Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood transcriptome based biomarkers for human circadian phase

Diagnosis and treatment of circadian rhythm sleep-wake disorders both require assessment of circadian phase of the brain’s circadian pacemaker. The gold-standard univariate method is based on collection of a 24-hr time series of plasma melatonin, a suprachiasmatic nucleus-driven pineal hormone. We developed and validated a multivariate whole-blood mRNA-based predictor of melatonin phase which requires few samples. Transcriptome data were collected under normal, sleep-deprivation and abnormal sleep-timing conditions to assess robustness of the predictor. Partial least square regression (PLSR), applied to the transcriptome, identified a set of 100 biomarkers primarily related to glucocorticoid signaling and immune function. Validation showed that PLSR-based predictors outperform published blood-derived circadian phase predictors. When given one sample as input, the R2 of predicted vs observed phase was 0.74, whereas for two samples taken 12 hr apart, R2 was 0.90. This blood transcriptome-based model enables assessment of circadian phase from a few samples. DOI: http://dx.doi. org/10.7554/eLife.20214. 001
Intrinsic Morphing of Compatible Triangulations

Two planar triangulations with a correspondence between two vertex sets are compatible (isomorphic) if they are topologically equivalent. This work presents a simple and robust method for morphing two compatible planar triangulations with identical convex boundaries that locally preserves the intrinsic geometric properties of triangles throughout the morph. The method is based on the barycentric coordinates representation of planar triangulations, and thus, guarantees compatibility of all intermediate triangulations. The intrinsic properties are preserved by interpolating angles and edge lengths components of mean value barycentric coordinates, rather than interpolating the barycentric coordinates themselves. As a result, the method generates a natural-looking and guaranteed intersection-free morphing sequence.
Automated repair of HTML generation errors in PHP applications using string constraint solving

PHP web applications routinely generate invalid HTML. Modern browsers silently correct HTML errors, but sometimes malformed pages render inconsistently, cause browser crashes, or expose security vulnerabilities. Fixing errors in generated pages is usually straightforward, but repairing the generating PHP program can be much harder. We observe that malformed HTML is often produced by incorrect constant prints, i.e., statements that print string literals, and present two tools for automatically repairing such HTML generation errors. PHPQuickFix repairs simple bugs by statically analyzing individual prints. PHPRepair handles more general repairs using a dynamic approach. Based on a test suite, the property that all tests should produce their expected output is encoded as a string constraint over variables representing constant prints. Solving this constraint describes how constant prints must be modified to make all tests pass. Both tools were implemented as an Eclipse plugin and evaluated on PHP programs containing hundreds of HTML generation errors, most of which our tools were able to repair automatically.
Consumer Ethics Across Cultures

Consumer ethics are an understudied but important counterpart of business ethics. In this study we use qualitative methods and video ethnography to examine consumer beliefs and behaviors in eight countries, including both affluent and poor nations in Europe, North America and Australasia. Using depth interviews and projective methods, informants address three different ethical choices of products involving harm to the environment, poor labor conditions, and counterfeit goods. As the accompanying video reveals, there is a general lack of consumer concern for such issues across cultures. We examine the justifications offered for these views and consider implications for altering consumer behavior.
“Amount effect” of water isotopes and quantitative analysis of post‐condensation processes

A numerical model is proposed that describes the interaction between raindrops and water vapour near the planetary boundary layer to explain the “amount effect”. This model relates the intensity to the isotopic composition of precipitation. The model resolves raindrop sizes, and explicitly includes: (1) the isotopic equilibration time of raindrops that is drop‐size dependent; (2) raindrop transit times through the atmosphere; and (3) the evolution of the isotopic composition of vapour at various rain rates. At high rain rate, the precipitation through a layer is less equilibrated with the vapour because the isotopic equilibration time is long compared to the fast transit time, and there is a preponderance of large drops, which take longer to equilibrate. The δ18O of vapour in the lower atmosphere becomes lower as a result of the interaction with these raindrops of low δ18O, and the degree of depletion of 18O is higher when precipitation rates are high. The model reproduces time‐series observations of isotopic composition of precipitation in Japan, and a vapour replenishment rate is inferred by either advection or evaporation of about 5% of the precipitation rate. The results could be the basis for a new parameterization of the isotopic equilibration for different precipitation types and rates in General Circulation Models (GCMs). When the model is applied to a GCM, this parameterization is important for places where precipitation occurs at cold temperatures (<15 °C). Copyright © 2007 John Wiley & Sons, Ltd.
Renal nerves: are they essential?

