gebhart/patrepeval huggingface dataset:
Optimization of Important Early ADME(T) Parameters of NADPH Oxidase-4 Inhibitor Molecules (2012)

Through their reactive oxygen species (ROS) producing function, NADPH oxidase (NOX) enzymes have been linked to several oxidative stress related diseases. In our recently published paper [1] we have already shown the NOX4 inhibitory effect of diverse, molecule sub-libraries and their biological importance. We also presented our work connected to potential anti-tumour molecules and the relationship between their biological activity and physico-chemical properties [2]. As an extension of these studies further physico-chemical and biological investigation has been carried out on a molecule group included NOX4 inhibitory chromanone compounds. Here we describe the optimization of early ADME(T) parameters determining lipophilicity, phospholipophilicity and permeability linked to structure-activity relationship. We prove that optimal lipo- and phospholipophilicty can be also determined in case of NOX4 inhibitors and a comparison will be made between the chemically similar isochromanone and chromanone molecular libraries. It will be also shown how to predict the effect of different substituents on permeability, lipo- and phospholipophilicity and also the biological differences between anti-tumour molecules and NOX4 inhibitors according to their penetration ability.
Frailty, Length of Stay, and Mortality in Kidney Transplant Recipients (2016)

Frail KT recipients are more likely to experience a longer LOS. Longer LOS among nonfrail recipients may be a marker of increased mortality risk. Frailty is a measure of physiologic reserve that may be an important clinical marker of longer surgical LOS.
ChemInform Abstract: Chiral Ferrocenes as Novel Rotary Modules for Molecular Machines (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Stochastic EXIT Design for Low-Latency Short-Block LDPC Codes (2020)

We introduce a stochastic version of extrinsic information transfer (EXIT) chart which accounts for dispersion in finite-length LDPC decoding. The proposed approach can design short LDPC codes systematically, achieving about 1.2 dB gain over recently proposed scattered EXIT design.
Linear unification (1976)

A unification algorithm is described which tests a set of expressions for unifiability and which requires time and space which are only linear in the size of the input.
Transpiration efficiency: further insights from species, sink strength, and soil comparisons (2017)

During ID-IV we reported that TE was closely related to the capacity
to restrict transpiration under high vapor pressure deficit
(VPD). Experiments were undertaken to evaluate other possible
factors influencing TE. Experiments across seasons varying
in VPD conditions and across water regimes showed that
maize had a higher TE than sorghum and pearl millet. While
C4 cereals should, theoretically, have similar TE, 100 years of
breeding in maize could be responsible for these differences,
possibly from increased rates of carbon fixation deriving from
selective pressure underincreased planting densities. These
results then open an opportunity to accelerate breeding in
sorghum and pearl millet by specifically targeting the possible
reasons for these differences (RUE, density “resistance”). Further
experimentation was undertaken in which ears and panicles
were severed from the plants and showed that TE was depressed
in maize and sorghum, respectively, while it was not in
pearl millet, which produced many new tillers and nodal tillers.
This work then raised the question of source-sink relationship
in setting carbon demand and then photosynthetic activity. Finally,
TE assessed in C4 cereals, grown in four different soils
and two different VPD seasons, showed large TE differences
among soils during the high VPD season, with a degree of species-by-soil
interaction. We interpret these differences to be a
consequence of different hydraulic soil properties likely affecting
the transpiration response under high VPD. Results will be
discussed with regard to breeding targets in “less-bred” crops
(pearl millet, sorghum) and with regards to better understanding
GxExM interactions.
Death rate of populations of Bact. lactis aerogenes III. Interpretation of survival curves (1953)

Abstract Most theories of the survival curve postulate either a progressive action of the lethal agent on cells with large inherent differences of resistance, or random events such as encounters between the agent and a sensitive region of the cells. A survey of the experimental evidence, however, suggests that death of the bacterial cell involves not only a progressive destruction of essential cell activities, but may also be conditioned at some stage by a random combina­tion of various independent events. The form of the survival curve depends essentially on the speed of the former process in relation to the probability of the latter. Factors modifying this form are: (1) intrinsic differences between individual cells, which, however, appear not to be the major cause of variation of survival times, and (2) the occurrence, in favourable circumstances, of adaptive adjustments. It is the element of chance in survival that accounts for the frequent observation of extremely skew distributions of survival times (and in the limit nearly logarithmic decline curves). It probably arises from the fact that the concentrations of various molecular species show complex fluctuations, at the appropriate phase of which certain cell activities fall below a critical level for viability.
Using an oxidized porous silicon interferometer for determination of relative protein binding affinity through non‐covalent capture probe immobilization (2007)

