Miracle-dz/UniFAR-FTUs huggingface dataset:
Modification of the lattice thermal conductivity in silicon quantum wires due to spatial confinement of acoustic phonons

Lattice thermal conductivity in silicon quantum wires is theoretically investigated. The bulk of heat in silicon structures is carried by acoustic phonons within a small region in the first Brillouin zone. Our formalism rigorously takes into account modification of these acoustic phonon modes and phonon group velocities in freeand clamped-surface wires due to spatial confinement. From our numerical results, we predict a significant decrease (more than an order of magnitude) of the lattice thermal conductivity in cylindrical quantum wires with diameter D = 200 Å. The decrease is about two times stronger in quantum wires than in quantum wells of corresponding dimensions. Our theoretical results are in qualitative agreement with experimentally observed drop of the lattice thermal conductivity in silicon low-dimensional structures. c © 1999 Academic Press
Temporal Profiling of Gene Networks Associated with the Late Phase of Long-Term Potentiation In Vivo

Long-term potentiation (LTP) is widely accepted as a cellular mechanism underlying memory processes. It is well established that LTP persistence is strongly dependent on activation of constitutive and inducible transcription factors, but there is limited information regarding the downstream gene networks and controlling elements that coalesce to stabilise LTP. To identify these gene networks, we used Affymetrix RAT230.2 microarrays to detect genes regulated 5 h and 24 h (n = 5) after LTP induction at perforant path synapses in the dentate gyrus of awake adult rats. The functional relationships of the differentially expressed genes were examined using DAVID and Ingenuity Pathway Analysis, and compared with our previous data derived 20 min post-LTP induction in vivo. This analysis showed that LTP-related genes are predominantly upregulated at 5 h but that there is pronounced downregulation of gene expression at 24 h after LTP induction. Analysis of the structure of the networks and canonical pathways predicted a regulation of calcium dynamics via G-protein coupled receptors, dendritogenesis and neurogenesis at the 5 h time-point. By 24 h neurotrophin-NFKB driven pathways of neuronal growth were identified. The temporal shift in gene expression appears to be mediated by regulation of protein synthesis, ubiquitination and time-dependent regulation of specific microRNA and histone deacetylase expression. Together this programme of genomic responses, marked by both homeostatic and growth pathways, is likely to be critical for the consolidation of LTP in vivo.
Hydrometallurgical Recovery of Precious Metals and Removal of Hazardous Metals Using Persimmon Tannin and Persimmon Wastes

Novel and environmentally benign adsorbents were prepared via a simple sulfuric acid treatment process using the wastes of astringent persimmon, a type of biomass waste, along with persimmon tannin extract which is currently employed for the tanning of leather and as natural dyes and paints. The effectiveness of these new biosorbents was exemplified with regards to hydrometallurgical and environmental engineering applications for the adsorptive removal of uranium and thorium from rare earths, cesium from other alkaline metals such as sodium, hexa-valent chromium from zinc as well as adsorptive recovery of gold from chloride media. Furthermore, reductive coagulation of gold from chloride media for the direct recovery of metallic gold and adsorptive recovery of palladium and platinum using chemically modified persimmon tannin extract were studied. OPEN
Canada’s Smallest Satellite: The Canadian Advanced Nanospace Experiment (CanX-1)

The Canadian Advanced Nanospace eXperiment (CanX) Program of the Space Flight Laboratory at the University of Toronto Institute for Aerospace Studies (UTIAS/SFL) is a Canadian first, allowing engineering researchers to test nanoand micro-scale devices rapidly and inexpensively in space. CanX is a “picosatellite” program for research and education, with graduate students leading the design, development, testing, and operations of Canada’s smallest satellites having a mass under 1 kg. The first UTIAS/SFL picosatellite, CanX-1, is scheduled for launch in early 2003 together with CubeSats from other university and industry developers. The objective of the CanX-1 mission is to verify the functionality of several novel electronic technologies in orbital space. This paper outlines the features, capabilities and performance of CanX-1, including horizon and star-tracking experiments using two CMOS imagers, active threeaxis magnetic stabilization, GPS-based position determination, and an ARM7 central processor.
Pluripotency of human embryonic and induced pluripotent stem cells for cardiac and vascular regeneration

