gebhart/patrepeval huggingface dataset:
A Limited-Vocabulary Adaptive Speech-Recognition System (1967)

This paper describes a recently developed adaptive speech-recognition system. The system quantizes the spectrum of the speech signal in respect to frequency, amplitude, and time. A 20-bit binary feature matrix is obtained for each utterance. Each feature matrix, identified as to the word spoken, may be stored in a disk memory. With the system in its present form, up to 256 reference samples for 10 classes of words may be accumulated. When the desired number of reference samples have been obtained, the system may be used for the recognition of speech. Test words are spoken and quantized as before. The new feature matrix is compared serially with the contents of the disk memory. The degree of difference between each reference sample and the test sample is determined. If this difference is sufficiently small, the identifying information on the reference sample is decoded and a visual display actuated. This system, with the aid of the operator, adapts itself in an optimum manner to the characteristics of the speaker “training” the system. The contents of the memory may be readily changed for a different speaker or vocabulary.
Varys: protecting SGX enclaves from practical side-channel attacks (2018)

Numerous recent works have experimentally shown that Intel Software Guard Extensions (SGX) are vulnerable to cache timing and page table side-channel attacks which could be used to circumvent the data confidentiality guarantees provided by SGX. Existing mechanisms that protect against these attacks either incur high execution costs, are ineffective against certain attack variants, or require significant code modifications.

We present Varys, a system that protects unmodified programs running in SGX enclaves from cache timing and page table side-channel attacks. Varys takes a pragmatic approach of strict reservation of physical cores to security-sensitive threads, thereby preventing the attacker from accessing shared CPU resources during enclave execution. The key challenge that we are addressing is that of maintaining the core reservation in the presence of an untrusted OS.

Varys fully protects against all L1/L2 cache timing attacks and significantly raises the bar for page table side-channel attacks--all with only 15% overhead on average for Phoenix and PARSEC benchmarks. Additionally, we propose a set of minor hardware extensions that hold the potential to extend Varys' security guarantees to L3 cache and further improve its performance.
Brusatol enhances the efficacy of chemotherapy by inhibiting the Nrf2-mediated defense mechanism (2011)

The major obstacle in cancer treatment is the resistance of cancer cells to therapies. Nrf2 is a transcription factor that regulates a cellular defense response and is ubiquitously expressed at low basal levels in normal tissues due to Keap1-dependent ubiquitination and proteasomal degradation. Recently, Nrf2 has emerged as an important contributor to chemoresistance. High constitutive expression of Nrf2 was found in many types of cancers, creating an environment conducive for cancer cell survival. Here, we report the identification of brusatol as a unique inhibitor of the Nrf2 pathway that sensitizes a broad spectrum of cancer cells and A549 xenografts to cisplatin and other chemotherapeutic drugs. Mechanistically, brusatol selectively reduces the protein level of Nrf2 through enhanced ubiquitination and degradation of Nrf2. Consequently, expression of Nrf2-downstream genes is reduced and the Nrf2-dependent protective response is suppressed. In A549 xenografts, brusatol and cisplatin cotreatment induced apoptosis, reduced cell proliferation, and inhibited tumor growth more substantially when compared with cisplatin treatment alone. Additionally, A549-K xenografts, in which Nrf2 is expressed at very low levels due to ectopic expression of Keap1, do not respond to brusatol treatment, demonstrating that brusatol-mediated sensitization to cisplatin is Nrf2 dependent. Moreover, a decrease in drug detoxification and impairment in drug removal may be the primary mechanisms by which brusatol enhances the efficacy of chemotherapeutic drugs. Taken together, these results clearly demonstrate the effectiveness of using brusatol to combat chemoresistance and suggest that brusatol can be developed into an adjuvant chemotherapeutic drug.
A Direct Physical Interface for Navigation and Positioning of a Robotic Nursing Assistant (2011)

