gebhart/patrepeval huggingface dataset:
A Critical Assessment of Feature Selection Methods for Biomarker Discovery in Clinical Proteomics (2012)

In this paper, we compare the performance of six different feature selection methods for LC-MS-based proteomics and metabolomics biomarker discovery-t test, the Mann-Whitney-Wilcoxon test (mww test), nearest shrunken centroid (NSC), linear support vector machine-recursive features elimination (SVM-RFE), principal component discriminant analysis (PCDA), and partial least squares discriminant analysis (PLSDA)-using human urine and porcine cerebrospinal fluid samples that were spiked with a range of peptides at different concentration levels. The ideal feature selection method should select the complete list of discriminating features that are related to the spiked peptides without selecting unrelated features. Whereas many studies have to rely on classification error to judge the reliability of the selected biomarker candidates, we assessed the accuracy of selection directly from the list of spiked peptides. The feature selection methods were applied to data sets with different sample sizes and extents of sample class separation determined by the concentration level of spiked compounds. For each feature selection method and data set, the performance for selecting a set of features related to spiked compounds was assessed using the harmonic mean of the recall and the precision (f-score) and the geometric mean of the recall and the true negative rate (g-score). We conclude that the univariate t test and the mww test with multiple testing corrections are not applicable to data sets with small sample sizes (n = 6), but their performance improves markedly with increasing sample size up to a point (n > 12) at which they outperform the other methods. PCDA and PLSDA select small feature sets with high precision but miss many true positive features related to the spiked peptides. NSC strikes a reasonable compromise between recall and precision for all data sets independent of spiking level and number of samples. Linear SVM-RFE performs poorly for selecting features related to the spiked compounds, even though the classification error is relatively low.
High quality thin GaN templates grown by hydride vapor phase epitaxy on sapphire substrates (2006)

The growth by hydride vapor phase epitaxy (HVPE) of high quality thin GaN layers (d=8μm) on c-plane sapphire substrates with dislocation densities lower than 2×108cm−2 is demonstrated using a two-step process similar to that of metal organic vapor phase epitaxy (MOVPE). Ex situ surface preparation and nucleation layer thickness are shown to be critical factors in achieving these high quality epilayers as they allow controlling the polarity and the dislocation density, respectively. Furthermore, we demonstrate that in situ reflectivity monitoring applied to HVPE is a powerful technique for rapidly optimizing the growth parameters. As a result, thin HVPE-grown GaN layers with state of the art MOVPE GaN quality are obtained as demonstrated through structural and optical characterizations.
Extending VHE with the device unifying service (2003)

The virtual home environment is a powerful concept that enables personal service environment (PSE) portability across network boundaries and between terminals. The device unifying service (DUS) presented in this paper extends the VHE concept by allowing the usage of multiple devices simultaneously and the possibility of adding, removing or changing devices both on the fly or according to predefined profiles.. The user will be able to specify several different personal service environments, professional office environments, private home environments, travelling environments etc., and to select the most appropriate environment for a given time and according to his changing roles. This paper presents the concept of the device unifying service, which will take care of the management, coordination and configuration of all the devices that the user has at his disposal. A discussion regarding the system architecture is given, suggesting the best solution for where to locate this function. In addition, this paper discusses the technologies, emerging and existing, that are required for implementing the device unifying service.
Light-mediated changes in two proteins found associated with plasma membrane fractions from pea stem sections (1988)

Irradiation of etiolated pea (Pisum sativum L.) seedlings with white light affects two proteins, both of monomer molecular mass near 120 kDa. Both proteins have been detected in association with plasma membrane fractions. The first is identifiable in that it becomes heavily phosphorylated when the membranes are incubated with exogenous ATP. The second of these proteins is phytochrome, as determined by electrophoretic transfer (Western) blot analysis. Measurable phosphorylation and phytochrome (the latter detected by antigenicity) decline when the tissue is irradiated with white light prior to membrane isolation and in vitro phosphorylation. The phosphorylated protein is probably not phytochrome for three reasons. (i) It shows a slightly different distribution in sucrose gradients. (ii) Red light causes a gradual decline in the phytochrome that is associated with membrane fractions but has a negligible effect on the phosphorylatable protein; blue light, on the other hand, causes significantly slower loss of phytochrome than does red light but brings about a rapid decline in the phosphorylation signal. (iii) The molecular masses are not identical. The association of both proteins with membrane fractions is probably neither ionic nor, at least for the phosphorylatable protein, the consequence of entrapment of soluble proteins in vesicles formed during tissue extraction. Phytochrome is lost from the membrane fractions during irradiation, as judged by loss of antigenicity. Whether the phosphorylatable protein is lost, a specific kinase is lost, phosphatase activity increases, or phosphorylatable sites are blocked as a consequence of blue light treatment is not known.
Nonce-Disrespecting Adversaries:Practical Forgery Attacks on GCM in TLS (2017)

