gebhart/patrepeval huggingface dataset:
Generalization through Memorization: Nearest Neighbor Language Models (2019)

We introduce $k$NN-LMs, which extend a pre-trained neural language model (LM) by linearly interpolating it with a $k$-nearest neighbors ($k$NN) model. The nearest neighbors are computed according to distance in the pre-trained LM embedding space, and can be drawn from any text collection, including the original LM training data. Applying this augmentation to a strong Wikitext-103 LM, with neighbors drawn from the original training set, our $k$NN-LM achieves a new state-of-the-art perplexity of 15.79 - a 2.9 point improvement with no additional training. We also show that this approach has implications for efficiently scaling up to larger training sets and allows for effective domain adaptation, by simply varying the nearest neighbor datastore, again without further training. Qualitatively, the model is particularly helpful in predicting rare patterns, such as factual knowledge. Together, these results strongly suggest that learning similarity between sequences of text is easier than predicting the next word, and that nearest neighbor search is an effective approach for language modeling in the long tail.
An InAs channel heterojunction field-effect transistor with high transconductance (1990)

A report is presented on an InAs channel field-effect transistor (FET) based on AlGaSb/InAs/AlSb/AlGaSb structures grown by molecular-beam epitaxy. Excellent pinch-off characteristics have been obtained. An FET with a gate length of 1.7 mu m showed transconductances ranging from 460 mS/mm (at V/sub ds/=0.5 V) to 509 mS/mm (at V/sub ds/=1 V) and a K factor of 1450 mS/Vmm (at V/sub ds/=1 V) at room temperature.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The ECMWF Ensemble Prediction System: Methodology and validation (1996)

Abstract The European Centre for Medium‐Range Weather Forecasts (ECMWF) Ensemble Prediction System (EPS) is described. In addition to an unperturbed (control) forecast, each ensemble comprises 32 10‐day forecasts starting from initial conditions in which dynamically defined perturbations have been added to the operational analysis. The perturbations are constructed from singular vectors of a time‐evolution operator linearized around the short‐range‐forecast trajectory. These singular vectors approximately determine the most unstable phase‐space directions in the early part of the forecast period, and are estimated using a forward and adjoint linear version of the ECMWF numerical weather‐prediction model. An appropriate norm is chosen, and relationships between the structures of these singular vectors at initial time and patterns showing the sensitivity of short‐range forecast error to changes in the analysis are discussed. A methodology to perform a phase‐space rotation of the singular vectors is described, which generates hemispheric‐wide perturbations and renormalizes them according to analysis‐error estimates from the data‐assimilation system. The validation of the ensembles is given firstly in terms of scatter diagrams and contingency tables of ensemble spread and control‐forecast skill. The contingency tables are compared with those from a perfect‐model ensemble system; no significant differences are found in some cases. Brier scores for the probability of European flow clusters are presented, which indicate predictive skill up to forecast‐day 8 with respect to climatological probabilities. The dependence of these scores on flow‐dependent model errors is also discussed. Finally, ensemble‐member skill‐score distributions are presented, which confirm the overall satisfactory performance of the EPS, particularly in summer and autumn 1993. In winter, cases of poor performance over Europe were associated with the occurrence of a split westerly flow with a blocking high and/or a cut‐off low in the verifying analysis. Two cases are studied in detail, one having large ensemble dispersion, the other corresponding to a more predictable situation. The case studies are used to illustrate the range of ensemble products routinely disseminated to ECMWF Member States. These products include clusters of flow types, and probability fields of weather elements.
Activation of c-Jun N-terminal kinase in bacterial lipopolysaccharide-stimulated macrophages. (1996)

