gebhart/patrepeval huggingface dataset:
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding (2017)

Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data. The DNAphi method uses a sliding-window approach to mine results from non-linear Poisson-Boltzmann (NLPB) calculations on DNA structures derived from all-atom Monte Carlo simulations. We validated this approach, which only requires nucleotide sequence as input, based on direct comparison with NLPB calculations for available crystal structures. Using statistical machine-learning approaches, we showed that adding EP as a biophysical feature can improve the predictive power of quantitative binding specificity models across 27 transcription factor families. High-throughput prediction of EP offers a novel way to integrate biophysical and genomic studies of protein-DNA binding.
Weakly-Supervised Discovery of Geometry-Aware Representation for 3D Human Pose Estimation (2019)

Recent studies have shown remarkable advances in 3D human pose estimation from monocular images, with the help of large-scale in-door 3D datasets and sophisticated network architectures. However, the generalizability to different environments remains an elusive goal. In this work, we propose a geometry-aware 3D representation for the human pose to address this limitation by using multiple views in a simple auto-encoder model at the training stage and only 2D keypoint information as supervision. A view synthesis framework is proposed to learn the shared 3D representation between viewpoints with synthesizing the human pose from one viewpoint to the other one. Instead of performing a direct transfer in the raw image-level, we propose a skeleton-based encoder-decoder mechanism to distil only pose-related representation in the latent space. A learning-based representation consistency constraint is further introduced to facilitate the robustness of latent 3D representation. Since the learnt representation encodes 3D geometry information, mapping it to 3D pose will be much easier than conventional frameworks that use an image or 2D coordinates as the input of 3D pose estimator. We demonstrate our approach on the task of 3D human pose estimation. Comprehensive experiments on three popular benchmarks show that our model can significantly improve the performance of state-of-the-art methods with simply injecting the representation as a robust 3D prior.
Vertical Jump Performance and Selected Physiological Characteristics of Women (1994)

ABSTRACT Fifty healthy university women participated in a study measuring the association between two countermovement vertical jumps and a variety of structural and functional musculoskeletal variables. A squat incorporating “restricted” upper body motions served as the countermovement preceding the first style of jumping, while the second jumping style involved a depth jump with unrestricted upper body motions. Also, nine functional measurements for each of six isokinetic squat speeds ranging from 25 to 100° · s−1 were obtained. The squat exercises were modifications of previously reported protocols, therefore the reliabilities of all 54 measurements were assessed prior to their use as potential factors associated with jumping ability. Reliability coefficients ranged from very high to moderate, except for rise time at 180° · s−1 and peak hold time at 25° · s−1 being low. All force and power variables were significantly correlated with jumping performance. The highest correlations occurred with peak power at 70 and 85° · s−1 and average-force-to-body-weight ratio at 85° · s−1. No significant correlation was found between jumping performance and % body fat.
Blue Quantum Dot Light-Emitting Diodes with High Electroluminescent Efficiency (2017)

High-efficiency blue CdSe/ZnS quantum dots (QDs) have been synthesized for display application with emission peak over 460 nm with the purpose of reducing the harmful effect of short-wavelength light to human eyes. To reach a better charge balance, different size ZnO nanoparticles (NPs) were synthesized and electrical properties of ZnO NPs were analyzed. Quantum dot light-emitting diodes (QLEDs) based on as-prepared blue QDs and optimized ZnO NPs have been successfully fabricated. Using small-size ZnO NPs, we have obtained a maximum current efficiency (CE) of 14.1 cd A<sup>-1</sup> and a maximum external quantum efficiency (EQE) of 19.8% for QLEDs with an electroluminescence (EL) peak at 468 nm. To the best of our knowledge, this EQE is the highest value in comparison to the previous reports. The CIE 1931 color coordinates (0.136, 0.078) of this device are quite close to the standard (0.14, 0.08) of National Television System Committee (NTSC) 1953. The color saturation blue QLEDs show great promise for use in next-generation full-color displays.
Face detection and eyeglasses detection for thermal face recognition (2012)

Thermal face recognition becomes an active research direction in human identification because it does not rely on illumination condition. Face detection and eyeglasses detection are necessary steps prior to face recognition using thermal images. Infrared light cannot go through glasses and thus glasses will appear as dark areas in a thermal image. One possible solution is to detect eyeglasses and to exclude the eyeglasses areas before face matching. In thermal face detection, a projection profile analysis algorithm is proposed, where region growing and morphology operations are used to segment the body of a subject; then the derivatives of two projections (horizontal and vertical) are calculated and analyzed to locate a minimal rectangle of containing the face area. Of course, the searching region of a pair of eyeglasses is within the detected face area. The eyeglasses detection algorithm should produce either a binary mask if eyeglasses present, or an empty set if no eyeglasses at all. In the proposed eyeglasses detection algorithm, block processing, region growing, and priori knowledge (i.e., low mean and variance within glasses areas, the shapes and locations of eyeglasses) are employed. The results of face detection and eyeglasses detection are quantitatively measured and analyzed using the manually defined ground truths (for both face and eyeglasses). Our experimental results shown that the proposed face detection and eyeglasses detection algorithms performed very well in contrast with the predefined ground truths.
Molecular velocity imaging of supersonic flows using pulsed planar laser-induced fluorescence of NO (1989)

