Miracle-dz/UniFAR-FTUs huggingface dataset:
Pleiotropic Effects of a Methyl Donor Diet in a Novel Animal Model

Folate and other methyl-donor pathway components are widely supplemented due to their ability to prevent prenatal neural tube defects. Several lines of evidence suggest that these supplements act through epigenetic mechanisms (e.g. altering DNA methylation). Primary among these are the experiments on the mouse viable yellow allele of the agouti locus (Avy). In the Avy allele, an Intracisternal A-particle retroelement has inserted into the genome adjacent to the agouti gene and is preferentially methylated. To further test these effects, we tested the same diet used in the Avy studies on wild-derived Peromyscus maniculatus, a native North American rodent. We collected tissues from neonatal offspring whose parents were fed the high-methyl donor diet as well as controls. In addition, we assayed coat-color of a natural variant (wide-band agouti = ANb) that overexpresses agouti as a phenotypic biomarker. Our data indicate that these dietary components affected agouti protein production, despite the lack of a retroelement at this locus. Surprisingly, the methyl-donor diet was associated with defects (e.g. ovarian cysts, cataracts) and increased mortality. We also assessed the effects of the diet on behavior: We scored animals in open field and social interaction tests. We observed significant increases in female repetitive behaviors. Thus these data add to a growing number of studies that suggest that these ubiquitously added nutrients may be a human health concern.
Estimation and monitoring heat discharge rates using Landsat ETM+ thermal infrared data: a case study in Unzen geothermal field, Kyushu, Japan

The Unzen geothermal field, our study area is active fumaroles, situated in Shimabara Peninsula of Kyushu Island in Japan. Our prime objectives were (1) to estimate radiative heat flux (RHF), (2) to calculate approximately heat discharge rate (HDR) using the relationship of radiative heat flux with the total heat loss derived from two geothermal field studies and (3) finally, to monitor RHF as well as HDR in our study area using seven sets of Landsat 7 ETM+ images from 2000 to 2009. We used the NDVI (Normalized differential vegetation index) method for spectral emissivity estimation, the mono-window algorithm for land surface temperature (LST) and the Stefan-Boltzmann equation analyzing those satellite TIR images for RHF. We obtained a desired strong correlation of LST above ambient with RHF using random samples. We estimated that the maximum RHF was about 251 W/m2 in 2005 and minimum was about 27 W/m2 in 2001. The highest total RHF was about 39.1 MW in 2005 and lowest was about 12 MW in 2001 in our study region. We discovered that the estimated RHF was about 15.7 % of HDR from our studies. We applied this percentage to estimate heat discharge rate in Unzen geothermal area. The monitoring results showed a single fold trend of HDR from 2000 to 2009 with highest about 252 MW in 2005 and lowest about 78 MW in 2001. In conclusion, TIR remote sensing is thought as the best option for monitoring heat losses from fumaroles with high efficiency and low cost.
Comparison of Visual-Motor Performance and Nonverbal Reasoning among Child and Adolescent Patients in an Urban Psychiatric Hospital

Two groups of young psychiatric- inpatients were used to compare performance on the Test of Nonverbal Reasoning and the Developmental Test of Visual-motor Integration. The older group of 230 had a mean age of 15.7 yr. and produced a product-moment correlation of . 64 for the two tests. The younger group of 81 had a mean age of 11.3 yr; scores correlated . 53. On the TONI, the performance of the adolescent girls was superior to that of the boys. On the Test of Visual-motor Integration, the younger girls appeared to outscore the boys, but an analysis of variance of sex differences with age as covariate fell short of significance. Results were explained in terms of subjects' differing school experience in their development of vasomotor and visual-reasoning skills. Caution was advised in the application of age-based test norms to special populations.
Curvilinear 3-D Imaging Using Row-Column-Addressed 2-D Arrays With a Diverging Lens: Feasibility Study

