gebhart/patrepeval huggingface dataset:
Database Searching for Thymidine and Thymidylate Kinase Inhibitors Using Three-dimensional Structure-based Methods (2002)

Structure-based drug design methods were used to search for novel inhibitors of herpes simplex virus type 1 (HSV-1) thymidine kinase and Mycobacterium tuberculosis thymidylate kinase. The method involved the use of crystal structure complexes to guide database searching for potential inhibitors. A number of weak inhibitors of HSV-2 were identified, one of which was found to inhibit HSV-1 TK and HSV-1 TK-deficient viral strains. Each compound tested against M. tuberculosis thymidylate kinase was found to have some activity. The best of these compounds was only 4.6-fold less potent than 3'-azido-3'-deoxythymidine-5'-monophosphate (AZTMP). This study demonstrates the utility of structure-based drug design methods in the search for novel enzyme inhibitors.
Smartglasses/smartphone needle guidance AR system for transperineal prostate procedure (2019)

In transperineal prostate biopsy or ablation, a grid-template is typically used to guide the needle. The guidance method has limited positioning resolution and lack of needle angulation selections that are referenced to ultrasound imaging or TRUS-MRI fusion targets. To overcome the limitation, a novel augmented reality (AR) system that use smart see-through glasses and smartphone as a needle guidance device for transperineal prostate procedure was developed. The AR system is comprised of a MRI/CT scanner, a pre-procedural image analysis and visualization software, AR devices (smart-glasses, smartphone), a newly-developed AR app, as well as a local network. The AR app displays the lesion and planned needle trajectory, which are derived from the pre-procedural images, on the AR devices. A special designed image marker frame that affixed to the patient’s perineum was used to track the pre-procedural image with the AR devices. The displayed needle plan was always referenced to the patient and remains independent from the position and orientation of the devices. Multiple devices can be used simultaneously and communicate via a local network. We evaluated the AR system accuracy with iPhone and R-7 glasses in a phantom study. The image overlay accuracy was 0.58&plusmn;0.43<sup>o</sup> and 1.62&plusmn;1.52<sup>o</sup> in iPhone and R-7 glasses respectively. The accuracy of iPhone guidance was 1.9&plusmn;0.97 mm (lateral) and 1.0&plusmn;0.5 mm (in-direction), the accuracy of R-7 guidance was 2.8&plusmn;1.4mm (lateral) and 2.3&plusmn;1.5mm (indirection). AR system using smart-glasses and smartphone can provide accurate needle guidance and see-through-the-skin display for needle based transperineal prostate interventions like biopsy and ablation.
Distal bile duct carcinomas and pancreatic ductal adenocarcinomas: postulating a common tumor entity (2015)

The set definition of distal cholangiocarcinomas and adenocarcinomas of the pancreatic head is challenged by their close anatomical relation, similar growth pattern, and corresponding therapeutic outcome. They show a mutual development during embryologic organ formation and share phenotypic characteristics. This review will highlight the similarities with regard to the common origin of their primary organs, histopathological similarities, and modern clinical management. Thus, we propose to subsume those entities under a common superfamily.
Antibody Titer Correlates with Omicron Infection in Vaccinated Healthcare Workers (2022)

The advent of vaccines against SARS-CoV-2 has drastically reduced the level of hospitalization with severe COVID-19 disease in infected individuals. However, the diffusion of variants of concern still challenge the protection conferred by vaccines raised against the wild-type form of the virus. Here, we have characterized the antibody response to the BNT162b2 (Comirnaty) mRNA vaccine in patients infected with the Omicron variant. We analyzed a population of 4354 vaccinated healthcare workers (HCW) from 7 different hospitals in Italy and monitored infection with SARS-CoV-2 Omicron. We correlated infection with the antibody response after vaccination. We found that a lower level of IgG, younger age, and the presence of allergies correlate with increased infection during the Omicron wave, and that infections correlate with wild-type spike protein antibody titers below 350 BAU/mL. These results support the necessity of a fourth booster dose, particularly for individuals with lower levels of antibodies.
Apixaban inhibition of factor Xa: Microscopic rate constants and inhibition mechanism in purified protein systems and in human plasma (2010)

