gebhart/patrepeval huggingface dataset:
REAPR: Reconfigurable engine for automata processing (2017)

Finite automata have proven their usefulness in high-profile domains ranging from network security to machine learning. While prior work focused on their applicability for purely regular expression workloads such as antivirus and network security rulesets, recent research has shown that automata can optimize the performance for algorithms in other areas such as machine learning and even particle physics. Unfortunately, their emulation on traditional CPU architectures is fundamentally slow and further bottlenecked by memory. In this paper, we present REAPR: Reconfigurable Engine for Automata PRocessing, a flexible framework that synthesizes RTL for automata processing applications as well as I/O to handle data transfer to and from the kernel. We show that even with memory and control flow overheads, FPGAs still enable extremely high-throughput computation of automata workloads compared to other architectures.
BCL11A deletions result in fetal hemoglobin persistence and neurodevelopmental alterations (2015)

A transition from fetal hemoglobin (HbF) to adult hemoglobin (HbA) normally occurs within a few months after birth. Increased production of HbF after this period of infancy ameliorates clinical symptoms of the major disorders of adult β-hemoglobin: β-thalassemia and sickle cell disease. The transcription factor BCL11A silences HbF and has been an attractive therapeutic target for increasing HbF levels; however, it is not clear to what extent BCL11A inhibits HbF production or mediates other developmental functions in humans. Here, we identified and characterized 3 patients with rare microdeletions of 2p15-p16.1 who presented with an autism spectrum disorder and developmental delay. Moreover, these patients all exhibited substantial persistence of HbF but otherwise retained apparently normal hematologic and immunologic function. Of the genes within 2p15-p16.1, only BCL11A was commonly deleted in all of the patients. Evaluation of gene expression data sets from developing and adult human brains revealed that BCL11A expression patterns are similar to other genes associated with neurodevelopmental disorders. Additionally, common SNPs within the second intron of BCL11A are strongly associated with schizophrenia. Together, the study of these rare patients and orthogonal genetic data demonstrates that BCL11A plays a central role in silencing HbF in humans and implicates BCL11A as an important factor for neurodevelopment.
Cloning and sequencing of the <i>URA5</i> gene from the yeast <i>Yarrowia lipolytica</i> (1995)

The URA5 gene of Yarrowia lipolytica encoding the orotate phosphoribosyl transferase (OPRTase, EC2.4.2.10) was isolated by target integration in a mutant strain originally named ura2.21. The nucleotide sequence of the gene predicts a protein with high similarities with the OPRTases from Saccharomyces cerevisiae, Podospora anserina and Escherichia coli and to a lesser extent with that of Dictyostelium discoideum. The transcription start point has been mapped by primer extension analysis and indicates the existence of a long leader sequence in the corresponding mRNA. Northern-blot hybridization revealed the URA5 transcript to be approximately 0.94 kb. Deletion of the URA5 gene in Y. lipolytica produced a leaky phenotype similar to the one described for the ura5 mutation in S. cerevisiae. The URA5 gene of Y. lipolytica was able to complement functionally the ura5 mutation of S. cerevisiae.
Ka-Band 5-Bit MMIC Phase Shifter Using InGaAs PIN Switching Diodes (2011)

The design and performance of a Ka-band 5 b MMIC phase shifter using InGaAs PIN switching diodes is presented. In order to achieve low insertion loss and good phase shifting characteristics at Ka-band, a switched reactance type InGaAs PIN-diode phase shifter topology has been employed with a compact bias network. The fabricated InGaAs PIN MMIC phase shifter has demonstrated good performance characteristics such as a low insertion loss of less than 7.8 dB and a high P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> dB of 21.0 dBm compared to the previous results.
Exploration of an EEG-Based Cognitively Adaptive Training System in Virtual Reality (2019)

Virtual Reality (VR) is effective in various training scenarios across multiple domains, such as education, health and defense. However, most of those applications are not adaptive to the real-time cognitive or subjectively experienced load placed on the trainee. In this paper, we explore a cognitively adaptive training system based on real-time measurement of task related alpha activity in the brain. This measurement was made by a 32-channel mobile Electroencephalography (EEG) system, and was used to adapt the task difficulty to an ideal level which challenged our participants, and thus theoretically induces the best level of performance gains as a result of training. Our system required participants to select target objects in VR and the complexity of the task adapted to the alpha activity in the brain. A total of 14 participants undertook our training and completed 20 levels of increasing complexity. Our study identified significant differences in brain activity in response to increasing levels of task complexity, but response time did not alter as a function of task difficulty. Collectively, we interpret this to indicate the brain's ability to compensate for higher task load without affecting behaviourally measured visuomotor performance.
Efficient computation of personal aggregate queries on blogs (2008)

