gebhart/patrepeval huggingface dataset:
Transgenic mice harboring a full-length human mutant DRPLA gene exhibit age-dependent intergenerational and somatic instabilities of CAG repeats comparable with those in DRPLA patients (1999)

Dentatorubral-pallidoluysian atrophy (DRPLA) is one among an increasing number of hereditary neurodegenerative diseases determined as being caused by unstable expansion of CAG repeats coding for polyglutamine stretches. To investigate the molecular mechanisms underlying CAG repeat instability, we established three transgenic lines each harboring a single copy of a full-length human mutant DRPLA gene carrying a CAG repeat expansion. These transgenic mice exhibited an age-dependent increase (+0.31 per year) in male transmission and an age-dependent contraction (-1.21 per year) in female transmission. Similar tendencies in intergenerational instabilities were also observed in human DRPLA parent-offspring pairs. The intergenerational instabilities of the CAG repeats may be interpreted as being derived from the instability occurring during continuous cell division of spermatogonia in the male, and that occurring during the period of meiotic arrest in the female. The transgenic mice also exhibited an age-dependent increase in the degree of somatic mosaicism which occurred in a cell lineage-dependent manner, with the size range of CAG repeats being smaller in the cerebellum than in other tissues including the cerebrum, consistent with observations in autopsied tissues of DRPLA patients. Thus, the transgenic mice described in this study exhibited age-dependent intergenerational as well as somatic instabilities of expanded CAG repeats comparable with those observed in human DRPLA patients, and are therefore expected to serve as good models for investigating the molecular mechanisms of instabilities of CAG repeats.
Implementation of OFDM modem for the physical layer of IEEE 802.11a standard based on Xilinx Virtex-II FPGA (2005)

A prototype design, which is based on the orthogonal frequency division multiplexing (OFDM) technique, is presented for the physical layer of the IEEE 802.11a standard. Implementation aspects of an OFDM modem on a Xilinx field programmable gate array (FPGA) are addressed. The system includes synchronization circuitry used for packet detection and time synchronization. The demonstrated design flow shows an approach to implementing and prototyping the architecture of a real-time base-band OFDM modem. This design is efficiently synthesized on a 0.15 /spl mu/m/0.12 /spl mu/m CMOS 8-layer metal process Virtex-II FPGA. The resulting hardware implementation is analyzed and simulated for a system clock speed of 72 MHz to verify adequate performance.
DroidWalker: Generating Reproducible Test Cases via Automatic Exploration of Android Apps (2017)

Generating test cases through automatic app exploration is very useful for analyzing and testing Android apps. However, test cases generated by current app-exploration tools are not reproducible, i.e. when the generated test case is re-executed, the app cannot reach the same state as the explored one. As a result, app developers are not able to reproduce the failure or crash reported during the exploration, to conduct regression test after fixing the bug, or to execute the same test in different environments. In this paper, we present DroidWalker, a dynamic-analysis tool to generate reproducible test cases for Android apps. The key design of our tool is a dynamic-adaptive model that can abstract the app state in a proper granularity so every state in the model can be reached afterwards. Given an app under test, DroidWalker first explores the app to build the model. Then developers can select the state in the model to be reproduced. Finally, DroidWalker executes all the generated test cases and the app could reach exactly the same state as the explored one. We apply DroidWalker in three real usage scenarios to demonstrate its practical usage. The video of our tool is at https://youtu.be/ndUD8Gxs800.
Mechanism of Vitamin C Inhibition of Cell Death Induced by Oxidative Stress in Glutathione-depleted HL-60 Cells (2001)

