gebhart/patrepeval huggingface dataset:
Feature selection for ranking (2007)

Ranking is a very important topic in information retrieval. While algorithms for learning ranking models have been intensively studied, this is not the case for feature selection, despite of its importance. The reality is that many feature selection methods used in classification are directly applied to ranking. We argue that because of the striking differences between ranking and classification, it is better to develop different feature selection methods for ranking. To this end, we propose a new feature selection method in this paper. Specifically, for each feature we use its value to rank the training instances, and define the ranking accuracy in terms of a performance measure or a loss function as the importance of the feature. We also define the correlation between the ranking results of two features as the similarity between them. Based on the definitions, we formulate the feature selection issue as an optimization problem, for which it is to find the features with maximum total importance scores and minimum total similarity scores. We also demonstrate how to solve the optimization problem in an efficient way. We have tested the effectiveness of our feature selection method on two information retrieval datasets and with two ranking models. Experimental results show that our method can outperform traditional feature selection methods for the ranking task.
Bifunctional Opioid/Melanocortin Peptidomimetics for Use in Neuropathic Pain: Variation in the Type and Length of the Linker Connecting the Two Pharmacophores (2022)

Based on the mechanism of neuropathic pain induction, a new type of bifunctional hybrid peptidomimetics was obtained for potential use in this type of pain. Hybrids consist of two types of pharmacophores that are connected by different types of linkers. The first pharmacophore is an opioid agonist, and the second pharmacophore is an antagonist of the pronociceptive system, i.e., an antagonist of the melanocortin-4 receptor. The results of tests in acute and neuropathic pain models of the obtained compounds have shown that the type of linker used to connect pharmacophores had an effect on antinociceptive activity. Peptidomimetics containing longer flexible linkers were very effective at low doses in the neuropathic pain model. To elucidate the effect of linker lengths, two hybrids showing very high activity and two hybrids with lower activity were further tested for affinity for opioid (mu, delta) and melanocortin-4 receptors. Their complexes with the target receptors were also studied by molecular modelling. Our results do not show a simple relationship between linker length and affinity for particular receptor types but suggest that activity in neuropathic pain is related to a proper balance of receptor affinity rather than maximum binding to any or all of the target receptors.
Synthesis and gastric antisecretory properties of 4,5 unsaturated derivatives of 15-deoxy-16-hydroxy-16-methylprostaglandin E1 (1983)

The synthesis and gastric antisecretory activities of the delta 4,5-cis, delta 4,5-trans, and 4,5-acetylenic analogues of 15-deoxy-16-hydroxy-16-methyl prostaglandin E1 methyl ester are described. The key step in the preparation of these compounds involved the stereospecific conjugate addition of a cuprate reagent to the appropriate cyclopentenones. Although the trans and acetylenic derivatives were weak inhibitors of gastric acid secretion, the cis olefin was more potent and longer acting than the saturated parent compound. Selectivity with respect to unwanted diarrheagenic effects was found to be improved over that of both the parent 16-hydroxy compound and the reference standards, (15S)-15-methyl- and 16,16-dimethylprostaglandin E2.
Complementary thin-base symmetric lateral bipolar transistors on SOI (2011)

CMOS and bipolar technologies are intrinsically distinct. To take advantage of the beneficial attributes of both will drive expensive high mask count processes. We present a bipolar device architecture that will naturally integrate into an existing CMOS process flow without adding the complexity of vertical scaling present in the conventional high performance bipolar technologies. Symmetric thin-base silicon on insulator (SOI) lateral bipolar transistor is proposed. It overcomes the problems associated with conventional bipolar transistors including performance degradation at high current density and slow switching speed in saturation and fabricated samples show immunity to base-push-out effect. Simulation results suggest that THz f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</inf> is possible with current lithography capability and SOI thickness of 20 nm. Primary applications for low voltage and memory applications are discussed.
Bandwidth utilization improvement methods of Coarse Integral Holographic video displays (2018)

This paper introduces two methods to improve the bandwidth utilization in the Coarse Integral Holographic Display architecture, achieving doubled horizontal field of view and fully utilized bandwidth for the spatial light modulator in use.
Investigating Blood-Based, Cell-Specific Biomarkers of Acute Cardiac Allograft Rejection (2017)