Summary Cardiac and vascular abnormalities and disease syndromes are major causes of death both during human development and with aging. To identify the cause of congenital defects and to combat this epidemic in the aging population, new models must be created for scientific investigation and new therapies must be developed. Recent advances in pluripotent stem cell biology offer renewed hope for tackling these problems. Of particular importance has been the creation of induced pluripotent (iPS) cells from adult tissues and organs through the forced expression of two to four transcription factors. Moreover, iPS cells, which are phenotypically indistinguishable from embryonic stem (ES) cells, can be generated from any patient. This unique capacity when coupled with samples from patients who have congenital and genetic defects of unknown aetiology should permit the creation of new model systems that foment scientific investigation. Moreover, creation of patient-specific cells should overcome many of the immunological limitations that currently impede therapeutic applications associated with other pluripotent stem cells and their derivatives. The aims of this paper will be to discuss cardiac and vascular diseases and show how iPS cells may be employed to overcome some of the most significant scientific and clinical hurdles facing this field.
Reliability and Validity of the Belt-Stabilized Handheld Dynamometer in Hip- and Knee-Strength Tests.

CONTEXT The belt-stabilized handheld dynamometer (HHD) has been used to assess the strength of knee- and hip-muscle groups. However, few researchers have examined its reliability and validity for assessing the strength of these muscles. OBJECTIVE To evaluate the intra-examiner reliability of the belt-stabilized HHD and its validity and agreement with the isokinetic dynamometer for assessing the strength of knee- and hip-muscle groups. DESIGN Cross-sectional study. SETTING University laboratory. PATIENTS OR OTHER PARTICIPANTS We evaluated 26 healthy participants (13 men, 13 women; age = 23.5 ± 2.8 years, height = 1.7 ± 0.1 m, mass = 68.6 ± 12.4 kg) in 2 sessions using the belt-stabilized HHD and an isokinetic dynamometer for maximum strength of the hip adductors, abductors, flexors, extensors, internal rotators, and external rotators and the knee flexors and extensors. MAIN OUTCOME MEASURE(S) We used reliability values provided by the intraclass correlation coefficient (2,3), standard error of measurement (SEM and percentage SEM), and minimal detectable change; correlation values comparing the belt-stabilized HHD and the isokinetic instrument using the Pearson correlation coefficient (r); and the mean difference in values comparing the 2 instruments using the Bland-Altman method. RESULTS The intrarater HHD reliability was excellent for most measurements (range = 0.80-0.96; SEM = 1.3-5.3 kilograms of force or 4.8-18.9 Nm, percentage SEM = 7.0%-22.0%, minimal detectable change = 3.6-18.8 kilograms of force or 13.2-52.4 Nm) and was moderate only for bilateral knee flexion and left hip internal rotation (intraclass correlation coefficient [2,3] = 0.62-0.66 and 0.70, respectively). Correlation with the isokinetic dynamometer was moderate to high (r = 0.60-0.90), but the absolute values did not demonstrate concordance between results using the Bland-Altman method. CONCLUSIONS The belt-stabilized HHD measurements were reliable, and although they did not agree with those from the isokinetic dynamometer, the values were correlated for the hip- and knee-muscle groups.
Imaging of nuclear Overhauser enhancement at 7 and 3 T