We investigate nonce reuse issues with the GCM block cipher mode as used in TLS and focus in particular on AES-GCM, the most widely deployed variant. With an Internet-wide scan we identified 184 HTTPS servers repeating nonces, which fully breaks the authenticity of the connections. Affected servers include large corporations, financial institutions, and a credit card company. We present a proof of concept of our attack allowing to violate the authenticity of affected HTTPS connections which in turn can be utilized to inject seemingly valid content into encrypted sessions. Furthermore, we discovered over 70,000 HTTPS servers using random nonces, which puts them at risk of nonce reuse, in the unlikely case that large amounts of data are sent via the same session.
An Adaptive Tabu Search Heuristic for the Location Routing Pickup and Delivery Problem with Time Windows with a Theater Distribution Application (2006)

Abstract : The time constrained pickup and delivery problem (PDPTW) is a problem of finding a set of routes for a fleet of vehicles in order to satisfy a set of transportation requests. Each request represents a user-specified pickup and delivery location. The PDPTW may be used to model many problems in logistics and public transportation. The location routing problem (LRP) is an extension of the vehicle routing problem where the solution identifies the optimal location of the depots and provides the vehicle schedules and distribution routes. This dissertation seeks to blend the PDPTW and LRP areas of research and formulate a location scheduling pickup and delivery problem with time windows (LPDPTW) in order to model the theater distribution problem and find excellent solutions. This research utilizes advanced tabu search techniques, including reactive tabu search and group theory applications, to develop a heuristic procedure for solving the LPDPTW. Tabu search is a metaheuristic that performs an intelligent search of the solution space. Group theory provides the structural foundation that supports the efficient search of the neighborhoods and movement through the solution space.
UHF piezoelectric quartz mems magnetometers based on acoustic coupling of flexural and thickness shear modes (2015)

This paper reports the design, fabrication, and characterization of piezoelectric quartz MEMS magnetometers based on acoustic coupling between resonance modes. The magnetic sensors described herein employ a novel transduction scheme to upconvert the desired near-DC magnetic field signal (using the fundamental flexural mode) onto frequency modulated (FM) sidebands of the primary quartz thickness shear (TS) oscillation at frequencies above 500 MHz. First-generation devices exhibit flexural and TS resonances at 2.77 kHz and at 583.31 MHz, respectively, and magnetic sensitivity of 63.6 V/T was measured with an AC loop current of 9.2 mA. This novel sensing method, intended for electronic compassing, illuminates the interactions between low and high frequency acoustic modes within resonant devices.
Effect of sodium etidronate in adult cats. (1970)

Abstract Sodium etidronate is a phosphonate which prevents the conversion, of calcium phosphate into hydroxyapatite. It had been suggested as an agent for the treatment of osteoporosis. Sodium etidronate was given orally to adult cats at dosages of 500 or 50 mg. per kilogram per day for 6 weeks and 25, 10, and 1 mg. per kilogram per day for 6 months. The majority of the high-dosage group died and had high serum creatinine values. Both high- and low-dosage groups developed abnormally high serum calcium and phosphorus values compared with control animals. The experimental animals also demonstrated increased widths of osteoid tissue, indicating morphologic osteomalacia.
Rapid and Efficient One-Step Metabolic Pathway Integration in <i>E. coli</i> (2016)

