gebhart/patrepeval huggingface dataset:
Novel Chemical Space Exploration via Natural Products (2009)

Natural products (NPs) are a rich source of novel compound classes and new drugs. In the present study we have used the chemical space navigation tool ChemGPS-NP to evaluate the chemical space occupancy by NPs and bioactive medicinal chemistry compounds from the database WOMBAT. The two sets differ notably in coverage of chemical space, and tangible leadlike NPs were found to cover regions of chemical space that lack representation in WOMBAT. Property based similarity calculations were performed to identify NP neighbors of approved drugs. Several of the NPs revealed by this method were confirmed to exhibit the same activity as their drug neighbors. The identification of leads from a NP starting point may prove a useful strategy for drug discovery in the search for novel leads with unique properties.
SiC Charge-Balanced Devices Offering Breakthrough Performance Surpassing the 1-D Ron versus BV Limit (2019)

This work presents experimental validation of novel device design, based on charge-balance concept expected to expand SiC utilization space for industrial and transportation power conversion applications. Fabricated 2kV and 3kV SiC CB-JBS diodes have surpassed the 1-D BV versus R On,sp tradeoff with the highest reported breakdown voltage. Static and dynamic characteristics of these new diodes are reported.
Shape from Mixed Polarization (2016)

Shape from Polarization (SfP) estimates surface normals using photos captured at different polarizer rotations. Fundamentally, the SfP model assumes that light is reflected either diffusely or specularly. However, this model is not valid for many real-world surfaces exhibiting a mixture of diffuse and specular properties. To address this challenge, previous methods have used a sequential solution: first, use an existing algorithm to separate the scene into diffuse and specular components, then apply the appropriate SfP model. In this paper, we propose a new method that jointly uses viewpoint and polarization data to holistically separate diffuse and specular components, recover refractive index, and ultimately recover 3D shape. By involving the physics of polarization in the separation process, we demonstrate competitive results with a benchmark method, while recovering additional information (e.g. refractive index).
In Vitro and In Vivo Studies To Characterize the Clearance Mechanism and Potential Cytochrome P450 Interactions of Anidulafungin (2008)

Anidulafungin is a novel semisynthetic echinocandin with potent activity against Candida (including azole-resistant isolates) and Aspergillus spp. and is used for serious systemic fungal infections. The purpose of these studies was to characterize the clearance mechanism and potential for drug interactions of anidulafungin. Experiments included in vitro degradation of anidulafungin in buffer and human plasma, a bioassay for antifungal activity, in vitro human cytochrome P450 inhibition studies, in vitro incubation with rat and human hepatocytes, and mass balance studies in rats and humans. Clearance of anidulafungin appeared to be primarily due to slow chemical degradation, with no evidence of hepatic-mediated metabolism (phase 1 or 2). Under physiological conditions, further degradation of the primary degradant appears to take place. The primary degradation product does not retain antifungal activity. Anidulafungin was not an inhibitor of cytochrome P450 enzymes commonly involved in drug metabolism. Mass balance studies showed that anidulafungin was eliminated in the feces predominantly as degradation products, with only a small fraction (10%) eliminated as unchanged drug; fecal elimination likely occurred via biliary excretion. Only negligible renal involvement in the drug's elimination was observed. In conclusion, the primary biotransformation of anidulafungin is mediated by slow chemical degradation, with no evidence for hepatic enzymatic metabolism or renal elimination.
Discovery of a Novel Dopamine Transporter Inhibitor, 4-Hydroxy-1-methyl-4-(4-methylphenyl)-3-piperidyl 4-Methylphenyl Ketone, as a Potential Cocaine Antagonist through 3D-Database Pharmacophore Searching. Molecular Modeling, Structure−Activity Relationships, and Behavioral Pharmacological Studies (2000)