Nuclear Overhauser enhancement (NOE) is a type of magnetization transfer using cross‐relaxation. It originates from mobile macromolecules, which may have relevance to the evaluation of tumor features. We studied the value of NOE imaging at 7 and 3 T and suggest a utility for diagnosing human brain tumors. Two types of protein solution at different concentrations and pH values, and six normal Sprague Dawley (SD) rats, were used to detect NOE signal with a 7 T scanner. Then, six healthy volunteers and 11 patients with brain tumors (six gliomas and five meningiomas) were included at 3 T. Z‐spectra were measured and NOE weighted (NOE*) images were acquired with a three‐offset measurement. Wide spectral separation was shown at both 7 T and 3 T delineating the NOE peak in the Z‐spectrum. The concentration dependence and pH independence of NOE were confirmed in phantom experiments, and NOE values were greater in white matter than in gray matter in vivo. At 3 T, data indicated that NOE* maps were slightly hypointense in gliomas and were not obviously different from meningiomas. Thus, NOE imaging may help distinguish benign from malignant tumors, and as such may contribute to diagnosing brain tumors.
Cushing in a Leaf: Endocrine Disruption From a Natural Remedy.

BACKGROUND Information regarding the safety of herbal drugs is often not reported. We describe the case of a 65-year-old woman referred to us for a iatrogenic hypercortisolism, who denied any previous steroid consumption. She reported only a chronic application of a phytocosmetic cream, containing ethanol extract of the Cardiospermum halicacabum (CH) plant. Adrenal insufficiency occurred after the cream application was stopped. CH is used in traditional and Western medicine for its documented anti-inflammatory properties. Once the presence of synthetic glucocorticoids was ruled out in the phytocosmetic product, we investigated whether and how its chronic application could have caused the iatrogenic hypercortisolism. METHODS Liquid chromatography high-resolution mass spectrometry (LC-HRMS) was performed to exclude the presence of known glucocorticoids in the cream. ELISA assay and Western blot analysis were employed to assess ACTH secretion and the glucocorticoid receptor expression respectively in murine ACTH-secreting pituitary adenoma cells AtT-20/D16v-F2, treated with dexamethasone, CH tincture, and mifepristone alone or in combination. To detect specific interaction of CH extract with the glucocorticoid receptor, we performed a dual-luciferase reporter assay in HEK293 cells. RESULTS In AtT-20/D16v-F2 cells, CH extract showed to significantly reduce basal and CRH-induced ACTH secretion and the glucocorticoid receptor expression, similarly to dexamethasone; these effects were counteracted by mifepristone. In HEK293 cells, dexamethasone significantly induced luciferase activity after 24- and 36-hour treatment and CH tincture only after 36 hours; these effects were antagonized by mifepristone. CONCLUSIONS CH extract displays a glucocorticoid-like activity, by means of a direct binding to the glucocorticoid receptor.
Using a Mobile Device Fingerprint Sensor as a Gestural Input Device

With the spread of mobile device fingerprint sensors, there is an opportunity to allow interaction beyond biometric authentication on the same device. The fingerprint sensor can detect simple gestures, enabling an additional gestural input method. We conducted user research sessions with ten people to understand the usefulness of a fingerprint sensor that also functions as a gestural input device. We identified general user perceptions as well as reactions to specific gestures and interactions. We find that this concept has promise and point to gestures and interactions that can provide a compelling and useful new input method.
Scalable molecular dynamics with NAMD

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel platforms, as well as tens of processors on low‐cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks. uiuc.edu. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1781–1802, 2005
Deleting the DAG kinase Dgk1 augments yeast vacuole fusion through increased Ypt7 activity and altered membrane fluidity

