gebhart/patrepeval huggingface dataset:
Ion pairs and their role in modulating stability of cold‐ and warm‐active uracil DNA glycosylase (2007)

MD simulations and continuum electrostatics calculations have been used to study the observed differences in thermostability of cold- and warm-active uracil DNA glycosylase (UDG). The present study focuses on the role of ion pairs and how they affect the thermal stability of the two enzymes. Analysis of the MD generated structural ensembles show that cod UDG (cUDG) and human UDG (hUDG) have 11 and 12 ion pairs which are present in at least 30% of the conformations. The electrostatic contribution of the ion pairs, computed using continuum electrostatics, is slightly more favorable in cUDG at 298 K. This is primarily attributed to more optimized interactions between the ion pairs and nearby dipoles/charges in cUDG. More global salt bridges are found in hUDG and are more stabilizing when compared to cUDG, possibly playing a role in maintaining overall stability and reducing conformational entropy. Both enzymes contain one three-member ionic network, but the one found in hUDG is far more stabilizing. Our results also suggest that care should be taken when performing statistical analysis of crystal structures with respect to ion pairs, and that crystallization conditions must be carefully examined when performing such analysis.
Two-Stage Hand Gesture Recognition based on Hand Keypoints Localization (2022)

Hand gesture is an important component of non-verbal communication, and the appropriate categorization of the gestures is quintessential for fruitful communication. Hand gestures are used in many human-computer interfaces for their natural and simplistic contactless way of conveying instruction to the interface. However, the recognition of hand gestures is complicated by numerous factors. This paper addresses a few issues by proposing a two-stage recognition framework that uses a hand joint localization technique. Firstly, the proposed method predicts hand keypoints that localize the region of interest by encompassing the hand region through a bounding box. Subsequently, this region of interest is used in gesture recognizing. The proposed work uses only one input modality-RGB image and performs phenomenally despite background clutter and illumination variation.
ORIGINAL ARTICLE: The bone‐anchored hearing aid in the rehabilitation of single‐sided deafness: experience with 58 patients (2010)

Bone-anchored hearing aid rehabilitation for single-sided deafness is less successful than for other indications, reflected here by relatively low median Glasgow Benefit Inventory scores. There was also no significant difference between controls and bone-anchored hearing aid users in the Speech and Spatial Qualities of Hearing Questionnaire. Patients with a longer duration of deafness report greater subjective benefit than those more recently deafened, perhaps due to differing expectations.
A survey on level set methods for inverse problems and optimal design (2005)

The aim of this paper is to provide a survey on the recent development in level set methods in inverse problems and optimal design. We give introductions on the general features of such problems involving geometries and on the general framework of the level set method. In subsequent parts we discuss shape sensitivity analysis and its relation to level set methods, various approaches on constructing optimization algorithms based on the level set approach, and special tools needed for the application of level set based optimization methods to ill-posed problems. Furthermore, we provide a review on numerical methods important in this context, and give an overview of applications treated with level set methods. Finally, we provide a discussion of the most challenging and interesting open problems in this field, that might be of interest for scientists who plan to start future research in this field.
Optimizing Reaction Conditions of the NanoOrange® Protein Quantitation Method for Use with Microplate-based Automation (2001)

Because of the rapidly expanding need for higher sample throughput in drug discovery, automation of corresponding biochemical analyses is desirable. In particular, automation of protein quantitation is crucial since its results are used extensively. Recently, a single-reagent fluorescent protein quantitation method (NanoOrange®) with attractive performance attributes has become available. While it can potentially be automated with liquid handling workstations, several of this method's reaction parameters need to be optimized. We studied the time and a temperature dependence of the NanoOrange protein quantitation reaction in ninety-six well black microplates using either a temperature-regulated hot block or a microwave oven as heat sources. Fluorescence of the NanoOrange reaction was quantified with a multimode microplate spectral scanner. Time-dependent heating profiles of filled microplates placed on hot blocks at fixed temperatures (45, 55, 65, 75, and 95°C) revealed temperature differences of 4–7°C cooler for the outside wells compared to the inner wells, however the maximum well temperature did not exceed 65°C. Similar time-temperature studies of microwave-heated microplates revealed an equilibrium temperature of 45–49°C that was 10–16°C lower than microplates that were block heated. The bovine serum albumin (BSA): NanoOrange standard curves created using a hot block increased in slope from 45°C to 55°C, but then remained constant from 65 to 85°C. Fluorescence of the BSA: NanoOrange standard curve created using a microwave oven was about half the magnitude of the hot block-derived curves, possible reflecting a lower energy transfer rate of the microwave oven. We conclude that the NanoOrange protein quantitation method can be automated if a microplate-compatible hot block with a 65–85°C surface can heat the microplate for minimum of 15 min prior to quantifying the reaction's fluorescence.
ChemInform Abstract: Novel Catalytic Asymmetric Sulfoxidation in Water Using the Hypervalent Iodine Reagent Iodoxybenzene. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Deep learning based one-shot optically-sectioned structured illumination microscopy for surface measurement (2021)

