gebhart/patrepeval huggingface dataset:
DeepCT: Tomographic Combinatorial Testing for Deep Learning Systems (2019)

Deep learning (DL) has achieved remarkable progress over the past decade and has been widely applied to many industry domains. However, the robustness of DL systems recently becomes great concerns, where minor perturbation on the input might cause the DL malfunction. These robustness issues could potentially result in severe consequences when a DL system is deployed to safety-critical applications and hinder the real-world deployment of DL systems. Testing techniques enable the robustness evaluation and vulnerable issue detection of a DL system at an early stage. The main challenge of testing a DL system attributes to the high dimensionality of its inputs and large internal latent feature space, which makes testing each state almost impossible. For traditional software, combinatorial testing (CT) is an effective testing technique to balance the testing exploration effort and defect detection capabilities. In this paper, we perform an exploratory study of CT on DL systems. We propose a set of combinatorial testing criteria specialized for DL systems, as well as a CT coverage guided test generation technique. Our evaluation demonstrates that CT provides a promising avenue for testing DL systems.
Publisher Correction: An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonasis (2021)

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20623-0
Novel Interconnection Technologies for Integrated Microfluidic Systems (1998)

A new approach to realize silicon based integrated microfluidic sys tems is presented. By using a combination of silicon fusion bonding (SFB) and deep reactive ion etching (DRIE) [1, 2], multi-level flu idic "circuit boards" are fabricated and used to integrate microflu idic components into a hybrid system. As application examples, we demonstrate a multi-level laminating mixer and a multi-level mani fold with multiple pressure sensors. To interface the microfluidic system to the macroscopic world, three types of ORIE-fabricated, tight-fitting fluidic couplers for standard capillary tubes are described. One type of coupler is designed for minimal dead space, while another type reduces the risk of blocking capillaries with adhesive. A third design demonstrates for the first time a sili con/plastic coupler combining the DRIE coupler technology with injection-molded press fittings.
Analysis and Implementation of an Ultra-Wide Tuning Range CMOS Ring-VCO With Inductor Peaking (2016)

A novel ring voltage controlled oscillator (VCO) topology is proposed which uses monolithic inductors as a peaking load. Four design examples have been fabricated and tested to verify the proposed circuit structure. The highest measured oscillation frequency is 25.07 GHz, with a tuning range of more than four octaves, and the active area is 0.0085 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The design has the highest combined frequency and tuning range with the best figure of merit (≈ 195) comparable to previously published work.
THz Electric Field-Induced Second Harmonic Generation in Inorganic Ferroelectric (2017)

Second Harmonic Generation induced by the electric field of a strong nearly single-cycle terahertz pulse with the peak amplitude of 300 kV/cm is studied in a classical inorganic ferroelectric thin film of (Ba<sub>0.8</sub>Sr<sub>0.2</sub>)TiO<sub>3</sub>. The dependences of the SHG intensity on the polarization of the incoming light is revealed and interpreted in terms of electric polarization induced in the plane of the film. As the THz pulse pumps the medium in the range of phononic excitations, the induced polarization is explained as a dynamical change of the ferrolectric order parameter. It is estimated that under action of the THz pulse the ferroelectric order parameter acquires an in-plane component up to 6% of the net polarization.
Experimental comparison of multiple quantum-well GaInAs verticle-cavity SOAs (2004)

This paper presents the gain characterization and efficiency comparison of two reflection-format 1.3 /spl mu/m GaInNAs vertical-cavity semiconductor optical amplifiers (VCSOAs) having six and fifteen quantum-wells. A maximum gain operation of 19 dB and 17 dB, respectively, is reported.
Reduced Transcobalamin I Gene Expression Following Roux‐en‐Y Gastric Bypass Surgery Can Contribute to B12 Deficiency (2015)