The intrinsic innervation of the human kidney has been investigated for over 100 years. Until recently there has been no agreement concerning the distribution of these nerves. Studies using classic silver impregnation technics have shown, in addition to the nerve fibers of intrarenal blood vessels, what appeared to be nerve fibers innervating the nephrons of the kidney. Modern histochemical technics that allow differentiation of adrenergic from cholinergic nerves have demonstrated that both adrenergic and cholinergic nerves innervate the renal arteries and their branches. In addition, the major renal veins have been found to have a sparse adrenergic innervation. A cholinergic .
Automatic external Persian plagiarism detection using vector space model

Nowadays, extremely wide and facilitated access to the Internet has made the plagiarism and text reuse more common. Many studies have been conducted on automatic plagiarism detection. But there are few studies on automatic Persian plagiarism detection methods due to lack of a suitable Persian corpus. In this paper, an external Persian plagiarism detection method based on the vector space model (VSM) has been proposed. To implement and examine this method, a Persian corpus has been developed. Several optimizations have been done during the study. These optimizations make the algorithm very fast and accurate. The test results of the proposed method shows an accuracy of 0.87 and a processing time cost of less than 10 minutes.
Cluster consensus for heterogeneous multi-agent systems

This paper investigates the cluster consensus problem of heterogeneous multi-agent systems, where the considered systems are composed of first-order dynamics and second-order dynamics. The consensus protocol is designed to converge the position and velocity states of the heterogeneous multi-agent systems in two separate location. Stability analysis for heterogeneous multi-agent systems is presented based on Lyapunov function. Finally, some simulation results are provided to verify the effectiveness of the proposed methods.
Practical techniques to reduce skew and its variations in buffered clock networks

Clock skew is becoming increasingly difficult to control due to variations. Link based non-tree clock distribution is a cost-effective technique for reducing clock skew variations. However, previous works based on this technique were limited to unbuffered clock networks and neglected spatial correlations in the experimental validation. In this work, we overcome these shortcomings and make the link based non-tree approach feasible for realistic designs. The short circuit risk and multi-driver delay issues in buffered non-tree clock networks are investigated. Our approach is validated with SPICE based Monte Carlo simulations, considering spatial correlations among variations. The experimental results show that our approach can reduce the maximal skew by 47%, improve the skew yield from 15% to 73% on average with a decrease on the total wire and buffer capacitance.
ASYMMETRICAL PATTERNS OF SPECIATION UNIQUELY SUPPORT REINFORCEMENT IN DROSOPHILA

Understanding how often natural selection directly favors speciation, a process known as reinforcement, has remained an outstanding problem for over 70 years. Although reinforcement has been strongly criticized in the past, it is once again seen as more realistic due to the seminal discovery of enhanced prezygotic isolation among sympatric species and to a handful of well‐studied examples. Nevertheless, the pattern of enhanced isolation in sympatry has alternative explanations, highlighting the need to uncover unique signatures of reinforcement to determine its overall frequency in nature. Using a novel dataset on asymmetrical prezygotic and postzygotic isolation among Drosophila species, I uncover new patterns explicitly predicted by reinforcement. Broadly, I found that almost all sympatric species had concordant isolation asymmetries, where the more costly reciprocal mating has greater prezygotic isolation relative to the less costly mating. No such patterns exist in allopatry. Using simulations, I ruled out alternative explanations and showed that concordant isolation asymmetries in sympatry are likely unique signatures of reinforcement. These results allowed me to estimate that reinforcement may impact 60–83% of all sympatric Drosophila and enhance premating isolation by 18–26%. These findings suggest that reinforcement plays a key role in Drosophila speciation.
Seasonal variations in the equatorial Indian Ocean and their impact on the Lombok throughflow

In order to identify the origin of the nonequilibrated pressure field which introduces semiannual variations to the Lombok throughflow, one of the major components of the Indonesian throughflow, seasonal sea level records along the eastern boundary of the Indian Ocean and subsurface temperature records in the equatorial Indian Ocean are compared with the results from ocean general circulation models forced by climatological winds. It is shown, as discussed by Clarke and Liu [1993] using a simple analytical model, that the annual component of the sea level is excited locally by monsoonal winds, whereas the semiannual component is excited remotely by zonal winds in the central equatorial Indian Ocean during the monsoon transition periods. The eastward semiannual propagation observed both in the model and in the 20°C isotherm depth anomaly along the equatorial Indian Ocean is interpreted in terms of the second mode equatorial Kelvin wave excited by the zonal winds during the monsoon transition periods. The propagation direction is westward in the off-equatorial region along 4°N, suggesting that the equatorial Kelvin wave reflects as an equatorial Rossby wave twice a year at the coast of Sumatra. Since the seasonal winds responsible for those semiannual oceanic variations suffer short-term climate variabilities such as El Nino-Southern Oscillation events, they may introduce interannual modulations to the seasonal cycle of the Lombok throughflow. As a corollary, we suggest an ageostrophic limitation due to a nonequilibrated pressure field on the use of Godfrey's [1989] island rule in estimating the throughflow variations.
EFFECTS OF A KNEE LIGAMENT INJURY PREVENTION EXERCISE PROGRAM ON IMPACT FORCES IN WOMEN