Activation of macrophages by bacterial lipopolysaccharide (LPS) induces transcription of genes that encode for proinflammatory regulators of the immune response. Previous work has suggested that activation of the transcription factor activator protein 1 (AP-1) is one LPS-induced event that mediates this response. Consistent with this notion, we found that LPS stimulated AP-1-mediated transcription of a transfected reporter gene in the murine macrophage cell line RAW 264.7. As AP-1 activity is regulated in part by activation of the c-Jun N-terminal kinase (JNK), which phosphorylates and subsequently increases the transcriptional activity of c-Jun, we examined whether LPS treatment of macrophages resulted in activation of this kinase. LPS treatment of RAW 264.7 cells, murine bone marrow-derived macrophages, and the human monocyte cell line THP-1 resulted in rapid activation of the p46 and p54 isoforms of JNK. Treatment with wild-type and rough mutant forms of LPS and synthetic lipid A resulted in JNK activation, while pretreatment with the tyrosine kinase inhibitor herbimycin A inhibited this response. Binding of LPS-LPS binding protein (LBP) complexes to CD14, a surface receptor that mediates many LPS responses, was found to be crucial, as pretreatment of THP-1 cells with the monoclonal antibody 60b, which blocks this binding, inhibited JNK activation. These results suggest that LPS activation of JNK in monocyte/macrophage cells is a CD14- and protein tyrosine phosphorylation-dependent event that may mediate the early activation of AP-1 in regulating LPS-triggered gene induction.
The 13q- syndrome: the molecular definition of a critical deletion region in band 13q32. (1995)

Patients with interstitial deletions of the long arm of chromosome 13 may have widely varying phenotypes. From cytogenetic analysis, we have postulated that there is a discrete region in 13q32 where deletion leads to a syndrome of severe malformations, including digital and brain anomalies. To test this hypothesis at the molecular level, we have studied the deletions in 17 patients; 5 had severe malformations, while the remaining 12 had only minor malformations. Our results indicate that the deletions in the severely affected patients all involve an overlapping region in q32, while the deletions in the mildly affected patients include some, but not all, of this overlapping region. Our findings are consistent with the hypothesis that the severely malformed 13q- phenotype results from the deletion of a critical region in 13q32. This region is presently defined as lying between D13S136 and D13S147 and is on the order of 1 Mb in size.
H2-ARQ-Relaying: Spectrum and Energy Efficiency Perspectives (2011)

In this paper, we propose novel Hybrid Automatic Repeat re-Quest (HARQ) strategies used in conjunction with hybrid relaying schemes, named as H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -ARQ-Relaying. The strategies allow the relay to dynamically switch between amplify-and-forward/compress-and-forward and decode-and-forward schemes according to its decoding status. The performance analysis is conducted from both the spectrum and energy efficiency perspectives. The spectrum efficiency of the proposed strategies, in terms of the maximum throughput, is significantly improved compared with their non-hybrid counterparts under the same constraints. The consumed energy per bit is optimized by manipulating the node activation time, the transmission energy and the power allocation between the source and the relay. The circuitry energy consumption of all involved nodes is taken into consideration. Numerical results shed light on how and when the energy efficiency can be improved in cooperative HARQ. For instance, cooperative HARQ is shown to be energy efficient in long distance transmission only. Furthermore, we consider the fact that the compress-and-forward scheme requires instantaneous signal to noise ratios of all three constituent links. However, this requirement can be impractical in some cases. In this regard, we introduce an improved strategy where only partial and affordable channel state information feedback is needed.
Dental implants placed in expanded narrow edentulous ridges with the Extension Crest<sup>®</sup> device (2006)

Within the limits of this study, this technique appeared to be reliable and simple, with reduction of morbidity and times of dental rehabilitation as compared with other techniques such as autogenous bone grafts and guided bone regeneration. Survival and success rates of implants placed in the treated areas are consistent with those placed in native bone.
Tissue phantom for optical diagnostics based on a suspension of microspheres with a fractal size distribution (2005)