A technique is described for imaging components of velocity in a gaseous flow field by using pulsed planar laser-induced fluorescence. The technique is based on the fluorescence detection of Doppler-shifted absorption that results when a spectrally narrow absorption line is excited with a broadband laser. Results obtained in a Mach 7 underexpanded supersonic jet, seeded with NO, are presented. The practical extension of this technique to single-shot measurements of two velocity components is discussed.
Review of Nanosheet Transistors Technology (2021)

Nano-sheet transistor can be defined as a stacked horizontally gate surrounding the channel on all direction. This new structure is earning extremely attention from research to cope the restriction of current Fin Field Effect Transistor (FinFET) structure. To further understand the characteristics of nano-sheet transistors, this paper presents a review of this new nano-structure of Metal Oxide Semiconductor Field Effect Transistor (MOSFET), this new device that consists of a metal gate material. Lateral nano-sheet FET is now targeting for 3nm Complementary MOS (CMOS) technology node. In this review, the structure and characteristics of Nano-Sheet FET (NSFET), FinFET and NanoWire FET (NWFET) under 5nm technology node are presented and compared. According to the comparison, the NSFET shows to be more impregnable to mismatch in ON current than NWFET. Furthermore, as comparing with other nano-dimensional transistors, the NSFET has the superior control of gate all-around structures, also the NWFET realize lower mismatch in sub threshold slope (SS) and drain induced barrier lowering (DIBL).
<i>In Situ</i> Molecular Spectroscopic Evidence for CO<sub>2</sub> Intercalation into Montmorillonite in Supercritical Carbon Dioxide (2012)

The interaction of anhydrous supercritical CO(2) (scCO(2)) with both kaolinite and ~1W (i.e., close to but less than one layer of hydration) calcium-saturated montmorillonite was investigated under conditions relevant to geologic carbon sequestration (50 °C and 90 bar). The CO(2) molecular environment was probed in situ using a combination of three novel high-pressure techniques: X-ray diffraction, magic angle spinning nuclear magnetic resonance spectroscopy, and attenuated total reflection infrared spectroscopy. We report the first direct evidence that the expansion of montmorillonite under scCO(2) conditions is due to CO(2) migration into the interlayer. Intercalated CO(2) molecules are rotationally constrained and do not appear to react with waters to form bicarbonate or carbonic acid. In contrast, CO(2) does not intercalate into kaolinite. The findings show that predicting the seal integrity of caprock will have complex dependence on clay mineralogy and hydration state.
Fitting Hearing Aids to Adults Using Prescriptive Methods: An Evidence-Based Review of Effectiveness (2005)

The use of a prescriptive fitting approach for hearing aid selection has been a common practice for the past 60-70 years. While there are prescriptive approaches that have been validated, in recent years it has become popular to deviate from these validated methods and use manufacturers' proprietary algorithms, which in many cases are significantly different. This research review was designed to examine if there was evidence supporting the use of specific gain requirements for hearing aid fitting. Specifically, the question that was asked was "Are there real-world outcome measures from adult patients that show a preference for the gain prescribed by a specific prescriptive fitting procedure?" Inclusion criteria were as follows: adult subjects, consistent technology (e.g., different prescriptive methods compared using same hearing aids), real-ear verification of gain, and real-world outcome measures. For this review, in addition to subjective responses, preferred use gain was considered a real-world outcome measure. The National Acoustic Laboratories' revised (NAL-R), revised for severe/profound (NAL-RP), and the National Acoustic Laboratories-Non-Linear 1 (NAL-NL1) prescriptive methods were used as a common reference, as they have been the most commonly studied methods with adults. Eleven studies were identified that met the inclusion criteria. Eight of the studies supported gain similar to that prescribed by the NAL-R or NAL-RP methods; three studies supported prescribed gain less than the NAL-R or NAL-RP. There was no evidence that gain greater than that prescribed by the NAL methods should be used. The level of evidence was moderate, as the supporting studies were either Level 2 or Level 4, and the statistical power of the studies was low.
Modulation of Perfusion and Oxygenation by Red Blood Cell Oxygen Affinity during Acute Anemia (2007)

