gebhart/patrepeval huggingface dataset:
Ligand interaction energies and molecular recognition by chloramphenicol acetyltransferase (1991)

The apparent binding energy for the interaction of the 3-hydroxyl group of chloramphenicol (CM) with the proposed general base (His-195) in chloramphenicol acetyltransferase (CAT) was determined by comparison of the dissociation constants of CM and 3-deoxyCM with CAT. The delta Gapp for this hydrogen bond to the N-3 of the imidazole ring is 1.5 kcal mol-1. Extending the use of modified ligands, in an approach which is complementary to that of site-directed mutagenesis, the binding affinity of each of a family of 3-halo-3-deoxychloramphenicol derivatives was observed to increase in the series F less than Cl less than Br less than I and is dominated by hydrophobic considerations. There is a linear free energy relationship between the dissociation constants for binding to CAT and an empirical hydrophobicity scale derived from reverse-phase HPLC retention times. The existence of such a relationship allows a true estimate of the total energetic contribution of interactions between the 3-hydroxyl group of CM and its contacts at the active site of CAT to be made on the basis of a regression analysis. The calculated value of delta Gbind (2.7 kcal mol-1) must include not only the hydrogen bond but also some favorable van der Waals interactions. The results demonstrate some of the advantages of an analysis of the energetics of ligand binding using modified ligands, in an approach that is formally analogous with and complementary to the use of site-directed mutations.(ABSTRACT TRUNCATED AT 250 WORDS)
Opioid receptors and endogenous opioids in diverse human and animal cancers. (1987)

Receptor binding studies demonstrated specific high-affinity, saturable binding of a number of opioid ligands to a wide variety of neural and nonneural human and animal tumors. Radioimmunoassays revealed the presence of beta-endorphin and methionine-enkephalin in these tumors. Both methionine- and leucine-enkephalin were detected in tumor tissue by immunocytochemistry, with immunoreactivity related to the cortical cytoplasm of tumor cells, but not to cell nuclei. Endogenous opioids and receptors were found in benign and malignant tumors representative of ectodermal, mesodermal, and endodermal origin. Receptors and endogenous opioid peptides were present in tumors from many different species, including those transplanted into nude mice. These results suggest that opioid receptors and endogenous opioids are fundamental features of human and animal cancers.
Bioequivalence of a New Sustained‐Release Formulation of Sodium Valproate, Valproate Modified‐Release Granules, Compared with Existing Sustained‐Release Formulations After Once‐ or Twice‐Daily Administration (2004)

Valproate MR granules, administered once/day or twice/day, may be an attractive alternative to existing SR formulations for patients who have difficulties with swallowing tablets or who favor granules over tablets.
Studies on Naphthyridines. II. Synthesis of 2, 7-Naphthyridine. (1958)

Reaction of 4-methylnicotinic acid with formaldehyde or acetaldehyde gave a lactone, which was led to the amide, and this was oxidized to 1-hydroxy-2, 7-naphthyridine. 2, 7-Naphthyridine and 3-methyl-2, 7-naphthyridine were synthesized from 1-hydroxy derivatives via 1-chloro and 1-hydrazino compounds.
Pathogen Reduction of Fresh Whole Blood for Military and Civilian Use (2010)

Abstract : Hemorrhage resulting from combat-related injuries is the most common cause of potentially preventable deaths in military operations. Evidence indicates that the use of fresh whole blood (FWB) during massive transfusion (10 units) is independently associated with improved survival. The use of warm FWB currently persists only in emergency life-threatening scenarios when tested, stored blood components are not available, such as combat casualties. Risks of non-leukoreduced FWB transfusions include the transmission of infectious agents due to prior exposures or exposures in theater, alloimmunization to donor antigens and the potential for microchimerism. These risks may be mitigated in large part by a process capable of pathogen reduction and leukocyte inactivation. Such a technique, Pathogen Reduction Technology (PRT), can increase the safety of FWB and provide both an adequate and safe blood supply in a combat environment. This presentation will review work in progress on the development of such a system to treat fresh whole blood, which is capable of reducing infectious pathogen loads of bacteria, viruses, and parasites and inactivating white blood cells. This process is based on the use of riboflavin (vitamin B2) and UV light and relies on a photochemical process capable of disrupting nucleic acid replication processes in pathogens and white cells. Pre-clinical evaluations of device performance include tests of blood component quality, as well as tests of WBC inactivation, of virus reduction, and of bacteria reduction. The device is currently in clinical evaluation in the United States under an FDA approved Investigational Device Exemption. Early results with this system from pre-clinical and clinical studies will be provided. This work is supported through grants provided by the US Department of Defense.
Vector sampling expansion (2002)