Methods for importing heterologous genes into genetically tractable hosts are among the most desired tools of synthetic biology. Easy plug-and-play construction methods to rapidly test genes and pathways stably in the host genome would expedite synthetic biology and metabolic engineering applications. Here, we describe a CRISPR-based strategy that allows highly efficient, single step integration of large pathways in Escherichia coli. This strategy allows high efficiency integration in a broad range of homology arm sizes and genomic positions, with efficiencies ranging from 70 to 100% in 7 distinct loci. To demonstrate the large size capability, we integrated a 10 kb construct to implement isobutanol production in a single day. The ability to efficiently integrate entire metabolic pathways in a rapid and markerless manner will facilitate testing and engineering of novel pathways using the E. coli genome as a stable testing platform.
Technetium reduction and precipitation by sulfate‐reducing bacteria (1998)

Resting cells of the sulfate‐reducing bacterium Desulfovibrio desulfuricans ATCC 29577 were able to precipitate the radionuclide technetium, supplied as the pertechnetate anion (TcO4 ‐), under anaerobic conditions by two discrete mechanisms. Sulfidogenic cultures, supplied with sulfate and lactate as an electron acceptor and donor, respectively, precipitated the radionuclide as an insoluble sulfhide. Using electron microscopy in combination with energy‐dispersive x‐ray analysis (EDAX), the precipitate was shown to be extracellular, and contained S as the major element at a fivefold stoichiometric excess to Tc as quantified by proton‐induced x‐ray emission analysis (PIXE). With hydrogen supplied as the electron donor, the pertechnetate anion was utilized as an alternative electron acceptor in the absence of sulfate. The radionuclide was removed from solution, but in these cultures the precipitate was cell associated, with Tc as the major element detected by PIXE (Tc:S ratio of 2:1). Reduction of the radionuclide in lieu of sulfate was confirmed using XAS. Hydrogen uptake, coupled to metal reduction, was also monitored manometrically, with 1 mol H2 used to reduce 1 mol TcO4 ‐. The implications of these results on Tc mobility in the environment are discussed, and possible biotechnological uses of sulfate‐reducing bacteria in bioremediation programs to treat Tc‐contaminated waters are highlighted.
Urinary concentrating defect in the aged rat (1981)

The renal concentrating ability of Fischer 344 rats was studied at 23 and 4 mo of age. Maximum urine concentration after 40 h of dehydration with or without vasopressin injection was significantly lower (P less than 0.01) in old (2,550 +/- 70 and 2,363 +/- 107 mosmol/kg H2O2, respectively) vs. young (3,242 +/- 50 and 3,162 +/- 50 mosmol/kg H2O, respectively) rats. Free water reabsorption (TcH2O/GFR) rose progressively as a function of osmolar clearance, and at similar values of distal solute delivery TcH2O was clearly reduced in the old group. Free water formation (CH2O/GFR) rose linearly as a function of urine flow and was not different between old and young rats. Glomerular filtration rate was also not different between age groups under the conditions studied. Nonurea (sodium + potassium + ammonium) x 2 and urea solute concentrations as well as total calculated osmolality in the cortex, outer medulla, or inner medulla were not different between age groups. Because the indices of ascending limb solute delivery and transport and the solute gradient for water reabsorption were similar, we conclude that the concentrating defect in aged rats is most likely secondary to a decrease in water permeability along the collecting duct.
Proteome dynamics in complex organisms: Using stable isotopes to monitor individual protein turnover rates (2005)

The complete definition of changes in a proteome requires information about dynamics and specifically the rate at which the individual proteins are turned over intracellularly. Whilst this can be achieved in single-cell culture using stable isotope precursors, it is more challenging to develop methods for intact animals. In this study, we show how dietary administration of stable isotope-labelled amino acids can obtain information on the relative rates of synthesis and degradation of individual proteins in a proteome. The pattern of stable isotope-labelling in tryptic peptides can be deconstructed to yield a highly reliable measure of the isotope abundance of the precursor pool, a parameter that is often difficult to acquire. We demonstrate this approach using chickens fed a semisynthetic diet containing [(2)H(8)]valine at a calculated relative isotope abundance (RIA) of 0.5. When the labelling pattern of gel-resolved muscle proteins was analyzed, the intracellular precursor isotope abundance was 0.35, consistent with dilution of the amino acid precursor pool with unlabelled amino acids derived from degradation of pre-existing proteins. However, the RIA was stable over an extended labelling window, and permitted calculation of the rates of synthesis and degradation of individual proteins isolated by gel electrophoresis. For the first time, it is feasible to contemplate the analysis of turnover of individual proteins in intact animals.
Diastereodivergent Carbometalation/Oxidation/Selective Ring Opening: Formation of All‐Carbon Quaternary Stereogenic Centers in Acyclic Systems (2013)