Vitamin C is a well known antioxidant whose precise role in protecting cells from oxidative challenge is uncertain. In vitro results have been confounded by pro-oxidant effects of ascorbic acid and an overlapping role of glutathione. We used HL-60 cells as a model to determine the precise and independent role of vitamin C in cellular protection against cell death induced by oxidative stress. HL-60 cells do not depend on glutathione to transport or reduce dehydroascorbic acid. Depletion of glutathione rendered the HL-60 cells highly sensitive to cell death induced by H2O2, an effect that was not mediated by changes in the activities of glutathione reductase, glutathione peroxidase, catalase, or superoxide dismutase. The increased sensitivity to oxidative stress was largely reversed when glutathione-depleted cells were preloaded with ascorbic acid by exposure to dehydroascorbic acid. Resistance to H2O2 treatment in cells loaded with vitamin C was accompanied by intracellular consumption of ascorbic acid, generation of dehydroascorbic acid, and a decrease in the cellular content of reactive oxygen species. Some of the dehydroascorbic acid generated was exported out of the cells via the glucose transporters. Our data indicate that vitamin C is an important independent antioxidant in protecting cells against death from oxidative stress.
Performance and efficiency tradeoffs in blockchain overlay networks (2022)

Underlying blockchain's scalability and performance is a Peer-to-Peer (P2P) overlay network and protocols for relaying blocks and transactions among participating nodes. In this work, we model and perform a systematic analysis of blockchain communication protocols. We begin by introducing the performance metric of interest for blockchains, the sequence of ordered-completion-times, which captures the progress distributed nodes are making in jointly constructing a consistent blockchain. We then study the characteristics of block relaying protocols. In particular, we show that when nodes cannot perform cut-through relaying, there is no optimal causal block relaying protocol if block relaying times are deterministic. We propose a simple age-based block relaying protocol that is provably near-optimal in terms of minimizing ordered-completion-times when the P2P overlay network is a tree. This analysis is relevant to blockchain relay networks such as Bitcoin-Fibre, Bloxroute etc., where the core part of the overlay is a tree. Finally, using the insights derived for tree overlays, we explore the interplay between transaction and block relaying and prioritization (age, size, FCFS based) on both tree and fully connected overlays via simulation. We observe that policies that relay blocks and incorporate transactions into blocks based on 'age' outperform other natural policies. We also explore a fundamental tradeoff between mining and computational efficiencies and performance (in terms of ordered completion times).
Space-time cut-off rate for the flat Rayleigh fading channel (2002)

The computational cut-off rate is studied for the complex Rayleigh flat fading spatio-temporal channel under a peak power constraint. Any optimal finite constellation of signals must admit an equalizer distribution which equalizes the conditional decoding error probabilities. For small constellations the set of equiprobable mutually-orthogonal unitary matrices attains cut-off rate. For low SNR these matrices are rank one and a single transmit antenna is as good as multiple antennas.
Detection of Aromatic α-Hydroxyketones with Tetrazolium Salts (2003)

In principle there are two ways for the biocatalytic synthesis of α-hydroxyketones. Oxidoreductases may be used to convert diketones or diols into the respective α-hydroxyketones. This kind of reaction is exploited, e.g., in the industrial synthesis of the α-glucosidase inhibitor miglitol ([2R,3R,4R,5S]-1-[2-hydroxyethyl]-2-[hydroxymethyl]-3,4,5-piperidintriole) (). Alternatively, thiamine diphosphate dependent transketolases are capable of synthesizing α-hydroxyketones by catalyzing the transfer of activated glycolaldehyde (). In natural biosyntheses these enzymes are usually found in sugar metabolism. Another thiamine diphosphate-dependent enzyme is used for the industrial production of R-phenylacetylcarbinol ([1R]-1-hydroxy-1-phenyl-propan-2-one). R-phenylacetylcarbinol (R-PAC) is the first chiral intermediate in the production process of pseudoephedrine and ephedrine. Since 1921, it has been known that yeast (Saccharomyces cerevisiae) are able to catalyze the formation of R-PAC (,). The further synthetic steps from R-PAC to pseudoephedrine are carried out by classical chemical synthesis (). The actual enzyme in yeast catalyzing the synthesis of R-PAC is pyruvate decarboxylase (PDC; EC 4.1.1.1). In vivo this enzyme converts pyruvate to acetaldehyde. 2-α-Hydroxyethyl-thiamine diphosphate (“activated acetaldehyde”) is an intermediate of the catalytic cycle of PDC. Its α-carbanion reacts with several aldehydes in a nucleophilic attack to form the respective acyloins (). In this manner, benzaldehyde and pyruvic acid form R-PAC and CO2
Redox Proteomics: A New Approach to Investigate Oxidative Stress in Alzheimer's Disease (2006)