We demonstrate experimentally the possibility of reproducing the phase function, absorption, and scattering coefficients of a real biological tissue (adult brain white matter and liver) using a suspension of polystyrene microspheres with a fractal size distribution. The design of a light scattering goniometer with a cylindrical cell in air is discussed, and phase function measurements using the device are described. The scattering coefficient is measured using transmission spectrophotometry and the absorption and reduced scattering coefficients are measured using a time-resolved method. A good match between real tissue and phantom parameters is demonstrated.
All-du-path coverage for parallel programs (1998)

One significant challenge in bringing the power of parallel machines to application programmers is providing them with a suite of software tools similar to the tools that sequential programmers currently utilize. In particular, automatic or semi-automatic testing tools for parallel programs are lacking. This paper describes our work in automatic generation of all-du-paths for testing parallel programs. Our goal is to demonstrate that, with some extension, sequential test data adequacy criteria are still applicable to parallel program testing. The concepts and algorithms in this paper have been incorporated as the foundation of our DELaware PArallel Software Testing Aid, della pasta.
The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements (1992)

To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, each independently directing the accurate initiation of transcription from a specified set of start sites, EES1 and EES2, respectively. The sequence of TATA element I fits best with the compiled 'consensus' sequence found in eukaryotic gene promoters and is the most efficient in directing transcription initiation. Mutations which improve this fit can still increase the rate of transcription, confirming the theory of a correlation between the nucleotide sequence of a TATA element and its functional efficiency. Moreover, some mutations which simultaneously modify the angle of DNA curvature in the T + A-rich promoter region and the rate of transcription reveal a correlation between DNA bending and transcription initiation.
ClpE, a novel type of HSP100 ATPase, is part of the CtsR heat shock regulon of <i>Bacillus subtilis</i> (1999)

Clp ATPases, which include the ubiquitous HSP100 family, are classified according to their structural features and sequence similarities. During the course of the Bacillus subtilis genome sequencing project, we identified a gene encoding a new member of the HSP100 family. We designated this protein ClpE, as it is the prototype of a novel subfamily among the Clp ATPases, and have identified homologues in several bacteria, including Listeria monocytogenes, Enterococcus faecalis, Streptococcus pyogenes, Streptococcus pneumoniae, Lactobacillus sakei and Clostridium acetobutylicum. A unique feature of these Hsp100-type Clp ATPases is their amino-terminal zinc finger motif. Unlike the other class III genes of B. subtilis (clpC and clpP ), clpE does not appear to be required for stress tolerance. Transcriptional analysis revealed two sigmaA-type promoters, expression from which was shown to be inducible by heat shock and puromycin treatment. Investigation of the regulatory mechanism controlling clpE expression indicates that this gene is controlled by CtsR and is thus a member of the class III heat shock genes of B. subtilis. CtsR negatively regulates clpE expression by binding to the promoter region, in which five CtsR binding sites were identified through DNase I footprinting and sequence analysis.
Synthesis and Structure of Dinucleotides Featuring Canonical and Non‐canonical A‐Type Duplex α, β and δ Torsion Angle Combinations (LNA/α,β‐D‐CNA) (2007)

Abstract The synthesis of diastereoisomers of LNA/α,β‐D‐CNA dinucleotide building units of nucleic acids in which one δ torsional angle is constrained by an LNA structure and the α and β torsional angles are stereocontrolled by a dioxaphosphorinane ring structure (D‐CNA family) is described. NMR structural analysis showed that the δ a , α b and β b torsional angles of the ( R C5′ , R P )‐configured LNA/α,β‐D‐CNA TT dimer are restricted to the canonical {δ a ,α b ,β b } = { gauche (+)/ anticlinal (+), gauche (–), trans } conformation typically observed in A‐type duplexes. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
A Weighted Method to Update Network User Preference Profile Dynamically (2014)