A twofer: The title reaction sequence for cyclopropenes allows the preparation of aldehydes bearing α-quaternary stereocenters in a one pot-reaction from readily available starting materials. Through a diastereodivergent carbometalation reaction, both enantiomers of the corresponding aldehyde were obtained from the same cyclopropene derivative (see scheme).
Abscisic Acid and the Developmental Regulation of Embryo Storage Proteins in Maize (1991)

The relationship of abscisic acid (ABA) inhibition of precocious germination and ABA-induced storage protein accumulation was examined over the course of embryogenesis in wild-type and viviparous mutants of maize (Zea mays L.). We show that a high level of embryo ABA and the product of the Viviparous-1 gene are both required in early maturation phase for germination suppression and the accumulation of storage globulins encoded by the gene Glb1. Suppressing precocious germination with a high osmoticum is not sufficient to initiate Glb1 protein synthesis, although continued accumulation is contingent upon this inhibition; germination of immature or mature embryos leads to a decline in synthesis and the degradation of stored globulins. Late in embryogenesis, fragments of Glb1 protein accumulate, coinciding with the loss of ABA sensitivity. These results suggest that ABA influences storage globulin accumulation by initiating synthesis, suppressing degradation, and inhibiting precocious germination.
Dynamic characteristics of high voltage 4H-SiC vertical JFETs (2003)

We have developed a novel structure for a fully implanted, normally-on vertical junction field effect transistor (VJFET) and fabricated prototypes with blocking voltages between 600 and 1000 V. Mounting the SiC VJFET together with a 50 V Si MOSFET on a DCB substrate in a cascode circuit, we obtain a normally-off high voltage switch. The specific on-resistance of the VJFET was sufficiently low, in the range of 18 to 40 m/spl Omega/cm/sup 2/, for various blocking voltages. The dynamic behaviour shows turn-off times between 50 ns and 2 /spl mu/s due to the RC-product of two different p-gate networks.
Nitric oxide (NO) in expired air at rest and during exercise (1994)

Nitric oxide (NO) was analysed in expired air from 27 healthy human subjects. At rest the NO concentration was 10.5 +/- 0.9 ng 1-1 (mean +/- SEM) corresponding to 8.6 +/- 0.7 parts per billion (ppb). The expired NO concentration did not change when the subjects were switched from breathing NO-free tank gas to room air which contained 7.7 ng l-1 NO. Repeated measurements of expired NO with an interval of 1 day showed a mean variation of 2.2 +/- 0.7 ng l-1 NO. The NO concentration in the first portion in the expired tidal volume (44%) was insignificantly higher than in the latter expired portion, 6.9 +/- 1.9 vs. 5.1 +/- 1.0 ng l-1 (n = 5). During moderately heavy exercise on an ergometer bicycle (90 W for women, n = 4, 150 W for men, n = 4) the expired concentration of NO decreased, however because of increased minute ventilation, the expired amount of NO almost doubled (from 111 +/- 12 to 209 +/- 30 ng min-1). The source of the expired NO is not clear and both the airways and the pulmonary circulation may contribute.
Latex Assay for Serotyping of Group B <i>Streptococcus</i> Isolates (2003)

We developed a group B streptococcus (GBS) latex serotyping kit that reduces the numbers of GBS nontypeable isolates by nearly 50%. A total of 232 isolates were tested, and 203 isolates were serotyped by the GBS latex test, while the capillary precipitation test serotyped 184 isolates.
ChemInform Abstract: Efficient Synthesis of Imidazole‐Fused Benzodiazepines Using Palladium‐Catalyzed Intramolecular C—N Bond Formation Reaction. (2013)

