gebhart/patrepeval huggingface dataset:
Quantifying Uncertainties in Natural Language Processing Tasks (2018)

Reliable uncertainty quantification is a first step towards building explainable, transparent, and accountable artificial intelligent systems. Recent progress in Bayesian deep learning has made such quantification realizable. In this paper, we propose novel methods to study the benefits of characterizing model and data uncertainties for natural language processing (NLP) tasks. With empirical experiments on sentiment analysis, named entity recognition, and language modeling using convolutional and recurrent neural network models, we show that explicitly modeling uncertainties is not only necessary to measure output confidence levels, but also useful at enhancing model performances in various NLP tasks.
Historiography of the Russian revolution in the twenties (1973)

(1973). Historiography of the Russian revolution in the twenties. Critique: Vol. 1, No. 1, pp. 42-54.
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia (2012)

Thus, we have established an initial platform for computational evaluation and prediction of ataxia pathophysiology. Specifically, the model has been used to investigate SCA15/16, SCA1, SCA2, and SCA3. Results suggest that experimental studies treating mouse models of any of these ataxias with appropriately chosen peptides resembling the C-terminal of IP3R1 could adjust receptor sensitivity, and thereby modulate calcium release and normalize IP3 response. In addition, the model supports the hypothesis of IP3R1 supersensitivity in SCA1.
Identification of fatty acids from butterfat using a combined gas chromatograph-mass spectrometer (1967)

Summary The identification and approximate quantitative determination of methyl esters of fatty acids from commercial butterfat was obtained with a combined gaschromatograph-mass spectrometer instrument. Fifty-two components, straight chain saturated and unsaturated, as well as branched chain compounds, were identified. Seven monomethyl saturated fatty acid methyl ester isomers were identified for both C 15 and C 17 , i.e. with chain lengths of 14 and 16 carbon atoms, respectively. Multibranched fatty acids with molecular weights of 326 and 368 were found. The results were obtained in one day.
A novel intracellular isoform of VEGFR‐1 activates Src and promotes cell invasion in MDA‐MB‐231 breast cancer cells (2010)

Two types of VEGFR-1 receptors have been characterized: a full-length transmembrane receptor and a truncated extracellular soluble isoform (sVEGFR-1). We report here the characterization, in normal and cancer cells, of a new family of intracellular isoforms of VEGFR-1 resulting from alternative initiation of transcription in intronic sequences of the gene. While the classical isoforms of VEGFR-1 were barely detectable in MDA-MB-231 breast cancer cells, one of the intracellular isoforms transcribed from intron 21 (i(21)VEGFR-1) was the main isoform expressed in these cells. The new transcript encodes for a protein that contains only the phosphotransferase domain and the carboxyterminal tail of VEGFR-1. Treatment of MDA-MB-231 cells with siRNA specific for the tyrosine domain of VEGFR-1 suppressed the expression of i(21)VEGFR-1, downregulated phosphorylation of Src at tyrosine 418, and reduced markedly the invasion capacity of these cells in vitro. Accordingly, overexpression of transfected i(21)VEGFR-1 in MDA-MB-231 cells upregulated the active form of Src and increased invasiveness of MDA-MB-231 cells. The expression of i(21)VEGFR-1 in MDA-MB-231 cells was inhibited by retinoic acid. Both, activation of Src and downregulation by retinoic acid, have been reported in other intracellular members of the Fms/Kit/PDGFR family of tyrosine kinases, particularly in the intracellular isoform of c-kit, analogous structurally to i(21)VEGFR-1 and frequently expressed in cancer cells.
A slowly ADP-ribosylated pertussis-toxin-sensitive GTP-binding regulatory protein is required for vasopressin-stimulated Ca2+ inflow in hepatocytes (1994)