The objective of this study was to examine potential mechanisms leading to the often‐observed Vitamin B 12 deficiency following Roux‐en‐Y gastric bypass (RYGB). Vitamin B 12 absorption begins with release from food in the upper GI tract followed by transcobalamin I binding; duodenal enzyme degradation of transcobalamin I is then followed by intrinsic factor (IF) capture; IF is next degraded within the ileal enterocyte, releasing B 12 that then enters the plasma. Although IF levels are reduced with RYGB due to removal of the gastric fundus, other causes of modified B 12 transport may be involved. To examine these other potential mechanisms we used balloon endoscopy to acquire GI tissue at multiple sites in 20 obese women with adult‐onset diabetes before (age, 46.5±6.6 yrs; BMI, 45.7±4.1 kg/m 2 ) RYGB and at the identical India‐Ink marked sites three months following surgery (BMI, 37.7±3.4 kg/m 2 ). Microarray analysis was performed on all samples using a Human GeneChip 1.0 ST array (Affymetrix, Inc., Santa Clara, CA). There was significantly reduced gene expression (2.335‐fold, p&lt;0.05) of TCN1 in the remnant stomach following surgery (TCN1 translates transcobalamin I) . These findings suggest that B 12 deficiency following RYGB may be caused by a reduction in transcobalamin I in addition to the anatomical absence of IF. FAPESP 2011/09612‐3, BEPE 2014/07742‐5.
Resource Modelling for the QC Laboratory at XYZ Pharmaceuticals in Southern Africa (2021)

Quality control (QC) laboratories are critical components in drug manufacturing and running them efficiently contributes to better, consistent supply of cost-effective quality products, while also and preventing deaths due to untimely delivery or unavailability of medicines. Having a resource modelling tool to estimate resources needed to handle a particular demand in a given system is essential for efficient running of QC laboratory. This study was done to establish such a model at XYZ Pharmaceuticals. The list of all products manufactured by XYZ Pharmaceuticals Southern Africa was reviewed; and product families for all products were identified. Analysts’ hands on time (HOT) to process one sample of each of the product families was estimated. The number of analysts required to support the workload at XYZ Pharmaceuticals was calculated using the HOTs for the different product families and the Maslaton’s Calculation Model. A baseline resource model was established.
Distortions to the penetration depth and coherence length of superconductor/normal-metal superlattices (2020)

Superconducting (S) thin film superlattices composed of Nb and a normal-metal spacer (N) have been extensively utilized in Josephson junctions given their favorable surface roughness compared to Nb films of comparable thickness. In this work, we characterize the London penetration depth and Ginzburg-Landau coherence lengths of $S/N$ superlattices using polarized neutron reflectometry and electrical transport. Despite the normal-metal spacer layers being only approximately 8% of the total superlattice thickness, we surprisingly find that the introduction of these thin N spacers between S layers leads to a dramatic increase in the measured London penetration depth compared to that of a single Nb film of comparable thickness. Using the measured values for the effective in- and out-of-plane coherence lengths, we quantify the induced anisotropy of the superlattice samples and compare to a single Nb film sample. From these results, we find that the superlattices behave similarly to layered 2D superconductors.
Drug-free remission: is it already possible? (2011)

Drug-free remission can be achieved and sustained in a small group of RA patients. In early RA, retreatment is successful in the majority of patients. Disease flare after cessation of medication does not seem to increase joint damage progression. Sustained drug-free remission is predicted by autoantibody and shared epitope negativity and short disease duration before treatment initiation.
Full‐waveform inversion results when using acoustic approximation instead of elastic medium (2008)

Seismic marine data inversion is a very heavy process, especially for the 3D seismic case. Often, approximations are made to limit the number of physical parameters or to speed up the forward modeling. Because the data are often dominated by unconverted P waves, one popular approximation is to consider the earth as purely acoustic: no shear modulus; even sometimes with constant density. Non‐linear waveform seismic inversion consists in iteratively minimizing the misfit between the amplitudes of the measured and the modeled data. Approximations, such as acoustic medium, lead to model incorrectly the amplitudes of the seismic waves, especially with respect to offset (AVO) and therefore have a direct impact on the inversion results. For evaluation purposes, we performed series of inversions with different approximations and different constraints where the synthetic data set to recover is computed for a 1D elastic medium. The different physical approximations go from an acoustic medium to a fully elastic medium. The different geometrical constraints go from fixed interface positions to full 2D inversion and for the data: from near to far offset. As expected, the acoustic approximation is not minor and it impacts the inversion results, in some cases drastically.
Radio Resource Management in context of Network Slicing: What is Missing in Existing Mechanisms? (2019)