Abstract The intramolecular Buchwald—Hartwig cycloamination reaction of precursors (V) is the key‐step in the three‐step synthetic route to the title benzodiazepines (VI).
Effect of H2 on the etch profile of InP/InGaAsP alloys in Cl2/Ar/H2 inductively coupled plasma reactive ion etching chemistries for photonic device fabrication (2002)

This study demonstrates etch profile engineering of InP, In1−xGaxAs1−yPy, and In0.53Ga0.47As heterostructures results from adding H2 to standard Cl2/Ar inductively coupled plasma-reactive ion etching chemistries. Etch rate curves of bulk InP, In1−xGaxAs1−yPy, and In0.53Ga0.47As show a general parabolic trend as a function of the H2 component of the Cl2/Ar/H2 ratio. Three distinct etching profiles of InP/InGaAsP layers were realized by varying the Cl2/Ar/H2 ratio. Highly anisotropic profiles result for Cl2/Ar/H2 ratios between 2/3/1 and 2/3/2. Waveguiding structures fabricated using this technology are presented with a loss as low as 2 dB/cm. An InP racetrack resonator with a quality factor (Q)&gt;8000 is also presented.
Human papillomavirus 18-immortalized endocervical cells with in vitro cytokeratin expression characteristics of adenocarcinoma. (1994)

Both endo- and ectocervical cells are targets for immortalization by HPV 18. Based on cytokeratin expression patterns, immortalized endocervical cells, but not ectocervical cells, may be useful as a model for premalignant lesions that progress into adenocarcinoma.
Automatic parameter recommendation for practical API usage (2012)

Programmers extensively use application programming interfaces (APIs) to leverage existing libraries and frameworks. However, correctly and efficiently choosing and using APIs from unfamiliar libraries and frameworks is still a non-trivial task. Programmers often need to ruminate on API documentations (that are often incomplete) or inspect code examples (that are often absent) to learn API usage patterns. Recently, various techniques have been proposed to alleviate this problem by creating API summarizations, mining code examples, or showing common API call sequences. However, few techniques focus on recommending API parameters. In this paper, we propose an automated technique, called Precise, to address this problem. Differing from common code completion systems, Precise mines existing code bases, uses an abstract usage instance representation for each API usage example, and then builds a parameter usage database. Upon a request, Precise queries the database for abstract usage instances in similar contexts and generates parameter candidates by concretizing the instances adaptively. The experimental results show that our technique is more general and applicable than existing code completion systems, specially, 64% of the parameter recommendations are useful and 53% of the recommendations are exactly the same as the actual parameters needed. We have also performed a user study to show our technique is useful in practice.
Algorithm AS 253: Maximum Likelihood Estimation of the RC(M) Association Model (1990)

The subroutine RCM fits the RC(M) association model (Goodman) to a given two-way cross-classification of counts. The algorithm is based on the cyclic application of Newton's elementary (univariate) method. The user is provided with the option of specifying: (a) the dimension of the model, say M, (b) the weight vectors used to identify the association parameters (row and column scores) and (c) cells to be «banked out» (e.g. structural zeros)
Reflecting trackchanger: new acoustic-surface-wave component for folding long delay lines onto small substrates (1972)

A new acoustic-surface-wave component is described, which has the unique property of reflecting a freely propagating acoustic wave onto a path adjacent to the input path. This ‘trackchanging’ operation may be performed several times to fold a long acoustic-delay path onto a short substrate. The trackchanger has a loss below 3 dB over a 50% band-width, and is particularly suited to materials of large electro-mechanical-coupling constant. No external electrical components are required, and the device is constructed by standard photolithographic techniques.
Decreased incidence of prostate cancer with selenium supplementation: results of a double‐blind cancer prevention trial (1998)

Although selenium shows no protective effects against the primary endpoint of squamous and basal cell carcinomas of the skin, the selenium-treated group had substantial reductions in the incidence of prostate cancer, and total cancer incidence and mortality that demand further evaluation in well-controlled prevention trials.
Propionibacterium acnes and inflammation in acne; P. acnes has T-cell mitogenic activity (2002)

Two mechanisms of lymphocyte activation by P. acnes cells are proposed, antigen and mitogen driven. These results are consistent with the histological evidence of inflammation in acne lesions.