gebhart/patrepeval huggingface dataset:
Confidence measures for large vocabulary continuous speech recognition (2001)

In this paper, we present several confidence measures for large vocabulary continuous speech recognition. We propose to estimate the confidence of a hypothesized word directly as its posterior probability, given all acoustic observations of the utterance. These probabilities are computed on word graphs using a forward-backward algorithm. We also study the estimation of posterior probabilities on N-best lists instead of word graphs and compare both algorithms in detail. In addition, we compare the posterior probabilities with two alternative confidence measures, i.e., the acoustic stability and the hypothesis density. We present experimental results on five different corpora: the Dutch ARISE 1k evaluation corpus, the German Verbmobil '98 7k evaluation corpus, the English North American Business '94 20k and 64k development corpora, and the English Broadcast News '96 65k evaluation corpus. We show that the posterior probabilities computed on word graphs outperform all other confidence measures. The relative reduction in confidence error rate ranges between 19% and 35% compared to the baseline confidence error rate.
Dominant loss of responsiveness to sweet and bitter compounds caused by a single mutation in α-gustducin (2001)

Biochemical and genetic studies have implicated alpha-gustducin as a key component in the transduction of both bitter or sweet taste. Yet, alpha-gustducin-null mice are not completely unresponsive to bitter or sweet compounds. To gain insights into how gustducin mediates responses to bitter and sweet compounds, and to elicit the nature of the gustducin-independent pathways, we generated a dominant-negative form of alpha-gustducin and expressed it as a transgene from the alpha-gustducin promoter in both wild-type and alpha-gustducin-null mice. A single mutation, G352P, introduced into the C-terminal region of alpha-gustducin critical for receptor interaction rendered the mutant protein unresponsive to activation by taste receptor, but left its other functions intact. In control experiments, expression of wild-type alpha-gustducin as a transgene in alpha-gustducin-null mice fully restored responsiveness to bitter and sweet compounds, formally proving that the targeted deletion of the alpha-gustducin gene caused the taste deficits of the null mice. In contrast, transgenic expression of the G352P mutant did not restore responsiveness of the null mice to either bitter or sweet compounds. Furthermore, in the wild-type background, the mutant transgene inhibited endogenous alpha-gustducin's interactions with taste receptors, i.e., it acted as a dominant-negative. That the mutant transgene further diminished the residual bitter and sweet taste responsiveness of the alpha-gustducin-null mice suggests that other guanine nucleotide-binding regulatory proteins expressed in the alpha-gustducin lineage of taste cells mediate these responses.
Effects of Environment on Compensatory Mutations to Ameliorate Costs of Antibiotic Resistance (2000)

Most types of antibiotic resistance impose a biological cost on bacterial fitness. These costs can be compensated, usually without loss of resistance, by second-site mutations during the evolution of the resistant bacteria in an experimental host or in a laboratory medium. Different fitness-compensating mutations were selected depending on whether the bacteria evolved through serial passage in mice or in a laboratory medium. This difference in mutation spectra was caused by either a growth condition-specific formation or selection of the compensated mutants. These results suggest that bacterial evolution to reduce the costs of antibiotic resistance can take different trajectories within and outside a host.
Map, diagram, and web page navigation on mobile devices (2008)

This paper presents a study comparing two Zoomable User Interfaces with Overviews (ZUIOs) against a classic Zoomable User Interface (ZUI) in the context of user navigation of large information spaces on mobile devices. The study aims at exploring (i) if an overview is worth the space it uses as an orientation tool during navigation of an information space and (ii) if part of the lost space can be recovered by switching to a wireframe visualization of the overview and dropping semantic information in it. The study takes into consideration search tasks on three types of information space, namely maps, diagrams, and web pages, that widely differ in structural complexity. Results suggest that overviews bring enough benefit to justify the used space if (i) they highlight relevant semantic information that users can exploit during search and (ii) the structure of the considered information space does not provide appropriate orientation cues.
Cooperative hydrogen bond interactions in the streptavidin–biotin system (2006)