Previous research suggests high impact forces generated during landings contribute to noncontact anterior cruciate ligament (ACL) injuries. In women, neuromuscular differences appear to modify the ability to dissipate landing forces when compared to men. This study examined peak vertical impact forces (Fp) and rate of force development (RFD) following a 9-week, low-intensity (simple jump-landing-jump tasks) and volume (number of foot contacts per workout) plyometric-based knee ligament injury prevention (KLIP) program. Female subjects were randomly assigned into control (n = 14) and treatment (n = 14) groups. Treatment subjects attended KLIP sessions twice a week for 9 weeks, and control subjects received no intervention. Ground reaction forces (Fp and RFD) generated during a step-land protocol were assessed at study onset and termination. Significant reductions in Fp (p = 0.0004) and RFD (p = 0.0205) were observed in the treatment group. Our results indicate that 9 weeks of KLIP training altered landing strategies in women to lower Fp and RFD. These changes are considered conducive to a reduced risk of knee injury while landing.
Ectopic activation of Dpp signalling in the male Drosophila germline inhibits germ cell differentiation

The mechanisms that control differentiation of stem cells to specialised cell types probably include factors intrinsic to stem cells as well as extrinsic factors produced by the microenvironment of the stem cell niche. The Drosophila male germline is renewed from a population of stem cells located in the apical tip of the adult testis. The morphological relationship between germline stem cells and their surrounding somatic cells is well understood but the factors that regulate stem cell proliferation and differentiation are still being uncovered. This study examined the effect of stimulating Dpp signalling directly in male germ cells. Ectopic Dpp or Activin signalling resulted in overproliferation of both stem cell‐like and spermatogonial‐like cells in the apical region of the testis. A third cell population that expressed stem cell markers was seen to proliferate in the distal testis when Dpp signalling was either stimulated or repressed in germline stem cells. genesis 39:84–93, 2004. © 2004 Wiley‐Liss, Inc.
An overview of face recognition in an unconstrained environment

Face recognition in an unconstrained environment is still a challenging problem. Variations in aging, partially visible faces, expression, illumination, pose, disguise, and twin faces are considered as basic challenges in face recognition. This paper presents a comparative study of existing 2D and 3D face recognition methods which are suitable to work with in these environments.
Improved Classification Methods for BCI Based on Nonlinear Transform

Brain computer interface (BCI) aims at providing a new communication way without depending on brain's normal output through nerve and muscle. The electroencephalography (EEG) has been widely used for BCI because it is a non-invasive approach. For the EEG signals of left and right hand motor imagery, the event-related desynchronization(ERD) and event-related synchronization(ERS) are used as classification features in this paper. The raw data are transformed by nonlinear methods and classified by Fisher classifier. Compared with the linear methods, the classification accuracy can get an obvious increase to 86.25%. Two different nonlinear transform were arised and one of them is under the consideration of the relativity of two channels of EEG signals. With these nonlinear transform, different misclassifications can get balance.
PILOT DATA ON THE BEHAVIOR RATING INVENTORY OF EXECUTIVE FUNCTION ( BRIEF ) AND PERFORMANCE MEASURES OF EXECUTIVE FUNCTION IN PEDIATRIC TRAUMATIC BRAIN INJURY ( TBI

of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science PILOT DATA ON THE BEHAVIOR RATING INVENTORY OF EXECUTIVE FUNCTION (BRIEF) AND PERFORMANCE MEASURES OF EXECUTIVE FUNCTION IN PEDIATRIC TRAUMATIC BRAIN INJURY (TBI) By Michelle L. Benjamin August 2004 Chair: Eileen B. Fennell Major Department: Clinical and Health Psychology Executive dysfunction has been reported in several studies of pediatric traumatic brain injury (TBI). Research using the Behavior Rating Inventory of Executive Function (BRIEF) in pediatric TBI has focused on cases of severe TBI evaluated several years post-injury, and little is known about the relationship between the BRIEF and traditional tests of executive function. Furthermore, previous studies did not explore individual BRIEF scales and instead used global composite scores from the BRIEF. The current study presents pilot data examining ratings of individual scales of the BRIEF and performance on traditional tests of executive functioning for an acute pediatric TBI sample with a range of severity. These data are compared to an orthopedic control group within the first year of recovery.
Displacement and stress fields produced by a centre of dilation and by a pressure source in a viscoelastic half-space: application to the study of ground deformation and seismic activity at Campi Flegrei, Italy