This work extends Papoulis' general sampling expansion to the vector case where N bandlimited signals are passed through a multi-input multi-output (MIMO) LTI system that generates M (M/spl ges/N) output signals. We find necessary and sufficient conditions for reconstructing the N input signals from the samples of the M output signals, all sampled at N/M the Nyquist rate. A surprising necessary condition is that M/N must be an integer. This condition is no longer necessary when each of the output signals can be sampled at a different rate.
Attitudes regarding vaccinations of STDs and other diseases (2000)

The purpose of this study was to examine, among 2 groups of individuals with different risk profiles, the similarity of their attitudes towards vaccines for sexually transmitted diseases (STDs) and non-STDs. Subjects were recruited from an undergraduate psychology class at an urban university (n=518) or were participants in genital herpes vaccine trials (n=87). The participants were asked to complete a questionnaire regarding their attitudes about vaccines for selected diseases. The results of this study revealed that, in general, both groups supported vaccination for most diseases. There were differences, however, between groups regarding 3 diseases: measles, genital warts, and chlamydia. The vaccine trial participants were more likely to accept vaccines for measles and the college students were more likely to accept vaccines for chlamydia and genital warts. The results of this study suggest that negative attitudes regarding vaccination to control STDs may not be a significant barrier to use.
Impact of Sr‐Incorporation on Cr Oxidation and Water Dissociation in La(1–x)SrxCrO3 (2018)

Abstract The oxidation and reduction of metal oxides and their interaction with the environment play a critical role in material stability and the ability to catalyze reactions. The local change in valence and formation of surface adsorbates affect the oxide electronic structure and chemical reactivity, yet are challenging to probe experimentally. In this paper a detailed study of the oxidation and reduction of Cr in the perovskite oxide family of La (1– x ) Sr x CrO 3 using ambient pressure X‐ray photoelectron spectroscopy is presented. The incorporation of Sr increases the propensity to oxidize at the surface, leading to the presence of Cr 4+ and Cr 6+ principally confined to the top unit cell when in equilibrium with O 2 gas. These acidic sites are readily reduced to Cr 3+ in equilibrium with H 2 O vapor, and the resultant amount of hydroxyls formed from the dissociation of H 2 O is directly proportional to the density of surface sites formerly oxidized. The quantification of the redox stability of La (1– x ) Sr x CrO 3 and the relationship between the extent of oxidation, reduction, and hydroxylation with Sr yield important insight into the surface functionality during electrochemical applications.
Metal ion-doped sol-gel film for emulating synaptic activity and short-term non-volatile memory (2019)

We propose a hybrid device substituting the software synapse in artificial neural networks with an individual hardware transistor unit. The unit merges a silicon nanowire semiconductor channel with a metal-ion doped sol-gel film as hybrid gate of the transistor. The film, amorphous and transparent, shows a memristive property due to ion redistribution under bias, emulating synaptic plasticity with pulsed gate stimulation.
Synthesis of Linear Arrays and Apertures (2002)

This chapter develops techniques for choosing the weighting of each sensor output in order to obtain a frequency-wavenumber response and beam pattern with desirable properties. The weighting process is also referred to as shading or tapering in the literature. This chapter restricts its attention to linear arrays.
Design recommendations to prevent global out-of-plane instability of rectangular reinforced concrete ductile walls (2021)