Abstract People often use direct physical contact to guide a person to a desired location (e.g., leading a child by the hand) or to adjust a person's posture for a task (e.g., a dance instructor working with a dancer). When a user is in close proximity to a robot, physical contact becomes a potentially valuable channel for communication. We define a direct physical interface (DPI) as an interface that enables a user to influence a robot's behavior by making contact with its body. We evaluated a DPI in a controlled laboratory setting with 18 nurses and compared its performance with that of a comparable gamepad interface. The DPI significantly outperformed the gamepad according to several objective and subjective measures. Nurses also tended to exert more force at the robot's end-effectors and command higher velocities when using the DPI to perform a navigation task compared with using the DPI to perform a positioning task. Based on user surveys, we identify various nursing tasks where robotic assistance may be useful and provide design recommendations specifically in the area of healthcare. Keywords: HEALTHCARE ROBOTICSNURSINGDIRECT PHYSICAL INTERFACEHUMAN-ROBOT INTERACTIONUSER STUDY
Structure of the <i>β<sub>2</sub></i> homodimer of bacterial luciferase from <i>vibrio harveyi</i>: X‐ray analysis of a kinetic protein folding trap (1997)

Luciferase, as isolated from Vibrio harveyi, is an alpha beta heterodimer. When allowed to fold in the absence of the alpha subunit, either in vitro or in vivo, the beta subunit of enzyme will form a kinetically stable homodimer that does not unfold even after prolonged incubation in 5 M urea at pH 7.0 and 18 degrees C. This form of the beta subunit, arising via kinetic partitioning on the folding pathway, appears to constitute a kinetically trapped alternative to the heterodimeric enzyme (Sinclair JF, Ziegler MM, Baldwin TO. 1994. Kinetic partitioning during protein folding yields multiple native states. Nature Struct Biol 1: 320-326). Here we describe the X-ray crystal structure of the beta 2 homodimer of luciferase from V. harveyi determined and refined at 1.95 A resolution. Crystals employed in the investigational belonged to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 58.8 A, b = 62.0 A, and c = 218.2 A and contained one dimer per asymmetric unit. Like that observed in the functional luciferase alpha beta heterodimer, the major tertiary structural motif of each beta subunit consists of an (alpha/beta)8 barrel (Fisher AJ, Raushel FM, Baldwin TO, Rayment I. 1995. Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution. Biochemistry 34: 6581-6586). The root-mean-square deviation of the alpha-carbon coordinates between the beta subunits of the hetero- and homodimers is 0.7 A. This high resolution X-ray analysis demonstrated that "domain" or "loop" swapping has not occurred upon formation of the beta 2 homodimer and thus the stability of the beta 2 species to denaturation cannot be explained in such simple terms. In fact, the subunit:subunit interfaces observed in both the beta 2 homodimer and alpha beta heterodimer are remarkably similar in hydrogen-bonding patterns and buried surface areas.
End-of-life issues. (2001)

In the Western world we have not fully accepted the fact that dying is indeed part of the process of living. Even today in the 21st century, physicians who have historically been taught to diagnose and treat disease with the expectation of cure, still regard death as a failure. We need to be reminded of the 15th-century definition of medical care, "To cure sometimes, to relieve often, to comfort always." We must realise that we cannot defy death and that every individual on earth has no choice but to travel the journey, be it long or short, from birth to ultimate death.
Adaptation of H9N2 AIV in guinea pigs enables efficient transmission by direct contact and inefficient transmission by respiratory droplets (2015)

H9N2 avian influenza viruses circulate worldwide in poultry and have sporadically infected humans, raising concern whether H9N2 viruses have pandemic potential. Here, we use a guinea pig model to examine whether serial passage results in adaptive viral changes that confer a transmissible phenotype to a wild-type H9N2 virus. After nine serial passages of an H9N2 virus through guinea pigs, productive transmission by direct contact occurred in 2/3 guinea pig pairs. The efficiency of transmission by direct contact increased following the fifteenth passage and occurred in 3/3 guinea pig pairs. In contrast, airborne transmission of the passaged virus was less efficient and occurred in 1/6 guinea pig pairs and 0/6 ferret pairs after the fifteenth passage. Three amino acid substitutions, HA1-Q227P, HA2-D46E, and NP-E434K, were sufficient for contact transmission in guinea pigs (2/3 pairs). The two HA amino acid substitutions enhanced receptor binding to α2,3-linked sialic acid receptors. Additionally, the HA2-D46E substitution increased virus thermostability whereas the NP-E434K mutation enhanced viral RNA polymerase activity in vitro. Our findings suggest that adaptive changes that enhance viral receptor binding, thermostability, and replicative capacity in mammalian cells can collectively enhance the transmissibility of H9N2 AIVs by direct contact in the guinea pig model.
Repression of Dioxin Signal Transduction in Fibroblasts (1999)