A novel, fairly potent dopamine transporter (DAT) inhibitor, 4-hydroxy-1-methyl-4-(4-methylphenyl)-3-piperidyl 4-methylphenyl ketone (3, K(i) values of 492 and 360 nM in binding affinity and inhibition of dopamine reuptake, respectively), with significant functional antagonism against cocaine and a different in vitro pharmacological profile from cocaine at the three transporter sites (dopamine, serotonin, and norepinephrine) was discovered through 3D-database pharmacophore searching. Through structure-activity relationships and molecular modeling studies, we found that hydrophobicity and conformational preference are two additional important parameters that determine affinity at the DAT site. Chemical modifications of the lead compound (3) led to a high affinity analogue (6, K(i) values of 11 and 55 nM in binding affinity and inhibition of dopamine reuptake, respectively). In behavioral pharmacological testing, 6 mimics partially the effect of cocaine in increasing locomotor activity in mice but lacks cocaine-like discriminative stimulus effect in rats. Taken together, these data suggest that 6 represents a promising lead for further evaluations as potential therapy for the treatment of cocaine abuse.
ARTS: A Framework for AI-Rooted IoT System Design Automation (2022)

IoT systems are used for performing a variety of essential tasks in wide-ranging sectors, such as healthcare, smart cities, agriculture, and industrial automation. Most of these systems incorporate smartness for intelligent decision making using artificial intelligence (AI) approaches. To reduce the network bandwidth usage and load on the cloud server, there is a push to relegate most of these AI-related computations to edge IoT devices/systems. Hence, to ensure good performance, the edge devices must be systematically designed with an emphasis on the respective AI requirements from exploration to deployment. State-of-the-art IoT device and system design practices place little importance on the AI specifications during the early stages of the system development resulting in systems, which are unable to meet the AI specifications without additional redesigning and optimization efforts. In this letter, we propose an automated framework for AI-rooted IoT system design approach, where the AI specifications play a vital role in deciding the system components, design, and implementation from a very early stage of the design life cycle. The proposed framework employs an expert system and a machine-readable knowledge-base to automate the design process. Using a set of case studies, we demonstrate the benefits of the proposed framework.
Self-similarity in file systems (1998)

We demonstrate that high-level file system events exhibit self-similar behaviour, but only for short-term time scales of approximately under a day. We do so through the analysis of four sets of traces that span time scales of milliseconds through months, and that differ in the trace collection method, the filesystems being traced, and the chronological times of the tracing. Two sets of detailed, short-term file system trace data are analyzed; both are shown to have self-similar like behaviour, with consistent Hurst parameters (a measure of self-similarity) for all file system traffic as well as individual classes of file system events. Long-term file system trace data is then analyzed, and we discover that the traces' high variability and self-similar behaviour does not persist across time scales of days, weeks, and months. Using the short-term trace data, we show that sources of file system traffic exhibit ON/OFF source behaviour, which is characterized by highly variably lengthed bursts of activity, followed by similarly variably lengthed periods of inactivity. This ON/OFF behaviour is used to motivate a simple technique for synthesizing a stream of events that exhibit the same self-similar short-term behaviour as was observed in the file system traces.
Frontispiece: Rotaxanes Capped with Host Molecules: Supramolecular Behavior of Adamantylated Bisimidazolium Salts Containing a Biphenyl Centerpiece (2015)

Rotaxanes Bisimidazolium salts with one central biphenyl binding site and two terminal adamantyl binding sites form water-soluble binary or ternary aggregates with macrocyclic host molecules cucurbit[7]uril and β-cyclodextrin with rotaxane and pseudorotaxane architectures, as described by R. Vicha et al. in their Full Paper on page 11712 ff. The resultant arrangements are attributed to the binding strength of the supramolecular stopper and steric barriers against free slippage of the macrocyclic host molecules over the bisimidazolium guest axle.
Anion Recognition as a Supramolecular Switch of Cell Internalization (2016)

The cell internalization of designed oligoarginine peptides equipped with six glutamic acid residues and an anionic pyranine at the N-terminus is triggered upon addition of a supramolecular host. This host binds specifically to the pyranine moiety, enabling the complex to traverse the cell membrane. Interestingly, none of the components, neither the host nor the guest, are able to cross the cell membrane on their own.
Adaptive Channel Quantization on TDD Reciprocity Performance of Relative Antenna Calibration (2014)