Responses to exchange transfusion using red blood cells (RBCs) with modified hemoglobin (Hb) oxygen (O(2)) affinity were studied in the hamster window chamber model during acute anemia to determine its role on microvascular perfusion and tissue oxygenation. Allosteric effectors were introduced in the RBCs by electroporation. Inositol hexaphosphate (IHP) and 5-hydroxymethyl-2-furfural (5HMF) were used to decrease and increase Hb-O(2) affinity. In vitro P50s (partial pressure of O(2) at 50% Hb saturation) were modified to 10, 25, 45, and 50 mm Hg (normal P50 is 32 mm Hg). Allosteric effectors also decreased the Hill coefficient. Anemic condition was induced by isovolemic hemodilution exchanges using 6% dextran 70 kD to 18% hematocrit (Hct). Modified RBCs (at 18% Hct in 5% albumin solution) were infused by exchange transfusion of 35% of blood volume. Systemic parameters, microvascular perfusion, capillary perfusion (functional capillary density, FCD), and microvascular Po(2) levels were measured. RBcs with P50 of 45 mm Hg increased tissue Po(2) and decreased O(2) delivery (Do(2)) and extraction (Vo(2)) and RBCs with P50 of 60 mmHg reduced FCD, microvascular flow, tissue Po(2), Do(2) and Vo(2). Erythrocytes with increased Hb-O(2) affinity maintained hemodynamic conditions, Do(2) and decreased tissue Po(2). This study shows that in an anemic condition, maximal tissue Po(2) does not correspond to maximal Do(2) and Vo(2).
Population-based analysis of sporadic and type 2 neurofibromatosis-associated meningiomas and schwannomas (2000)

The current diagnostic criteria of type 2 neurofibromatosis (NF2) seem valid because NF2 patients were differentiated rather easily from patients with sporadic schwannomatosis and meningiomatosis. Familial meningiomatosis, if it truly exists, is very rare, and familial schwannomatosis is uncommon.
Modeling the effects of treating diabetic wounds with engineered skin substitutes (2007)

In this paper, a novel mathematical model of wound healing in both normal and diabetic cases is presented, focusing upon the effects of adding two currently available commercial engineered skin substitute therapies to the wound (Apligraf) and Dermagraft). Our work extends a previously developed model, which considers inflammatory and repair macrophage dynamics in normal and diabetic wound healing. Here, we extend the model to include equations for platelet-derived growth factor concentration, fibroblast density, collagen density, and hyaluronan concentration. This enables us to examine the variation of these components in both normal and diabetic wound healing cases, and to model the treatment protocols of these therapies. Within the context of our model, we find that the key component to successful healing in diabetic wounds is hyaluronan and that the therapies work by increasing the amount of hyaluronan available in the wound environment. The time-to-healing results correlate with those observed in clinical trials and the model goes some way to establishing an understanding of why diabetic wounds do not heal, and how these treatments affect the diabetic wound environment to promote wound closure.
Research on real-time display Algorithm of Cascading Screen for Automated Reserve Warehouse in EMU Depot (2010)

Taking real-time display algorithm of storage/retrieval operation and its guidance information for automated reserve warehouse as the research object,the relevant algorithms (information acquired and preliminary computation,information pretreatment algorithm and quasi-synchronous output algorithm,etc.) of the cascading screens were analyzed and designed in detail.Some problems such as information quasi-synchronous display among to the various screens and information reappearance when data message lost,were solved.Making the related operation of automated reserve warehouse in electric multiple unit depot possessed information real-time display and guidance function,meanwhile,ensuring rapid,high efficiency and ordered circulation for nondurable materials and recycle articles in automated reserve depot.
Innate Immune Receptors in the Regulation of Tumor Immunity (2017)

Innate immune receptors, also called pattern recognition receptors (PRRs), have gained much attention for their ability to evoke innate immune responses and regulate adaptive immunity. While the recent advent of immunotherapy for the treatment of cancer has primarily focused on harnessing the adaptive immune responses, signal-transducing innate receptors have come under extensive investigation in the context of regulating antitumor immune responses. Indeed, while these innate receptor classes are well known for the critical roles they play in the recognition of invading pathogens, a mounting body of evidence indicates that they also have the capacity to recognize ligands that are expressed by live or dead cancer cells. Although generally beneficial to the host’s innate responses against pathogens, these receptors appear to manifest either beneficial or harmful role in the host’s immune responses to cancers. Here, we summarize our current knowledge of the role of signal-transducing innate immune receptors in the regulation of cancer progression. We believe that a better understanding of these receptor functions may contribute to the development of effective strategies for cancer immunotherapies.
The Stanford Health Assessment Questionnaire: a review of its history, issues, progress, and documentation. (2003)