Fifth generation (5G) of mobile networks are expected to serve multiple heterogeneous use cases. These use cases are extremely diverse in terms of service requirements and bundling them in a single monolithic network is a challenge. Network slicing is identified as one of the main enablers of 5G systems, where multiple logical End-to-End (E2E) networks share the resources of a single physical network. Radio Resource Management (RRM) in a sliced network should be able to simultaneously fulfill the required services of slices, dynamically share the network and assure the independence of slices so that slices cannot affect each other negatively. In this paper, we study the existing mechanisms that provide similar features in legacy networks and demonstrate the contributions and shortcomings of such existing RRM mechanisms in a sliced network. Thereafter, we argue the need for a new entity that will complement the existing RRM mechanisms to be slice-aware. With the aid of system-level simulations, we compare different slicing schemes and illustrate the drawbacks of legacy networks in fulfilling the objectives of a fully sliced network. Moreover, we illustrate the capabilities of the slice-aware RRM in steering the network's Key Performance Indicators (KPIs).
<scp>cDNA</scp> microarray assays to evaluate immune responses following intracranial injection of baculoviral vectors in non‐human primates (2016)

Recombinant insect baculoviral vectors efficiently transduce several types of cells in the brain and can possibly be used in gene therapy for brain disorders. However, together with contaminating insect cell proteins, they trigger immune responses that might damage host brain cells. To substantially reduce unwanted immune responses due to the insect cell impurities, we purified and concentrated baculoviral vectors by combining an ion-exchange membrane chromatography method with high-speed centrifugation and demonstrated reduced immune responses of the vector preparations in the mouse brain. To verify the suitability of using these viral vectors for gene therapy strategies in the brain, we evaluated immune reactions and vector toxicity upon acute administration of baculoviral vectors into the brains of cynomolgus macaques. We demonstrated that the virus inoculation caused no abnormalities to non-human primates but induced host anti-viral responses in the brain. With global cellular gene expression profiling, using cDNA microarray technology, we detected that the affected genes were mainly associated with innate immunity, involving the genes of RIG-1-like receptor signaling pathway as the major interferon production pathway. These findings in non-human primates, which share close physiological and genomic similarities with man, may better mimic the responses to baculoviral transduction in the human brain and should be useful in guiding rational therapeutic applications of baculoviral vectors to treat brain disorders.
Klotho as a regulator of fibroblast growth factor signaling and phosphate/calcium metabolism (2006)

Klotho protein binds to fibroblast growth factor receptors and functions as a regulator of FGF23 signaling. It also functions as an enzyme that modifies sugar chains of transient receptor potential vanilloid-5 and regulates its activity. Klotho is a multi-functional protein that regulates phosphate/calcium metabolism as well as aging.
A pyroelectric liquid crystal polymer (PLCP) for second-harmonic generation (1996)

Abstract In order for a material to show a non-vanishing second order non-linear susceptibility, the material has to have a polar axis. This is hard to achieve in a liquid crystal system because of the strong quadrupolar order along the director. Electrostatic poling of polymers and polymer liquid crystals at high temperature and subsequent quenching to lower temperature only gives a small value of the polar order parameter and, in addition, results in materials which are not in thermodynamic equilibrium and therefore not stable over long times. Starting with a ferroelectric liquid crystal (which has polar order perpendicular to the director) we have succeeded in making a material with true polar order. It is not ferroelectric, although the ferroelectric properties of the starting and intermediate materials are basic for the procedure and for the final product which can be used for frequency doubling, of importance, for instance, in a wide area of optic communication applications.
ChemInform Abstract: Chemistry of 2‐Oxazolines (1985‐Present) (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dielectric Barrier Discharge Ionization for Liquid Chromatography/Mass Spectrometry (2009)