There is an exploding amount of user-generated content on theWeb due to the emergence of "Web 2.0" services, such as Blogger,MySpace, Flickr, and del.icio.us. The participation of a large number of users in sharing their opinion on the Web has inspired researchers to build an effective "information filter" by aggregating these independent opinions. However, given the diverse groups of users on the Web nowadays, the global aggregation of the information may not be of much interest to different groups of users. In this paper, we explore the possibility of computing personalized aggregation over the opinions expressed on the Web based on a user's indication of trust over the information sources. The hope is that by employing such "personalized" aggregation, we can make the recommendation more likely to be interesting to the users. We address the challenging scalability issues by proposing an efficient method, that utilizes two core techniques: Non-Negative Matrix Factorization and Threshold Algorithm, to compute personalized aggregations when there are potentially millions of users and millions of sources within a system. We show that, through experiments on real-life dataset, our personalized aggregation approach indeed makes a significant difference in the items that are recommended and it reduces the query computational cost significantly, often more than 75%, while the result of personalized aggregation is kept accurate enough.
Evaluation of the safety, pharmacokinetics and treatment effects of an α<sub>ν</sub>β<sub>3</sub> integrin inhibitor on bone turnover and disease activity in men with hormone‐refractory prostate cancer and bone metastases (2010)

MK-0429 was generally well tolerated, with the most common side-effect being nausea. There was some evidence of an early reduction of bone turnover, indicating a potential for clinical use in the treatment of MBD although serum PSA was unexpectedly increased during the study.
An International Survey of Computer Models for Fire and Smoke (1992)

At the request of the Forum for International Cooperation on Fire Research, a worldwide survey was conducted of operational computer programs relevant to fire protection. A total of 62 programs, from 10 countries, were identified, and include compartment fire models, fire-sprinkler interaction models, and submodels for fire endurance, building evacuation, thermal detector actuation, fire spread on a wall, and smoke movement. These are listed, plus 12 additional models, including models from three additional coun tries. Then a general discussion is provided of the difficulties in achieving an accurate model of a growing fire in an enclosure, and of assessing the accuracy of a given model.
Interactions between the double-stranded RNA binding motif and RNA: definition of the binding site for the interferon-induced protein kinase DAI (PKR) on adenovirus VA RNA. (1995)

The protein kinase DAI, the double-stranded RNA activated inhibitor of translation (also known as PKR), regulates cell growth, virus infection, and other processes. DAI represents a class of proteins containing a recently recognized RNA binding motif, the dsRBM, but little is known about the contacts between these proteins and their RNA ligands. In adenovirus-infected cells, DAI activation is prevented by VA RNAI, a highly structured RNA that binds to the kinase. VA RNA contains three chief structural features: a terminal stem, an apical stem-loop, and a complex central domain. We used enzymatic and chemical footprinting to identify the interactions between DAI and VA RNAI. DAI protects the proximal part of the apical stem structure, an adjacent region in the central domain, and a region surrounding a conserved stem in the central domain from nuclease attack. During binding the RNA undergoes a conformational change that is mainly restricted to the central domain. A similar change is induced by magnesium ions alone. Footprinting and interference binding assays using base-specific chemical probes suggest that the protein does not make major contacts with RNA bases. On the other hand, footprinting with probes specific for the RNA backbone shows that DAI engages in a strong interaction with the minor groove of the apical stem and a weaker interaction in the central domain. A truncated form of DAI, p20, containing only the RNA binding domain, gives a similar protection pattern in the apical stem but protects the central domain less effectively. We conclude that the RNA binding domain of DAI interacts directly with the apical stem and central domain of VA RNA, and that other regions of the protein contribute to interactions with the central domain.
Mueller and Kennaugh matrices in radar polarimetry (1994)

This paper is concerned with the notions of the Mueller matrix and the Kennaugh (or Stokes scattering) matrix, that are commonly used in the field of radar polarimetry. Although these two matrices are quite similar, there exists a basic difference between them that seems to have been overlooked by a number of researchers, resulting in a great deal of confusion. An attempt is made to clarify this point and to present the basic relationships of radar polarimetry in a compact form.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Shiga Toxin 2-Producing <i>Acinetobacter haemolyticus</i> Associated with a Case of Bloody Diarrhea (2006)

We report the first Shiga toxin 2-producing Acinetobacter haemolyticus strain that was isolated from the feces of a 3-month-old infant with bloody diarrhea. Usual enteropathogenic bacteria were not detected. This finding suggests that any Shiga toxin-producing microorganism capable of colonizing the human gut may have the potential to cause illness.
ChemInform Abstract: Report from Commission on Nomenclature of Organic Chemistry. (1976)

Abstract Rules for the Nomenclature of Organic Chemistry. Section E: Stereochemistry.
Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres (2015)