Introduction: Cardiac transplantation is the main intervention for patients with end-stage heart failure. Despite great improvements in maintenance immunosuppressive therapies, acute allograft rejection remains a clinical problem. Timely detection of moderate rejection allows for treatment to be modified, preventing organ damage, graft failure and patient death. Regular monitoring for rejection is thus crucial. The endomyocardial biopsy (EMB) is the current standard for monitoring the allograft, but the procedure is highly invasive and costly. Consequently, there is great interest in developing blood-based biomarker tests to monitor for allograft rejection. Blood is a complex tissue, however, and accounting for its dynamic cellular heterogeneity is likely key to identifying robust biomarkers. We investigated whether integrating cellular composition estimates can lead to better performing biomarkers in the context of acute cardiac allograft rejection. Methods: Genome-wide transcript abundance was assayed from PAXgene peripheral whole blood samples obtained from patients undergoing biopsy-confirmed acute allograft rejection (≥2R; n = 29) or not (n = 198), using Affymetrix Human Gene 1.1 ST microarrays. The cellular composition of the blood samples was inferred from their gene expression profiles. Elastic net classifier panels were then identified using the whole blood gene expression, either unadjusted for cellular composition, adjusted for cellular composition for all cell types, or all but one cell type. Out-of-sample performance of the various models was estimated using stratified 5-fold cross-validation. Results: Best cross-validation performance (AUC = 0.75) was achieved by an NK cell-specific classifier panel. Both cell-adjusted and cell-specific classifiers outperformed those identified using unadjusted whole blood gene expression data. Conclusion: Cell-adjusted/specific biomarker panels outperformed those derived from unadjusted whole blood gene expression. Best performance was achieved by an NK cell-specific biomarker panel. The method presented here is a promising way to incorporate cellular composition in the context of biomarker discovery from gene expression in tissue admixtures.Figure
Non‐invasive temperature mapping using temperature‐responsive water saturation shift referencing (T‐WASSR) MRI (2014)

We present a non-invasive MRI approach for assessing the water proton resonance frequency (PRF) shifts associated with changes in temperature. This method is based on water saturation shift referencing (WASSR), a method first developed for assessing B0 field inhomogeneity. Temperature-induced water PRF shifts were determined by estimating the frequency of the minimum intensity of the water direct saturation spectrum at each temperature using Lorentzian line-shape fitting. The change in temperature was then calculated from the difference in water PRF shifts between temperatures. Optimal acquisition parameters were first estimated using simulations and later confirmed experimentally. Results in vitro and in vivo showed that the temperature changes measured using the temperature-responsive WASSR (T-WASSR) were in good agreement with those obtained with MR spectroscopy or phase-mapping-based water PRF measurement methods,. In addition, the feasibility of temperature mapping in fat-containing tissue is demonstrated in vitro. In conclusion, the T-WASSR approach provides an alternative for non-invasive temperature mapping by MRI, especially suitable for temperature measurements in fat-containing tissues.
Computing with a difference neuron (1992)

AbstractThe need for efficient implementation of neural networks in silicon is used to motivate the investigation of alternatives to the McCulloch-Pitts neuron; in particular, one which computes the norm of a difference rather than an inner product. Earlier work is reviewed briefly and formal relationships between the two types are provided. The two types are shown to be equivalent under certain circumstances. Hopfield-like networks and multilayer feedforward networks of the difference neuron are simulated and analysed by comparing them to conventional types. Outside the domain of equivalence, the difference networks are found to perform less well than networks of identical architecture but which incorporate the McCulloch-Pitts neuron.
Conditionally Cycle-Free Generalized Tanner Graphs: Theory and Application to High-Rate Serially Concatenated Codes (2007)

