gebhart/patrepeval huggingface dataset:
Fragment‐based quantitative structure–activity relationship (FB‐QSAR) for fragment‐based drug design (2008)

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus.
Human Embryonic Gastric Xenografts in Nude Mice: a New Model of <i>Helicobacter pylori</i> Infection (1999)

In vitro or animal models have been used to investigate the pathogenesis of Helicobacter pylori infection. However, extrapolation to humans of results obtained with these heterologous models remains difficult. We have developed a new model for the study of H. pylori infection that uses human entire embryonic stomachs engrafted in nude mice. At 80 days after implantation, 22 of these xenografts, which exhibited a mature gastric epithelium, were inoculated with 10(7) to 10(8) CFU of either H. pylori LB1, a freshly isolated H. pylori strain (n = 12), or H. pylori ATCC 49503 (n = 10). After 12-week examination, H. pylori LB1 persistently colonized the antrum of all inoculated grafts, as assessed by culture (mucus and mucosa), immunohistochemistry (mucosa), and a rapid urease test (mucus). H. pylori ATCC 49503, either before or after in vivo passage, permitted only a transient 2-week colonization in one of the five inoculated grafts in both groups. Colonization was always associated with an increase of gastric juice pH. A mild neutrophil infiltration of the gastric mucosa was noted solely in infected grafts. Transmission electron microscopy showed adherence of H. pylori organisms to epithelial cell surface. In six animals, intracytoplasmic location of this bacterium was observed in the antrum or the fundus. These results allow us to propose this model as a new ex vivo model for the study of specific H. pylori-gastric cell interactions.
Transient receptor potential (TRP) channels as drug targets for diseases of the digestive system (2011)

Approximately 20 of the 30 mammalian transient receptor potential (TRP) channel subunits are expressed by specific neurons and cells within the alimentary canal. They subserve important roles in taste, chemesthesis, mechanosensation, pain and hyperalgesia and contribute to the regulation of gastrointestinal motility, absorptive and secretory processes, blood flow, and mucosal homeostasis. In a cellular perspective, TRP channels operate either as primary detectors of chemical and physical stimuli, as secondary transducers of ionotropic or metabotropic receptors, or as ion transport channels. The polymodal sensory function of TRPA1, TRPM5, TRPM8, TRPP2, TRPV1, TRPV3 and TRPV4 enables the digestive system to survey its physical and chemical environment, which is relevant to all processes of digestion. TRPV5 and TRPV6 as well as TRPM6 and TRPM7 contribute to the absorption of Ca²⁺ and Mg²⁺, respectively. TRPM7 participates in intestinal pacemaker activity, and TRPC4 transduces muscarinic acetylcholine receptor activation to smooth muscle contraction. Changes in TRP channel expression or function are associated with a variety of diseases/disorders of the digestive system, notably gastro-esophageal reflux disease, inflammatory bowel disease, pain and hyperalgesia in heartburn, functional dyspepsia and irritable bowel syndrome, cholera, hypomagnesemia with secondary hypocalcemia, infantile hypertrophic pyloric stenosis, esophageal, gastrointestinal and pancreatic cancer, and polycystic liver disease. These implications identify TRP channels as promising drug targets for the management of a number of gastrointestinal pathologies. As a result, major efforts are put into the development of selective TRP channel agonists and antagonists and the assessment of their therapeutic potential.
Volatile Internet evidence extraction from Windows systems (2014)

