gebhart/patrepeval huggingface dataset:
Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase (2020)

β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition. X-ray crystallography validated the dimeric mechanism of inhibition, and compounds demonstrated high selectivity against related proteases, good target engagement, and tryptase inhibition in HMC1 xenograft models. Screening 3872 possible combinations from 44 boronic acid and 88 diol derivatives revealed several combinations that produced nanomolar inhibition, and seven unique pairs produced greater than 100-fold improvement in potency over monomeric inhibition. These heterodimeric tryptase inhibitors demonstrate the power of target-driven combinatorial chemistry to deliver bivalent drugs in a small molecule form.
Dispersion of nonlinear refraction and two-photon absorption using a white-light continuum Z-scan (2005)

We use a white-light continuum (WLC) Z-scan technique to measure the degenerate two-photon absorption spectrum and associated dispersion of the nonlinear refraction in ZnSe. The spectral components of the WLC source are separated by using a narrow band variable filter to minimize nondegenerate nonlinearities. We observe a change in sign of the ultrafast nonlinear refractive index around 0.7 of the bandgap energy as predicted by theory.
Professional disposition of wildland-urban interface recreation managers in Southern California: policy implications for the USDA Forest Service. (1991)

The professional disposition of USDA Forest Service recreation managers is reported from a study on the implementation of recreation policy on four southern California national forests. Inquiry focused on managers' education and training in recreation management, professional contacts related to recreation management, and relationships with visitors. Line and staff officers from recreation and other functions, and district-level agency and nonagency recreation personnel were interviewed or completed questionnaires. Managers were predominantly educated in resource, as opposed to social, management, indicating a lack of emphasis on people. Training occurred almost exclusively on the job, a concern in a setting requiring innovation and adaptation to diverse visitor needs. Visitor accommodation was supported, though public behavior was expected to change rather than the agency's. Recommendations to improve dispositions toward the recreation function include establishing a new federal recreation job classification, improving affiliation of agency personnel with professional organizations, and improving practices to increase understanding of forest visitors.
Editor's evaluation: Dorsal striatum coding for the timely execution of action sequences (2021)

In adolescent rats, whose actions are more impulsive, neuronal striatal activity that precedes self-initiated action sequences has a steeper modulation by waiting time compared to the modulation found in adults.
Protection from Toxicants (2007)

Exposures to skin irritants frequently occur in daily life at the workplace, in laboratories and during housekeeping. Apart from the physical protective countermeasures, there is a need for pharmacological preparations for the topical treatment of the exposed skin to prevent the development of burns. Exposure of the skin to a chemical irritant initiates an inflammatory response which progressively intensifies, leading to epidermal and dermal lesions. Topical treatment with povidone-iodine (PI) or iodine ointment significantly reduced skin damage induced by mustard gas (sulfur mustard), hydrofluoric acid and other chemical irritants. Human studies showed the efficacy of PI and iodine against thermal burns. The combination of anti-inflammatory agents and iodine increased the counterirritating activity. Both human and experimental animal studies demonstrated that the ointment should be immediately applied after occurrence: the earlier the treatment, the better the therapeutic effect. In addition, the ointment should be left on the skin long enough for achieving the therapeutic effect. This simple topical treatment can prevent suffering, skin transplantation and complications associated with skin burns.
Rodajes: cóltel de verano; en busca de taquilla (2011)

A fundamental problem in computer vision is face detection. In this paper, an experimentally derived ensemble made by a set of six face detectors is presented that maximizes the number of true positives while simultaneously reducing the number of false positives produced by the ensemble. False positives are removed using different filtering steps based primarily on the characteristics of the depth map related to the subwindows of the whole image that contain candidate faces. A new filtering approach based on processing the image with different wavelets is also proposed here. The experimental results show that the applied filtering steps used in our best ensemble reduce the number of false positives without decreasing the detection rate. This finding is validated on a combined dataset composed of four others for a total of 549 images, including 614 upright frontal faces acquired in unconstrained environments. The dataset provides both 2D and depth data. For further validation, the proposed ensemble is tested on the well-known BioID benchmark dataset, where it obtains a 100% detection rate with an acceptable number of false positives.
OCELOT: An infrastructure for data-driven research to discover and design crystalline organic semiconductors (2021)

Materials design and discovery are often hampered by the slow pace and materials and human costs associated with Edisonian trial-and-error screening approaches. Recent advances in computational power, theoretical methods, and data science techniques, however, are being manifest in a convergence of these tools to enable in silico materials discovery. Here, we present the development and deployment of computational materials data and data analytic approaches for crystalline organic semiconductors. The OCELOT (Organic Crystals in Electronic and Light-Oriented Technologies) infrastructure, consisting of a Python-based OCELOT application programming interface and OCELOT database, is designed to enable rapid materials exploration. The database contains a descriptor-based schema for high-throughput calculations that have been implemented on more than 56 000 experimental crystal structures derived from 47 000 distinct molecular structures. OCELOT is open-access and accessible via a web-user interface at https://oscar.as.uky.edu.
ARTIC3D: Learning Robust Articulated 3D Shapes from Noisy Web Image Collections (2023)