This chapter contains sections titled: Introduction Brain Tissue and Models Used in Studying Aβ(1–42)-Induced Oxidative Stress and Neurotoxicity in AD Redox Proteomics Oxidatively Modified Proteins in AD and AD Models by Redox Proteomics Conclusion
The effect of haemoglobin on tissue oxygenation in critical illness (2011)

University of Nottingham, Department of Anaesthesiology and Intensive Care, Nottingham, United Kingdom
Basis for design of industrial wastewater treatment plants (2016)

Designs for wastewater treatment plants associated with petrochemical production and petroleum-refining facilities are most reliable when wastewaters have been fully characterized and the performance characteristics of alternative treatment processes have been fully evaluated. Physical-chemical treatment is and will continue to serve as an important adjunct for pretreatment of specialty streams. While oxygen requirements can be established in a fairly forthright manner, bench-scale units do not lend themselves to meaningful prediction of sludge production. With these wastewaters, designers mayhave to use sophisticated concepts to ensure biological removal of ammonia nitrogen. High concentrations of amines may present particular challenges. Treatability studies can identify waste streams and perhaps even component discharges that can be removed or pretreated to promote nitrification of the total wastewaters. An appropriate treatment sequence for a particular wastewater treatment and disposal requirement can only be developed after detailed treatability studies have been conducted involving biological treatment, chemical addition, powdered activated carbon addition, postfiltration, and fixed-bed carbon polishing. The applicability of the activated carbon process in treating industrial wastewaters, for example, is contingent on many factors, including the amenability of the dissolved constituents to sorption, the presence of other substances that enhance or impede the sorption process, the soundness ofmore » engineering,, the degree of pretreatment, and the proper operation and maintenance of the system. As activated carbon was one of the primary processes factored into the development of the 1983 BAT guidelines for many industrial categories, some of which have been remanded by the courts, it is important to fully understand the process and its limitations. 12 figures, 1 table.« less
Fault Injection Based Interventional Causal Learning for Distributed Applications (2023)

We apply the machinery of interventional causal learning with programmable interventions to the domain of applications management. Modern applications are modularized into interdependent components or services (e.g. microservices) for ease of development and management. The communication graph among such components is a function of application code and is not always known to the platform provider. In our solution we learn this unknown communication graph solely using application logs observed during the execution of the application by using fault injections in a staging environment. Specifically, we have developed an active (or interventional) causal learning algorithm that uses the observations obtained during fault injections to learn a model of error propagation in the communication among the components. The “power of intervention” additionally allows us to address the presence of confounders in unobserved user interactions. We demonstrate the effectiveness of our solution in learning the communication graph of well-known microservice application benchmarks. We also show the efficacy of the solution on a downstream task of fault localization in which the learned graph indeed helps to localize faults at runtime in a production environment (in which the location of the fault is unknown). Additionally, we briefly discuss the implementation and deployment status of a fault injection framework which incorporates the developed technology.
The study of chemical micromechanism governing detonation initiation of somem-dinitrobenzopolyazaarenes (2002)

Abstract Electronic charges, q, at nitrogen atoms of twelve m-dinitrobezopolyazaarenes were calculated by means of ab initio HF/6–31G∗∗ and semi-empirical AM1 methods. The relationships have been confirmed between squares of the detonation velocities or, as the case may be, the detonation heats of the azaarenes and q-values for primarily split off nitro groups. These relationships were considered as an analogue of modified Evans-Polanyi-Semenov equation and so they directly specify the most reactive nitro groups of m-dinitrobenzopolyazaarene molecules in the detonation.
Medial Temporal Theta/Alpha Power Enhancement Precedes Successful Memory Encoding: Evidence Based on Intracranial EEG (2011)