Constructing a double-curved row-column-addressed (RCA) 2-D array or applying a diverging lens over the flat RCA 2-D array can extend the imaging field-of-view (FOV) to a curvilinear volume without increasing the aperture size, which is necessary for applications, such as abdominal and cardiac imaging. Extended FOV and low channel count of double-curved RCA 2-D arrays make 3-D imaging possible with equipment in the price range of conventional 2-D imaging. This paper proposes a delay-and-sum beamformation scheme specific to double-curved RCA 2-D arrays and validates its focusing ability based on simulations. A synthetic aperture imaging sequence with single element transmissions is designed for imaging down to 14 cm at a volume rate of 88 Hz. Using a diverging lens with an f-number of −1 circumscribing the underlying RCA array, the imaging quality of a double-curved $\lambda /2$ -pitch 3-MHz 62 + 62 RCA 2-D array is investigated as a function of depth within a curvilinear FOV of 60 $^{\circ }\times 60^{\circ }$ . The simulated double-curved 2-D array exhibits the same full-width-at-half-maximum values for a point scatterer within its curvilinear FOV at a fixed radial distance compared with a flat 2-D array within its rectilinear FOV. The results of this paper demonstrate that the proposed beamforming approach is accurate for achieving correct time-of-flight calculations, and hence avoids geometrical distortions.
CARBONATE DEPOSITIONAL ENVIRONMENTS, SEQUENCE STRATIGRAPHY AND EXCEPTIONAL SKELETAL PRESERVATION IN THE MUCH WENLOCK LIMESTONE FORMATION (SILURIAN) OF DUDLEY, ENGLAND

Abstract: The Much Wenlock Limestone Formation of the Dudley inliers, West Midlands, contains one of the world's richest and most exquisitely preserved Silurian marine biotas. However, for most museum specimens, little is known of their exact provenance and mode of preservation. Detailed comparisons between outcrops and museum collections allow the identification of five faunal‐lithological associations and numerous horizons of exceptional skeletal preservation. The associations are interpreted as a series of transient carbonate mid‐platform environments extending from below storm wave‐base to above fair‐weather wave‐base. Erosive surfaces, condensed sections, flooding surfaces and the stacking patterns of genetically related bed‐sets (parasequences) have allowed the formation to be interpreted as a single third‐order sequence stratigraphic cycle of sea‐level change. The articulated preservation of taxa such as pelmatozoan echinoderms and trilobites can be attributed to either rapid burial by obrution deposits close to fair‐weather wave‐base or smothering by storm sequestered muds in slightly deeper‐water settings. Such intervals of exceptional preservation are commonly associated with flooding surfaces, presumably reflecting reduced likelihood of reworking once rapid burial had taken place.
A circuit-driven design methodology for a linear-to-circular polarizer

The paper presents a fast design methodology to achieve a circular polarizer with a relatively low thickness of one-fifth of a free-space wavelength. A three-layer planar structure is devised to exhibit transparency to both TE and TM polarized fields while imparting a quadrature phase difference between them, as required for the generation of circularly-polarized fields. The structure is designed using a circuit-driven approach whereby an independent equivalent circuit describes the behavior of each constituent polarization. Meanwhile, the small unit cell size endows the structure with a low sensitivity to the angle of incidence of the impinging waves. This polarizer with a unit cell volume of 0. 13λ0×θ. 13λ0×0. 21λ0 renders axial ratios of less than 3dB and 1dB over 12.5% and 4.4% fractional bandwidths, respectively. Numerical simulations verify the accuracy of the circuit-driven approach and its applicability as a design tool in the synthesis of this class of polarizer.
Attitude of bachelor of dental surgery students and interns toward teaching-learning process in Government Dental College, Kottayam, Kerala, India