There are many alternatives in a Recommender System (RS) that can be represented by numerical attributes. One of the most challenging tasks in developing RS is the design of techniques that can infer user preferences through observation of their actions. A RS usually stores a personal preference profile associated with each user, but the initial profile of a user is usually incomplete and imprecise. Therefore, it is necessary to update a user's preference profile dynamically. Some previous research has covered this area, but neglected an important fact in real situations, where different weights should be considered for every attribute when selecting alternatives and updating a user preference profile. This paper provides a realistic and weighted method to update network user preferences through analysis of user selections. More specifically, an algorithm to compute and update weights of different attributes in a dynamic way is presented. The weights are used in the adaptation process of network user preference profile. The method is tested by extensive simulations and the obtained results show that it is more effective than previous methods.
Galvanic Corrosion of Magnesium Coupled to Steel at High Cathode-to-Anode Area Ratios (2015)

In this study, the impact of galvanic coupling of magnesium to steel on the corrosion rate, surface morphology, and surface film formation was investigated. In particular, the role of self-corrosion was quantified as previous studies showed discrepancies between model predictions and experimental results that were likely due to significant self-corrosion. This experimental study examined the corrosion of Mg coupled to steel in 5 wt% NaCl at cathode-to-anode area ratios that ranged from 5 to 27. Results showed that self-corrosion was significant and accounted for, on average, one-third of total corrosion. Moreover, self-corrosion varied with time and cathode size, and was accelerated by the high dissolution rate. Film formation was observed on the magnesium surface that inhibited the corrosion rates. This film contained approximately 30% of the Mg lost to corrosion. The morphology of the coupled Mg showed the rapid formation of pits with considerable depth, and was quite distinct from previously studied filiform and disk corrosion for uncoupled Mg. This study demonstrates the important role of self-corrosion during galvanic corrosion of Mg and the need to account for such corrosion when predicting corrosion rates. This study also provides important insight into the processes that control Mg corrosion under several conditions.
Evolution of nicotinic acetylcholine receptor subunits (1998)

A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may have appeared first in the nervous system. Moreover, we suggest that the alpha 1 subunits in the muscle system originated from the common ancestor of alpha 2, alpha 3, alpha 4, alpha 5, alpha 6, and beta 3 in the nervous system, whereas the beta 1, gamma, delta, and epsilon subunits in the muscle system shared a common ancestor with the beta 2 and beta 4 subunits in the nervous system. Using the ratio (f) of the number of nonsynonymous substitutions to that of synonymous substitutions, we predicted the functional importance of subunits. We found that the alpha 1 and alpha 7 subunits had the lowest f values in the muscle and nervous systems, respectively, indicating that very strong functional constraints work on these subunits. This is consistent with the fact that the alpha 1 subunit has sites binding to the ligand, and the alpha 7-containing receptor regulates the release of the transmitter. Moreover, the window analysis of the f values showed that strong functional constraints work on the so-called M2 region in all five types of muscle subunits. Thus, the window analysis of the f values is useful for evaluating the degree of functional constraints in not only the entire gene region, but also the within-gene subregion.
Human Gene Mutation Database: towards a comprehensive central mutation database (2008)

We write in response to a number of very specific criticisms of the Human Gene Mutation Database (HGMD; www.hgmd.org) made in the recently published article by George et al ( see review on p 65 ).1 All seven claims made were amenable to empirical testing. Having tested these claims, we find all of them to be either false or highly misleading. In the text that follows, we refute or rebut each claim in turn. HGMD represents an attempt to collate known (published) gene lesions responsible for human inherited disease. HGMD comprises various types of germ-line mutation within the coding, splicing and regulatory regions of human nuclear genes. HGMD currently (1 December 2007) contains 76 011 different mutations in 2876 human genes. Claim 1: 143 genes are present in OMIM but have no corresponding HGMD entry Response —This claim is wholly misleading. OMIM (Online Mendelian Inheritance in Man) records many types of gene mutation which HGMD does not, such as somatic lesions, neutral polymorphisms and mitochondrial mutations. It is therefore to be expected that there will be some entries in OMIM that do not have a corresponding HGMD entry. We received the list of 143 genes from George et al and performed our own analysis. After careful comparison with OMIM, we found the following:
Use of tertiarybutylarsine for GaAs growth (1987)