In brain regions containing crossing fibre bundles, voxel-average diffusion MRI measures such as fractional anisotropy (FA) are difficult to interpret, and lack within-voxel single fibre population specificity. Recent work has focused on the development of more interpretable quantitative measures that can be associated with a specific fibre population within a voxel containing crossing fibres (herein we use fixel to refer to a specific fibre population within a single voxel). Unfortunately, traditional 3D methods for smoothing and cluster-based statistical inference cannot be used for voxel-based analysis of these measures, since the local neighbourhood for smoothing and cluster formation can be ambiguous when adjacent voxels may have different numbers of fixels, or ill-defined when they belong to different tracts. Here we introduce a novel statistical method to perform whole-brain fixel-based analysis called connectivity-based fixel enhancement (CFE). CFE uses probabilistic tractography to identify structurally connected fixels that are likely to share underlying anatomy and pathology. Probabilistic connectivity information is then used for tract-specific smoothing (prior to the statistical analysis) and enhancement of the statistical map (using a threshold-free cluster enhancement-like approach). To investigate the characteristics of the CFE method, we assessed sensitivity and specificity using a large number of combinations of CFE enhancement parameters and smoothing extents, using simulated pathology generated with a range of test-statistic signal-to-noise ratios in five different white matter regions (chosen to cover a broad range of fibre bundle features). The results suggest that CFE input parameters are relatively insensitive to the characteristics of the simulated pathology. We therefore recommend a single set of CFE parameters that should give near optimal results in future studies where the group effect is unknown. We then demonstrate the proposed method by comparing apparent fibre density between motor neurone disease (MND) patients with control subjects. The MND results illustrate the benefit of fixel-specific statistical inference in white matter regions that contain crossing fibres.
Cachexia: prevalence and impact in medicine (2008)

There is a high prevalence of (pre)cachexia in patients with chronic diseases. The cachexia syndrome is probably less frequent but has a significant impact in terms of morbidity and mortality.
Photoacidic and Photobasic Behavior of Transition Metal Compounds with Carboxylic Acid Group(s) (2016)

Excited state proton transfer studies of six Ru polypyridyl compounds with carboxylic acid/carboxylate group(s) revealed that some were photoacids and some were photobases. The compounds [Ru(II)(btfmb)2(LL)](2+), [Ru(II)(dtb)2(LL)](2+), and [Ru(II)(bpy)2(LL)](2+), where bpy is 2,2'-bipyridine, btfmb is 4,4'-(CF3)2-bpy, and dtb is 4,4'-((CH3)3C)2-bpy, and LL is either dcb = 4,4'-(CO2H)2-bpy or mcb = 4-(CO2H),4'-(CO2Et)-2,2'-bpy, were synthesized and characterized. The compounds exhibited intense metal-to-ligand charge-transfer (MLCT) absorption bands in the visible region and room temperature photoluminescence (PL) with long τ > 100 ns excited state lifetimes. The mcb compounds had very similar ground state pKa's of 2.31 ± 0.07, and their characterization enabled accurate determination of the two pKa values for the commonly utilized dcb ligand, pKa1 = 2.1 ± 0.1 and pKa2 = 3.0 ± 0.2. Compounds with the btfmb ligand were photoacidic, and the other compounds were photobasic. Transient absorption spectra indicated that btfmb compounds displayed a [Ru(III)(btfmb(-))L2](2+)* localized excited state and a [Ru(III)(dcb(-))L2](2+)* formulation for all the other excited states. Time dependent PL spectral shifts provided the first kinetic data for excited state proton transfer in a transition metal compound. PL titrations, thermochemical cycles, and kinetic analysis (for the mcb compounds) provided self-consistent pKa* values. The ability to make a single ionizable group photobasic or photoacidic through ligand design was unprecedented and was understood based on the orientation of the lowest-lying MLCT excited state dipole relative to the ligand that contained the carboxylic acid group(s).
Offline Impairment-Aware Routing and Wavelength Assignment Algorithms in Translucent WDM Optical Networks (2009)

Physical impairments in optical fiber transmission necessitate the use of regeneration at certain intermediate nodes, at least for certain lengthy lightpaths. We design and implement impairment-aware algorithms for routing and wavelength assignment (IA-RWA) in translucent optical networks. We focus on the offline version of the problem, where we are given a network topology, the number of available wavelengths and a traffic matrix. The proposed algorithm selects the 3R regeneration sites and the number of regenerators that need to be deployed on these sites, solving the regenerator placement problem for the given set of requested connections. The problem can be also posed in a slightly different setting, where a (sparse) placement of regenerators in the network is given as input and the algorithm selects which of the available regenerators to use, solving the regenerator assignment problem. We formulate the problem of regenerator placement and regenerator assignment, as a virtual topology design problem, and address it using various algorithms, ranging from a series of integer linear programming (ILP) formulations to simple greedy heuristic algorithms. Once the sequence of regenerators to be used by the non-transparent connections has been determined, we transform the initial traffic matrix by replacing non-transparent connections with a sequence of transparent connections that terminate and begin at the specified 3R intermediate nodes. Using the transformed matrix we then apply an IA-RWA algorithm designed for transparent (as opposed to translucent) networks to route the traffic. Blocked connections are re-routed using any remaining regenerator(s) in the last phase of the algorithm.
Fourier Transform Infrared Spectroscopy of Skin Cancer Cells and Tissues (2009)