Introduction: The educational environment affects the academic performance of students. One of the most widely utilized tools for measuring the educational environment is Dundee Ready Education Environment Measure (DREEM). The objective of the study was to assess the attitude toward study environment, as measured using DREEM questionnaire, and to find out the differences in perception of various batches of dental students. Materials and Methods: All Bachelor of Dental Surgery students from Government Dental College, Kottayam, Kerala, India, were included in the study. They were given the well-established DREEM questionnaire. A total of 234 students took part in the study, belonging to 2009, 2010, 2011, 2012, 2013, and 2014 batches. DREEM subcategories were analyzed for significance using analysis of variance. The significance of DREEM score across the different batches was further analyzed using post hoc test. Results: Overall, DREEM score was positive (111.14), but there is need for improvement. Individual questions also were given positive score for most questions. The maximum score was obtained for 3rd year students. Similar results are obtained for three of the five subcategories of DREEM. Conclusion: The total DREEM score was positive (111.14). The total score as well as the scores for the subcategories was highest in 3rd year dental students. The increase might be due to the excitement of clinical exposure for the first time in 3rd year students.
Normal human mammary epithelial cells proliferate rapidly in the presence of elevated levels of the tumor suppressors p53 and p21WAF1/CIP1

In normal cells, p53 protein is maintained at low levels, but the levels increase after stress or inappropriate growth signals to coordinate growth arrest or apoptosis. Human mammary epithelial cells (HMECs) are unusual in that they exhibit two phases of growth. The second growth phase, referred to as post-selection, follows a period of temporary growth arrest and is characterized by the absence of p16INK4a (also known as CDK4I and p16-INK4a) expression. Previously, we observed that post-selection HMECs have elevated levels of p53. Exogenous p16INK4a expression decreased levels of both p53 transcript and protein, and this effect was inhibited by nutlin-3a, indicating that p16INK4a can regulate p53 expression by affecting both p53 transcription and Mdm2-dependent degradation of p53. The p53 in post-selection HMECs was wild type and, as expected, increased p53 expression was associated with elevated p21WAF1/CIP1 and Mdm2 levels; the p53 response to DNA damage seemed normal. Despite elevated levels of wild-type p53 and p21WAF1/CIP1, post-selection cells grew more rapidly than their pre-selection HMEC precursors. We found that the post-selection HMECs contain a truncated Mdm2 protein (p60), which presumably lacks the p53 ubiquitylation domain. We propose that the increased levels of p53 in post-selection HMECs are due to the presence of an Mdm2 fragment that binds p53 but does not result in its degradation.
Provenance Analysis of the Cretaceous Hornbrook Formation of northern California and southern Oregon

The provenance of the Cretaceous Hornbrook Formation, deposited unconformably on the eastern terranes of the Klamath Mountains of northern California and southern Oregon, may prove critical to reconstructing the complex Cretaceous paleogeography of this region. Sandstone petrography from each of the five members of the Hornbrook Formation indicates a variable source region with elements from basement uplift, transitional continent, recycled orogen, and dissected arc sources. A conglomerate clast count from the Klamath River Conglomerate member is broadly consistent with sandstone petrography, but yielded more quartzite and fewer volcanic clasts than the sand-sized fraction. This reflects the different susceptibility to weathering and diagenesis of these rock types. Likewise, Klamath River Conglomerate quartzite clasts contain a Precambrian detrital zircon age distribution very similar to that found in the Antelope Mountain Quartzite within the Yreka subterrane of the eastern Klamath Mountains while all the other Precambrian zircons from the Hornbrook Formation resemble northern Sierra Nevada terranes. This discrepancy suggests that the quartzite was not broken down into sand-sized grains during transport, but rocks from plutonic arc sources were disaggregated. In addition, detrital zircon age spectra from sandstones throughout the strata of the Hornbrook Formation clearly show that the provenance of the Hornbrook Formation changed with time and was not limited to the Klamath Mountains, contrary to past assumptions. In the Mesozoic detrital zircon age distribution, the reduction in the Early Cretaceous peak and the appearance of a Late Cretaceous peak suggests increasing input from an active magmatic arc other than a Klamath Mountain source. This age signature is supported by the variability of the sandstone petrography, the decreasing volcanic input, and the decreasing
Accuracy assessment of game-based crowdsourced land-use/land cover image classification