The thermodynamic and structural cooperativity between the Ser45- and D128-biotin hydrogen bonds was measured by calorimetric and X-ray crystallographic studies of the S45A/D128A double mutant of streptavidin. The double mutant exhibits a binding affinity approximately 2x10(7) times lower than that of wild-type streptavidin at 25 degrees C. The corresponding reduction in binding free energy (DeltaDeltaG) of 10.1 kcal/mol was nearly completely due to binding enthalpy losses at this temperature. The loss of binding affinity is 11-fold greater than that predicted by a linear combination of the single-mutant energetic perturbations (8.7 kcal/mol), indicating that these two mutations interact cooperatively. Crystallographic characterization of the double mutant and comparison with the two single mutant structures suggest that structural rearrangements at the S45 position, when the D128 carboxylate is removed, mask the true energetic contribution of the D128-biotin interaction. Taken together, the thermodynamic and structural analyses support the conclusion that the wild-type hydrogen bond between D128-OD and biotin-N2 is thermodynamically stronger than that between S45-OG and biotin-N1.
Electroencephalography (EEG)-near-infrared spectroscopy (NIRS) based online imaging during non-invasive electrical brain stimulation (2014)

Transcranial direct current stimulation (tDCS) has been shown to modulate cortical neural activity (Nitsche and Paulus 2000). During neural activity, the electric currents from excitable membranes of brain tissue superimpose at a given location in the extracellular medium and generate a potential, which is referred to as the electroencephalogram (EEG) when recorded from the scalp (Nunez and Srinivasan 2006). Respective neural activity has been shown to be closely related, spatially and temporally, to cerebral blood flow (CBF) that supplies glucose via neurovascular coupling (Girouard and Iadecola 2006). The hemodynamic response to neural activity can be captured by near-infrared spectroscopy (NIRS), which enables continuous monitoring of cerebral oxygenation and blood volume (Siesler et al. 2008). Here, the CBF is increased in the brain regions with neural activity via metabolic coupling mechanisms (Attwell et al. 2010). Cerebral autoregulation mechanisms ensure that the blood flow is maintained during changes in the perfusion pressure (Lucas et al. 2010). We proposed a phenomological model for metabolic coupling mechanisms (Attwell et al. 2010) to capture cerebrovascular reactivity (CVR) that represented the capacity of blood vessels to dilate during anodal tDCS due to neuronal activity-caused increased demands of oxygen (Dutta et al. 2013). Crosssectional studies suggest that impaired cerebral hemodynamics precedes stroke and transient ischaemic attacks (TIA). CVR reflects the capacity of blood vessels to dilate, and is an important marker for brain vascular reserve (Markus and Cullinane 2001). Therefore, cerebrovascular reserve capacity may have a predictive value for the risk of cerebral infarction in patients with reduced cerebrovascular reserve capacity such that it might evolve as a part of routine diagnostic neuroangiologic program (Stoll and Hamann 2002).
SignalSLAM: Simultaneous localization and mapping with mixed WiFi, Bluetooth, LTE and magnetic signals (2013)