The roles of heterotrimeric GTP-binding regulatory proteins (G-proteins) and inositol polyphosphates in the mechanism by which vasopressin stimulates Ca2+ inflow in hepatocytes were investigated by using single cells loaded with fura2 by microinjection. Vasopressin-stimulated Ca2+ inflow was mimicked by microinjection of guanosine 5'-[gamma-thio]triphosphate (GTP[S]) or guanosine 5'-[beta gamma-imido]triphosphate to the cells, but not adenosine 5'-[gamma-thio]triphosphate (ATP[S]) or guanosine 5'-[beta-thio]diphosphate (GDP[S]). Extracellular Gd3+ (5 microM) inhibited both vasopressin- and GTP[S]-stimulated Ca2+ inflow. GDP[S], but not GMP, administered to hepatocytes by microinjection, completely inhibited vasopressin-stimulated Ca2+ inflow and partially inhibited vasopressin-induced release of Ca2+ from intracellular stores. The microinjection of pertussis toxin had no effect either on the release of Ca2+ from intracellular stores or on Ca2+ inflow induced by vasopressin, but completely inhibited changes in these processes induced by epidermal growth factor (EGF). Hepatocytes isolated from rats treated with pertussis toxin for 24 h exhibited no vasopressin- or GTP[S]-stimulated Ca2+ inflow, whereas the vasopressin-stimulated release of Ca2+ from intracellular stores was similar to that observed for control cells. Heparin or ATP[S] inhibited, or delayed the onset of, both vasopressin-induced release of Ca2+ from intracellular stores and vasopressin-stimulated Ca2+ inflow. Vasopressin-induced oscillations in intracellular [Ca2+] were observed in some heparin-treated cells. It is concluded that the stimulation by vasopressin of Ca2+ inflow to hepatocytes requires inositol 1,4,5-trisphosphate (InsP3) and, by implication, the pertussis-toxin-insensitive G-protein required for the activation of phospholipase C beta [Taylor, Chae, Rhee and Exton (1991) Nature (London) 350, 516-518], and another G-protein which is slowly ADP-ribosylated by pertussis toxin and acts between InsP3 and the putative plasma-membrane Ca2+ channel. EGF-stimulated Ca2+ inflow involves at least one G-protein which is rapidly ADP-ribosylated and is most likely required for InsP3 formation.
Design of a Si-based lattice-matched room-temperature GeSn/GeSiSn multi-quantum-well mid-infrared laser diode (2010)

This paper presents modeling and simulation of a silicon-based group IV semiconductor injection laser diode in which the active region has a multiple quantum well structure formed with Ge(0.9)Sn(0.1) quantum wells separated by Ge(0.75)Si(0.1)Sn(0.15) barriers. These alloy compositions were chosen to satisfy three conditions simultaneously: a direct band gap for Ge(0.9)Sn(0.1), type-I band alignment between Ge(0.9)Sn(0.1) and Ge(0.75)Si(0.1)Sn(0.15,) and a lattice match between wells and barriers. This match ensures that the entire structure can be grown strain free upon a relaxed Ge(0.75)Si(0.1)Sn(0.15) buffer on a silicon substrate - a CMOS compatible process. Detailed analysis is performed for the type I band offsets, carrier lifetime, optical confinement, and modal gain. The carrier lifetime is found to be dominated by the spontaneous radiative process rather than the Auger process. The modal gain has a rather sensitive dependence on the number of quantum wells in the active region. The proposed laser is predicted to operate at 2.3 μm in the mid infrared at room temperature.
Activated Ras displaces 14-3-3 protein from the amino terminus of c-Raf-1. (1996)

The serine/threonine protein kinase c-Raf-1 interacts with a number of cellular proteins including 14-3-3 isoforms which may be regulators or substrates of c-Raf-1 in signal transduction pathways. In vivo and in vitro binding analyses of c-Raf-1 and mutant proteins with 14-3-3 zeta indicate bivalent binding of 14-3-3 zeta to the amino terminus as well as to the carboxy terminus of c-Raf-1. Although 14-3-3 zeta and Ras use different binding regions on the amino terminal regulatory domain of c-Raf-1 (c-Raf-NT), 14-3-3 zeta is displaced from the amino terminus upon binding of activated Ras. In contrast, if c-Raf-1 full length is analysed instead of the separately expressed c-Raf-NT, binding of 14-3-3 zeta is only slightly effected by co-expression of activated Ras. This is explained by a second binding site of 14-3-3 zeta at the carboxy terminus of c-Raf-1. The mutant c-Raf-NT (S259A) cannot bind 14-3-3 zeta, suggesting a regulatory role of this in vivo phosphorylation site. However, c-Raf-NT phosphorylated or unphosphorylated at S259, is able to bind 14-3-3 zeta. Even though 14-3-3 zeta can be phosphorylated in vivo, only the unphosphorylated form binds to the amino terminus of c-Raf-1. The data presented indicate, that 14-3-3 zeta binds to c-Raf-1 in a bivalent fashion in unstimulated cells. 14-3-3 zeta is displaced from the amino terminus but not from the carboxy terminus of c-Raf-1 by binding of activated Ras to c-Raf-1.
Value-maximizing deadline scheduling and its application to animation rendering (2005)

