabetes education and management programs in response to the growing diabetes prevalence among Chinese Americans. The investigators hypothesized that participants will have improved diabetes knowledge and practices, hemoglobin A1C, and social support. The study objectives were at least: 50% will have significant improvements in diabetes knowledge and practice activities, 30% of participants will have significant improvements in A1C, and 50% will report a gain in emotional support. Methods The program consisted of 12 90-minute diabetes education and support group sessions offered in a medical office setting. The sample included 23 Chinese Americans with either type 1 or type 2 diabetes. Using a single-group, pre-post test design, A1C and diabetes knowledge were assessed at baseline and 6 months. Data were collected through clinical assessments and written questionnaires. Results The results indicated high attendance and statistically significant increases in glycemic control and diabetes knowledge. Statistically insignificant differences were shown in diabetes management practices. Secondary outcomes assessed participants’ perceived diabetes management and emotional and social support. Conclusions Diabetes Self-Management: A Cultural Approach (DSMCA) support group model demonstrates that a culturally tailored support group utilizing a community-based participatory research approach is an effective format to improve diabetes self-management skills among Chinese Americans. The program can be adapted for other ethnic populations. The efficacy of the intervention can be further tested in larger randomized trials.