This paper studies a relative antenna calibration scheme for time division duplex (TDD) systems, which relies on user equipment (UE) for the estimation of transceiver response via multiple forward and reverse link channel measurements. Since the downlink channel knowledge at the base station (BS) needs to be accurate, UE feeds the quantized channel coefficients back to BS. Once accurate channel estimation is available at BS within a calibration phase, the transceiver response can be approximated by total least squares method. We propose an adaptive quantization method for downlink channel state information, which selects the number of feedback bits based on the estimation quality of the instantaneous uplink channel. We also discuss two reference UE selection methods based on channel quality indication feedback and UE-BS channel signal-to-noise ratio measurement.
Monolithically Integrated Balanced Uni-Traveling-Carrier Photodiode with Tunable MMI Coupler for Microwave Photonic Circuits (2006)

A monolithically integrated balanced uni-traveling-carrier photodiode (UTC-PD) with a tunable 2times2 multimode interference (MMI) coupler has been fabricated and tested. Two waveguide UTC-PDs are electrically isolated using high-energy Helium implantation, and then connected in series using a monolithic metal interconnect. On chip metal-insulator-semiconductor (MIS) capacitors provide some DC decoupling. The tunable MMI coupler allows for tuning of the power balance in the PDs. Output saturation currents greater than 40 mA at 1 GHz are demonstrated for a single 10 mum times 150 mum UTC-PD. The third order intermodulation distortion (IMD3) is also measured and exhibits an output intercept point (OIP3) of 43 dBm at 20 mA and 34 dBm at 40 mA for this same UTC-PD. In the balanced configuration, the OIP3 values are therefore 49 dBm and 40 dBm. The balanced UTC-PD is also highly symmetric; the common mode rejection ratio (CMRR) was measured to be around 40 dB.
Amino Acid Sequence Analysis of Two Mouse Calbindin-D9k Isoforms by Tandem Mass Spectrometry (1989)

Two forms of calbindin-D9k have sometimes been observed within a single tissue. Sequencing of these proteins has been complicated by the presence of blocked amino termini. Tandem mass spectrometry is a powerful tool for comparing related proteins, and its use does not depend upon an unblocked amino terminus. In the present studies, calbindin-D9k was purified from the intestines of mice (270 animals per purification) by use of gel permeation chromatography and two preparative electrophoresis steps in the presence and absence of EDTA. The purified protein appeared to be homogeneous following electrophoresis under nondenaturing conditions, but two components were identified by sodium dodecyl sulfate-gel electrophoresis and immunoblotting. Two forms of the protein were isolated by reverse-phase high performance liquid chromatography. In each of three preparations, the average ratio of the major:minor isoforms was 2:1. The major form contained 77 amino acids and lacked the amino-terminal serine found in 78-amino acid calbindins from rat and pig. The amino acid sequence was identical with the deduced sequence reported for rat intestinal calbindin-D9k in 73 of 77 positions. In the minor form, a glutamine was found in a location between Lys-43 and Ala-44 of the major form and between the two calcium binding sites of the protein. The minor form was otherwise identical with the major form, including the presence of a blocked amino terminus. The inserted glutamine was located at the site of an intron in the rat calbindin gene, suggesting the possibility that alternative splicing produced the two forms of calbindin-D9k. The functional significance of an inserted amino acid between the two calcium binding sites remains to be explored.
Theoretical and experimental investigation of the nonlinear response of an electrically actuated imperfect microbeam (2012)

In this study a theoretical and experimental investigation of the nonlinear response of an electrically actuated microbeam is performed. A mechanical model is proposed, which accounts for two common imperfections of microbeams, due to microfabrications, which are the compliant support conditions and the initially deformed profile. A computationally efficient single-mode reduced-order model is derived by combining the Ritz technique and the Padé approximation. Numerical simulations of the harmonic response of the device near primary resonance are shown illustrating nonlinear phenomena arising in the device response. Experimental investigation is conducted on a polysilicon imperfect microbeam confirming the simulation results. The concurrence between the theoretical results and the experimental data reveals that this model, while simple, is capable of properly capturing the response both at low and, especially, at higher electrodynamic voltages.
Ethyl Pyruvate, a Potentially Effective Mitigator of Damage after Total-Body Irradiation (2007)