Apixaban is a potent, direct, selective, and orally active inhibitor of coagulation factor Xa. Rate constants for apixaban binding to free and prothrombinase-bound factor Xa were measured using multiple techniques. The inhibition mechanism was determined in purified systems and in a plasma prothrombin clotting time assay. Apixaban inhibits factor Xa with a K(i) of 0.25 nM at 37°C, an association rate constant of approximately 20 μM(-1) s(-1), and a dissociation half-life of 1-2 min. Under physiological conditions apixaban exhibits mixed-type inhibition and maintains high factor Xa affinity with a K(i) of 0.62 nM and association rate constant of 12 μM(-1) s(-1) for prothrombinase, and a K(i) of 1.7 nM and association rate constant of 4 μM(-1) s(-1) for the prothrombinase:prothrombin complex. Experiments in prothrombin depleted human plasma showed that the mechanism and kinetics of inhibition are maintained in plasma. The mechanistic detail derived from these experiments can be used to understand and interpret the pharmacodynamic action of apixaban.
H2O2 Decomposition and Its Impact on Silicon Surface Roughening and Gate Oxide Integrity (1995)

In this study the impact of temperature and metal contamination on the stability of hydrogen peroxide in the two most common wet chemical cleaning mixtures for wafer process operations has been investigated. The stability of the caustic mixture ( NH 4 OH/H 2 O 2 /H 2 O) was found to be very sensitive to certain metallic contaminations in the sub-ppb range, while the stability of the acid mixture ( HCl/H 2 O 2 /H 2 O) is mainly influenced by non metallic, anionic components of the solution itself. We observed also a strong oscillating behaviour of the rate of the oxygen gas evolution caused by the decomposition of H 2 O 2 . Furthermore it was found, that the oxygen gas bubbles, formed by the decomposition of hydrogen peroxide cause a certain kind of micro-roughness on the silicon surface through a micro masking mechanism. In a series of experiments we could prove that this kind of surface roughness has a significant impact on the integrity of thin gate oxides.
The control of protein phosphatase‐1 by targetting subunits (1992)

The major protein phosphatase that dephosphorylates smooth-muscle myosin was purified from chicken gizzard myofibrils and shown to be composed of three subunits with apparent molecular masses of 130, 37 and 20 kDa, the most likely structure being a heterotrimer. The 37-kDa component was the catalytic subunit, while the 130-kDa and 20-kDa components formed a regulatory complex that enhanced catalytic subunit activity towards heavy meromyosin or the isolated myosin P light chain from smooth muscle and suppressed its activity towards phosphorylase, phosphorylase kinase and glycogen synthase. The catalytic subunit was identified as the beta isoform of protein phosphatase-1 (PP1) and the 130-kDa subunit as the PP1-binding component. The distinctive properties of smooth and skeletal muscle myosin phosphatases are explained by interaction of PP1 beta with different proteins and (in conjunction with earlier analysis of the glycogen-associated phosphatase) establish that the specificity and subcellular location of PP1 is determined by its interaction with a number of specific targetting subunits.
Supplementary Figure S1 from Promoter Methylation of <i>CDO1</i> Identifies Clear-Cell Renal Cell Cancer Patients with Poor Survival Outcome (2023)

&lt;p&gt;Ten-year survival of clear-cell renal cell cancer patients from the population-based series according to CDO1 methylation in patients A) aged {greater than or equal to}55 to &lt;65 years, B) aged {greater than or equal to} 65 to &lt;75 years and C) aged {greater than or equal to}75 years at diagnosis.&lt;/p&gt;
Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities (2008)

Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumors were high-grade serous or undifferentiated type. None of the endometrioid (n=5), clear cell (n=4), or low grade serous (n=2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumors with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.
High‐Efficiency Inverted Polymer Photovoltaics via Spectrally Tuned Absorption Enhancement (2014)

The trade-off between light absorption and exciton diffusion length must be addressed before widespread deployment of organic photovoltaics can be realized. Optical transfer matrix modeling is used in inverted, high-efficiency organic photovoltaics, employing a poly[[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b′]dithiophene-2,6-diyl] [3-fluoro-2-[(2-ethyl­hexyl)carbonyl] thieno[3,4-b]thiophene­diyl]] (PTB7):[6,6]-phenyl C71 butyric acid methyl-ester (PC71BM) active layer to spectrally sculpt absorption enhancement by tuning the layer thicknesses of both the photoactive layer and the ZnO interfacial layer (IFL). As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Nipple Loss following Nipple-Sparing Mastectomy (2016)

Therapeutic, IV.
CoVE: Towards Confidential Computing on RISC-V Platforms (2023)