Over the last 2 decades, assessment of patient health status has undergone a dramatic paradigm shift, evolving from a predominant reliance on biochemical and physical measurements to an emphasis upon health outcomes based on the patient's personal appreciation of their illness. The Health Assessment Questionnaire (HAQ), published in 1980, was among the first instruments based on patient centered dimensions. The HAQ was designed to represent a model of patient oriented outcome assessment and has played a major role in diverse areas such as prediction of successful aging, inversion of the therapeutic pyramid in rheumatoid arthritis (RA), quantification of nonsteroidal antiinflammatory drug gastropathy, development of risk factor models for osteoarthrosis, and examination of mortality risks in RA. The HAQ has established itself as a valuable, effective, and sensitive tool for measurement of health status. It has increased the credibility and use of validated self-report measurement techniques as a quantifiable set of hard data endpoints and has contributed to a new appreciation of outcome assessment. We review the development, content, and dissemination of the HAQ and provide reference sources for its uses, translations, and validations. We discuss contemporary issues regarding outcome assessment instruments relative to the HAQ's identity and utility. These include: (1) the issue of labeling instruments as generic versus disease-specific; (2) floor and ceiling effects in scales such as "disability"; (3) distances between values on scales; and (4) the continuing introduction of new measurement instruments and their potential effects.
A role for G‐CSF and GM‐CSF in nonmyeloid cancers (2014)

Granulocyte colony-stimulating factor (G-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) modulate progression of certain solid tumors. The G-CSF- or GM-CSF-secreting cancers, albeit not very common are, however, among the most rapidly advancing ones due to a cytokine-mediated immune suppression and angiogenesis. Similarly, de novo angiogenesis and vasculogenesis may complicate adjuvant use of recombinant G-CSF or GM-CSF thus possibly contributing to a cancer relapse. Rapid diagnostic tools to differentiate G-CSF- or GM-CSF-secreting cancers are not well developed therefore hindering efforts to individualize treatments for these patients. Given an increasing utilization of adjuvant G-/GM-CSF in cancer therapy, we aimed to summarize recent studies exploring their roles in pathophysiology of solid tumors and to provide insights into some complexities of their therapeutic applications.
Nasal fluid release of eotaxin‐3 and eotaxin‐2 in persistent sinonasal eosinophilic inflammation (2014)

Our data suggest that CCL26 and CCL24 are likely involved in the pathogenesis of chronic nasal hypereosinophilia, with a complex cooperation and different involvement of the various members of eotaxin family. Further studies are necessary to better understand the actual physiopathologic mechanism, possible clinical relevance, and therapeutic implications.
Implantation of the Semicircular Canals With Preservation of Hearing and Rotational Sensitivity (2012)

It is possible to implant the vestibular system with prosthetic stimulating electrodes without loss of rotational sensitivity or hearing. Because electrically evoked eye movements can be reliably obtained with the assistance of intraoperative electrophysiology, it is appropriate to consider treatment of a variety of vestibular disorders using prosthetic electrical stimulation. Based on these findings, and others, a feasibility study for the treatment of human subjects with disabling Ménière's disease has begun.
Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies (2016)

Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence allowing sample origin to be determined after sequencing. The use of indexed primers assumes they behave no differently than standard primers; however, we found that indexed primers cause substantial template sequence-specific bias, resulting in radically different profiles of the same environmental sample. Likely the outcome of differential amplification efficiency due to primer-template mismatch, two indexed primer sets spuriously change the inferred sequence abundance from the same DNA extraction by up to 77.1%. We demonstrate that a double PCR approach alleviates these effects in applications where indexed primers are necessary.
Clopidogrel Resistance Is Associated With Increased Risk of Recurrent Atherothrombotic Events in Patients With Acute Myocardial Infarction (2004)

Up to 25% of STEMI patients undergoing primary PCI with stenting are resistant to clopidogrel and therefore may be at increased risk for recurrent cardiovascular events.
CMOS photonics for optical engines and interconnects (2012)

In this contribution the CMOS photonics technology (LuxG) developed and commercialized by Luxtera is reviewed. The advantages of integration and usage of a standard CMOS foundry toolset/process/practice are discussed with mention to a newly developed 14Gbps transceiver chip.
Hardware realization of inverse kinematics for robot manipulators (1994)

For real-time processing of kinematic information required for intelligent robotic applications, a hardware realization of an inverse kinematics algorithm is a challenging task. This paper adopts an incremental unit computation method to accomplish the inverse kinematics of a three-axis articulated robot. This method starts from defining incremental units in joint and Cartesian spaces, which represent the position resolutions in each space. With this approach, calculation of the inverse Jacobian matrix can be realized through a simple combinational logic gate circuit. Furthermore, the incremental direct kinematics can be solved by using a digital differential analyzer (DDA) integrator. The hardware architecture to implement the algorithm is also described. Applying the hardware implemented by an erasable programmable logic device (EPLD) to the straight-line trajectory of an experimental robot, the authors have obtained an end-effector's maximum speed of 12.6 m/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>