Abstract An oxidized porous Si interferometer was used to measure binding of immunoglobulin G (IgG) to an immobilized protein A capture probe. Protein A was non‐covalently immobilized on a thermally oxidized porous Si (PSiO 2 ) sample and exposed to IgG originating from different species. The resulting order of IgG affinity toward the protein A‐coated surface (human &gt; rabbit ≫ sheep IgG) agrees with previous inhibition studies for protein A/IgG binding. No signal change was observed when a protein A coated sample was exposed to bovine serum albumin (BSA), demonstrating that the adsorbed sensing layer sufficiently coats the PSiO 2 surface to prevent non‐specific binding. This strategy is excellent for qualitative measurements of protein binding affinity because it is label‐free, requires minimal sample preparation, and can be implemented using an inexpensive CCD‐based spectrometer coupled to a tungsten lamp. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
A Modular GPS Remote Sensing Receiver for Small Platforms (2006)

This paper focuses on the processing of experimental data collected with a small modular GPS bistatic radar software receiver on a balloon flight. The receiver is designed for remote sensing purposes and the design process will be covered in some detail. GPS bistatic radar focuses on the surfacereflected signal, which can be used to determine properties of the reflection surface, including roughness, ocean wave height and also ranging to the surface. In the past, a mixture of both ASIC-based and software receivers have been used, but these require desktop or laptop computers to operate them. Previous receiver configurations have been prohibitively large and could not be mounted on smaller platforms. This design features two analog front-ends with a common clock, a FPGA and USB bridge to move the digital samples to a Linux-based Single Board Computer. The system features a modular design and allows for easy integration with other analog frontends.Airborne data collected with this instrument near Boulder, Colorado during a balloon flight will be presented. The data from the balloon flight has been processed to extract the height above ground using GPS bistatic radar as an altimeter and the GPS position as a reference. GTOPO30 Digital Elevation Models have been used to estimate the surface elevation used for height estimates in the altimeter. This project opens up new opportunities to perform remote sensing with cheaper and smaller platforms.
Evolving Lessons on Nanomaterial-Coated Viral Vectors for Local and Systemic Gene Therapy (2016)

Viral vectors are promising gene carriers for cancer therapy. However, virus-mediated gene therapies have demonstrated insufficient therapeutic efficacy in clinical trials due to rapid dissemination to nontarget tissues and to the immunogenicity of viral vectors, resulting in poor retention at the disease locus and induction of adverse inflammatory responses in patients. Further, the limited tropism of viral vectors prevents efficient gene delivery to target tissues. In this regard, modification of the viral surface with nanomaterials is a promising strategy to augment vector accumulation at the target tissue, circumvent the host immune response, and avoid nonspecific interactions with the reticuloendothelial system or serum complement. In the present review, we discuss various chemical modification strategies to enhance the therapeutic efficacy of viral vectors delivered either locally or systemically. We conclude by highlighting the salient features of various nanomaterial-coated viral vectors and their prospects and directions for future research.
Integrated Magneto-Chemical Sensor For On-Site Food Allergen Detection (2017)

Adverse food reactions, including food allergies, food sensitivities, and autoimmune reaction (e.g., celiac disease) affect 5-15% of the population and remain a considerable public health problem requiring stringent food avoidance and epinephrine availability for emergency events. Avoiding problematic foods is practically difficult, given current reliance on prepared foods and out-of-home meals. In response, we developed a portable, point-of-use detection technology, termed integrated exogenous antigen testing (iEAT). The system consists of a disposable antigen extraction device coupled with an electronic keychain reader for rapid sensing and communication. We optimized the prototype iEAT system to detect five major food antigens in peanuts, hazelnuts, wheat, milk, and eggs. Antigen extraction and detection with iEAT requires <10 min and achieves high-detection sensitivities (e.g., 0.1 mg/kg for gluten, lower than regulatory limits of 20 mg/kg). When testing under restaurant conditions, we were able to detect hidden food antigens such as gluten within "gluten-free" food items. The small size and rapid, simple testing of the iEAT system should help not only consumers but also other key stakeholders such as clinicians, food industries, and regulators to enhance food safety.
PTB domain and leucine zipper motif 1 (APPL1) inhibits myocardial ischemia/hypoxia-reperfusion injury via inactivation of apoptotic protease activating factor-1 (APAF-1)/Caspase9 signaling pathway (2021)