Estimating 3D articulated shapes like animal bodies from monocular images is inherently challenging due to the ambiguities of camera viewpoint, pose, texture, lighting, etc. We propose ARTIC3D, a self-supervised framework to reconstruct per-instance 3D shapes from a sparse image collection in-the-wild. Specifically, ARTIC3D is built upon a skeleton-based surface representation and is further guided by 2D diffusion priors from Stable Diffusion. First, we enhance the input images with occlusions/truncation via 2D diffusion to obtain cleaner mask estimates and semantic features. Second, we perform diffusion-guided 3D optimization to estimate shape and texture that are of high-fidelity and faithful to input images. We also propose a novel technique to calculate more stable image-level gradients via diffusion models compared to existing alternatives. Finally, we produce realistic animations by fine-tuning the rendered shape and texture under rigid part transformations. Extensive evaluations on multiple existing datasets as well as newly introduced noisy web image collections with occlusions and truncation demonstrate that ARTIC3D outputs are more robust to noisy images, higher quality in terms of shape and texture details, and more realistic when animated. Project page: https://chhankyao.github.io/artic3d/
Modifications of Epitaxial Graphene on SiC for the Electrochemical Detection and Identification of Heavy Metal Salts in Seawater (2022)

The electrochemical detection of heavy metal ions is reported using an inexpensive portable in-house built potentiostat and epitaxial graphene. Monolayer, hydrogen-intercalated quasi-freestanding bilayer, and multilayer epitaxial graphene were each tested as working electrodes before and after modification with an oxygen plasma etch to introduce oxygen chemical groups to the surface. The graphene samples were characterized using X-ray photoelectron spectroscopy, atomic force microscopy, Raman spectroscopy, and van der Pauw Hall measurements. Dose-response curves in seawater were evaluated with added trace levels of four heavy metal salts (CdCl<sub>2</sub>, CuSO<sub>4</sub>, HgCl<sub>2</sub>, and PbCl<sub>2</sub>), along with detection algorithms based on machine learning and library development for each form of graphene and its oxygen plasma modification. Oxygen plasma-modified, hydrogen-intercalated quasi-freestanding bilayer epitaxial graphene was found to perform best for correctly identifying heavy metals in seawater.
Evaluating Feature Selection Methods for Short-Term Load Forecasting (2019)

Identifying an appropriate set of predictors is important for making efficient and accurate forecasting models. In this paper, we study the application of some feature selection methods for prediction of household energy consumption. This study follows a two-stage framework. First, it identifies candidate features based on literature study and data characteristics of a load profile and then it selects a subset of relevant features using four different feature selection methods; F-regression, Mutual Information, Recursive Feature Elimination and Elastic Net. We evaluate the effectiveness of these methods, in conjunction with an ensemble-based prediction algorithm (Gradient Boosted Regression Tree), using smart meter data of 23 houses in Norway. To study the performance of these methods for different load profiles, we grouped households into clusters of similar consumption behaviour and computed average performance of each mechanism over clusters' members. Test results show that all feature selection methods could identify a custom-made subset of highly relevant features for each household. Across all clusters, building predictive models utilizing feature selection techniques led to considerable improvements in training speed and simplicity, as well as comparable prediction accuracy with models without feature engineering.
Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation (2016)

The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavorable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here, we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
Models for photochemical electron transfer at fixed distances. Porphyrin-bicyclo[2.2.2]octane-quinone and porphyrin-bisbicyclo[2.2.2]octane-quinone (1984)

We report the syntheses of three rigidly linked side-by-side porphyrinquinone molecules 2-4 whose edge-to-edge distances are fixed at 6, 10, and 14 Å (Figure 1). The spacer units bicyclo[2.2.2]octane and bibicyclo[2.2.2]octane prevent translational&#13;\ndisplacement and only allow rotational freedom. Our preliminary studies of the fluorescence yields of both the free base PLQ 2a-4a and Zn PLQ 2b-4b systems, relative to 1, a similar porphyrin not equipped with a quinone, reveal a distance dependence. This suggests that 2-4 will be useful systems for studying the incremental effect of distance on photochemical electron transfer from excited-state porphyrins to quinones.
Balancing Properties with Carboxylates: A Lead Optimization Campaign for Selective and Orally Active CDK9 Inhibitors (2021)