Indoor localization typically relies on measuring a collection of RF signals, such as Received Signal Strength (RSS) from WiFi, in conjunction with spatial maps of signal fingerprints. A new technology for localization could arise with the use of 4G LTE telephony small cells, with limited range but with rich signal strength information, namely Reference Signal Received Power (RSRP). In this paper, we propose to combine an ensemble of available sources of RF signals to build multi-modal signal maps that can be used for localization or for network deployment optimization. We primarily rely on Simultaneous Localization and Mapping (SLAM), which provides a solution to the challenge of building a map of observations without knowing the location of the observer. SLAM has recently been extended to incorporate signal strength from WiFi in the so-called WiFi-SLAM. In parallel to WiFi-SLAM, other localization algorithms have been developed that exploit the inertial motion sensors and a known map of either WiFi RSS or of magnetic field magnitude. In our study, we use all the measurements that can be acquired by an off-the-shelf smartphone and crowd-source the data collection from several experimenters walking freely through a building, collecting time-stamped WiFi and Bluetooth RSS, 4G LTE RSRP, magnetic field magnitude, GPS reference points when outdoors, Near-Field Communication (NFC) readings at specific landmarks and pedestrian dead reckoning based on inertial data. We resolve the location of all the users using a modified version of Graph-SLAM optimization of the users poses with a collection of absolute location and pairwise constraints that incorporates multi-modal signal similarity. We demonstrate that we can recover the user positions and thus simultaneously generate dense signal maps for each WiFi access point and 4G LTE small cell, “from the pocket”. Finally, we demonstrate the localization performance using selected single modalities, such as only WiFi and the WiFi signal maps that we generated.
Monitoring protein kinase and phosphatase reactions with matrix-assisted laser desorption/ionization mass spectrometry and capillary zone electrophoresis: Comparison of the detection efficiency of peptide-phosphopeptide mixtures (1994)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and capillary zone electrophoresis (CZE) were evaluated for monitoring protein phosphatase and kinase reactions in vitro. Varying concentrations of peptide C (YIHLEKKYVRRDSG), peptide S (YLIEDNEYTARQGA) and kemptide (LARRSALG) mixed with their corresponding phosphorylated peptides, pC, pS and pkemptide, were analyzed. Comparison between the two techniques indicated that MALDI MS was less quantitative than CZE, showing a bias towards detection of the unphosphorylated peptide S and kemptide. In terms of sensitivity, the MALDI MS and CZE techniques are comparable. Protein kinase A phosphorylation of kemptide was monitored with both MALDI MS and CZE, whereas alkaline phosphatase dephosphorylation of pC could only be monitored with MALDI MS. The absence of inhibition with phosphatase or kinase buffers is a significant advantage of MALDI MS. In contrast to CZE, the MALDI spectra allow identification of the species analyzed by virtue of their mass. The results obtained emphasize the advantage of monitoring enzymatic reactions in buffer solutions using MALDI MS compared with CZE.
Low cost, high performance, self-aligning miniature optical systems (2009)

The most expensive aspects in producing high quality miniature optical systems are the component costs and long assembly process. A new approach for fabricating these systems that reduces both aspects through the implementation of self-aligning LIGA (German acronym for lithographie, galvanoformung, abformung, or x-ray lithography, electroplating, and molding) optomechanics with high volume plastic injection molded and off-the-shelf glass optics is presented. This zero alignment strategy has been incorporated into a miniature high numerical aperture (NA = 1.0 W) microscope objective for a fiber confocal reflectance microscope. Tight alignment tolerances of less than 10 microm are maintained for all components that reside inside of a small 9 gauge diameter hypodermic tubing. A prototype system has been tested using the slanted edge modulation transfer function technique and demonstrated to have a Strehl ratio of 0.71. This universal technology is now being developed for smaller, needle-sized imaging systems and other portable point-of-care diagnostic instruments.
Construction and expression of a monomeric c-Jun protein that binds and activates transcription of AP-1-responsive genes. (1992)

c-Jun is a typical member of the bZIP (basic zipper) family of dimeric transcriptional activators. These proteins contain a basic region responsible for DNA sequence recognition and a leucine zipper that mediates dimerization. bZIP proteins regulate a large number of important physiological functions and, therefore, present an interesting target for molecular interference and mimicry. As a step toward the development of peptide and nonpeptide analogs of such proteins, we constructed a derivative of c-Jun that binds DNA as a monomer. This construction was done by connecting a second basic region to the natural basic region of c-Jun by means of a short peptide loop. Although the polypeptide backbone of the second basic region has an inverted polarity relative to that of the natural basic region, the monomeric c-Jun protein binds DNA with reasonably high affinity and indistinguishable specificity from the wild-type, dimeric c-Jun protein. Furthermore, the monomeric c-Jun protein can activate transcription in vivo. These findings indicate that the polypeptide backbone of the basic region contributes little to sequence recognition and that the leucine zipper is not directly involved in transcriptional activation.
Characterization of chimeric antibody producing CHO cells in the course of dihydrofolate reductase-mediated gene amplification and their stability in the absence of selective pressure (1998)