Internet users are increasing day by day and hence browser related evidence provides crucial information regarding a cyber crime. The rate of possible cyber crimes are increased unimaginably with this high usage of popular social networking Web sites and online Internet services for banking, shopping etc. Thus the need for collecting Internet browsing related information through a Browser Forensics Analysis is inevitable in a cyber crime investigation. Browser Forensics can be done as part of offline forensics by analyzing browser related files containing cookies, cache and other history information available in the hard disk. But, these files usually stores limited information and its content varies based on user settings. On the other hand, when a live forensics approach is adopted, the prime source of forensically relevant information is physical memory. So, in an Internet related cyber crime, the chance of getting crucial information by analyzing physical memory content collected from the Suspect's machine is very high. This paper presents a methodology for extracting user credentials of popular Web applications by analyzing a Windows system's physical memory content. It helps cyber crime investigators to retrieve usernames and associated passwords used in various Web based mail accounts, online banking and shopping sites etc. Another important methodology the paper presents is for the retrieval of high profile browser forensics information related to the suspect's Internet activity by memory dump analysis.
A Development Platform to Evaluate UAV Runtime Verification Through Hardware-in-the-loop Simulation (2020)

The popularity and demand for safe autonomous vehicles are on the rise. Advances in semiconductor technology have led to the integration of a wide range of sensors with high-performance computers, all onboard the autonomous vehicles. The complexity of the software controlling the vehicles has also seen steady growth in recent years. Verifying the control software using traditional verification techniques is difficult and thus increases their safety concerns. Runtime verification is an efficient technique to ensure the autonomous vehicle's actions are limited to a set of acceptable behaviors that are deemed safe. The acceptable behaviors are formally described in linear temporal logic (LTL) specifications. The sensor data is actively monitored to verify its adherence to the LTL specifications using monitors. Corrective action is taken if a violation of a specification is found. An unmanned aerial vehicle (UAV) development platform is proposed for the validation of monitors on configurable hardware. A high-fidelity simulator is used to emulate the UAV and the virtual environment, thereby eliminating the need for a real UAV. The platform interfaces the emulated UAV with monitors implemented on configurable hardware and autopilot software running on a flight controller. The proposed platform allows the implementation of monitors in an isolated and scalable manner. Scenarios violating the LTL specifications can be generated in the simulator to validate the functioning of the monitors.
DART: Dependable VLSI test architecture and its implementation (2012)

Although many electronic safety-related systems require very high reliability, it is becoming harder and harder to achieve it because of delay-related failures, which are caused by decreased noise margin. This paper describes a technology named DART and its implementation. The DART repeatedly measures the maximum delay of a circuit and the amount of degradation in field, in consequence, confirms the marginality of the circuit. The system employing the DART will be informed the significant reduction of delay margin in advance of a failure and be able to repair it at an appropriate time. The DART also equips a technique to improve the test coverage using the rotating test and a technique to consider the test environment such as temperature or voltage using novel ring-oscillator-based monitors. The authors applied the proposed technology to an industrial design and confirmed its effectiveness and availability with reasonable resources.
Chemical Dynamics in Condensed Phases (2006)

This text provides a uniform and consistent approach to diversified problems encountered in the study of dynamical processes in condensed phase molecular systems. Given the broad interdisciplinary aspect of this subject, the book focuses on three themes: coverage of needed background material, in-depth introduction of methodologies, and analysis of several key applications. The uniform approach and common language used in all discussions help to develop general understanding and insight on condensed phases chemical dynamics. The applications discussed are among the most fundamental processes that underlie physical, chemical and biological phenomena in complex systems. The first part of the book starts with a general review of basic mathematical and physical methods (Chapter 1) and a few introductory chapters on quantum dynamics (Chapter 2), interaction of radiation and matter (Chapter 3) and basic properties of solids (chapter 4) and liquids (Chapter 5). In the second part the text embarks on a broad coverage of the main methodological approaches. The central role of classical and quantum time correlation functions is emphasized in Chapter 6. The presentation of dynamical phenomena in complex systems as stochastic processes is discussed in Chapters 7 and 8. The basic theory of quantum relaxation phenomena is developed in Chapter 9, and carried on in Chapter 10 which introduces the density operator, its quantum evolution in Liouville space, and the concept of reduced equation of motions. The methodological part concludes with a discussion of linear response theory in Chapter 11, and of the spin-boson model in chapter 12. The third part of the book applies the methodologies introduced earlier to several fundamental processes that underlie much of the dynamical behaviour of condensed phase molecular systems. Vibrational relaxation and vibrational energy transfer (Chapter 13), Barrier crossing and diffusion controlled reactions (Chapter 14), solvation dynamics (Chapter 15), electron transfer in bulk solvents (Chapter 16) and at electrodes/electrolyte and metal/molecule/metal junctions (Chapter 17), and several processes pertaining to molecular spectroscopy in condensed phases (Chapter 18) are the main subjects discussed in this part.
Monitoring neutron generator output in a mixed neutron-gamma field using a plastic scintillator (2007)