Cyclin-dependent kinase 9 (CDK9) is a serine/threonine kinase involved in the regulation of transcription elongation. An inhibition of CDK9 downregulates a number of short-lived proteins responsible for tumor maintenance and survival, including the antiapoptotic BCL-2 family member MCL-1. As pan-CDK inhibitors under development have faced dosing and toxicity challenges in the clinical setting, we generated selective CDK9 inhibitors that could be amenable to an oral administration. Here, we report the lead optimization of a series of azaindole-based inhibitors. To overcome early challenges with promiscuity and cardiovascular toxicity, carboxylates were introduced into the pharmacophore en route to compounds such as <b>14</b> and <b>16</b>. These CDK9 inhibitors demonstrated a reduced toxicity, adequate pharmacokinetic properties, and a robust in vivo efficacy in mice upon oral dosing.
Supplementary Table S2 from Predictive Biomarkers of Sensitivity to the Phosphatidylinositol 3′ Kinase Inhibitor GDC-0941 in Breast Cancer Preclinical Models (2023)

Supplementary Table S2 from Predictive Biomarkers of Sensitivity to the Phosphatidylinositol 3′ Kinase Inhibitor GDC-0941 in Breast Cancer Preclinical Models
Operation of Saturable-Absorber-Based Autotracking Filter for a Stabilized Single-Frequency Erbium Fiber Laser (2005)

A fiber ring laser with the wavelength tunability and single-longitudinal-mode oscillation based on a C-band erbium-doped waveguide amplifier is proposed and demonstrated. A saturable-absorber-based autotracking filter, consisting of an unpumped erbium-doped fiber and an optical reflector, is utilized to provide fine mode restriction and guarantee the single-frequency operation.
Non-directed aromatic C–H amination: catalytic and mechanistic studies enabled by Pd catalyst and reagent design (2016)

This manuscript describes the systematic development of pyridine-type ligands, which promote the Pd catalyzed, non-directed amination of benzene in combination with novel, hydroxylamine-based electrophilic amination reagents. DFT calculations and mechanistic experiments provide insights into the factors influencing the arene C-H amination protocol.
Simultaneous Separation And Segmentation In Layered Music. (2016)

[TODO] Add abstract here.
Characterization of polycrystalline silicon wafers for solar cells sliced with novel fixed‐abrasive wire (2010)

Abstract For slicing crystalline silicon ingots, we have developed a novel fixed‐abrasive wire where diamond grit is fixed onto a bare wire by resin bonding. The properties of the wafers sliced using a multi‐wire saw with the fixed‐abrasive wire have been investigated. When compared with the wafers sliced with the loose‐abrasive wire, the slicing speed is improved by approximately 2.5‐fold and the thicknesses of saw‐damage layers are reduced by more than a factor of two. Polycrystalline silicon solar cells have been fabricated for the first time utilizing the wafers sliced with the fixed‐abrasive wire, and the cells with the saw‐damage etching depth of 7 µm have shown photovoltaic properties comparable to those prepared using the wafers sliced with the loose‐abrasive wire and subsequently etched to remove the damage layers up to 15 µm. It has been clarified that wafer slicing using the fixed‐abrasive wire is promising as a next‐generation slicing technique for fabrication of solar cells, particularly thin silicon cells where the wafer thicknesses approach or become less than 150 µm. Copyright © 2010 John Wiley &amp; Sons, Ltd.
SAFETY EVALUATION OF 3M LIGHTED GUIDANCE TUBES (1994)

The Lighted Guidance Tube (LGT) is a delineation device used to reduce the frequency of vehicles impacting wide hazard crash cushions and longitudinal barrier systems. Prototype installations of the LGT have indicated that the device is very effective at reducing accident frequencies. This research project provides a preliminary evaluation of the safety performance of the LGT system for both wide hazard crash cushions and longitudinal barriers. The static tests on the longitudinal LGT system indicate that, due to the low load required to deflect the tube, it is possible for it to project into the windshields of oncoming traffic. Preliminary testing and evaluation of the LGT crash cushion system indicates that supporting the front sign with two structural tubes will greatly improve the safety of the system.
Towards a High Performance Fiber Laser Hydrophone (2011)

The operating principle and theory of a fiber laser bender hydrophone is presented. We report experimental results for a micro-engineered silicon fiber laser hydrophone. The hydrophone has a flat pressure responsivity of 107 dB re Hz/Pa over a bandwidth exceeding 5 kHz, corresponding to ocean noise limited acoustic sensitivity. The first structural resonance of the hydrophone is 9 kHz in water and the acceleration rejection is in excess of 0 dB re ms <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{{-}2}$</tex></formula> /Pa up to 5 kHz.
Gene Therapy Studies in a Canine Model of X-Linked Severe Combined Immunodeficiency (2015)