Generalized Tanner graphs have been implicitly studied by a number of authors under the rubric of generalized parity-check matrices. This work considers the conditioning of binary hidden variables in such models in order to break all cycles and thus derive optimal soft-in soft-out (SISO) decoding algorithms. Conditionally cycle-free generalized Tanner graphs are shown to imply optimal SISO decoding algorithms for the first order Reed-Muller codes and their duals - the extended Hamming codes - which are substantially less complex than conventional bit-level trellis decoding. The study of low-complexity optimal SISO decoding algorithms for the family of extended Hamming codes is practically motivated. Specifically, it is shown that exended Hamming codes offer an attractive alternative to high- rate convolutional codes in terms of both performance and complexity for use in very high-rate, very low-floor, serially concatenated coding schemes.
Pancreatic stone protein as a novel marker for neonatal sepsis (2012)

Background: Most clinical trials of sepsis treatment modalities fail at their primary objective of establishing superiority over placebo when added to background standard of care. While there is no definitive explanation for the high failure rate, it might be stated that our attempts to insert a new therapeutic agent into standard of care encounters severe problems with definition of exactly what stage is ongoing, and what are the criteria for progression or resolution from that time point onwards. Clearly there is need for a means of defining steps in the septic process that would apply to individuals, and to better define the course of sepsis in each patient after they are enrolled in a trial. Methods: For core model development, 30 septic patients were studied for time-related progression in relation to biomarkers, employing a Load Model in a neural net algorithm in MatLab. Causative bacterial infections were linked to primary infection sites. In order to minimize overparameterization, the model was allowed to estimate outputs using the best three input parameters. Bacterial load was tracked from origin using clinical and microbiologic data to provide an estimate at the start of sepsis. The bacterial load as well as clinical and laboratory parameters were model inputs with the output parameter being organ failures and/ or mortality. Results: At onset of sepsis, human bacterial load estimates ranged from between 10 8 and 10 11 CFU, which is consistent with inocula in animal models of sepsis. Sepsis proceeds to organ failures and mortality in a series of steps that are initially linked to bacterial load and inflammatory response, followed by coagulopathy, ischemia, oxygen deprivation in organs and tissues, and culminating in organ failures. The later stages of sepsis are all driven by metabolic parameters, and there seems to be little benefit to blocking inflammation at later stages. Substrate and oxygen deficiencies must be addressed first. Conclusion: Neural net progression models based on biomarkers and physiological markers are able to describe the evolution of sepsis to septic shock, organ failures, and provide some evidence that mortality may be a consequence of the stages of sepsis. Overall, these models appear useful to the task of sorting out organ failure endpoints and mechanisms in individual patients with sepsis progression across sepsis to septic shock.
The effect of proline insertions on the thermostability of a barley α-glucosidase (2002)

The thermal stability of alpha-glucosidase is important because the conversion of starch to fermentable sugars during industrial production of ethanol (e.g. brewing, fuel ethanol production) typically takes place at temperatures of 65-73 degrees C. In this study we investigate the thermostability of alpha-glucosidases from four plant species, compare their deduced amino acid sequences, and test the effect of substituting a proline for the residue present in the wild-type enzyme on the thermostability of alpha-glucosidase. The alpha-glucosidase from barley (Hordeum vulgare) was significantly less thermostable than the other three alpha-glucosidases. A comparison of the published deduced amino acid sequences of these four alpha-glucosidases revealed conserved proline residues in the three most thermostable alpha-glucosidases that were not found in the barley enzyme. Site-directed mutagenesis was done on recombinant barley alpha-glucosidase to create proteins with prolines at these conserved positions. The thermostability (T(50)) of one of these mutant enzymes, T340P, was 10 degrees C higher than the non-mutated enzyme.
Mumps Virus Matrix, Fusion, and Nucleocapsid Proteins Cooperate for Efficient Production of Virus-Like Particles (2009)