Observations of out-of-plane (OOP) instability in the 2010 Chile earthquake and in the 2011 Christchurch earthquake resulted in concerns about the current design provisions of structural walls. This mode of failure was previously observed in the experimental response of some wall specimens subjected to in-plane loading. Therefore, the postulations proposed for prediction of the limit states corresponding to OOP instability of rectangular walls are generally based on stability analysis under in-plane loading only. These approaches address stability of a cracked wall section when subjected to compression, thereby considering the level of residual strain developed in the reinforcement as the parameter that prevents timely crack closure of the wall section and induces stability failure. The New Zealand code requirements addressing the OOP instability of structural walls are based on the assumptions used in the literature and the analytical methods proposed for mathematical determination of the critical strain values. In this study, a parametric study is conducted using a numerical model capable of simulating OOP instability of rectangular walls to evaluate sensitivity of the OOP response of rectangular walls to variation of different parameters identified to be governing this failure mechanism. The effects of wall slenderness (unsupported height-to-thickness) ratio, longitudinal reinforcement ratio of the boundary regions and length on the OOP response of walls are evaluated. A clear trend was observed regarding the influence of these parameters on the initiation of OOP displacement, based on which simple equations are proposed for prediction of OOP instability in rectangular walls.
3P-209 Role of Asp252 in chloride transport by pharaonis halorhodopsin(Photobiology:Vision & Photoreception,The 47th Annual Meeting of the Biophysical Society of Japan) (2009)

Phetemtermediates of Ndtrenomonav pharaonts phoborhodopsm rLNealed bi iegollante Raman spectrogLepy "Iasashi Unno (1) Yusuke 1iteshi (]) YutdkdNakao {2} Jun Timogirn
Association between Exposure to HSV1 and Cognitive Functioning in a General Population of Adolescents. The TRAILS Study (2014)

Both presence and level of HSV1 antibodies are prospectively associated with reduced cognitive performance in a large cohort of adolescents.
Pathogenesis of non-alcoholic fatty liver disease (2009)

Non-alcoholic fatty liver disease (NAFLD) represents a spectrum of disease ranging from hepatocellular steatosis through steatohepatitis to fibrosis and irreversible cirrhosis. The prevalence of NAFLD has risen rapidly in parallel with the dramatic rise in obesity and diabetes,1,2 and is rapidly becoming the most common cause of liver disease in Western countries.3 Indeed, NAFLD is now recognized to be the aetiology in many cases previously labelled as cryptogenic cirrhosis.4

In Western populations, estimates of NAFLD prevalence vary between 20 and 30%,5,6 rising up to 90% in morbidly obese individuals.7 The more severe, and clinically significant form of NAFLD, non-alcoholic steatohepatitis (NASH) is less common, affecting an estimated 2–3% of the general population,8 and up to 37% of the morbidly obese.7 Of particular concern, and with significant implications for future disease burden, is the increasing prevalence of NAFLD in children and young adults. Studies have reported a 3% prevalence of NAFLD in the general paediatric population, rising to 53% in obese children.9,10 NAFLD has a strong association with type 2 diabetes, with steatosis present in 70% of type 2 diabetics screened with ultrasound,11 and thus it is now recognized to represent the hepatic manifestation of the metabolic syndrome.

NAFLD occurs in all ethnic groups although it appears to have a lower prevalence in African-Americans compared with Hispanic and European Americans. This difference remains even after controlling for obesity and insulin resistance (IR)5,12 and may be related to ethnic differences in lipid homeostasis.5

There are no laboratory, imaging or histological findings which can accurately distinguish between NAFLD and alcohol-induced steatosis or steatohepatitis, and the diagnosis can therefore only be made in the absence of a history of significant alcohol intake. Other specific causes … 

Address correspondence to J. K. Dowman, Centre for Liver Research, Institute of Biomedical Research, University of Birmingham, Wolfson Drive, B15 2TT, Birmingham, UK. email: j.k.dowman{at}bham.ac.uk
Design and Synthesis of trans-N-[4-[2-(6-Cyano-1,2,3,4-tetrahydroisoquinolin-2- yl)ethyl]cyclohexyl]-4-quinolinecarboxamide (SB-277011):  A Potent and Selective Dopamine D3 Receptor Antagonist with High Oral Bioavailability and CNS Penetration in the Rat (2000)