Quantitative neutron-induced gamma-ray spectroscopy employing neutron generators (NGs) entails monitoring them for possible fluctuations in their neutron output. We accomplished this using a plastic scintillator and recording a spectrum from which we selected a neutron region- of-interest (nROI) to discriminate between neutrons and the accompanying high-energy gamma-rays. We show that the selected nROI is insensitive to changes in the gamma-ray background, thus allowing satisfactory normalization of the gamma-ray spectra of an in-situ system for analyzing soil carbon.
Energy-efficient congestion detection and avoidance in sensor networks (2011)

Event-driven sensor networks operate under an idle or light load and then suddenly become active in response to a detected or monitored event. The transport of event impulses is likely to lead to varying degrees of congestion in the network depending on the distribution and rate of packet sources in the network. It is during these periods of event impulses that the likelihood of congestion is greatest and the information in transit of most importance to users. To address this challenge we propose an energy-efficient congestion control scheme for sensor networks called CODA (COngestion Detection and Avoidance) that comprises three mechanisms: (i) receiver-based congestion detection; (ii) open-loop hop-by-hop backpressure; and (iii) closed-loop multisource regulation. We present the detailed design, implementation, and evaluation of CODA using simulation and experimentation. We define three important performance metrics (i.e., energy tax, fidelity penalty, and power) to evaluate the impact of CODA on the performance of sensing applications. We discuss the performance benefits and practical engineering challenges of implementing CODA in an experimental sensor network testbed based on Berkeley motes using CSMA. Simulation results indicate that CODA significantly improves the performance of data dissemination applications such as directed diffusion by mitigating hotspots, and reducing the energy tax and fidelity penalty on sensing applications. We also demonstrate that CODA is capable of responding to a number of congestion scenarios that we believe will be prevalent as the deployment of these networks accelerates.
High-k MOSFET performance degradation by plasma process-induced charging damage &#x2014; Impacts on device parameter variation (2012)

We discuss plasma charging damage (PCD) to high-k gate dielectrics, in particular, the threshold voltage shift (ΔV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) in metal-oxide-semiconductor field-effect transistors (MOSFETs). The PCD induced by the antenna effect is focused on, and ΔV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> and its variation are estimated for MOSFETs treated by various plasma processes. The direction of threshold voltage shift in damaged high-k MOSFETs was found to depend on the amount of damage, i.e., the polarity itself results in "negative" or "positive" as the charging damage varies. We demonstrate a model prediction based on both the power-law dependence of ΔV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> on the antenna ratio r (= exposed metal interconnect area/gate area) and the r distribution deduced from an interconnect-length distribution function (ILDF) in a large-scale integrated (LSI) circuit. Then, we simulate the variation in ΔV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> [σ(ΔV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> )]. PCD to high-k dielectrics may lead to a considerable contribution to MOSFET-parameter fluctuations.
Browning of Mozzarella Cheese During High Temperature Pizza Baking (1994)