Not only poststimulus, but also prestimulus neural activity has been shown to be predictive for later successful memory encoding. However, it is still not clear which medial temporal lobe processes precede effective memory formation. Here, our aim was to investigate whether such prestimulus markers for successful memory encoding can be specified based on intracranial recordings directly from the hippocampus and rhinal cortex. For this purpose, we analyzed subsequent memory effects during a continuous word recognition paradigm in 31 presurgical epilepsy patients. We found that rhinal and hippocampal theta and successive alpha power enhancement before word presentation predicted successful memory encoding. Previous studies suggest that stimulus-triggered hippocampal theta activity is particularly related to memory retrieval and activation of a mnemonic context, whereas the alpha rhythm reflects inhibitory top-down control of task processing and executive functioning. In line with these suggestions, we propose that the observed medial temporal theta and alpha power increases before stimulus presentation reflect activation of contextual information and inhibitory top-down control processes preparing for stimulus-triggered memory processing.
Minichromosome maintenance-2 (MCM2) expression differentiates oral squamous cell carcinoma from pre-cancerous lesions. (2015)

The findings indicated that Mcm-2 could be a useful marker for early detection of oral SCC and dysplasia. Also, due to the overexpression of this marker in OSCC, there exists the possibility of application of Mcm-2 for molecular target therapy in these patients.
Uncovering a tumor-suppressor function for Drosophila Polycomb group genes (2010)

Comment on: Martinez AM, et al. Nat Genet 2009; 41:1076-82.
N-Substituent modulation of opiate agonist/antagonist activity in resolved 3-methyl-3-(m-hydroxyphenyl)piperidines (1986)

A series of 3-methyl-3-(m-hydroxyphenyl)piperidines with N-substituent variations have been synthesized and resolved, and an X-ray crystal structure of one analogue was determined. The compounds have been characterized, pharmacologically, by detailed opiate receptor binding studies and determination of in vivo analgesia and opiate antagonism. The results indicate that all compounds bind with high selectivity and moderate affinity to mu-receptors with no qualitative difference between enantiomeric pairs. By contrast a striking difference in activities is found, with the (-) enantiomers being pure agonists and the (+) enantiomers having both agonist and antagonist activity. The effect of N-substituents on relative agonist and antagonist potency does not mimic that of fused ring opiates with the N-phenethyl compound, the most potent antagonist. These results together with the X-ray structure obtained suggest that agonist and antagonist activity is initiated by a bimodel binding of the compounds in two different orientations at the mu-receptor site.
The Critical Role of Materials’ Interaction in Realizing Organic Field-Effect Transistors Via High-Dilution Blending with Insulating Polymers (2020)

High-performance low-band-gap polymer semiconductors are visibly colored, making them unsuitable for transparent and imperceptible electronics without reducing film thickness to the nanoscale range. Herein, we demonstrate polymer/insulator blends exhibiting favorable miscibility that improves the transparency and carrier transport in an organic field-effect transistor (OFET) device. The mesoscale structures leading to more efficient charge transport in ultrathin films relevant to the realization of transparent and flexible electronic applications are explored based on thermodynamic material interaction principles in conjunction with optical and morphological studies. By blending the commodity polymer polystyrene (PS) with two high-performing polymers, PDPP3T and P (NDI2OD-T2) (known as N2200), a drastic difference in morphology and fiber network are observed due to considerable differences in the degree of thermodynamic interaction between the conjugated polymers and PS. Intrinsic material interaction behavior establishes a long-range intermolecular interaction in the PDPP3T polymer fibrillar network dispersed in the majority (80%) PS matrix resulting in a ca. 3-fold increased transistor hole mobility of 1.15 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup> (highest = 1.5 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>) as compared to the pristine material, while PS barely affects the electron mobility in N2200. These basic findings provide important guidelines to achieve high mobility in transparent OFETs.
Weak Calcium-Mediated Interactions between Lewis X-Related Trisaccharides Studied by NMR Measurements of Residual Dipolar Couplings (2007)