A selective dopamine D(3) receptor antagonist offers the potential for an effective antipsychotic therapy, free of the serious side effects of currently available drugs. Using clearance and brain penetration studies as a screen, a series of 1,2,3, 4-tetrahydroisoquinolines, exemplified by 13, was identified with high D(3) affinity and selectivity against the D(2) receptor. Following examination of molecular models, the flexible butyl linker present in 13 was replaced by a more conformationally constrained cyclohexylethyl linker, leading to compounds with improved oral bioavailability and selectivity over other receptors. Subsequent optimization of this new series to improve the cytochrome P450 inhibitory profile and CNS penetration gave trans-N-[4-[2-(6-cyano-1, 2,3, 4-tetrahydroisoquinolin-2-yl)ethyl]cyclohexyl]-4-quinolinecarbo xamide (24, SB-277011). This compound is a potent and selective dopamine D(3) receptor antagonist with high oral bioavailability and brain penetration in the rat and represents an excellent new chemical tool for the investigation of the role of the dopamine D(3) receptor in the CNS.
Can Systemic Anti-CD20 B Cell-Depleting Antibodies Eliminate Meningeal Follicles in Multiple Sclerosis? (2021)

2] However, the impact of anti-CD20 mAb therapy on preventing long-term disability in progressive forms of MS is modest. It has been postulated that this relative lack of efficacy is because of the inadequate penetration by anti-CD20 mAb across the blood-brain barrier (BBB) 5 into the CNS, where there is evidence of ongoing CNS B cell activation. Those CNS B cells reside in meningeal ectopic lymphoid follicles (mELT) and are associated with subpial inflammation in patients with MS, particularly in secondary progressive MS (SPMS), where they may contribute to progression and neurodegeneration. The effect of anti-CD20 mAb therapy on mELT remains unknown, and there continues to be several unanswered questions regarding its efficacy against the B cells within them.
Growth kinetics and inhibition of growth of chemical vapor deposited thin tungsten films on silicon from tungsten hexafluoride (1992)

The growth kinetics and inhibition of growth of chemical vapor deposited thin W films on Si(100) from WF6 was studied with in situ growth stress and reflectivity measurements and ex situ weight gain measurements. A systematic series of experiments at varying WF6 flow, total pressure, and temperature show that the thickening kinetics and inhibition of the growth are controlled by two processes: WF6 diffusion through the gas phase and Si diffusion through the thickening columnar film. The steady state growth kinetics are controlled by WF6 diffusion in the gas phase whereas inhibition of the growth occurs at the transition from WF6 gas diffusion limited to Si solid state diffusion limited growth. A simple model based on WF6 gas phase diffusion and Si solid state diffusion is presented which gives a quantitative description of the experimental results.
Face Antispoofing Method Using Color Texture Segmentation on FPGA (2021)

User authentication for accurate biometric systems is becoming necessary in modern real-world applications. Authentication systems based on biometric identifiers such as faces and fingerprints are being applied in a variety of fields in preference over existing password input methods. Face imaging is the most widely used biometric identifier because the registration and authentication process is noncontact and concise. However, it is comparatively easy to acquire face images using SNS, etc., and there is a problem of forgery via photos and videos. To solve this problem, much research on face spoofing detection has been conducted. In this paper, we propose a method for face spoofing detection based on convolution neural networks using the color and texture information of face images. The color-texture information combined with luminance and color difference channels is analyzed using a local binary pattern descriptor. Color-texture information is analyzed using the Cb, S, and V bands in the color spaces. The CASIA-FASD dataset was used to verify the proposed scheme. The proposed scheme showed better performance than state-of-the-art methods developed in previous studies. Considering the AI FPGA board, the performance of existing methods was evaluated and compared with the method proposed herein. Based on these results, it was confirmed that the proposed method can be effectively implemented in edge environments.
INCENTIVES AND PERFORMANCE IN LARGE-SCALE LEAN SOFTWARE DEVELOPMENT - An Agent-based Simulation Approach (2011)