Diacylglycerol (DAG) is a fusogenic lipid that can be produced through phospholipase C activity on phosphatidylinositol 4,5‐bisphosphate [PI(4,5)P2 ], or through phosphatidic acid (PA) phosphatase activity. The fusion of Saccharomyces cerevisiae vacuoles requires DAG, PA and PI(4,5)P2 , and the production of these lipids is thought to provide temporally specific stoichiometries that are critical for each stage of fusion. Furthermore, DAG and PA can be interconverted by the DAG kinase Dgk1 and the PA phosphatase Pah1. Previously we found that pah1 Δ vacuoles were fragmented, blocked in SNARE priming and showed arrested endosomal maturation. In other pathways the effects of deleting PAH1 can be compensated for by additionally deleting DGK1 ; however, deleting both genes did not rescue the pah1 Δ vacuolar defects. Deleting DGK1 alone caused a marked increase in vacuole fusion that was attributed to elevated DAG levels. This was accompanied by a gain in resistance to the inhibitory effects of PA as well as inhibitors of Ypt7 activity. Together these data show that Dgk1 function can act as a negative regulator of vacuole fusion through the production of PA at the cost of depleting DAG and reducing Ypt7 activity.
Similarity indexing: algorithms and performance

Efficient indexing support is essential to allow content-based image and video databases using similarity-based retrieval to scale to large databases (tens of thousands up to millions of images). In this paper, we take an in depth look at this problem. One of the major difficulties in solving this problem is the high dimension (6-100) of the feature vectors that are used to represent objects. We provide an overview of the work in computational geometry on this problem and highlight the results we found are most useful in practice, including the use of approximate nearest neighbor algorithms. We also present a variant of the optimized k-d tree we call the VAM k-d tree, and provide algorithms to create an optimized R-tree we call the VAMSplit R-tree. We found that the VAMSplit R-tree provided better overall performance than all competing structures we tested for main memory and secondary memory applications. We observed large improvements in performance relative to the R*-tree and SS-tree in secondary memory applications, and modest improvements relative to optimized k-d tree variants.
Meta‐analytic approaches to determine gender differences in the age‐incidence characteristics of schizophrenia and related psychoses

A recent systematic review and meta‐analysis of the incidence and prevalence of schizophrenia and other psychoses in England investigated the variation in the rates of psychotic disorders. However, some of the questions of interest, and the data collected to answer these, could not be adequately addressed using established meta‐analysis techniques. We developed a novel statistical method, which makes combined use of fractional polynomials and meta‐regression. This was used to quantify the evidence of gender differences and a secondary peak onset in women, where the outcome of interest is the incidence of schizophrenia. Statistically significant and epidemiologically important effects were obtained using our methods. Our analysis is based on data from four studies that provide 50 incidence rates, stratified by age and gender. We describe several variations of our method, in particular those that might be used where more data is available, and provide guidance for assessing the model fit. Copyright © 2013 John Wiley & Sons, Ltd.
Looking to Parallel Algorithms for ILP and Decentralization

We introduce explicit multi-threading (XMT), a decentralized architecture that exploits fine-grained SPMD-style programming; a SPMD program can translate directly to MIPS assembly language using three additional instruction primitives. The motivation for XMT is: (i) to define an inherently decentralizable architecture, taking into account that the performance of future integrated circuits will be dominated by wire costs, (ii) to increase available instruction-level parallelism (ILP) by leveraging expertise in the world of parallel algorithms, and (iii) to reduce hardware complexity by alleviating the need to detect ILP at run-time: if parallel algorithms can give us an overabundance of work to do in the form of thread-level parallelism, one can extract instructionlevel parallelism with greatly simplified dependence-checking. We show that implementations of such an architecture tend towards decentralization and that, when global communication is necessary, overall performance is relatively insensitive to large on-chip delays. We compare the performance of the design to more traditional parallel architectures and to a high-performance superscalar implementation, but the intent is merely to illustrate the performance behavior of the organization and to stimulate debate on the viability of introducing SPMD to the single-chip processor domain. We cannot offer at this stage hard comparisons with wellresearched models of execution. When programming for the SPMD model, the total number of operations that the processor has to perform is often slightly higher. To counter this, we have observed that the length of the critical path through the dynamic execution graph is smaller than in the serial domain, and the amount of ILP is correspondingly larger. Fine-grained SPMD programming connects with a broad knowledge base in parallel algorithms and scales down to provide good performance relative to high-performance superscalar designs even with small input sizes and small numbers of functional units.
Mediator Directs Co-transcriptional Heterochromatin Assembly by RNA Interference-Dependent and -Independent Pathways

Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism, which is coupled with the transcription of non-coding RNA from the repeats by RNA polymerase II. In addition, Rrp6, a component of the nuclear exosome, also contributes to heterochromatin assembly and is coupled with non-coding RNA transcription. The multi-subunit complex Mediator, which directs initiation of RNA polymerase II-dependent transcription, has recently been suggested to function after initiation in processes such as elongation of transcription and splicing. However, the role of Mediator in the regulation of chromatin structure is not well understood. We investigated the role of Mediator in pericentromeric heterochromatin formation and found that deletion of specific subunits of the head domain of Mediator compromised heterochromatin structure. The Mediator head domain was required for Rrp6-dependent heterochromatin nucleation at the pericentromere and for RNAi-dependent spreading of heterochromatin into the neighboring region. In the latter process, Mediator appeared to contribute to efficient processing of siRNA from transcribed non-coding RNA, which was required for efficient spreading of heterochromatin. Furthermore, the head domain directed efficient transcription in heterochromatin. These results reveal a pivotal role for Mediator in multiple steps of transcription-coupled formation of pericentromeric heterochromatin. This observation further extends the role of Mediator to co-transcriptional chromatin regulation.
Rich Locomotion Skills with the Oncilla Robot

We are motivated to better understand how adaptive locomotion (rough terrain locomotion, turning, gait transition, etc) can be realized using a quadrupedal platform with constrained resources. These constraints include computational power limitation, no accurate force/torque sensing, and partial sensing of robot’s kinematic states. These constraints arise from the fact that we are designing and experimenting with autonomous light-weight and (comparatively) cheap quadruped robots. The practical benefit of such robots is fast experimentation: experiments can be safely done with presence of one or two humans, and repairs are cheap and quick.
log N-log S Relations and Spectral Properties of Sources from the ASCA Large Sky Survey: Their Implications for the Origin of the Cosmic X-Ray Background (CXB)

We carried out the first wide-area unbiased survey with the ASCA satellite in the 0.7-10 keV band around a north Galactic-pole region covering a continuous area of 7 deg2 (Large Sky Survey; LSS). To make the best use of ASCA's capabilities, we developed a new source-detection method in which the complicated detector responses are fully taken into account. Applying this method to the entire LSS data independently in the total (0.7-7 keV), hard (2-10 keV), and soft (0.7-2 keV) bands, we detected 107 sources altogether, with sensitivity limits of 6 × 10-14 (0.7-7 keV), 1 × 10-13 (2-10 keV), and 2 × 10-14 ergs s-1 cm-2 (0.7-2 keV), respectively. A complete list of the detected sources is presented. Based on detailed studies by Monte Carlo simulations, we evaluated the effects of the source confusion and accurately derived the log N-log S relation in each survey band. The log N-log S relation in the hard band is located on the extrapolation from Ginga and HEAO1 results with a Euclidean slope of -3/2, while that in the soft band is consistent with the results from ROSAT. At these flux limits, 30% ± 3% of the CXB in the 0.7-7 keV band and 23% ± 3% in the 2-10 keV band have been resolved into discrete sources. The average spectrum of faint sources detected in the total band shows a photon index of 1.63 ± 0.07 in the 0.7-10 keV range, consistent with the comparison of source counts between the hard and soft energy bands. Those detected in the hard band show a photon index of 1.49 ± 0.10 in the 2-10 keV range. These spectral properties suggest that the contribution of sources with hard energy spectra becomes significant at a flux of 10-13 ergs s-1 cm-2 (2-10 keV). The most plausible candidates are type II active galactic nuclei, as indicated by on-going optical identifications.