An atmospheric pressure microplasma ionization source based on a dielectric barrier discharge with a helium plasma cone outside the electrode region has been developed for liquid chromatography/mass spectrometry (LC/MS). For this purpose, the plasma was realized in a commercial atmospheric pressure ionization source. Dielectric barrier discharge ionization (DBDI) was compared to conventional electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photoionization (APPI) in the positive ionization mode. Therefore, a heterogeneous compound library was investigated that covered polar compounds such as amino acids, water-soluble vitamins, and nonpolar compounds like polycyclic aromatic hydrocarbons and functionalized hydrocarbons. It turned out that DBDI can be regarded as a soft ionization technique characterized by only minor fragmentation similar to APCI. Mainly protonated molecules were detected. Additionally, molecular ions were observed for polycyclic aromatic hydrocarbons and derivatives thereof. During DBDI, adduct formation with acetonitrile occurred. For aromatic compounds, addition of one to four oxygen atoms and to a smaller extend one nitrogen and oxygen was observed which delivered insight into the complexity of the ionization processes. In general, compounds covering a wider range of polarities can be ionized by DBDI than by ESI. Furthermore, limits of detection compared to APCI are in most cases equal or even better.
Retrospective analysis of Hemoporfin-mediated photodynamic therapy in the treatment of naïve port-wine stains (2022)

Hemoporfin-PDT is an effective and safe treatment for PWS. The number of treatments was a favorable factor for Hemoporfin-PDT, smaller lesion sizes showed a better effect than the larger one, and the location of extremity and trunk was a negative factor.
Assembling the puzzle of superconducting elements: a review (2004)

Superconductivity in the simple elements is of both technological relevance and fundamental scientific interest in the investigation of superconductivity phenomena. Recent advances in the instrumentation of physics under pressure have enabled the observation of superconductivity in many elements not previously known to superconduct, and at steadily increasing temperatures. This article offers a review of the state of the art in the superconductivity of elements, highlighting underlying correlations and general trends.
Trends of Earlier and Later Responses of C-peptide to Oral Glucose Challenges With Progression to Type 1 Diabetes in Diabetes Prevention Trial–Type 1 Participants (2009)

OBJECTIVE We studied the C-peptide response to oral glucose with progression to type 1 diabetes in Diabetes Prevention Trial-Type 1 (DPT-1) participants. RESEARCH DESIGN AND METHODS Among 504 DPT-1 participants <15 years of age, longitudinal analyses were performed in 36 progressors and 80 nonprogressors. Progressors had oral glucose tolerance tests (OGTTs) at baseline and every 6 months from 2.0 to 0.5 years before diagnosis; nonprogressors had OGTTs over similar intervals before their last visit. Sixty-six progressors and 192 nonprogressors were also studied proximal to and at diagnosis. RESULTS The 30-0 min C-peptide difference from OGTTs performed 2.0 years before diagnosis in progressors was lower than the 30-0 min C-peptide difference from OGTTs performed 2.0 years before the last visit in nonprogressors (P < 0.01) and remained lower over time. The 90-60 min C-peptide difference was positive at every OGTT before diagnosis in progressors, whereas it was negative at every OGTT before the last visit in nonprogressors (P < 0.01 at 2.0 years). The percentage whose peak C-peptide occurred at 120 min was higher in progressors at 2.0 years (P < 0.05); this persisted over time (P < 0.001 at 0.5 years). However, the peak C-peptide levels were only significantly lower at 0.5 years in progressors (P < 0.01). The timing of the peak C-peptide predicted type 1 diabetes (P < 0.001); peak C-peptide levels were less predictive (P < 0.05). CONCLUSIONS A decreased early C-peptide response to oral glucose and an increased later response occur at least 2 years before the diagnosis of type 1 diabetes.
The Common Marmoset as a Target Preclinical Primate Model for Cytokine and Gene Therapy Studies (1999)