Ethyl pyruvate (EP), a simple aliphatic ester of pyruvic acid, has been shown to improve survival and ameliorate organ damage in animal models of sepsis, ischemia/reperfusion injury and hemorrhagic shock. Incubating IL3-dependent mouse hematopoietic progenitor cell 32Dcl3 cells before or after irradiation with 10 mM EP increased resistance to radiation as assessed by clonogenic radiation survival curves, decreased release of mitochondrial cytochrome C into the cytoplasm, and decreased apoptosis. EP inhibited radiation-induced caspase 3 activation and poly(ADP-ribose) polymerase (PARP) cleavage in 32Dcl3 cells in a concentration-dependent fashion. EP was given i.p. to C57BL/6NHsd mice irradiated with 9.75 Gy total-body irradiation (TBI). This treatment significantly improved survival. The survival benefit was apparent irrespective of whether treatment with EP was started 1 h before TBI and continued for 5 consecutive days after TBI or the compound was injected only 1 h before or only for 5 days after TBI. In all of the in vitro and in vivo experiments, ethyl lactate, an inactive analogue of EP, had no detectable radioprotective or mitigating effects. EP may be an effective radioprotector and mitigator of the hematopoietic syndrome induced by TBI.
KP-CoT-23 (CCDC83) is a novel immunogenic cancer/testis antigen in colon cancer (2012)

Cancer/testis (CT) antigens are considered target molecules for cancer immunotherapy. To identify novel CT antigens, immunoscreening of a testicular cDNA library was performed using serum obtained from a colon cancer patient who was immunized with a new dendritic cell vaccine. We isolated 64 positive cDNA clones comprised of 40 different genes, designated KP-CoT-1 through KP-CoT-40. Three of these putative antigens, including KP-CoT-23 (CCDC83), had testis-specific expression profiles in the Unigene database. RT-PCR analysis showed that the expression of 2 KP-Cot-23 variants was restricted to the testis in normal adult tissues. In addition, KP-CoT-23 variants were frequently expressed in a variety of tumors and cancer cell lines, including colon cancer. A serological western blot assay showed IgG antibodies to the KP-CoT-23 protein in 26 of 37 colon cancer patients and in 4 of 21 healthy patients. These data suggest that KP-CoT-23 is a novel CT antigen that may be useful for the diagnosis and immunotherapy of cancer.
Imaging and pathology findings after an initial negative MRI-US fusion-guided and 12-core extended sextant prostate biopsy session (2014)

In patients with a negative MRI-US fusion prostate biopsy and indications for repeat biopsy, the detection rate of the follow-up sessions was lower than the initial detection rate. Of the prostate cancers subsequently found, 93% were low grade (≤ 3+4). In this low risk group of patients, increasing the follow-up time interval should be considered in the appropriate clinical setting.
Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy (2015)

Non-synonymous single nucleotide variants (nsSNVs) in coding DNA regions can result in phenotypic differences between individuals; however, only some nsSNVs are causative for a certain disease. As just a fraction of respective nsSNVs is annotated in databases, computational biology tools are applied to predict the pathogenicity in silico. In addition to applications in oncology, novel molecular diagnostic tests have been developed for cardiovascular disorders as a leading cause of morbidity and mortality in industrialized nations. We explored the concordance and performance of 13 nsSNV pathogenicity prediction tools on panel sequencing results of dilated cardiomyopathy. The analyzed data set from the INHERITANCE study contained 842 nsSNVs discovered in 639 patients, screened for the full sequence of 76 genes related to cardiomyopathies. The single tools prediction revealed a surprisingly high heterogeneity and discordance based on the implemented prediction method. Known disease associations were not reported by the tools, limiting usability in clinics. Because different tools have different advantages, we combined their results. By clustering of correlated methods using similar prediction strategies and calculating a majority vote-based consensus, we found that the prediction accuracy and sensitivity can be further improved. Although challenges remain, different in silico tools bear the potential to predict the malignancy of nsSNVs, especially if different algorithms are combined. Most tools rely mainly on sequence features; beyond these, structural information is important to analyze the relationship of nsSNVs with disease phenotypes. Likewise, current tools consider single nsSNVs, which may, however, show a cumulative effect and turn neutral mutations in an ensemble into pathogenic variants.
Minerals of Washington, D.C. and vicinity (1976)