Previously, the highest producing (HP) recombinant CHO subclones isolated at various methotrexate (MTX) levels showed different antibody production stability during long-term culture, although they were clonally derived from CS13 transformant. In this study, genetic basis for their difference in antibody production stability was investigated using southern blot hybridization and fluorescence in situ hybridization (FISH) techniques. Southern analysis of HP subclones revealed that light-chain (LC) and heavy-chain (HC) cDNAs were located closely within 23 kb on an amplification unit, and the configuration of LC and HC cDNAs within this amplification unit was not disrupted during long-term culture in the absence of MTX. However, when LC and HC genes were localized on the metaphase chromosomes of HP subclones using FISH, the amplified sequences were present as an extended array on diverse marker chromosomes. HP subclones selected at higher MTX level had more kinds of marker chromosomes. CS13*-002 isolated at 0.02 microM MTX had only one marker chromosome (m002), whereas CS13*-1.0 isolated at 1 microM MTX had five different ones (m10A, m10B, m10C, m10D, and m10E). Each marker chromosome showed different fate during long-term culture of HP subclones in the absence of MTX, resulting in different degrees of stability among the HP subclones. The m10A and m10B remained unchanged, whereas the others disappeared or evolved to variants with shortened amplified arrays. The cells containing stable marker chromosomes constituted dominant subpopulations in CS13*-1.0, and thereby CS13*-1.0 became most stable in regard to antibody production during long-term culture. Furthermore, our dual-color FISH showed that the telomeric ends of amplified arrays on the stable marker chromosomes were always surrounded by (TTAGGG)(n) sequences, indicating that (TTAGGG)(n) sequences are closely related to the stability and evolution of amplified sequences. Taken together, our data show that the assessment of genotypic stability of amplified CHO cells is a prerequisite for understanding their production stability during long-term culture in the absence of selection pressure.
From Point Defects in Graphene to Two-Dimensional Amorphous Carbon (2011)

While crystalline two-dimensional materials have become an experimental reality during the past few years, an amorphous 2D material has not been reported before. Here, using electron irradiation we create an sp2-hybridized one-atom-thick flat carbon membrane with a random arrangement of polygons, including four-membered carbon rings. We show how the transformation occurs step by step by nucleation and growth of low-energy multivacancy structures constructed of rotated hexagons and other polygons. Our observations, along with first-principles calculations, provide new insights to the bonding behavior of carbon and dynamics of defects in graphene. The created domains possess a band gap, which may open new possibilities for engineering graphene-based electronic devices.
A Broader Understanding of Moral Distress (2016)

On the traditional view, moral distress arises only in cases where an individual believes she knows the morally right thing to do but fails to perform that action due to various constraints. We seek to motivate a broader understanding of moral distress. We begin by presenting six types of distress that fall outside the bounds of the traditional definition and explaining why they should be recognized as forms of moral distress. We then propose and defend a new and more expansive definition of moral distress and examine how it can enable the development of a taxonomy of moral distress.
A comparison of data prefetching on an access decoupled and superscalar machine (1997)