The application of lean principles and agile project management techniques in the domain of large-scale software product development has gained tremendous momentum over the last decade. However, a simple transfer of good practices from the automotive industry combined with experiences from agile development on a team level is not possible due to fundamental differences stemming from the particular domain specifics – i.e. different types of products and components (material versus immaterial goods), knowledge work versus production systems as well as established business models. Especially team empowerment and the absence of a a hierarchical control on all levels impacts goal orientation and business optimization. In such settings, the design of adequate incentive schemes in order to align local optimization and opportunistic behavior with the overall strategy of the company is a crucial activity of central importance. Following an agent-based simulation approach with reinforcement learning, we (i) address the question of how information regarding backlog item dependencies is shared within and in between development teams on the product level subject to different incentive schemes. We (ii) compare different incentive schemes ranging from individual to team-based compensation. Based on our results, we are (iii) able to provide recommendations on how to design such incentives, what their effect is, and how to chose an adequate development structure to foster overall software product development flow by means of more economic decisions and thus resulting in a shorter time to market. For calibrating our simulation, we rely on practical experience from a very large software company piloting and implementing lean and agile for about three years.
Real-time PCR quantification analysis of five mucosal transcripts in patients with Crohnʼs disease (2008)

The mucosal transcript pattern in Crohn's disease may, based on the known biological function of the transcripts, explain some of the typical features of Crohn's disease and indicate a possible pathophysiological role of microbes. Our results may thereby contribute to the understanding of the pathogenesis and manifestations of Crohn's disease.
Plasma omega-3 PUFA and white matter mediated executive decline in older adults (2013)

Executive decline with age appears to be a cognitive domain particularly sensitive to plasma O3PUFA in longitudinal examination. O3PUFA may modulate executive functioning by mechanisms underlying the development of WMH, a biologically plausible hypothesis that warrants further investigation.
Removal of inhomogeneous internal multiples (1994)

Removal of surface-related multiples and interral multiples can be considered as the first step in the inversion of seismic data. The removal of surface-related multiples can be formulated by means of Rayleigh&apos;s reciprocity theorem, which leads to an integral equation of the second kind for the reflected pressure wavefield (Fokkema and van den Berg, 1993). The method requires no a priori information about the subsurface geology, nor structural nor material. In this paper a method is proposed to remove interral multiples of the first layer. Application of Rayleigh&apos;s reciprocity theorem leads to two integral relations that must be satisfied simultaneously: the first requires consistency in the first layer, implemented as an integral equation, while the other requires consistency with the measured data in the form of an integral representation. The result of simultaneous manipulation of the two integral relations is that the homogeneous domain has been extended downwardly, removing the first layer. This process can be continued to deeper levels to remove internal multiples from deeper layers. The method presented requires a priori infomation on the material properties in the layer from which the internal multiples are to be removed.
Demystifying Multitask Deep Neural Networks for Quantitative Structure–Activity Relationships (2017)

Deep neural networks (DNNs) are complex computational models that have found great success in many artificial intelligence applications, such as computer vision1,2 and natural language processing.3,4 In the past four years, DNNs have also generated promising results for quantitative structure-activity relationship (QSAR) tasks.5,6 Previous work showed that DNNs can routinely make better predictions than traditional methods, such as random forests, on a diverse collection of QSAR data sets. It was also found that multitask DNN models-those trained on and predicting multiple QSAR properties simultaneously-outperform DNNs trained separately on the individual data sets in many, but not all, tasks. To date there has been no satisfactory explanation of why the QSAR of one task embedded in a multitask DNN can borrow information from other unrelated QSAR tasks. Thus, using multitask DNNs in a way that consistently provides a predictive advantage becomes a challenge. In this work, we explored why multitask DNNs make a difference in predictive performance. Our results show that during prediction a multitask DNN does borrow "signal" from molecules with similar structures in the training sets of the other tasks. However, whether this borrowing leads to better or worse predictive performance depends on whether the activities are correlated. On the basis of this, we have developed a strategy to use multitask DNNs that incorporate prior domain knowledge to select training sets with correlated activities, and we demonstrate its effectiveness on several examples.