The Lewis X (LeX) determinant, a trisaccharide with the carbohydrate sequence Galbeta(1-->4)[Fucalpha(1-->3)]GlcNAcbeta, is believed to be responsible for Ca2+-mediated cell-cell interactions. In partly oriented phases composed of mixtures of penta(ethyleneglycol)monododecyl ether HO(CH2CH2O)5C12H25 and n-hexanol in the presence of Ca2+ ions, the variation of the residual dipolar couplings 1DCH of various CiHi vectors in LeX as a function of the concentration of the trisaccharide demonstrates the existence of very weak LeX-Ca2+-LeX complexes in solution. Synthetic 3-, 4-, and 6-deoxy-LeX variants were also shown to form complexes in the presence of calcium ions, despite the replacement of one of their hydroxyl groups by hydrogen atoms. This is the first direct observation in solution of a calcium-mediated interaction between LeX molecules.
Thermo-mechanical and electrical characterization of through-silicon vias with a vapor deposited polyimide dielectric liner (2012)

A study using a vapor deposited polyimide (VDP) dielectric liner to electrically isolate through-silicon vias (TSVs) has demonstrated electrical and thermo-mechanical performance superior to sub-atmospheric chemically vapor deposited (SACVD) tetraethyl orthosilicate (TEOS) liner in 5 μm × 50 μm TSVs. The VDP liner is continuous and highly conformal, with a worst-case coverage of 85% relative to the target deposition thickness. Moreover, the material integrates through TSV metallization, anneal, and polish. Electrically, VDP provides lower inter-via capacitance than the more conventional SACVD TEOS liner. Mechanically, blanket film stress of VDP measured as a function of temperature shows no hysteresis up to 400°C and a stress delta during cycling of only 45 MPa. The delta is an order of magnitude lower than SACVD TEOS. The thermo-mechanical behavior of VDP also results in a lower residual stress in the silicon area surrounding the structure, which enables a smaller keep-away zone for TSVs and effectively increases the density of transistors in silicon for 3D integrated systems.
Support Vector Method for Novelty Detection (1999)

Suppose you are given some dataset drawn from an underlying probability distributionPand you want to estimate a “simple ” subsetSof input space such that the probability that a test point drawn from P lies outside of Sequals some a priori specified between0and1. We propose a m ethod to approach this problem by trying to estimate a function f which is positive on S and negative on the complement. The functional form offis given by a kernel expansion in terms of a potentially small subset of the training data; it is regularized by controlling the length of the weight vector in an associated feature space. We provide a theoretical analysis of the statistical performance of our algorithm. The algorithm is a natural extension of the support vector algorithm to the case of unlabelled data.
Asymptotic similarity of turbulence structures in smooth- and rough-walled pipes (1977)

Work recently reported by the authors (Perry &amp; Abell 1975) on smooth-walled pipe flow showed support for the Townsend (1976) structural similarity principle as regards viscosity not being directly relevant in controlling the mean relative motions and the energy-containing turbulent motions. The work also supported a universal spectral behaviour in the wall region of the flow. In many hypotheses for rough-walled pipe flow, surface roughness, like viscosity, enters the problem only via external boundary conditions. Data obtained in a rough pipe are reported here and on first appearance the results seem to contradict the Townsend hypothesis and to threaten the very foundation upon which many similarity laws for rough-walled flows are based. However, on closer examination of the spectrum scaling of smooth-walled pipe flow the low and high wavenumber energy not necessarily associated with the universal similarity range can be accounted for. The broad-band longitudinal turbulence results for a rough-walled pipe can then be predicted from the smooth-wall scaling. The conclusion is that, despite the apparent anomalies, the turbulence structure in a rough pipe appears to follow the same scaling laws as for a smooth pipe, given a sufficient length of flow development in both cases. The deduced functional forms are consistent with Townsend's (1976) attached-eddy hypothesis.
Equivalent network modeling of cylindrical systems with conductors in motion (1993)

Equivalent network models for the analysis of electromagnetic field distributions and forces in axisymmetric systems with linear ferromagnetic conductors in motion are presented. The infinite equivalent network model calculates the inductive parameters of the equivalent network by means of analytical expressions, obtained under the hypothesis of an infinite axial length of the system, in order to have a quick first evaluation of the system performance. The finite equivalent network model uses the magnetization vector and a magnetic scalar potential to take into account the actual finite axial length of the system in the evaluation of the inductive parameters of the equivalent network. The equivalent network model calculated results were compared with results obtained from an analytical model, and the models were then tested comparing calculated results with experimental data on a linear motor prototype.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>