Summary. Analytical expressions for the static displacement field produced by a centre of dilation and by a pressure source in a viscoelastic half-space are derived. The associated stress fields are also computed. The rheology of a standard linear solid (SLS) is adopted for the shear modulus, while the incompressibility is kept elastic. An instantaneous dilation or variation of pressure is considered as responsible for the deformation. In the centre of dilation model, if the two rigidities of the SLS are of the same order of magnitude, the viscoelastic contribution to the deformation is negligible; if the short-term rigidity is at least two orders of magnitude higher than the other one, the results are indistinguishable from those obtained with a Maxwell solid rheology. In this case, it is found that the initial elastic displacement is amplified by 20 per cent. In the pressure source model, if the rigidities of the SLS are of the same order of magnitude, the initial elastic displacement is amplified by a factor of about 2, but unrealistically high pressure values are required. On the other hand, for a Maxwell solid rheology the displacement grows indefinitely in time, following a sudden application of a finite pressure. The uplift rate is evaluated and it is shown that, for obtaining values of the order of 1 m over one characteristic relaxation time, more reasonable values of pressure are allowed. Applications to ground deformation in volcanic areas are discussed, taking as an example the Campi Flegrei zone, near Naples, Italy.
Spatial Representations From Perception and Cognitive Mediation

Spatial representations can be derived not only by direct perception, but also through cognitive mediation. Conventional or ex-situ ultrasound displays, which displace imaged data to a remote screen, require both types of process. To determine the depth of a target hidden beneath a surface, ultrasound users must both perceive how deeply the ultrasound transducer indents the surface and interpret the on-screen image to visualize how deeply the target lies below the transducer. Combining these perceptual and cognitive depth components requires a spatial representation that has been called amodal. We report experiments measuring errors in perceptual and cognitively mediated depth estimates and show that these estimates can be concatenated (linked) without further error, providing evidence for an amodal representation. We further contrast conventional ultrasound with an in-situ display whereby an ultrasound image appears to float at the precise location being imaged, enabling the depth of a target to be directly perceived. The research has the potential to enhance ultrasound-guided surgical intervention.
Thermochronologic insight into late Cenozoic deformation in the basement‐cored Terskey Range, Kyrgyz Tien Shan

Basement‐cored ranges formed by reverse faulting within intracontinental mountain belts are often composed of poly‐deformed lithologies. Geological data capable of constraining the timing, magnitude, and distribution of the most recent deformational phase are usually missing in such ranges. In this paper, we present new low temperature thermochronological and geological data from a transect through the basement‐cored Terskey Range, located in the Kyrgyz Tien Shan. Using these data, we are able to investigate the range's late Cenozoic deformation for the first time. Displacements on reactivated faults are constrained and deformation of thermochronologically derived structural markers is assessed. These structural markers postdate the earlier deformational phases, providing the only record of Cenozoic deformation and of the reactivation of structures within the Terskey Range. Overall, these structural markers have a southern inclination, interpreted to reflect the decreasing inclination of the reverse fault bounding the Terskey Range. Our thermochronological data are also used to investigate spatial and temporal variations in the exhumation of the Terskey Range, identifying a three‐stage Cenozoic exhumation history: (1) virtually no exhumation in the Paleogene, (2) increase to slightly higher exhumation rates at ~26–20 Ma, and (3) significant increase in exhumation starting at ~10 Ma.
High Fat Feeding in Mice Is Insufficient to Induce Cardiac Dysfunction and Does Not Exacerbate Heart Failure

Feeding high fat diet (HFD) to mice is a commonly used model to investigate the impact of risk factors on cardiovascular physiology and the development of disease. Therefore, we sought to investigate whether a high fat diet (HFD) alone could produce cardiac dysfunction. Mice were fed a normal chow diet, a milk‐based HFD (60% cal from fat), or a lard‐based HFD (60% cal from fat) for a period of 28 weeks. Neither anesthetized (at 18 weeks) nor conscious echocardiography (28 weeks) revealed any evidence of cardiac dysfunction, despite elevated body fat in the two HFD groups. We next evaluated whether a HFD would exacerbate cardiac dysfunction during heart failure. Mice fed a HFD were subjected to myocardial infarction but experienced no more significant ventricular dysfunction than normal diet fed mice. These largely negative results compelled us to investigate a more severe model of hyperglycemia/obesity. Next, db/db mice were subjected to myocardial ischemia‐reperfusion and demonstrated a significant reduction in fractional shortening compared to wild‐type (WT) littermates. Interestingly, when subjected to pressure overload, db/db mice did not exhibit more severe dysfunction than WT littermates. In conclusion, our findings, coupled with several similar reports from other groups, indicate that a HFD may not reliably replicate the pathophysiological impact of a western diet on the murine heart.