We describe a new class of utility-maximization scheduling problem with precedence constraints, the disconnected staged scheduling problem (DSSP). DSSP is a nonpreemptive multiprocessor deadline scheduling problem that arises in several commercially-important applications, including animation rendering, protein analysis, and seismic signal processing. DSSP differs from most previously-studied deadline scheduling problems because the graph of precedence constraints among tasks within jobs is disconnected, with one component per job. Another difference is that in practice we often lack accurate estimates of task execution times, and so purely offline solutions are not possible. However we do know the set of jobs and their precedence constraints up front and therefore some offline planning is possible.Our solution decomposes DSSP into an offline job selection phase followed by an online task dispatching phase. We model the former as a knapsack problem and explore several solutions to it, describe a new dispatching algorithm for the latter, and compare both with existing methods. Our theoretical results show that while DSSP is NP-hard and inapproximable in general, our two-phase scheduling method guarantees a good performance bound for many special cases. Our empirical results include an evaluation of scheduling algorithms on a real animation-rendering workload; we present a characterization of this workload in a companion paper. The workload records eight weeks of activity on a 1,000-CPU cluster used to render portions of the full-length animated feature film Shrek 2 in 2004. We show that our improved scheduling algorithms can substantially increase the aggregate value of completed jobs compared to existing practices. Our new task dispatching algorithm LCPF performs well by several metrics, including job completion times as well as the aggregate value of completed jobs.
Comparison between the pseudo-spectral time domain method and the discrete dipole approximation for light scattering simulations (2012)

The pseudo-spectral time domain (PSTD) and the discrete dipole approximation (DDA) are two popular and robust methods for the numerical simulation of dielectric particle light scattering. The present study compares the numerical performances of the two methods in the computation of the single-scattering properties of homogeneous dielectric spheres and spheroids for which the exact solutions can be obtained from the Lorenz-Mie theory and the T-matrix theory. The accuracy criteria for the extinction efficiency and the phase function are prescribed to be the same for the PSTD and DDA in order that the computational time can be compared in a fair manner. The computational efficiency and applicability of the two methods are each shown to depend on both the size parameter and the refractive index of the scattering particle. For a small refractive index, a critical size parameter, which decreases from 80 to 30 as the refractive index increases from 1.2 to 1.4, exists below which the DDA outperforms the PSTD. For large refractive indices (>1.4), the PSTD is more efficient than the DDA for a wide size parameter range and has a larger region of applicability. Furthermore, the accuracy shown by the two methods in the computation of backscatter, linear polarization, and asymmetry factor is comparable. The comparison was extended to include spheroids with typical refractive indices of ice and dust and similar conclusions were drawn.
Aminocyclopentadienyl Ruthenium Complexes as Racemization Catalysts for Dynamic Kinetic Resolution of Secondary Alcohols at Ambient Temperature (2004)

Aminocyclopentadienyl ruthenium complexes, which can be used as room-temperature racemization catalysts with lipases in the dynamic kinetic resolution (DKR) of secondary alcohols, were synthesized from cyclopenta-2,4-dienimines, Ru(3)(CO)(12), and CHCl(3): [2,3,4,5-Ph(4)(eta(5)-C(4)CNHR)]Ru(CO)(2)Cl (4: R = i-Pr; 5: R = n-Pr; 6: R = t-Bu), [2,5-Me(2)-3,4-Ph(2)(eta(5)-C(4)CNHR)]Ru(CO)(2)Cl (7: R = i-Pr; 8: R = Ph), and [2,3,4,5-Ph(4)(eta(5)-C(4)CNHAr)]Ru(CO)(2)Cl (9: Ar = p-NO(2)C(6)H(4); 10: Ar = p-ClC(6)H(4); 11: Ar = Ph; 12: Ar = p-OMeC(6)H(4); 13: Ar = p-NMe(2)C(6)H(4)). The tests in the racemization of (S)-4-phenyl-2-butanol showed that 7 is the most active catalyst, although the difference decreased in the DKR. Complex 4 was used in the DKR of various alcohols; at room temperature, not only simple alcohols but also functionalized ones such as allylic alcohols, alkynyl alcohols, diols, hydroxyl esters, and chlorohydrins were successfully transformed to chiral acetates. In mechanistic studies for the catalytic racemization, ruthenium hydride 14 appeared to be a key species. It was the major organometallic species in the racemization of (S)-1-phenylethanol with 4 and potassium tert-butoxide. In a separate experiment, (S)-1-phenylethanol was racemized catalytically by 14 in the presence of acetophenone.
PubMed related articles: a probabilistic topic-based model for content similarity (2007)

Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search.
Article : Biochemistry,Molecular Biology ; Classification and Expression Analysis of Cytochrome P450 Genes from Soybean (2004)

Cytochrome P450 monooxygenases in plants are involved in various metabolic pathways. Synthetic pathways for phenylpropanoid, fatty acid, terpenoid and various plant hormones are only parts in which P450s are involved. With vast information available from various plant genome projects, many P450 sequences from several plants can be accessed. However, only few of their functions are known. Based on P450 classification system, eight-two soybean P450 genes were classified and their expression patterns in different tissues and upon UV-B irradiation analyzed by RT-PCR. In most soybean P450 genes, its expression pattern is correlated with P450 clan to which individual P450 belongs. It would be a first step to understand biological functions of individual P450s from soybean.
Stability of Buffered Lidocaine and Epinephrine Used for Local Anesthesia (1991)

Buffered lidocaine has been recently recommended for local anesthesia, as there is less pain on injection of the buffered solution. Reduced pain on injection of lidocaine and epinephrine buffered to a neutral pH was confirmed in 20 subjects (P less than .01). Concentrations of buffered lidocaine and epinephrine were performed in order to evaluate their stability. Buffered lidocaine dropped to 66.1% of initial concentrations after 4 weeks when stored at 25 degrees C. Buffered epinephrine fell to 1.34% of its initial concentration under similar conditions. Buffered lidocaine and epinephrine maintained 94.54% and 82.04%, respectively, of their initial concentrations after 4 weeks when refrigerated at 0-4 degrees C. Both lidocaine and epinephrine maintained greater than 90% concentration 2 weeks after buffering when stored at 0-4 degrees C. This permits batch buffering of lidocaine with epinephrine and storage for periods up to 2 weeks when properly refrigerated.
Active thread compaction for GPU path tracing (2011)

Modern GPUs like NVidia's Fermi internally operate in a SIMD manner by ganging multiple (32) scalar threads together into SIMD warps; if a warp's threads diverge, the warp serially executes both branches, temporarily disabling threads that are not on that path. In this paper, we explore and thoroughly analyze the concept of active thread compaction---i.e., the process of taking multiple partially-filled warps and compacting them to fewer but fully utilized warps---in the context of a CUDA path tracer. Our results show that this technique can indeed lead to significant improvements in SIMD utilization, and corresponding savings in the amount of work performed; however, they also show that certain inadequacies of today's hardware wipe out most of the achieved gains, leaving bottom-up speed-ups of a mere 12--16%. We believe our analysis of why this is the case will provide insight to other researchers experimenting with this technique in different contexts.
Transcriptional Repression of the Interleukin-2 Gene by Vitamin D <sub>3</sub> : Direct Inhibition of NFATp/AP-1 Complex Formation by a Nuclear Hormone Receptor (1995)

T-lymphocyte proliferation is suppressed by 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], the active metabolite of vitamin D3, and is associated with a decrease in interleukin 2 (IL-2), gamma interferon, and granulocyte-macrophage colony-stimulating factor mRNA levels. We report here that 1,25(OH)2D3-mediated repression in Jurkat cells is cycloheximide resistant, suggesting that it is a direct transcriptional repressive effect on IL-2 expression by the vitamin D3 receptor (VDR). We therefore examined vitamin D3-mediated repression of activated IL-2 expression by cotransfecting Jurkat cells with IL-2 promoter/reporter constructs and a VDR overexpression vector and by DNA binding. We delineated an element conferring both DNA binding by the receptor in vitro and 1,25(OH)2D3-mediated repression in vivo to a short 40-bp region encompassing an important positive regulatory element, NF-AT-1, which is bound by a T-cell-specific transcription factor, NFATp, as well as by AP-1. VDR DNA-binding mutants were unable to either bind to this element in vitro or repress in vivo; the VDR DNA-binding domain alone, however, bound the element but also could not repress IL-2 expression. These results indicate that DNA binding by VDR is necessary but not sufficient to mediate IL-2 repression. By combining partially purified proteins in vitro, we observed the loss of the bound NFATp/AP-1-DNA complex upon inclusion of VDR or VDR-retinoid X receptor. Order of addition and off-rate experiments indicate that the VDR-retinoid X receptor heterodimer blocks NFATp/AP-1 complex formation and then stably associates with the NF-AT-1 element. This direct inhibition by a nuclear hormone receptor of transcriptional activators of the IL-2 gene may provide a mechanistic explanation of how vitamin derivatives can act as potent immunosuppressive agents.
Retinoic acid induces secretion of latent transforming growth factor beta 1 and beta 2 in normal and human papillomavirus type 16-immortalized human keratinocytes. (1992)