Nonhuman primate models are useful to evaluate the safety and efficacy of new therapeutic modalities, including gene therapy, before the inititation of clinical trials in humans. With the aim of establishing safe and effective approaches to therapeutic gene transfer, we have been focusing on a small New World monkey, the common marmoset, as a target preclinical model. This animal is relatively inexpensive and easy to breed in limited space. First, we characterized marmoset blood and bone marrow progenitor cells (BMPCs) and showed that human cytokines were effective to maintain and stimulate in culture. We then examined their susceptibility to transduction by retroviral vectors. In a mixed culture system containing both marmoset stromal cells and retroviral producer cells, the transduction efficiency into BMPCs and peripheral blood progenitor cells (PBPCs) was 12% to 24%. A series of marmosets then underwent transplantation with autologous PBPCs transduced with a retroviral vector carrying the multidrug resistance 1 gene (MDR1) and were followed for the persistence of these cells in vivo. Proviral DNA was detectable by polymerase chain reaction (PCR) in peripheral blood granulocytes and lymphocytes in the recipients of gene transduced progenitors up to 400 days posttransplantation. To examine the function of the MDR1 gene in vivo, recipient maromsets were challenged with docetaxel, an MDR effluxed drug, yet the overall level of gene transfer attained in vivo (<1% in peripheral blood granulocytes) was not sufficient to prevent the neutropenia induced by docetaxel treatment. Using this model, we safely and easily performed a series of in vivo studies in our small animal center. Our results show that this small nonhuman primate, the common marmoset, is a useful model for the evaluation of gene transfer methods targeting hematopoietic stem cells.
IL17 Mediates Pelvic Pain in Experimental Autoimmune Prostatitis (EAP) (2015)

Chronic pelvic pain syndrome (CPPS) is the most common form of prostatitis, accounting for 90-95% of all diagnoses. It is a complex multi-symptom syndrome with unknown etiology and limited effective treatments. Previous investigations highlight roles for inflammatory mediators in disease progression by correlating levels of cytokines and chemokines with patient reported symptom scores. It is hypothesized that alteration of adaptive immune mechanisms results in autoimmunity and subsequent development of pain. Mouse models of CPPS have been developed to delineate these immune mechanisms driving pain in humans. Using the experimental autoimmune prostatitis (EAP) in C57BL/6 mice model of CPPS we examined the role of CD4+T-cell subsets in the development and maintenance of prostate pain, by tactile allodynia behavioral testing and flow cytometry. In tandem with increased CD4+IL17A+ T-cells upon EAP induction, prophylactic treatment with an anti-IL17 antibody one-day prior to EAP induction prevented the onset of pelvic pain. Therapeutic blockade of IL17 did not reverse pain symptoms indicating that IL17 is essential for development but not maintenance of chronic pain in EAP. Furthermore we identified a cytokine, IL7, to be associated with increased symptom severity in CPPS patients and is increased in patient prostatic secretions and the prostates of EAP mice. IL7 is fundamental to development of IL17 producing cells and plays a role in maturation of auto-reactive T-cells, it is also associated with autoimmune disorders including multiple sclerosis and type-1 diabetes. More recently a growing body of research has pointed to IL17's role in development of neuropathic and chronic pain. This report presents novel data on the role of CD4+IL17+ T-cells in development and maintenance of pain in EAP and CPPS.
Male Germline and Embryonic Stem Cell Lines from NOD Mice: Efficient Derivation of GS Cells from a Nonpermissive Strain for ES Cell Derivation1 (2009)

The nonobese diabetic (NOD) mouse is a valuable model for human type 1 diabetes and the development of humanized mice. Although the importance of this mouse strain is widely recognized, its usefulness is constrained by the absence of NOD embryonic stem (ES) lines with adequate germline transmission competence. In the present study, we established two germline transmission-competent types of cell lines from NOD mice; these cell lines, male germline stem (GS) cells and ES cells, were derived from NOD spermatogonia and blastocysts, respectively. NOD-GS cells proliferated in vitro and differentiated into mature sperm after transplantation into testis. NOD-ES cell lines were effectively established from NOD blastocysts using culture medium containing inhibitors for fibroblast growth receptor, MEK, and GSK3. Both the NOD-GS and NOD-ES cell lines transmitted their haplotypes to progeny, revealing a novel strategy for gene modification in a pure NOD genetic background. Our results also suggest that the establishment of GS cells is an effective procedure in nonpermissive mouse strains or other species for ES cell derivation.