Heterodimeric complexes of basic helix-loop-helix/PAS transcription factors are involved in regulation of diverse physiological phenomena such as circadian rhythms, reaction to low oxygen tension, and detoxification. In fibroblasts, the basic helix-loop-helix/PAS heterodimer consisting of the ligand-inducible dioxin receptor and Arnt shows DNA-binding activity, and the receptor and Arnt are able to activate transcription when fused to a heterologous DNA-binding domain. However, fibroblasts are nonresponsive to dioxin with regard to induction mediated by the DNA response element recognized by the receptor and Arnt. Here we demonstrate that Arnt is associated with a fibroblast-specific factor, forming a complex that is capable of binding the dioxin response element. This factor may function as a repressor since negative regulation of target gene induction appears to be abolished by inhibition of histone deacetylase activity by trichostatin A. Finally, the negative regulatory function of this factor appears to be restricted for dioxin signaling since Arnt was able to mediate, together with hypoxia-inducible factor-1alpha, transcriptional activation in hypoxic cells. Taken together, these data suggest that fibroblast-specific inhibition of dioxin responsiveness involves recruitment by Arnt of a cell type- and signaling pathway-specific corepressor associated with a histone deacetylase.
Role of the eosinophil in allergic reactions. (1996)

The eosinophil may have several functions in health and in the pathogenesis of allergic and other diseases. Some roles of the eosinophil are based on the acute, effector responses of this cell, its capacity to generate biologically active lipid mediators and release its granule contents, including its distinctive cationic proteins. Whilst the effector responses of eosinophils are important for their contribution to the acute pathogenesis of allergic diseases, a fuller understanding of the eosinophil requires evaluation of the role this cell may play at tissue sites, especially submucosal sites, where the cell is normally localized in the absence of disease. Moreover, for the long-lived, tissue-resident eosinophil, definition of the interactions that occur between the eosinophil and other immune cells is germane to understanding the functions of eosinophils both in acute and chronic diseases. Many allergic diseases are characterized by heightened accumulation of eosinophils and are chronic ongoing diseases.
Montelukast, a Leukotriene-Receptor Antagonist, for the Treatment of Mild Asthma and Exercise-Induced Bronchoconstriction (1998)

As compared with placebo, once-daily treatment with montelukast provided significant protection against exercise-induced asthma over a 12-week period. Tolerance to the medication and rebound worsening of lung function after discontinuation of treatment were not seen.
Thioredoxin-1 and oxidative stress status in pregnant women at early third trimester of pregnancy: relation to maternal and neonatal characteristics (2012)

This study examined the clinical and biological importance of thioredoxin-1, a redox-active defensive protein that controls multiple biological functions, in pregnant women. We measured serum concentrations of thioredoxin-1, total hydroperoxides, and redox potential in 60 pregnant women at the early third trimester: gestational age of 27-29 weeks. The thioredoxin-1 concentration (mean ± SD) was 90 ± 42 ng/ml. Total hydroperoxides was 471 ± 105 U.CARR (1 U.CARR = 0.08 mg/dl H(2)O(2)). Redox potential was 2142 ± 273 µmol/l. The total hydroperoxides: redox potential ratio (oxidative stress index) was 0.23 ± 0.08. Thioredoxin-1, total hydroperoxides, and oxidative stress index were higher and redox potential was lower than in blood of healthy adults. Total hydroperoxides and redox potential were mutually correlated significantly and negatively. Thioredoxin-1 correlated significantly and negatively and redox potential correlated significantly and positively with body weight and body mass index. Thioredoxin-1 and redox potential correlated significantly and positively with uric acid and albumin, respectively. Thioredoxin-1 and oxidative stress index correlated significantly and negatively and redox potential significantly and positively with neonatal birth weight. These results suggest that high concentrations of thioredoxin-1 are linked to high oxidative stress status in pregnant women and that neonatal birth weight is affected by the maternal oxidative condition during later pregnancy.
Adopting New Orphans into the Family of Metabolic Regulators (2008)