Before proceeding, a few aspects of mineral collecting in the region should be mentioned. First, it cannot be stressed too strongly 15--'
Communication Avoiding 2D Stencil Implementations over PaRSEC Task-Based Runtime (2020)

Stencil computation or general sparse matrix-vector product (SpMV) are key components in many algorithms like geometric multigrid or Krylov solvers. But their low arithmetic intensity means that memory bandwidth and network latency will be the performance limiting factors. The current architectural trend favors computations over bandwidth, worsening the already unfavorable imbalance. Previous work approached stencil kernel optimization either by improving memory bandwidth usage or by providing a Communication Avoiding (CA) scheme to minimize network latency in repeated sparse vector multiplication by replicating remote work in order to delay communications on the critical path. Focusing on minimizing communication bottleneck in distributed stencil computation, in this study we combine a CA scheme with the computation and communication overlapping that is inherent in a dataflow task-based runtime system such as PaRSEC to demonstrate their combined benefits. We implemented the 2D five point stencil (Jacobi iteration) in PETSc, and over PaRSEC in two flavors, full communications (base-PaRSEC) and CA-PaRSEC which operate directly on a 2D compute grid. Our results running on two clusters, NaCL and Stampede2 indicate that we can achieve 2× speedup over the standard SpMV solution implemented in PETSc, and in certain cases when kernel execution is not dominating the execution time, the CA-PaRSEC version achieved up to 57% and 33% speedup over base-PaRSEC implementation on NaCL and Stampede2 respectively.
Fabrication of Nanolaminates with Ultrathin Nanolayers Using Atomic Layer Deposition: Nucleation & Growth Issues (2009)

Abstract : This AFOSR grant concentrated on the fabrication of nanolaminates with ultrathin nanolayers using atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques. Nanolaminates are multilayered thin film structures with nanometer dimensions and very high interfacial density. These multilayer structures can display novel properties that can be optimized by manipulating the thickness and composition of the individual nanolayers. During this grant, the research examined nucleation and growth issues involved in the fabrication of W/Al203 nanolaminates. These studies are important because W/Al203 nanolaminates are important for thermal barrier coatings and x-ray mirrors. Subsequent studies examined Si02/Al203 nanolaminates for gas diffusion barriers on polymers. The brittleness of these Si02/Al203 nanolaminates motivated new work on molecular layer deposition (MLD) to develop flexible nanolaminate films using polymeric interlayers. New MLD growth methods were used to fabricate organic-inorganic nanolaminates that may serve as excellent flexible coatings.
Violation of Hund's third rule in structurally disordered ferromagnets (2011)

Violation of Hund's third rule caused by structural disorder is observed for the induced magnetic moment of Zr, using x-ray magnetic circular dichroism. The induced spin and orbital magnetic moments are antiparallel in the crystalline state, but parallel in an amorphous state of the investigated Co- and Fe-based materials. First-principles calculations are used to provide physical insight into the dependency of the spin-orbit coupling on the interatomic distance and coordination number.
ChemInform Abstract: New Triquinane‐Type Sesquiterpenoids from Macrocystidia cucumis (Basidiomycetes). (1998)

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.
Journal Club (1998)

Warner, David S.; Eliasson, M JL; Sampei, K; Mandir, A S; Hum, P D; Traystman, R J; Bao, J; Pieper, A; Wang, Z-Q; Dawson, T M; Snyder, S H; Dawson, V L. Author Information
Focused X-ray Beams from Van der Waals Heterostructures (2022)

We present the concept of customized van der Waals heterostructures with periodicity tailored to generate pre-designed X-ray patterns from free electrons. As an example, we demonstrate focused X-ray beams.