Myocardial ischemia/hypoxia-reperfusion injury mediates the progression of multiple cardiovascular diseases. It has been reported that knockdown of adaptor protein containing a PH domain, PTB domain and leucine zipper motif 1 (APPL1) is a significant factor for the progression of myocardial injury. However, the role of APPL1 in myocardial ischemia remains unclear. Hence, the aim of the present study was to investigate the specific mechanism underlying the role of APPL1 in myocardial ischemia.In our study, the mRNA level of APPL1 was detected by quantitative real-time PCR (RT-qPCR). The expressions of APPL1, Apoptotic protease activating factor-1 (APAF-1), cleaved caspase9 and other inflammation- and apoptosis-related proteins were determined by western blotting. The secretion of inflammatory cytokines and lactate dehydrogenase (LDH) levels were measured by commercial assay kits. The H9C2 cell viability was analyzed by cell counting kit-8 (CCK-8) assay. The apoptosis rate of H9C2 cells was analyzed by TUNEL assay. The interaction between APPL1 and APAF-1/caspase9 was determined by Immunoprecipitation (IP).Our findings demonstrated that APPL1 was low expressed in myocardial ischemia tissues and cells. APPL1 knockdown suppressed the viability of myocardial ischemia cells and aggravated hypoxia/reperfusion-induced LDH hypersecretion, inflammation and apoptosis. In addition, the overexpression of APPL1 induced inactivation of APAF-1/Caspase9 signaling pathway. Significantly, APAF1 inhibitor reversed the effect of APPL1 knockdown on viability, LDH secretion, inflammation and apoptosis.We conclude that APPL1 inhibits myocardial ischemia/hypoxia-reperfusion injury via inactivation of APAF-1/Caspase9 signaling pathway. Hence, APPL1 may be a novel and effective target for the treatment of myocardial ischemia.
Graphene-Based Interconnect Exploration for Large SRAM Caches for Ultrascaled Technology Nodes (2022)

Graphene-based interconnects are considered promising replacements for traditional copper (Cu) interconnect due to their great electric properties. In this article, an interconnect-memory co- design framework is developed to efficiently optimize various graphene-based interconnect technologies. Four interconnect materials and heterogeneous design schemes are benchmarked against their traditional Cu counterparts to optimize large cache-level SRAM performance in terms of delay and energy per access, energy-delay product (EDP), and energy-delay-area product (EDAP). A large design space exploration is performed based on realistic subarray design and device technology. Various interconnect- and array-level design parameters are studied to quantify the true potential of graphene-based wires for optimal memory performance.
Home-Based Resistance Training Is Not Sufficient to Maintain Improved Glycemic Control Following Supervised Training in Older Individuals With Type 2 Diabetes (2005)

In older adults with type 2 diabetes, home-based progressive resistance training was effective for maintaining the gymnasium-based improvements in muscle strength and LBM but not glycemic control. Reductions in adherence and exercise training volume and intensity seem to impede the effectiveness of home-based training for maintaining improved glycemic control.
Plasma Cell Granuloma in Cyclosporine-Induced Gingival Overgrowth: A Report of Two Cases with Immunohistochemical Positivity of Interleukin-6 and Phospholipase C-gamma1 (2002)

We report two cases of gingival plasma cell granuloma in a 34-yr-old and 40-yr-old two male renal transplant recipients with cyclosporine A (CsA)-induced gingival overgrowth (GO). Histologically, these lesions were composed of mature plasma cells, showing polyclonality for both lambda and kappa light chains and fibrovascular connective tissue stroma. In addition to the fact that CsA-induced plasma cell granuloma is rare, the salient features of our cases were the secretion of interleukin-6 and overexpression of phospholipase C- gamma 1 of the tumor cells, which may explain the mechanisms of CsA- induced GO.
<title>Real-time in-vivo endoscopic imaging of fluorescence from human colonic adenomas</title> (1998)

Previous in vitro studies showed that autofluorescence images of colonic mucosa collected endoscopically can be used to detect dysplasia with high sensitivity. This method is extended to collection of fluorescence images of adenomatous polyps in vivo. Fluorescence images were collected during colonoscopy in 30 patients. A total of 12 adenomatous and 6 hyperplastic polyps were identified. An optical fiber excitation probe, located in the instrument channel of the colonoscope, delivered 300 mW of near- ultraviolet light at (lambda) <SUB>ex</SUB> equals 351 and 364 nm. Mucosal fluorescence in the spectral bandwidth between 400 and 700 nm was imaged, processed, and displayed with various likelihoods of associated dysplasia. Adenomatous polyps exhibited decreased fluorescence intensity compared to adjacent mucosa with normal appearance. With the fluorescence threshold set to 80% of the average intensity of normal mucosa, a sensitivity of 83% for dysplasia detection was achieved. All hyperplastic polyps were correctly identified as being non-dysplastic. Optimal identification of dysplastic regions was obtained with the colonoscope oriented at near-normal incidence to the polyps. At higher angles of incidence, artifacts due to illumination shadows were introduced. The dysplasia associated with adenomatous polyps can be detected in vivo on fluorescence imaging with high sensitivity, thus demonstrating the potential to guide endoscopic biopsy.
Compensation mechanisms and the response of high resistivity GaAs photoconductive switches during high-power applications (2000)