Paramyxovirus particles, like other enveloped virus particles, are formed by budding from membranes of infected cells. To define mumps virus (MuV) proteins important for this process, viral proteins were expressed either singly or in combination in mammalian cells to produce virus-like particles (VLPs). Only the MuV matrix (M) protein when expressed by itself was capable of inducing particle release, but the quantity of these M-alone particles was very small. Efficient production of mumps VLPs occurred only when the M protein was coexpressed together with other viral proteins, with maximum production achieved upon coexpression of the viral M, nucleocapsid (NP), and fusion (F) proteins together. Electron microscopy analysis confirmed that VLPs were morphologically similar to MuV virions. The two MuV glycoproteins were not equal contributors to particle formation. The F protein was a major contributor to VLP production, while the hemagglutinin-neuraminidase protein made a smaller contribution. Evidence for the involvement of class E protein machinery in VLP budding was obtained, with mumps VLP production inhibited upon expression of dominant-negative versions of the class E proteins Vps4A and Chmp4b. Disruption of the sequence 24-FPVI-27 within the MuV M protein led to poor VLP production, consistent with findings of earlier studies of a related sequence, FPIV, important for the budding of parainfluenza virus 5. Together, these results demonstrate that different MuV structural proteins cooperate together for efficient particle production and that particle budding likely involves host class E protein machinery.
Salivary glucose oxidase: Multifunctional roles forHelicoverpa zea? (1999)

Labial glands of Helicoverpa zea produced a glucose oxidase (GOX), which was present in the saliva and midgut lumen. We purified GOX 23-fold by isoelectric focusing of labial gland homogenates and investigated physical and kinetic properties of the enzyme. D-glucose and 6-deoxy-D-glucose were the optimal substrates of 22 carbohydrates tested with GOX. The enzyme was not inhibited by several inhibitors of fungal GOX but was sensitive to HgCl2. Labial gland GOX activities varied daily during larval development with highest activities found when larvae were actively feeding. Based on pH optimum, pI, molecular weight estimate and Km(glucose), the insect enzyme is not derived from fungal GOXs but appears to have similar kinetic and physical attributes to other insect GOXs. Some possible functions are discussed, including antimicrobial properties, manipulating midgut O2<B> levels, altering host plant defense responses, and metabolizing carbohydrates. Arch. Insect Biochem. Physiol. 42:99–109, 1999. © 1999 Wiley-Liss, Inc.
Global Analysis of Outer Membrane Proteins from <i>Leptospira interrogans</i> Serovar Lai (2002)

Recombinant leptospiral outer membrane proteins (OMPs) can elicit immunity to leptospirosis in a hamster infection model. Previously characterized OMPs appear highly conserved, and thus their potential to stimulate heterologous immunity is of critical importance. In this study we undertook a global analysis of leptospiral OMPs, which were obtained by Triton X-114 extraction and phase partitioning. Outer membrane fractions were isolated from Leptospira interrogans serovar Lai grown at 20, 30, and 37 degrees C with or without 10% fetal calf serum and, finally, in iron-depleted medium. The OMPs were separated by two-dimensional gel electrophoresis. Gel patterns from each of the five conditions were compared via image analysis, and 37 gel-purified proteins were tryptically digested and characterized by mass spectrometry (MS). Matrix-assisted laser desorption ionization-time-of-flight MS was used to rapidly identify leptospiral OMPs present in sequence databases. Proteins identified by this approach included the outer membrane lipoproteins LipL32, LipL36, LipL41, and LipL48. No known proteins from any cellular location other than the outer membrane were identified. Tandem electrospray MS was used to obtain peptide sequence information from eight novel proteins designated pL18, pL21, pL22, pL24, pL45, pL47/49, pL50, and pL55. The expression of LipL36 and pL50 was not apparent at temperatures above 30 degrees C or under iron-depleted conditions. The expression of pL24 was also downregulated after iron depletion. The leptospiral major OMP LipL32 was observed to undergo substantial cleavage under all conditions except iron depletion. Additionally, significant downregulation of these mass forms was observed under iron limitation at 30 degrees C, but not at 30 degrees C alone, suggesting that LipL32 processing is dependent on iron-regulated extracellular proteases. However, separate cleavage products responded differently to changes in growth temperature and medium constituents, indicating that more than one process may be involved in LipL32 processing. Furthermore, under iron-depleted conditions there was no concomitant increase in the levels of the intact form of LipL32. The temperature- and iron-regulated expression of LipL36 and the iron-dependent cleavage of LipL32 were confirmed by immunoblotting with specific antisera. Global analysis of the cellular location and expression of leptospiral proteins will be useful in the annotation of genomic sequence data and in providing insight into the biology of Leptospira.
Comparison of an Improved Polymerase Chain Reaction Protocol and the Indirect Hemagglutination Assay in the Detection of<i>Eperythrozoon Suis</i>Infection (1994)