Optically-sectioned structured illumination microscopy (OS-SIM) is broadly used for biological imaging and engineering surface measurement owing to its simple, low-cost, scanning-free experimental setup and excellent optical sectioning capability. However, the efficiency of current optically-sectioned methods in OS-SIM is yet limited for surface measurement because a set of wide-field images under uniform or structured illumination are needed to derive an optical section at each scanning height. In this paper, a deep-learning-based one-shot optically-sectioned method, called Deep-OS-SIM, is proposed to improve the efficiency of OS-SIM for surface measurement. Specifically, we develop a convolutional neural network (CNN) to learn the statistical invariance of optical sectioning across structured illumination images. By taking full advantage of the high entropy properties of structured illumination images to train the CNN, fast convergence and low training error are achieved in our method even for low-textured surfaces. The well-trained CNN is then applied to a plane mirror for testing, demonstrating the ability of the method to reconstruct high-quality optical sectioning from only one instead of two or three raw structured illumination frames. Further measurement experiments on a standard step and milled surface show that the proposed method has similar accuracy to OS-SIM techniques but with higher imaging speed.
Management of ovine vaginal prolapse (1998)

PREPARTUM vaginal prolapse raises major animal welfare and economic concerns, affecting up to 15 per cent of ewes in modern intensively managed lowland sheep flocks in the UK. While some control can be effected by culling ewes which have previously prolapsed, this policy does not address the immediate treatment and management needs of vaginal prolapse cases presented to the veterinary practitioner or (of much greater concern) those cases which receive no veterinary care. This article outlines an approach to the treatment and management of ewes with vaginal prolapse based upon the authors' practical experience, and reasons that the treatment of vaginal prolapse must be considered an act of veterinary surgery, not least for animal welfare reasons. Furthermore, complications associated with vaginal prolapse cannot be dealt with by the shepherd.
Minimal residual disease (2006)

A multitude of clinical and biologic factors have been associated with a variable response to treatment in patients with acute leukemia, but their predictive power is far from absolute, and their usefulness for guiding clinical decisions in individual patients is inherently limited. Rather than predicting treatment response, in vivo measurements of leukemia cytoreduction provide direct information on the effectiveness of treatment in each patient. This information should have great clinical utility, but estimates by conventional morphologic techniques have a relatively low sensitivity and accuracy: in most cases, leukemic cells can be detected in bone marrow with certainty only when they constitute 5% or more of the total cell population. These limitations are overcome by methods for detecting minimal (i.e. submicroscopic) residual disease (MRD), which can be 100 times more sensitive than morphology and allow a more objective assessement of treatment response. The definition of "remission" in patients with acute leukemia by these methods is becoming the standard at many cancer centers.
Fast diffusion kurtosis imaging in acute ischemic stroke shows mean kurtosis‐diffusivity mismatch (2022)

In this pilot study, we demonstrated the feasibility of incorporating a fast DKI sequence into a clinical MRI protocol. Acute infarcts were depicted on kurtosis maps, and MK lesion volumes were smaller than MD, in accordance with prior works. Future studies are needed to determine the role of DKI in acute stroke treatment selection and prognostication.
High fragmentation in platelet concentrates impacts the activation, procoagulant, and aggregatory capacity of platelets (2023)