The use of AsH3 in the organometallic vapor phase epitaxial (OMVPE) growth of GaAs and other As containing III/V semiconductors has a number of disadvantages, including toxicity hazard, purity problems associated with storage cylinders, and low pyrolysis rate at the low temperatures often desirable in OMVPE growth. A new organometallic source, tertiarybutylarsine (TBAs), has recently become available. In this letter we report the results of OMVPE growth of GaAs using trimethylgallium (TMGa) and TBAs in a one atmosphere ambient. The major results of the study are (1) the vapor pressure of TBAs is measured to be 96 Torr at 10 °C, (2) the pyrolysis rate of TBAs appears to be greater than that of AsH3 under similar conditions, (3) as a consequence of (2), excellent morphology GaAs layers can be grown at lower values of V/III ratio (approximately unity) using TBAs than using AsH3 (4) no additional carbon incorporation is produced by the use of the organometallic group V source. These factors make TBAs a promising candidate to replace AsH3 in vapor phase epitaxial growth of GaAs.
Identification of a Minimal Peptide Tag for <i>in Vivo</i> and <i>in Vitro</i> Loading of Encapsulin (2016)

The encapsulation of enzymes and other proteins within a proteinaceous shell has been observed in many bacteria and archaea, but the function and utility of many such compartments are enigmatic. Efforts to study these functions have been complicated by the size and complexity of traditional protein compartments. One potential system for investigating the effect of compartmentalization is encapsulin, a large and newly discovered class of protein shells that are typically composed of two proteins: a protomer that assembles into the icosahedral shell and a cargo protein packaged inside. Encapsulins are some of the simplest known protein shell systems and readily self-assemble in vivo. Systematic characterization of the effects of compartmentalization requires the ability to load a wide range of cargo proteins. Here, we demonstrate that foreign cargo can be loaded into the encapsulin from Thermotoga maritima both in vivo and in vitro by fusion of the cargo protein with a short C-terminal peptide present in the native cargo. To facilitate biochemical characterization, we also develop a simple and rapid purification protocol and demonstrate the thermal and pH stability of the shell. Efforts to study the biophysical effects of protein encapsulation have been problematic in complex compartments, but the simplicity of assembling and loading encapsulin makes it an ideal system for future experiments exploring the effects of encapsulation on proteins.
A radiation-tolerant, low-power non-volatile memory based on silicon nanocrystal quantum dots (2001)

Nanocrystal nonvolatile floating-gate memories are a good candidate for space applications - initial results suggest they are fast, more reliable and consume less power than conventional floating gate memories. In the nanocrystal based NVM device, charge is not stored on a continuous polysilicon layer (so-called floating gate), but instead on a layer of discrete nanocrystals. Charge injection and storage in dense arrays of silicon nanocrystals in SiO_2 is a critical aspect of the performance of potential nanocrystal flash memory structures. The ultimate goal for this class of devices is few- or single-electron storage in a small number of nanocrystal elements. In addition, the nanocrystal layer fabrication technique should be simple, 8-inch wafer compatible and well controlled.
Modelling and Visualising Traces for Reflexivity in Synchronous Collaborative Systems (2009)

This article addresses issues related to traces modelling and visualization in synchronous collaborative learning. The objective is to propose models and tools for representing, transforming, sharing and visualizing traces of users' experiences. The traces here represent the users' activities in their interactions with the learning platform. Our proposition is based on reflexive learning defined as the ability to interact with the situation, in order to meet one's own limitations. This work takes place in the ITHACA project which aims at developing an on-line learning platform that uses interaction traces as knowledge sources on, and for, the learners' learning as individuals or groups. In this paper, we propose a general framework for trace management and sharing, a generic model of synchronous collaborative activity based on the notion of interaction modes, which we specialized for whiteboard sharing and text chatting. We modelled an IRC client and developed a first implementation.