The ability of an improved polymerase chain reaction (PCR) protocol to detect Eperythrozoon suis DNA in the blood of experimentally infected nonsplenectomized pigs was evaluated. The protocol utilizes previously described E. suis-specific primers and a proprietary DNA-releasing reagent in a 2-step amplification cycle followed by visualization of the 492-bp amplification product on agarose gels. This PCR protocol successfully amplified E. suis DNA in blood from all postinfection samples and from the preinfection samples of 2 pigs, indicating preexisting natural infections. Results of the indirect hemagglutination test on serum samples from these pigs revealed that only 1 pig developed detectable antibody titers to E. suis infection during the 43-day study; that pig was determined by PCR to have been infected naturally with E. suis prior to experimental inoculation. These results confirm previous reports of poor antibody response of young pigs to E. suis infection and demonstrate the potential of PCR as a valuable tool for the diagnosis and study of E. suis infection in pigs.
A humidity-controlled fast integrated mobility spectrometer (HFIMS) for rapid measurements of particle hygroscopic growth (2017)

Abstract. We present a humidity-controlled fast integrated mobility spectrometer (HFIMS) for rapid particle hygroscopicity measurements. The HFIMS consists of a differential mobility analyzer (DMA), a relative humidity (RH) control unit and a water-based FIMS (WFIMS) coupled in series. The WFIMS (Pinterich et al., 2017) combines the fast integrated mobility spectrometer (Kulkarni and Wang, 2006a, b) with laminar flow water condensation methodologies (Hering and Stolzenburg, 2005; Spielman et al., 2017). Inside the WFIMS, particles of different electrical mobilities are spatially separated in an electric field, condensationally enlarged and imaged to provide 1 Hz measurements of size distribution spanning a factor of ∼ 3 in particle diameter, which is sufficient to cover the entire range of growth factor (GF) for atmospheric aerosol particles at 90 % RH. By replacing the second DMA of a traditional hygroscopicity tandem DMA (HTDMA) system with the WFIMS, the HFIMS greatly increases the speed of particle growth factor measurement. The performance of the HFIMS was evaluated using NaCl particles with well-known hygroscopic growth behavior and further through measurements of ambient aerosols. Results show that the HFIMS can reproduce, within 2 %, the literature values for hygroscopic growth of NaCl particles. NaCl deliquescence was observed between 76 and 77 % RH in agreement with the theoretical value of 76.5 % (Ming and Russell, 2001), and efflorescence relative humidity (43 %) was found to lie within the RH range of 41 to 56 % reported in the literature. Ambient data indicate that the HFIMS can measure the hygroscopic growth of five standard dry particle sizes ranging from 35 to 165 nm within less than 3 min, which makes it about 1 order of magnitude faster than traditional HTDMA systems.
Recurrent group A <i>Streptococcus</i> tonsillitis is an immunosusceptibility disease involving antibody deficiency and aberrant T <sub>FH</sub> cells (2019)

"Strep throat" is highly prevalent among children, yet it is unknown why only some children develop recurrent tonsillitis (RT), a common indication for tonsillectomy. To gain insights into this classic childhood disease, we performed phenotypic, genotypic, and functional studies on pediatric group A <i>Streptococcus</i> (GAS) RT and non-RT tonsils from two independent cohorts. GAS RT tonsils had smaller germinal centers, with an underrepresentation of GAS-specific CD4<sup>+</sup> germinal center T follicular helper (GC-T<sub>FH</sub>) cells. RT children exhibited reduced antibody responses to an important GAS virulence factor, streptococcal pyrogenic exotoxin A (SpeA). Risk and protective human leukocyte antigen (HLA) class II alleles for RT were identified. Lastly, SpeA induced granzyme B production in GC-T<sub>FH</sub> cells from RT tonsils with the capacity to kill B cells and the potential to hobble the germinal center response. These observations suggest that RT is a multifactorial disease and that contributors to RT susceptibility include HLA class II differences, aberrant SpeA-activated GC-T<sub>FH</sub> cells, and lower SpeA antibody titers.