Platelets are transfused to patients to prevent bleeding. Since both preparation and storage can impact the hemostatic functions of platelets, we studied platelet concentrates (PCs) with different initial composition in regard to platelet fragmentation and its impact on storage-induced changes in activation potential. Ten whole blood derived PCs were assessed over 7 storage days. Using flow cytometry, platelet (CD41+) subpopulations were characterized for activation potential using activation markers (PAC-1, P-selectin, and LAMP-1), phosphatidylserine (Annexin V), and mitochondrial integrity (DiIC<sub>1</sub>(5)). Aggregation response, coagulation, and soluble activation markers (cytokines and sGPVI) were also measured. Of the CD41+ events, the PCs contained a median of 82% normal-sized platelets, 10% small platelets, and 8% fragments. The small platelets exhibited procoagulant hallmarks (increased P-selectin and Annexin V and reduced DiIC<sub>1</sub>(5)). Normal-sized platelets responded to activation, whereas activation potential was decreased for small and abolished for fragments. Five PCs contained a high proportion of small platelets and fragments (median of 28% of CD41+ events), which was significantly higher than the other five PCs (median of 9%). A high proportion of small platelets and fragments was associated with procoagulant hallmarks and decreased activation potential, but, although diminished, they still retained some activation potential throughout 7 days storage.
Integrated assessment of methods for calculating harm caused by vehicles in transport of heavy cargoes (2018)

This article presents a comparative analysis of methods for calculating the harm caused by vehicles carrying large-tonnage cargo on roads of regional importance in the North-Western Federal District. An exponential distribution model was used for the analysis. It is revealed that the regions do not have a single methodology for calculating harm, which has brought inconvenience to carriers of large-sized and heavy cargoes. The developed methodology is considered that takes into account the load-carrying capacity and wear of road surfaces.
Finding frequent substructures in chemical compounds (1998)

The discovery of the relationships between chemical structure and biological function is central to biologi-cal science and medicine. In this paper we apply data mining to the problem of predicting chemical carcino-genicity. This toxicology application was launched at IJCAI’97 as a research challenge for artificial intelli-gence. Our approach to the problem is descriptive rather than based on classification; the goal being to find common substructures and properties in chemi-cal compounds, and in this way to contribute to sci-entific insight. This approach contrasts with previous machine learning research on this problem, which has mainly concentrated on predicting the toxicity of un-known chemicals. Our contribution to the field of data mining is the ability to discover useful frequent pat-terns that are beyond the complexity of association rules or their known variants. This is vital to the prob-lem, which requires the discovery of patterns that are out of the reach of simple transformations to frequent itemsets. We present a knowledge discovery method for structured data, where patterns reflect the one-to-many and many-to-many relationships of several ta-bles. Background knowledge, represented in a uniform manner in some of the tables, has an essential role here, unlike in most data mining settings for the discovery of frequent patterns.
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011)

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.
Phage Orf Family Recombinases: Conservation of Activities and Involvement of the Central Channel in DNA Binding (2014)

Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination.
Abstract B89: Expression of DNA damage repair enzymes determine the efficacy of a novel dUTPase inhibitor, TAS-114. (2013)

Abstract Background: Deoxyuridine 5'-triphosphate nucleotidehydrolase (dUTPase) is a pyrophosphatase, which selectively catalyzes FdUTP and dUTP hydrolysis, and tightly restricts 5-fluorouracil (5-FU) and uracil misincorporation into DNA. TAS-114 is a novel potent inhibitor of dUTPase, and is under clinical development as a fluoropyrimidine enhancer. TAS-114 potentiates the antitumor activity of fluoropyrimidines through increasing misincorporation of 5-FU and uracil into DNA, however, precise mechanisms of cytotoxicity after misincorporation of the aberrant base is unknown. Here, we report relationships between the DNA damage repair function and the efficacy of TAS-114 on the anticancer activity of fluoropyrimidine. Materials and Methods: The antitumor activities of 5-FU or 5-FU/TAS-114 were evaluated in 9 human tumor xenograft models. Intratumor dUTPase protein was measured by Western blotting, and phosphorylation of histone H2AX was detected by immunohistochemistry. Tissue concentrations of FdUMP and dUMP were measured by HPLC and a thymidylate synthase (TS) binding assay, respectively. Suppression of DNA damage repair proteins were performed by RNA interference technology in HeLa cells, and then, the cells were used to assess an antiproliferative activity of FdUrd/TAS-114. Results: Oral administration of TAS-114 inhibited dUTPase and synergistically increased antitumor activity of 5-FU in various human tumor xenograft models. The magnitude of dUTPase inhibition was estimated by the change of dUTPase enzymatic products (FdUMP and dUMP) and it appeared to correlate with dUTPase expression and synergistic effect. These data suggest that 5-FU and uracil misincorporation is a primary mechanism of TAS-114 efficacy. In addition, TAS-114 combination with 5-FU increased phosphorylation of histone H2AX, suggesting a TAS-114 activated DNA damage response pathway. Suppression of DNA damage repair proteins involved in base excision repair (BER) and homologous recombination repair (HR) revealed that these DNA repair pathways were important in TAS-114’s synergistic increase of 5-FU cytotoxicity. Conclusion: Expression levels of DNA damage repair proteins in BER and HR affect TAS-114 sensitivity. DNA repair response appears to be a determinant of TAS-114 efficacy as well as dUTPase expression. These factors will be measured inTAS-114/fluoropyrimidines combination clinical trial. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B89. Citation Format: Sayaka Tsukioka, Wakako Yano, Tatsushi Yokogawa, Takeshi Wakasa, Akio Fujioka, Keisuke Yamamura, Satoko Itoh, Masayoshi Fukuoka, Kenichi Matsuo, Kazuharu Noguchi, Teruhiro Utsugi. Expression of DNA damage repair enzymes determine the efficacy of a novel dUTPase inhibitor, TAS-114. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B89.
SSAGA (2017)