Abstract The aim of this review is to combine all the information related to the characterization of skin tissues and cells, focusing on the identification of the specific biochemical characteristics of skin cancer. We have characterized two types of melanoma by FTIR spectroscopy: a murine melanoma (B16F10 cell line) and a human melanoma (C8161 cell line). The cells were deposited on IR transparent CaF2 windows, the spectral range used lay between 900-4000 cm− 1, transmission mode with 2 cm− 1 resolution, and 32 scans. A biochemical association is presented for all the absorption bands identified in this study. Besides the characterization of both cell lines above, a collection of works done in the area of skin cancer was also carried out, in this review; some interesting results obtained by different authors with respect to the characterization of different samples (melanomas, follicle sheath, basal cell carcinoma, epidermis tissues, dermis tissue, and human stratum corneum) are presented and compared to the chemical and biological associations performed in each case. The identification of biochemical injuries provides important information that, associated with clinical examination, can assist the diagnosis of diseases. Several FTIR techniques can be used in the diagnosis of biochemical changes in biological tissues, by identifying molecular markers associated with malignant and benign changes or variations in the composition of amino acids in tissues and cells. In the near future, a further study to compare histopatological analysis and biochemical characterization by FTIR spectroscopy would be interesting, in order to verify the accuracy and validate the applicability of this technique in the diagnosis of skin lesions from a statistical viewpoint. Keywords: MelanomacarcinomamicrospectroscopyATRFTIR ACKNOWLEDGEMENTS This research was supported by Capes (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) and FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo). Notes (∗) have a distinct assignment from that indicated by most of the other authors.
Suppression of Specific and Bystander IgE Responses in a Mouse Model of Oral Sensitization to β-Lactoglobulin (2001)

In orally sensitized mice, bystander IgE suppression depended on the dose of tolerogen, but also on its mode of administration. Mucosally induced IgE responses were suppressed by a mechanism that was distinct from that operating in the periphery.
Inappropriate closeness in fieldwork?: A view from anthropology of education (2008)

In the earliest decades of anthropological fieldwork in the late nineteenth century, fieldwork relationships with informants appear to have been anything but overly close. The stereotype of the anthropologist in the American Southwest is that of a white man who sat on the steps of the trading post and paid Indians to tell him words in their language. Attempts were made to elicit information on kinship systems through direct and imperious questioning: “What do you call your mother's brother?” The analogous British and German stereotypes were of those who sat on the verandah of the local colonial officer's house, conducting themselves similarly with “the natives.”
Retracted: Regional Differences in Brain-Derived Neurotrophic Factor Levels and Dendritic Spine Density Confer Resilience to Inescapable Stress (2015)

The results suggest that regional differences in BDNF levels and spine density in rat brain may contribute to resilience to inescapable stress.
Design and Synthesis of Novel α<sub>1</sub><sub>a</sub> Adrenoceptor-Selective Antagonists. 1. Structure−Activity Relationship in Dihydropyrimidinones (1999)

Dihydropyrimidinones such as compound 12 exhibited high binding affinity and subtype selectivity for the cloned human alpha(1a) receptor. Systematic modifications of 12 led to identification of highly potent and subtype-selective compounds such as (+)-30 and (+)-103, with high binding affinity (K(i) = 0.2 nM) for alpha(1a) receptor and greater than 1500-fold selectivity over alpha(1b) and alpha(1d) adrenoceptors. The compounds were found to be functional antagonists in human, rat, and dog prostate tissues. Compound (+)-103 exhibited excellent selectively to inhibit intraurethral pressure (IUP) as compared to lowering diastolic blood pressure (DBP) in mongrel dogs (K(b)(DBP)/K(b)(IUP) = 40) suggesting uroselectivity for alpha(1a)-selective compounds.
Adaptive admission congestion control (1991)

In this paper, we describe a novel congestion control scheme for high-speed networks. The scheme is based on periodic transmission through the network of time-stamped sampling packets that sense the congestion status of the network. Upon reception, the sampling packet delays are calculated, averaged, and used to determine the state of the network. The information on the state of the network is then used to drive the network adaptive admission control. The major advantage of the proposed scheme over conventional congestion control techniques is that it copes with traffic surges that are shorter than the network round-trip delay. This is achieved by controlling traffic admission with continuous estimate of the network state. The scheme is targeted toward networks that carry aggregated traffic, and can be applied to ATM-based networks.