Similar cellular responses are elicited by retinoic acid (RA) and transforming growth factor beta (TGF-beta). We investigated the ability of RA to modulate the production of TGF-beta in normal human keratinocytes (HKc) and HKc lines immortalized by transfection with human papillomavirus type 16 DNA (HKc/HPV16). RA treatment of both normal HKc and HKc/HPV16 resulted in a 2-3-fold induction in secreted levels of latent TGF-beta. The induction in TGF-beta secretion by RA was dose dependent, with significant increases observed with RA concentrations as low as 1-10 nM, and time dependent, with maximal induction occurring about 3 days after initiation of RA exposure. In addition, RA induced intracellular levels of TGF-beta almost 5-fold. Sandwich enzyme-linked immunosorbent assays were used to specifically quantify TGF-beta 1 and TGF-beta 2 secreted by normal HKc and HKc/HPV16 cultured in the absence or presence of RA. RA increased the secreted levels of latent TGF-beta 1 and TGF-beta 2 an average of 2- and 5-fold, respectively, with no major differences in the fold induction between normal HKc and HKc/HPV16. Northern blot analysis of mRNA isolated from HKc/HPV16 demonstrated that RA treatment induced specific transcripts for TGF-beta 1 and TGF-beta 2 about 3- and 50-fold, respectively. RA treatment of HKc had no significant effect on the binding affinity of TGF-beta for its receptors or receptor number. Normal HKc and HKc/HPV16 displayed similar dose-dependent inhibition of proliferation by TGF-beta 1. These studies indicate that RA may regulate growth control in both normal HKc and HKc/HPV16 by enhancing TGF-beta 1 and TGF-beta 2 production, which, after activation at the cell surface, could inhibit cellular proliferation in an autocrine and/or paracrine manner.
Tau association with synaptic vesicles causes presynaptic dysfunction (2017)

Tau is implicated in more than 20 neurodegenerative diseases, including Alzheimer's disease. Under pathological conditions, Tau dissociates from axonal microtubules and missorts to pre- and postsynaptic terminals. Patients suffer from early synaptic dysfunction prior to Tau aggregate formation, but the underlying mechanism is unclear. Here we show that pathogenic Tau binds to synaptic vesicles via its N-terminal domain and interferes with presynaptic functions, including synaptic vesicle mobility and release rate, lowering neurotransmission in fly and rat neurons. Pathological Tau mutants lacking the vesicle binding domain still localize to the presynaptic compartment but do not impair synaptic function in fly neurons. Moreover, an exogenously applied membrane-permeable peptide that competes for Tau-vesicle binding suppresses Tau-induced synaptic toxicity in rat neurons. Our work uncovers a presynaptic role of Tau that may be part of the early pathology in various Tauopathies and could be exploited therapeutically.
A new bandwidth guaranteed routing algorithm for MPLS traffic engineering (2003)

In this paper, we present a new online algorithm for dynamically routing bandwidth guaranteed label switched paths (LSPs). LSP set-up requests are represented in terms of a pair of ingress and egress routers as well as its bandwidth requirement, and arrive one by one. There is no a priori knowledge regarding future LSP set-up requests and their characteristics. Our proposed algorithm considers not only the importance of critical links, but also the degree of their importance to routing possible future LSP set-up requests by characterizing their normalized bandwidth contribution to routing future LSP demands. Moreover, link residual bandwidth information, i.e., the link's capability of routing future LSPs, is also incorporated. Simulation results show that our proposed algorithm performs better than the best known bandwidth guaranteed routing algorithm, the minimum interference routing algorithm, in terms of LSP rejection rate under both static and dynamic LSP set-up request arrivals.
Measuring Human Skin Colour (2015)

Human skin colour measurements from four ethnic groups including 188 subjects were accumulated. Five to ten locations of each subject were measured by using two different instruments, a tele-spectroradiometer and a spectrophotometer. Three repeated measurements were accumulated for each location. Repeatability of the measurements at different locations from different ethnicities was examined using the mean CIELAB colour difference from the mean (MCDM). The colour distribution between different locations of different ethnic groups was also studied by plotting the data in a*b* and L*C*ab planes. Systematic trends were found between different ethnicities and instruments.