The emergence of GPGPU applications, bolstered by flexible GPU programming platforms, has created a tremendous challenge in maintaining high energy efficiency in modern GPUs. In this article, we demonstrate that customizing a Streaming Multiprocessor (SM) of a GPU at a lower frequency is significantly more energy efficient compared to employing DVFS on an SM designed for a high-frequency operation. Using a system-level CAD technique, we propose SSAGA—Streaming Multiprocessors Synthesized for Asymmetric GPGPU Applications —an energy-efficient GPU design paradigm. SSAGA creates architecturally identical SM cores, customized for different voltage-frequency domains. Our rigorous cross-layer methodology demonstrates an average of 20% improvement in energy efficiency over a spatially multitasking GPU across a range of GPGPU applications.
Inline Reaction Monitoring of Amine-Catalyzed Acetylation of Benzyl Alcohol Using a Microfluidic Stripline Nuclear Magnetic Resonance Setup (2019)

We present an in-depth study of the acetylation of benzyl alcohol in the presence of N, N-diisopropylethylamine (DIPEA) by nuclear magnetic resonance (NMR) monitoring of the reaction from 1.5 s to several minutes. We have adapted the NMR setup to be compatible to microreactor technology, scaling down the typical sample volume of commercial NMR probes (500 μL) to a microfluidic stripline setup with 150 nL detection volume. Inline spectra are obtained to monitor the kinetics and unravel the reaction mechanism of this industrially relevant reaction. The experiments are combined with conventional 2D NMR measurements to identify the reaction products. In addition, we replace DIPEA with triethylamine and pyridine to validate the reaction mechanism for different amine catalysts. In all three acetylation reactions, we find that the acetyl ammonium ion is a key intermediate. The formation of ketene is observed during the first minutes of the reaction when tertiary amines were present. The pyridine-catalyzed reaction proceeds via a different mechanism.
SIMOX with epitaxial silicon: point defects and positive charge (1991)

Electron paramagnetic resonance (EPR), capacitance-voltage (CV) and point contact transistor measurements are used to investigate the radiation response of the SIMOX substrate emphasizing the difference between those samples with and without an epitaxial Si layer. It is shown that the hydrogen present during epitaxial deposition is responsible for a tenfold increase in radiation induced defects. Furthermore, the measurements indicate that the density of positive charge and oxygen vacancy related defects (E' centers) typically associated with this charge are not correlated in the case of hydrogen treated buried oxides. A model for E' generation in epitaxial SIMOX will be developed based on the known influence of hydrogen and lack of positive charge creation. Results of etch back measurements are briefly addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Organizational Beliefs and Managerial Vision (2005)

Can managers have an impact on their firm that goes beyond their direct actions and decisions? This article shows that a manager with strong beliefs about the right course of action will attract, through sorting in the labor market, employees with similar beliefs. This alignment of beliefs gives direction to the firm and has important implications for incentives and coordination. The article then defines vision, in accordance with the management literature, as a strong belief about the right course of action, and shows that it may be optimal to hire managers with such strong beliefs. Vision will be most important when uncertainty is high and actions are difficult to contract on.