The importance of the adopted metabolite receptors, such as peroxisome proliferator-activated receptor, liver X receptor, and farnesoid X receptor, in transcriptional control of metabolic pathways has been appreciated for many years. However, it is becoming increasingly clear that the number of nuclear receptors with roles in metabolism is much larger than initially suspected. Recent years have brought an intense effort to define the biological functions of the most enigmatic group of the nuclear receptor superfamily, the true orphan receptors, including nuclear receptor 4As, estrogen-related receptors, retinoid-related orphan receptors, and Rev-erbs. Unexpectedly, several of these receptors also turn out to have important functions in various aspects of metabolic control.
Theoretical Insights into a CO Dimerization Mechanism in CO<sub>2</sub> Electroreduction (2015)

In this work, we present DFT simulations that demonstrate the ability of Cu to catalyze CO dimerization in CO2 and CO electroreduction. We describe a previously unreported CO dimer configuration that is uniquely stabilized by a charged water layer on both Cu(111) and Cu(100). Without this charged water layer at the metal surface, the formation of the CO dimer is prohibitively endergonic. Our calculations also demonstrate that dimerization should have a lower activation barrier on Cu(100) than Cu(111), which, along with a more exergonic adsorption energy and a corresponding higher coverage of *CO, is consistent with experimental observations that Cu(100) has a high activity for C–C coupling at low overpotentials. We also demonstrate that this effect is present with cations other than H+, a finding that is consistent with the experimentally observed pH independence of C2 formation on Cu.
Comprehensive interpretation of the preferred orientation of vapor-phase grown polycrystalline silicon films (1995)

A comprehensive interpretation of the preferred orientations (PO) of poly-Si films prepared from various vapor-phase methods is presented. Existing theories and models are examined by comparing a wide variety of experimental results of PO published so far. Preferential nucleation and the conventional concept of the surface free energy are found to apply only to a limited range of deposition parameters. On the other hand, a combination of two concepts, i.e., the microscopic geometry of growing surfaces and the surface kinetics, proves to be very important in interpreting the wide variation of PO. The concept of the microscopic geometry of the surface considers the minimum numbers of atoms and bonds required for nucleation, lateral growth, and etching that characterizes the growth ability of planes. In addition, interpretation of the deposition parameter dependencies of the PO requires the concept of surface kinetics including diffusion of precursors, hydrogen coverage, and the surface reaction time which depends on the substrate temperature and gas pressure. The combined concepts can account for most of the observed POs (mainly 〈100〉 and 〈110〉) which depend on feed gases and the deposition parameters. Other specific growth modes such as facet growth or microtwins are considered for the 〈111〉 PO. The POs for n- and p-type doped films are different from those of undoped films, and their origin is also discussed in terms of their growth rates.
One-step fast deposition of thick epitaxial CdZnTe film on (001)GaAs by close-spaced sublimation (2012)

Thick epitaxial CdZnTe film has been successfully deposited on (001)GaAs substrate through a simple one-step process by close-spaced sublimation with a deposition rate of up to 1 μm min−1. Well-defined epitaxial features of the film are proved by the plan view SEM, XRDθ–2θ and ϕ scan, and the cross-sectional SEM and HRTEM analysis. A novel epitaxy mode has been discovered. The film is polycrystalline at the early stage and develops into an epitaxial layer as the deposition proceeds. The polycrystalline to single crystalline transition is completed through the lateral overgrowth and the self-organization of the layer-structured grains.
The Role of<i>NDR1</i>in Avirulence Gene-Directed Signaling and Control of Programmed Cell Death in Arabidopsis (2001)