Abstract The objective of this study was to evaluate various properties of low browning Mozzarella cheese. Low moisture, part skim type Mozzarella cheese was made using strains of Streptococcus spp. and Lactobacillus helveticus that release inappreciable amounts of galactose into the cheese curd and was compared with high browning cheese made using cultures that release galactose into the curd. Cheese composition differed only for galactose content. The browning potentials of the cheeses were significantly different. Pizzas were made using 125g of each cheese type and evaluated for appearance, texture, and flavor by a consumer panel. Panelists could distinguish between pizza samples based on color of the baked pizza, although no differences or preferences based on any of the other criteria were discernible. Both brown and low browned pizza were acceptable by the panelists, indicating that browning of Mozzarella cheese on pizza was not an undesirable property.
LiDAR Sensor modeling and Data augmentation with GANs for Autonomous driving (2019)

In the autonomous driving domain, data collection and annotation from real vehicles are expensive and sometimes unsafe. Simulators are often used for data augmentation, which requires realistic sensor models that are hard to formulate and model in closed forms. Instead, sensors models can be learned from real data. The main challenge is the absence of paired data set, which makes traditional supervised learning techniques not suitable. In this work, we formulate the problem as image translation from unpaired data and employ CycleGANs to solve the sensor modeling problem for LiDAR, to produce realistic LiDAR from simulated LiDAR (sim2real). Further, we generate high-resolution, realistic LiDAR from lower resolution one (real2real). The LiDAR 3D point cloud is processed in Bird-eye View and Polar 2D representations. The experimental results show a high potential of the proposed approach.
Novel phosphoric acid-doped PBI-blends as membranes for high-temperature PEM fuel cells (2015)

We present novel acid–base blend membranes with improved chemical stability and competitive fuel cell performance compared to conventional PBI membranes.
A conserved region in .alpha.-macroglobulins participates in binding to the mammalian .alpha.-macroglobulin receptor (1989)

Efforts to characterize the receptor recognition domain of alpha-macroglobulins have primarily focused on human alpha 2-macroglobulin (alpha 2M). In the present work, the structure and function of the alpha-macroglobulin receptor recognition site were investigated by amino acid sequence analysis, plasma clearance, and cell binding studies using several nonhuman alpha-macroglobulins: bovine alpha 2M, rat alpha 1-macroglobulin (alpha 1M), rat alpha 1-inhibitor 3 (alpha 1I3), and proteolytic fragments derived from these proteins. Each alpha-macroglobulin bound to the murine peritoneal macrophage alpha-macroglobulin receptor with comparable affinity (Kd approximately 1 nM). A carboxyl-terminal 20-kDa fragment was isolated from each of these proteins, and this fragment bound to alpha-macroglobulin receptors with Kd values ranging from 10 to 125 nM. The amino acid identity between the homologous carboxyl-terminal 20-kDa fragments of human and bovine alpha 2M was approximately 90%, while the overall sequence homology between all carboxyl-terminal fragments studied was 75%. The interchain disulfide bond present in the human alpha 2M carboxyl-terminal 20-kDa fragment was conserved in bovine alpha 2M and rat alpha 1I3, but not in rat alpha 1M. The clearance of each intact alpha-macroglobulin-proteinase complex was significantly retarded following treatment with cis-dichlorodiammineplatinum(II) (cis-DDP). cis-DDP treatment, however, did not affect receptor recognition of purified carboxyl-terminal 20-kDa fragments of these alpha-macroglobulins. A carboxyl-terminal 40-kDa subunit, which can be isolated from rat alpha 1M, bound to the murine alpha-macroglobulin receptor with a Kd of 5 nM.(ABSTRACT TRUNCATED AT 250 WORDS)
Potentiation of magnesium-deficiency-induced foetotoxicity by concomitant iron deficiency and its prevention by adequate supply via drinking water. (1994)