Photoconductive semiconductor switches (PCSSs) made from semi-insulating (SI) GaAs are the primary switching component of one class of high-power, ultra-wideband (UWB) microwave sources. The high resistivity of the GaAs can be achieved through different processing techniques. The resultant device characteristics of the PCSS such as breakdown voltage, rise time, and turn-on delay will depend on the actual processing technique that was used for the material. Simulation studies comparing an intrinsic material and a high resistivity SI GaAs PCSS grown through the liquid-encapsulated Czochralski (LEC) process with a deep donor and shallow acceptor compensation mechanism highlight these differences. Simulations also elucidate the role of an n/sup +/-doped layer placed next to the cathode, which increases the breakdown voltage of the device. Extending the n/sup +/ layer length beyond the cathode does not yield further improvement but leads to current confinement along a narrow strip that can initiate local heating or burnout. The doping profile of the n/sup +/ layer also affects hold-off characteristics, a faster gradient ensuring better protection of the cathode against the substrate field, and electron injection. Doping the n/sup +/ region with a higher concentration of carbon impurities does not produce the same effect as doping the n/sup +/-SI interface. These material-related issues are critical to further extending the performance characteristics of PCSSs.
Assertional reasoning about pairwise transient interactions in mobile computing (1996)

Mobile computing represents a major point of departure from the traditional distributed computing paradigm. The potentially very large number of independent computing units, a decoupled computing style, frequent disconnections, continuous position changes, and the location-dependent nature of the behavior and communication patterns of the individual components present designers with unprecedented challenges in the areas of modularity and dependability. The paper describes two ideas regarding a modular approach to specifying and reasoning about mobile computing. The novelty of our approach rests with the notion of allowing transient interactions among programs which move in space. We restrict our concern to pairwise interactions involving variable sharing and action synchronization. The motivation behind the transient nature of the interactions comes from the fact that components can communicate with each other only when they are within a certain range. The notation we propose is meant to simplify the writing of mobile applications and is a direct extension of that used in UNITY. Reasoning about mobile computations relies on the UNITY proof logic.
Sulfur cleaning for (100), (111)A, and (111)B InGaAs surfaces with In content of 0.53 and 0.70 and their Al<inf>2</inf>O<inf>3</inf>/InGaAs MOS interface properties (2012)

We have studied the impact of sulfur cleaning for (100), (111)A, and (111)B InGaAs surfaces with In content of 0.53 and 0.70 and their Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /InGaAs MOS interfaces using an (NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> solution. We found that the sulfur cleaning can effectively remove native oxides from InGaAs surfaces and passivate the InGaAs surfaces by sulfur atoms. Combining with trivalent oxide passivation using Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , the Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /InGaAs MOS interfaces with sulfur cleaning can realize good interface properties with the small frequency dispersion of the capacitance versus voltage (C - V) curves in accumulation region with independent of In content and the surface orientations.
A high-throughput platform for feedback-controlled directed evolution (2020)

Continuous directed evolution rapidly implements cycles of mutagenesis, selection, and replication to accelerate protein engineering. However, individual experiments are typically cumbersome, reagent-intensive, and require manual readjustment, limiting the number of evolutionary trajectories that can be explored. We report the design and validation of Phage-and-Robotics-Assisted Near-Continuous Evolution (PRANCE), an automation platform for the continuous directed evolution of biomolecules that enables real-time activitydependent reporter and absorbance monitoring of up to 96 parallel evolution experiments. We use this platform to characterize the evolutionary stochasticity of T7 RNA polymerase evolution, conserve precious reagents with miniaturized evolution volumes during evolution of aminoacyl-tRNA synthetases, and perform a massively parallel evolution of diverse candidate quadruplet tRNAs. Finally, we implement a feedback control system that autonomously modifies the selection strength in response to real-time fitness measurements. By addressing many of the limitations of previous methods within a single platform, PRANCE simultaneously enables multiplexed, miniaturized, and feedback-controlled continuous directed evolution.
Trends in shared memory multiprocessing (1997)

Current application and technology trends are causing researchers and developers to revisit shared memory multiprocessing. The authors look at what is needed to maintain growth, particularly for commercial applications. The first step is to carefully examine the current use of shared memory multiprocessing and arrive at intelligent projections of future use based on application and technology trends. The second step is to begin filling gaps in programming models and architectures for shared memory multiprocessing. Finally-and possibly concurrently with the second step-researchers must look at ways to make the development of parallel software more feasible, including the development of compilers and tools. We look at the issues in these three steps. We also show how architectural issues are tightly interwoven with application trends.