Arabidopsis plants containing the ndr1-1 mutation are incapable of mounting a hypersensitive response to bacteria carrying avrRpt2, but show an exaggerated cell death response to bacteria carrying avrB (Century et al., 1995). We show here that ndr1-1 plants are severely impaired in induction of systemic acquired resistance and PR1-driven transcription of a reporter gene in response to Pseudomonas syringae strains carrying avrRpt2 but not in response to P. syringae carrying avrB. The ndr1-1 mutation also impaired salicylic acid (SA) accumulation in response to treatments that produced reactive oxygen species (ROS) and impaired induction of systemic acquired resistance in response to in situ production of ROS. Hydrogen peroxide accumulated in wild-type Arabidopsis leaves beginning 4 to 7 h postinoculation with P. syringae carrying either avrRpt2 or avrB. In ndr1-1 plants, P. syringae carrying avrRpt2 elicited no detectable hydrogen peroxide production. Hydrogen peroxide production in response to bacteria carrying avrB was similar to that of Columbia in kinetics but of lesser intensity at early time points. These data are interpreted to indicate that NDR1 links ROS generation to SA production and that the phenotypic consequences of the ndr1-1 mutation are caused by a reduced ability to accumulate SA upon pathogen infection.
MRShare (2010)

Large-scale data analysis lies in the core of modern enterprises and scientific research. With the emergence of cloud computing, the use of an analytical query processing infrastructure (e.g., Amazon EC2) can be directly mapped to monetary value. MapReduce has been a popular framework in the context of cloud computing, designed to serve long running queries (jobs) which can be processed in batch mode. Taking into account that different jobs often perform similar work, there are many opportunities for sharing. In principle, sharing similar work reduces the overall amount of work, which can lead to reducing monetary charges incurred while utilizing the processing infrastructure. In this paper we propose a sharing framework tailored to MapReduce. Our framework, MRShare, transforms a batch of queries into a new batch that will be executed more efficiently, by merging jobs into groups and evaluating each group as a single query. Based on our cost model for MapReduce, we define an optimization problem and we provide a solution that derives the optimal grouping of queries. Experiments in our prototype, built on top of Hadoop, demonstrate the overall effectiveness of our approach and substantial savings.
Primary glioma spheroids maintain tumourogenicity and essential phenotypic traits after cryopreservation (2006)

Tumour spheroids initiated from glioma biopsy specimens provide a valuable three-dimensional cell culture system that share several biological features of malignant brain tumours in situ. Upon xenotransplantation in immunodeficient rats, tumours derived from such spheroids exhibit a highly infiltrative growth. Successful cryopreservation of spheroid specimens therefore represents an excellent tool for future comparative studies of tumour growth and progression. Thus, if frozen stocks of human glioma spheroids can be established, similar to those obtained from cancer cell lines, it would ease the planning of biopsy-based experiments. In this context, it is crucial that cryopreservation does not alter the biological behaviour of the tumour spheroids. The biopsy spheroids were frozen to -40 degrees Celsius, stored for 1 week at -196 degrees Celsius, thawed rapidly and cultured for 1 week. The viability of the spheroids was compared against controls using a two-colour fluorescence assay, which demonstrated that cryopreservation was well tolerated. Using an in vitro invasion assay, it is shown that the freezing procedures did not affect the spheroids ability to invade a collagen gel. Cryopreserved and control tumour spheroids were equally tumourogenic, and produced overlapping survival curves when transplanted into the brains of immunocompromised rats. Immunohistochemical analyses showed no significant changes regarding microvessel density or proliferation index. Furthermore, gene expression profiling using a macroarray system detected no significant changes following cryopreservation. The present data show that cryopreservation is well tolerated, and represent a methodologically reliable storage method for biopsy spheroids that can be used in experimental studies at later time points.