In this paper we investigate the behavior of data prefetching on an access decoupled machine and a superscalar machine. We assess if there are benefits to using the decoupling paradigm given that an out-of-order (o-o-o) superscalar architecture could in principle prefetch to the same degree as an access decoupled machine. We have found that for large issue width the access decoupled machine can hide memory latency more effectively than a single instruction window o-o-o superscalar architecture. Our findings also demonstrate that an access decoupled machine offers the benefit of reducing the complexity of window issue logic.
Structure of the MscL Homolog from <i>Mycobacterium tuberculosis</i> : A Gated Mechanosensitive Ion Channel (1998)

Mechanosensitive ion channels play a critical role in transducing physical stresses at the cell membrane into an electrochemical response. The MscL family of large-conductance mechanosensitive channels is widely distributed among prokaryotes and may participate in the regulation of osmotic pressure changes within the cell. In an effort to better understand the structural basis for the function of these channels, the structure of the MscL homolog from Mycobacterium tuberculosis was determined by x-ray crystallography to 3.5 angstroms resolution. This channel is organized as a homopentamer, with each subunit containing two transmembrane alpha helices and a third cytoplasmic alpha helix. From the extracellular side, a water-filled opening approximately 18 angstroms in diameter leads into a pore lined with hydrophilic residues which narrows at the cytoplasmic side to an occluded hydrophobic apex that may act as the channel gate. This structure may serve as a model for other mechanosensitive channels, as well as the broader class of pentameric ligand-gated ion channels exemplified by the nicotinic acetylcholine receptor.
Urothelial lesion formation is mediated by TNFR1 during neurogenic cystitis (2006)

Interstitial cystitis (IC) is a chronic bladder inflammatory disease of unknown etiology that shares similarities with Crohn's disease and psoriasis. IC, often regarded as a neurogenic cystitis, is associated with urothelial lesions that likely compromise the bladder permeability barrier and thereby contribute to patient morbidity. Here, we use a murine model of neurogenic cystitis to investigate the mechanism of urothelial lesion formation and find that urothelial apoptosis induces formation of lesions. Lesions formed in wild-type mice but not in mice deficient in TNF, TNF receptors, or mast cells. In urothelial cultures, only siRNAs targeting TNFR1, but not TNFR2, blocked TNF-induced apoptosis, indicating a primary role for TNFR1. Trans-epithelial resistance, a measure of bladder barrier function, decreased during neurogenic cystitis in wild-type and TNFR2(-/-) mice but was stabilized in TNF(-/-) mice. Anti-TNF antibodies both altered bladder mast cell localization and stabilized barrier function. Based on these findings, we conclude that mast cell activation and release of TNF drive urothelial apoptosis and lesion formation in a murine neurogenic cystitis model, and we hypothesize that anti-TNF therapy may stabilize bladder barrier function in IC patients.
HIV/HBV and HIV/HCV coinfection, and outcomes following highly active antiretroviral therapy (2003)

Coinfection with HBV or HCV is relatively common among HIV-infected participants in AHOD. HIV disease outcomes following HAART do not appear to be adversely affected by HBV/HCV coinfection, except for slightly poorer CD4 count responses in HIV/HCV coinfected patients.
Genetic dissection of Alzheimer disease, a heterogeneous disorder. (1995)

The genetics of Alzheimer disease (AD) are complex and not completely understood. Mutations in the amyloid precursor protein gene (APP) can cause early-onset autosomal dominant AD. In vitro studies indicate that cells expressing mutant APPs overproduce pathogenic forms of the A beta peptide, the major component of AD amyloid. However, mutations in the APP gene are responsible for 5% or less of all early-onset familial AD. A locus on chromosome 14 is responsible for AD in other early-onset AD families and represents the most severe form of the disease in terms of age of onset and rate of decline. Attempts to identify the AD3 gene by positional cloning methods are underway. At least one additional early-onset AD locus remains to be located. In late-onset AD, the apolipoprotein E gene allele epsilon 4 is a risk factor for AD. This allele appears to act as a dose-dependent age-of-onset modifier. The epsilon 2 allele of this gene may be protective. Other late-onset susceptibility factors remain to be identified.