Multi-tenant computing platforms are typically comprised of several software and hardware components including platform firmware, host operating system kernel, virtualization monitor, and the actual tenant payloads that run on them (typically in a virtual machine, container, or application). This model is well established in large scale commercial deployment, but the downside is that all platform components and operators are in the Trusted Computing Base (TCB) of the tenant. This aspect is ill-suited for privacy-oriented workloads that aim to minimize the TCB footprint. Confidential computing presents a good stepping-stone towards providing a quantifiable TCB for computing. Confidential computing [1] requires the use of a HW-attested Trusted Execution Environments for data-in-use protection. The RISC-V architecture presents a strong foundation for meeting the requirements for Confidential Computing and other security paradigms in a clean slate manner. This paper describes a reference architecture and discusses ISA, non-ISA and system-on-chip (SoC) requirements for confidential computing on RISC-V Platforms. It discusses proposed ISA and non-ISA Extension for Confidential Virtual Machine for RISC-V platforms, referred to as CoVE.
A Sealing Technique for Stacking MEMS on LSI Using Spin-Coating Film Transfer and Hot Pressing (2003)

This paper describes a novel sealing technique that uses spin-coating film transfer and hot pressing (STP). STP is a key technique in integrating microelectromechanical systems (MEMS) on large-scale integrated circuits (LSIs). It enables us to form a film over cavities and concavities easily by hot-pressing a dielectric in vacuum. Based on an analytical model, the effect of critical parameters for sealing was clarified. In the experiments, concave line-patterns 100 µm wide were sealed with a 20-µm-thick dielectric. The sealing characteristics were also examined experimentally with regard to film thickness and width of cavities, which quantitatively shows that the technique has the possibility of sealing patterns of various sizes. We applied this technique to the fabrication of a MEMS fingerprint sensor, whose MEMS structures with cavities must be stacked on an LSI. Using the fabricated sensor, we succeeded in capturing a fingerprint image, which indicates that the sealing technique does not cause damage and is compatible with the underlying LSI. This sealing technique will be a driving force in extending seamless integration technology to produce high-functionality MEMS devices on LSIs.
Application of Ultrasound Time-Domain Correlation Method to Turbulent Pipe Flow at Low Reynolds Number (2002)

This paper presents the applicability of a ultrasound time-domain correlatioon (UTDC) method to turbulent flows. The system is based on the cross-correlation between two consecutive echoes of ultrasonic pulses to detect the velocity. The UTDC has two advantages over a conventional ultrasound pulsed Doppler method. First, the system has a better time resolution than the pulse Doppler method. Second, the system does not have a limitation in maximum measurable velocity, which is limited by Nyquist's sampling theorem. We measured velocity profiles in turebulent pipe flows at low Reynolds number, and compared the results with the data obtained by a direct numerical simulations and by a laser Doppler velocimetry.
Anti-inflammatory Activity of Eudesmane-Type Sesquiterpenoids from Salvia plebeia (2017)

Nine new sesquiterpenoid lactones and 11 known analogues were isolated from the aerial parts of Salvia plebeia R.Br. Their structures were elucidated via HRESIMS and NMR data, and their absolute configurations were defined via electronic circular dichroism data, X-ray crystallographic analysis, and the modified Mosher's ester method. Compounds 1-20 were investigated for their ability to inhibit LPS-stimulated nitric oxide production in murine macrophage cells. Of the isolates, epi-eudebeiolide C (20) showed the highest inhibitory effect (IC<sub>50</sub> of 17.9 μM). mRNA and protein expression of inducible nitric oxide synthase (iNOS), but not that of cyclooxygenase-2 (COX-2), was dose-dependently decreased by 20 in LPS-activated RAW 264.7 cells. Based on a mechanistic study involving the nuclear factor-κB (NF-κB) signaling pathway, the anti-inflammatory effect of 20 was attributed to NF-κB activation blockade via inhibition of NF-κB (IκB) phosphorylation. Therefore, 20 might be a potential candidate for relieving inflammatory diseases.
Formation of Single-Orientation Epitaxial Islands of TiSi2 on Si (001) using Sr Passivation (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
Impact of a microfluidic jet onto a pendant droplet (2021)

High speed microfluidic jets can be generated by a thermocavitation process: from the evaporation of the liquid inside a microfluidic channel, a rapidly expanding bubble is formed and generates a jet through a flow focusing effect. Here, we study the impact and traversing of such jets on a pendant liquid droplet. Upon impact, an expanding cavity is created, and, above a critical impact velocity, the jet traverses the entire droplet. We predict the critical traversing velocity (i) from a simple energy balance and (ii) by comparing the Young-Laplace and dynamic pressures in the cavity that is created during impact. We contrast the model predictions against experiments, in which we vary the liquid properties of the pendant droplet and find good agreement. In addition, we asses how surfactants and viscoelastic effects influence the critical impact velocity. Our results are relevant for the study of needle-free injections, where jets of similar velocities and dimensions are being used. Given the simplicity of our system we can systematically vary the target properties and unravel their effect on the impact dynamics, a true challenge when injecting into real skin.
Partial DiGeorge Syndrome at the Age of Thirty-Four. (1994)