Since the occurrence of T cell leukemias in the original human γ-retroviral gene therapy trials for X-linked severe combined immunodeficiency (XSCID), considerable effort has been devoted to developing safer vectors. This review summarizes gene therapy studies performed in a canine model of XSCID to evaluate the efficacy of γ-retroviral, lentiviral, and foamy viral vectors for treating XSCID and a novel method of vector delivery. These studies demonstrate that durable T cell reconstitution and thymopoiesis with no evidence of any serious adverse events and, in contrast to the human XSCID patients, sustained marking in myeloid cells and B cells with reconstitution of normal humoral immune function can be achieved for up to 5 years without any pretreatment conditioning. The presence of sustained levels of gene-marked T cells, B cells, and more importantly myeloid cells for almost 5 years is highly suggestive of transduction of either multipotent hematopoietic stem cells or very primitive committed progenitors.
Development of sulfanegen for mass cyanide casualties (2016)

Cyanide is a metabolic poison that inhibits the utilization of oxygen to form ATP. The consequences of acute cyanide exposure are severe; exposure results in loss of consciousness, cardiac and respiratory failure, hypoxic brain injury, and dose-dependent death within minutes to hours. In a mass-casualty scenario, such as an industrial accident or terrorist attack, currently available cyanide antidotes would leave many victims untreated in the short time available for successful administration of a medical countermeasure. This restricted therapeutic window reflects the rate-limiting step of intravenous administration, which requires both time and trained medical personnel. Therefore, there is a need for rapidly acting antidotes that can be quickly administered to large numbers of people. To meet this need, our laboratory is developing sulfanegen, a potential antidote for cyanide poisoning with a novel mechanism based on 3-mercaptopyruvate sulfurtransferase (3-MST) for the detoxification of cyanide. Additionally, sulfanegen can be rapidly administered by intramuscular injection and has shown efficacy in many species of animal models. This article summarizes the journey from concept to clinical leads for this promising cyanide antidote.
The Radial Pulse Wave And Blood Viscosity (2009)

The aim of this study was to investigate the effect of blood viscosity on the radial pulse wave. For this, we obtained the radial pulse wave of 15 males with abnormal high hematocrit level and 47 males with normal hematocrit level at the age of thirties and forties. Various variables of the radial pulse wave between two groups were analyzed and compared by Student's T test. There are significant differences in several variables about height, time and area of the pulse wave. The first peak of the radial pulse wave was higher in abnormal high hematocrit group, but the third peak was higher and longer in normal hematocrit group. Our results suggest that the radial pulse wave can be used for diagnosis of high blood viscosity and more clinical application.
Automatically estimating noise-induced signal variance in magnitude reconstructed MRI using kernel estimator (2005)

2 2 σ = σnoise . Note that the value of M for which p(M) in (2) is maximum is equal to σ . This finding can be easily checked by differentiating (2) with respect to M, setting the result equal to zero, and solving for M (4). This information can be used to extract the standard deviation of the intensity σ in the images by simply identifying the peak of the noise distribution. We use the kernel or the Parzen density estimator (5) for this purpose, the most popular technique for nonparametric density estimation. The choice of basis function is not very important so long as it is smooth and bell-shaped (5). We chose the Gaussian kernel because it is easy to manipulate and derive. The kernel size or window width is very important and sometimes is adapted to the application. There is a trade-off between too much variability on one hand (if the window width is too small) and increased bias on the other (if it is too large). The window width can be computed by minimizing the mean square error between the true and estimated density. In our simulation, we set the window width equal 1.06*(sample standard deviation)*n -1/5 where n is the sample size as suggested in (5). We created synthetic images containing different size objects and added Gaussian distributed noise in quadrature to simulate images with different S/N. Our objective is to test the accuracy of the proposed method. RESULTS Figure 1 shows the simulation result on the amount of background required for the proposed method to properly estimate the peak of the noise distribution. If the error of the estimated standard deviation is set within 10%, 65% of the background in an image is required when S/N =3, 22% is required when S/N=4, and only a small amount of background is needed when S/N 5. In general, more background would provide a better result. If the background is less than required, for example, less than 60% when S/N=3, the estimated standard deviation is somewhat over-estimated. This is understandable because the noise distribution is contaminated by the signal and the mixture of noise and object will always cause the estimated peak to be shift to the right. We use echo-planar diffusion weighted images as a test application. We carefully chose 30 regions manually from the background and compute the average of variance from those regions. Our preliminary result shows that the estimated variance using the Parzen window approach has similar results when compared with this conventional estimation (has the error rate within 10% in our testing data sets). Simulations with artifacts will be conducted to further verify our preliminary findings. CONCLUSION An automatic method for estimating the variance in magnitude reconstructed MRI is presented. This method needs only one image, does not require any user interaction as no background pixels need to be selected, and does not require prior brain segmentation. The result is promising when compared with the conventional manual object-free background selection.