Crowd-sourced data has been used as alternative for ground truth data. However, the accuracy of crowd-sourced land use and land cover classification information has not been explored in an African land cover and land use context. The compares traditional classification techniques to crowd-sourced classification, highlighting the high accuracy of crowd-sourced responses and short turnaround time compared to other supervised and unsupervised methods. Crowd-sourcing is found to be an acceptable method for high speed classification of land use and land cover, and further study is recommended.
COMPARING LEARNING METHODS FOR CLASSIFICATION

We address the consistency property of cross validation (CV) for classification. Sufficient conditions are obtained on the data splitting ratio to ensure that the better classifier between two candidates will be favored by CV with probability approaching 1. Interestingly, it turns out that for comparing two general learning methods, the ratio of the training sample size and the evaluation size does not have to approach 0 for consistency in selection, as is required for comparing parametric regression models (Shao (1993)). In fact, the ratio may be allowed to converge to infinity or any positive constant, depending on the situation. In addition, we also discuss confidence intervals and sequential instability in selection for comparing classifiers.
Overexpression of S4D Mutant of Leishmania donovani ADF/Cofilin Impairs Flagellum Assembly by Affecting Actin Dynamics

ABSTRACT Leishmania, like other eukaryotes, contains large amounts of actin and a number of actin-related and actin binding proteins. Our earlier studies have shown that deletion of the gene corresponding to Leishmania actin-depolymerizing protein (ADF/cofilin) adversely affects flagellum assembly, intracellular trafficking, and cell division. To further analyze this, we have now created ADF/cofilin site-specific point mutants and then examined (i) the actin-depolymerizing, G-actin binding, and actin-bound nucleotide exchange activities of the mutant proteins and (ii) the effect of overexpression of these proteins in wild-type cells. Here we show that S4D mutant protein failed to depolymerize F-actin but weakly bound G-actin and inhibited the exchange of G-actin-bound nucleotide. We further observed that overexpression of this protein impaired flagellum assembly and consequently cell motility by severely impairing the assembly of the paraflagellar rod, without significantly affecting vesicular trafficking or cell growth. Taken together, these results indicate that dynamic actin is essentially required in assembly of the eukaryotic flagellum.
The hyaluronate receptor is a member of the CD44 (H-CAM) family of cell surface glycoproteins [published erratum appears in J Cell Biol 1991 Feb;112(3):following 513]

The present study was undertaken to determine the relationship between the hyaluronate receptor and CD44 (H-CAM), cell-surface glycoproteins of similar molecular weights that have been implicated in cell adhesion. In initial experiments, a panel of monoclonal antibodies directed against CD44 were tested for their ability to cross react with the hyaluronate receptor. These antibodies immunoprecipitated [3H]hyaluronate binding activity from detergent extracts of both mouse and human cells, indicating that the hyaluronate receptor is identical to CD44. In addition, one of these antibodies (KM-201 to mouse CD44) directly blocked the binding of labeled hyaluronate to the receptor and inhibited hyaluronate dependent aggregation of SV-3T3 cells. CD44 has also been implicated in lymphocyte binding to high endothelial venules during lymphocyte homing. Interestingly, the monoclonal antibody Hermes- 3, which blocks lymphocyte binding to the high endothelial venules of mucosal lymphoid tissue, had no effect on the binding of labeled hyaluronate. Furthermore, the binding of lymphocytes to high endothelial cells of lymph nodes and mucosal lymphoid tissue was not significantly affected by treatment with agents that block the binding of hyaluronate (hyaluronidase, excess hyaluronate and specific antibodies). Thus, CD44 appears to have at least two distinct functional domains, one for binding hyaluronate and another involved in interactions with mucosal high endothelial venules.
Macro constitutive law for rupture dynamics derived from micro constitutive law measured in laboratory