A 34-year-old man with partial DiGeorge syndrome suffered from seizures and mental retardation from the age of three years. He was diagnosed as having primary hypoparathyroidism by the Ellsworth-Howard test at the age of 22. He was also found to have a right aortic arch. Immunological studies revealed the presence of immature T cells (CD 38+, OKT 9+), although the subsets and function of his T cells were almost normal. The facts that the cardiovascular anomaly and immunodeficiency were mild and the hypoparathyroidism was well controlled, may account for his survival to this age.
Behavioral Effects of α2/α3 Subtype‐Selective GABA A Receptor Positive Allosteric Modulators (2018)

Millions of individuals suffer from chronic pain. Opioids are effective for treating chronic pain but their use is limited due to undesirable side‐effects. Previous studies have shown that different subunits of the GABA A receptor are associated with different actions of the benzodiazepine site. While α2/α3 subunit‐containing GABA A receptors mediate antinociceptive effects, α1 subunit‐containing GABA A receptors mediate sedative and abuse‐related effects. This study sought to examine the behavioral effects of two α2/α3‐subtype selective PAMs: KRM‐II‐81 and NS16085. In a rat model of inflammatory pain (complete Freund's adjuvant) and a rat model of neuropathic pain (chronic constriction injury), both PAMs and the classical benzodiazepine midazolam attenuated mechanical hyperalgesia (as measured by von Frey test). In the procedure of food‐maintained operant responding, KRM‐II‐81 and NS16085 did not significantly decrease the response rate at doses that produced maximal antinociception. Contrastingly, midazolam significantly reduced the response rate at doses that attenuated mechanical hyperalgesia. In a horizontal wire test aimed to measure muscle relaxation, within the dose range that produced antinociception, only midazolam dose‐dependently increased the percentage of rats unable to grasp the wire, indicating muscle‐relaxant activity. These behavioral effects can be attenuated by benzodiazepine receptor antagonist flumazenil, confirming that the behavioral effects of these subtype‐selective GABA A PAMs are mediated through the benzodiazepine site of GABA A receptors. Taken together, while midazolam produced antinociceptive, rate‐suppressing, and muscle‐relaxant activity at similar doses, both subtype‐selective GABA A receptor PAMs selectively produced antinocicpetive effects. Collectively, these data support the notion of α2/α3‐subtype selective GABA A PAMs as novel analgesics. Support or Funding Information R01DA034806 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Flexible Filter Bank Dimensioning for Multicarrier Modulation and Frequency Domain Equalization (2006)

This paper investigates both transmultiplexer (TMUX) and analysis-synthesis filter banks where the two sides of the filter bank system are of different sizes. Such configurations find applications in filter bank based multicarrier communication systems on one hand and in fractionally-spaced frequency domain equalizers on the other. The errors due to mismatched filter banks are analyzed. Based on this analysis, it is shown how to modify the subband processing to compensate the reconstruction error in the analysis-synthesis configuration, or the inter-carrier and inter-symbol interferences in the multicarrier case. The needed subband processing can be incorporated to the subband-wise channel equalizers with no additional complexity during data processing and minor additional complexity in the equalizer coefficient calculation and their adaptation
Solvent-driven chirality for luminescent self-assembled structures: experiments and theory (2020)

We describe, for a single platinum complex bearing a dipeptide moiety, a solvent-driven interconversion from twisted to straight micrometric assembled structures with different chirality. The photophysical and morphological properties of the aggregates have been investigated as well as the role of the media and concentration. A real-time visualization of the solvent-driven interconversion processes has been achieved by confocal microscopy. Finally, atomistic and coarse-grained simulations, providing results consistent with the experimental observations, allow to obtain a molecular-level insight into the interesting solvent-responsive behavior of this system.
Anisotropic thermal expansion of RuCo alloys in carbon nanotube matrix (2009)

Ru 1 − x Co x alloys exhibit hexagonal close packed phase for x≤0.75. The nanocrystalline samples of Ru1−xCox alloys in the presence of carbon nanotubes were prepared by organometallic synthesis and their thermal expansion coefficients were determined using high resolution x-ray diffraction over a temperature range of 25–250 °C. The coefficients of linear thermal expansions (CTE) showed anisotropy along the c- and a-axis. The CTE values showed dependence on the composition and varied between 8.8×10−6/°C to 16.1×10−6/°C for c-axis (α∥) and 5.9×10−6/°C to 12.6×10−6/°C for a-axis (α⊥). These results suggest that RuCo alloys have low thermal expansivity and allow the tailoring of their thermal properties. The radial thermal expansion coefficient (αc) of carbon nanotube was 26×10−6/°C.