Magnesium (Mg) and iron (Fe) deficiency frequently develop during pregnancy. Therefore these factors were studied alone (Mg-L, resp. Fe-L) or in combination (Mg-L/Fe-L) on 16 female and 8 male adult fertile Sprague-Dawley rats. The animals were offered a basal diet containing 30 per cent and 17 per cent of the rat's requirement for magnesium and iron, respectively, starting 21 days before mating (2:1) until 49 days after mating. Offspring were also kept on this regimen during a 3-week lactation period and 7 days post weaning. Drinking water was either enriched with 101 ppm Fe2+ (ferrous gluconate): Mg-L, or 365 ppm magnesium (magnesium-L-aspartate hydrochloride trihydrate, MAH): Fe-L, or with any: Mg-L/Fe-L or with both electrolytes: Controls. Fertility remained unaffected under these conditions. Clinically, Fe-L induced iron deficiency and growth retardation of offspring. Pronounced reproductive toxicity was elicited by Mg-L and was even potentiated by Mg-L/Fe-L. In the parental generation, too, adverse effects of Mg-L were aggravated by Mg-L/Fe-L despite the fact that no iron accumulation occurred. Bioavailability of iron was not impaired by magnesium as MAH. With respect to human pregnancy magnesium supplementation has higher priority over iron supplements. To improve tolerance and compliance both minerals are suggested to be taken simultaneously.
社会問題学習としての実践的態度形成 ―アメリカ中等後期カリキュラムユニット 『変化する世界の論争問題』を手がかりとして― (2014)

本研究は，実践的態度形成を目指した社会問題学習のあり方をアメリカ中等後期段階のカリキュラム『変化する世界の論争問題』を手掛かりとして明らかにすることを目的としている。社会問題学習はこれまでも様々な学習論が提案されており，その有効性が示されてきた。しかし，社会問題を扱った学習は，教師による価値注入・態度形成に陥る可能性がある。本研究では，社会問題学習に関するこの課題を克服し，学習者自身の実践的態度形成を促す社会問題学習のあり方を，米国の優れた社会科教材の分析を通して明らかにした。
Agricultural Research Priorities (1989)

The scientific community worldwide is slowly accepting the fact that the overall cost of R&D is now so enormous that economic factors cannot be ignored and that recipients of grants must accept a measure of accountability and assessment of their performance. This article reviews in general terms, but with special reference to agricultural research what criteria should be taken into account in taking decisions about funding.
The Determination of the Contents of Tanshinone II_A and Prediction of the Shelf-life of Danshen Injection (2010)

Objective:To establish a HPLC method for determination of the content of tanshinone ⅡA in Danshen injection and estimate the shelf-lifes of Danshen injection and Danshen injectable powder.Methods: Taking tanshinone ⅡA as target,the shelf-lifes of Danshen injection and its injectable powder were compared by classical isotermal method.Results:The content of tanshinone ⅡA was gradually decreased while temperature rising and time prolonging.The result showed the shelf-life of Danshen injection was only 0.43 years,while the period of validity of its powder for injection could be above two years.Conclusion: Preparing lyophilized powder could increase the compounds stability and extend its shelf-life.The result suggests the potential use of the lyophilized powder for improving the stability of tanshinone ⅡA.
Principles of cardiovascular magnetic resonance feature tracking and echocardiographic speckle tracking for informed clinical use (2016)

Tissue tracking technology of routinely acquired cardiovascular magnetic resonance (CMR) cine acquisitions has increased the apparent ease and availability of non-invasive assessments of myocardial deformation in clinical research and practice. Its widespread availability thanks to the fact that this technology can in principle be applied on images that are part of every CMR or echocardiographic protocol. However, the two modalities are based on very different methods of image acquisition and reconstruction, each with their respective strengths and limitations. The image tracking methods applied are not necessarily directly comparable between the modalities, or with those based on dedicated CMR acquisitions for strain measurement such as tagging or displacement encoding. Here we describe the principles underlying the image tracking methods for CMR and echocardiography, and the translation of the resulting tracking estimates into parameters suited to describe myocardial mechanics. Technical limitations are presented with the objective of suggesting potential solutions that may allow informed and appropriate use in clinical applications.