The relation between a macro constitutive law of friction during faulting with specified local or micro laws is assessed by means of numerical simulation. A 3‐D numerical model based on the Discrete Element Method was used to simulate the rupture of a fault, in which each local grid point on the fault is assumed to follow the micro friction law. Then, the macro friction model is estimated by averaging, on a selected area, relevant variables monitored during rupture. After considering a homogeneous material, the influence of non‐homogeneity was evaluated by assuming that mass density, Young's modulus and friction coefficient were correlated Gaussian random fields. In both cases, only minor variations in the parameters of the macro constitutive law in relation to the micro constitutive law were perceived. However, the presence of indentations on the fault was found to affect the macro constitutive law.
Integrated Movement Therapy™: Yoga-Based Therapy as a Viable and Effective Intervention for Autism Spectrum and Related Disorders

Integrated Movement Therapy™ is an individual and group therapy approach that combines speech-language pathology, behavioral and mental health counseling, and Yoga. It is taught by master-degreed therapists who are also certified Yoga instructors. Although this approach has been successfully implemented with children with Attention Deficit Hyperactivity Disorder (ADHD), Learning Disabilities, Pervasive Developmental Delay, Sensory Integration Dysfunction, Dyspraxia, and other specific motor-based disorders, it has had especially consistent and remarkable results with children diagnosed with Autism Spectrum Disorders. Integrated Movement Therapy has six core principles: structure and continuity, social interaction, language stimulation, self-calming, physical stimulation, and direct self-esteem building. The following article will describe Autism Spectrum Disorders in depth and will show how each of the six core principles of Integrated Movement Therapy specifically addresses the characteristics associated with Autism. It will also note specific, documented improvements in all areas addressed based on qualitative ratings scales and parent feedback.
A Non-Local Model for Fluid-Structure Interaction with Applications in Hydraulic Fracturing

Modeling important engineering problems related to flow-induced damage (in the context of hydraulic fracturing among others) depends critically on characterizing the interaction of porous media and interstitial fluid flow. This work presents a new formulation for incorporating the effects of pore pressure in a non-local representation of solid mechanics. The result is a framework for modeling fluid-structure interaction problems with the discontinuity capturing advantages of an integral-based formulation. A number of numerical examples are used to show that the proposed formulation can be applied to measure the effect of leak-off during hydraulic fracturing as well as modeling consolidation of fluid-saturated rock and surface subsidence caused by fluid extraction from a geologic reservoir. The formulation incorporates the effect of pore pressure in the constitutive description of the porous material in a way that is appropriate for nonlinear materials, easily implemented in existing codes, straightforward in its evaluation (no history dependence), and justifiable from first principles. A mixture theory approach is used (deviating only slightly where necessary) to motivate an alteration to the peridynamic pressure term based on the fluid pore pressure. The resulting formulation has a number of similarities to the effective stress principle developed by Terzaghi and Biot and close correspondence is shown between the proposed method and the classical effective stress principle.
Software-based register file vulnerability reduction for embedded processors

Register File (RF) is extremely vulnerable to soft errors, and traditional redundancy based schemes to protect the RF are prohibitive not only because RF is often in the timing critical path of the processor, but also since it is one of the hottest blocks on the chip. Software approaches would be ideal in this case, but previous approaches based on instruction scheduling are only moderately effective due to local scope. In this article we present a compiler approach, based on interprocedural program analysis, to reduce the vulnerability of registers by temporarily writing live variables to protected memory. We formulate the problem as an integer linear programming problem and also present a very efficient heuristic algorithm. Further we present an iterative optimization method based on Kernighan-Lin's graph partitioning algorithm. Our experiments demonstrate that our proposed techniques can reduce the vulnerability of a RF by 33 ∼ 37% on average and up to 66%, with a small 2% increase in runtime. In addition, our overhead reduction optimization can effectively reduce the code size overhead, by more than 40% on average, to a mere 5 ∼ 6%, compared to highly optimized binaries.