gebhart/patrepeval huggingface dataset:
An Adaptive-Resolution Quasi-Level-Crossing Delta Modulator With VCO-Based Residue Quantizer (2020)

This brief introduces an adaptive-resolution (AR) quasi-level-crossing delta modulator ADC with a voltage-controlled oscillator (VCO)-based residue quantizer for Internet-of-Things (IoT) wireless sensor nodes. The residue voltage signal is digitized by a VCO-based residue quantizer, thus leading to a straightforward implementation of level-crossing (LC) and AR algorithms in digital domain. The inherent and mismatch-induced dithering provided by the VCO-based residue quantizer increases the proposed modulator's dynamic range and average sampling rate for slowly-varying input signals, enabling accurate sampling and conversion. For fast-varying signals, the AR algorithm is adopted to reduce the average sampling rate by a factor of three compared to the straightforward LC algorithm at the edge of the modulator's signal bandwidth. Fabricated in 28-nm CMOS, the proposed modulator achieves a peak SNDR of 53dB over a signal bandwidth of 1.78MHz.
Temperature-responsive genetic loci in the plant pathogen Pseudomonas syringae pv. glycinea The GenBank accession numbers for the nucleotide sequences of mutants 560, 561, 562, 563, 564, 568, 570, 574, 590, 591, 593, 596, 599, 601, 605, 608, 613, 617, 618, 626 and 632 determined in this work are AF274322–AF274342, respectively. (2000)

Plant-pathogenic bacteria may sense variations in environmental factors, such as temperature, to adapt to plant-associated habitats during pathogenesis or epiphytic growth. The bacterial blight pathogen of soybean, Pseudomonas syringae pv. glycinea PG4180, preferentially produces the phytotoxin coronatine at 18 degrees C and infects the host plant under conditions of low temperature and high humidity. A miniTn5-based promoterless glucuronidase (uidA) reporter gene was used to identify genetic loci of PG4180 preferentially expressed at 18 or 28 degrees C. Out of 7500 transposon mutants, 61 showed thermoregulated uidA expression as determined by a three-step screening procedure. Two-thirds of these mutants showed an increased reporter gene expression at 18 degrees C whilst the remainder exhibited higher uidA expression at 28 degrees C. MiniTn5-uidA insertion loci from these mutants were subcloned and their nucleotide sequences were determined. Several of the mutants induced at 18 degrees C contained the miniTn5-uidA insertion within the 32.8 kb coronatine biosynthetic gene cluster. Among the other mutants with increased uidA expression at 18 degrees C, insertions were found in genes encoding formaldehyde dehydrogenase, short-chain dehydrogenase and mannuronan C-5-epimerase, in a plasmid-borne replication protein, and in the hrpT locus, involved in pathogenicity of P. syringae. Among the mutants induced at 28 degrees C, insertions disrupted loci with similarities to a repressor of conjugal plasmid transfer, UV resistance determinants, an isoflavanoid-degrading enzyme, a HU-like DNA-binding protein, two additional regulatory proteins, a homologue of bacterial adhesins, transport proteins, LPS synthesis enzymes and two proteases. Genetic loci from 13 mutants did not show significant similarities to any database entries. Results of plant inoculations showed that three of the mutants tested were inhibited in symptom development and in planta multiplication rates. Temperature-shift experiments suggested that all of the identified loci showed a rather slow induction of expression upon change of temperature.
Supplementary Tables 1-5 for scRNAseq marker genes from HER2 Isoforms Uniquely Program Intratumor Heterogeneity and Predetermine Breast Cancer Trajectories During the Occult Tumorigenic Phase (2023)

&lt;p&gt;Supplementary Table 1: Cluster-specific markers from all cells (8,486 cells) Supplementary Table 2: Cluster-specific markers from all epithelial cells (3,843 cells) Supplementary Table 3: Cluster-specific markers from all immune cells (1,803 cells) Supplementary Table 4: Cluster-specific markers from all fibroblast cells (922 cells) Supplementary Table 5a: State-specific markers from all d16:HBOW epithelial cells (1,421 cells) Supplementary Table 5b: State-specific markers from all p95:HBOW epithelial cells (1,258 cells)&lt;/p&gt;
Recent Developments of Nanomaterial Doped Paints for the Minimization of Biofouling in Submerged Structures (2010)

Biofouling prevention remains a major challenge to the chemists, and researchers around the world who are engaged in the development of antifouling paints that can prevent growth of organisms like barnacles, algae and tubeworms on the submerged structures. Growth of organisms on the surfaces exposed to marine and freshwater environment not only reduces the efficiency of such structures, e.g. reduction of heat transfer etc, but also causes structural damages. In order to prevent the growth of organisms on surfaces of the marine and freshwater environments, coatings containing biocides are generally used. However, use of biocides not only leads to the corrosion of the metallic structures in some cases, but it also inflicts severe damage to the aquatic ecosystem. It is thus necessary to develop anti-biofouling paints that are innocuous to both the environment and the structures. One alternative approach may be incorporation of nanoparticles, and preventing bacterial bio-film formation as well as the attachment of larger organisms. Various nanoparticles of metal and their oxides have been recognized to possess antibacterial properties. The development of such materials is a challenge to both the chemist and the biologist, where effective choice of methods that provide relevant information regarding application of the metal nanoparticles in anti-fouling materials, becomes the central objective. The present article is a short review in the area of nanoparticle doped antifouling paints. In addition, some aspects covering our experimental results on the selected bio-fouling paints with dispersed nanoparticles of ZnO, CuO, Al2O3, MgO, TiO2 and Co3O4. It also discusses the techniques used for the characterization of the nanoparticle-doped materials and methods for the determination of their efficacy against bio-film formation.
Synthesis and characterization of ionic conducting sulfonated polybenzimidazoles (2010)

Abstract By copolymerization of the disodium‐2,2′‐disulfonate‐4,4′‐oxydibenzoic acid (SODBA), the 4,4′‐oxybis(benzoic acid) (OBBA) with the bis 3,4‐(diaminophenyl)sulfone (BDAPS), a series of high molecular weight sulfonated polybenzimidazoles (sPBI) were prepared by varying the ratio of monomers SODBA/OBBA. Polymers with ion exchange capacity (IEC) ranging from 0 to 3.2 meqH + /g were obtained. The chemical structure of the sPBI was confirmed by NMR, Fourier‐transform infra‐red (FTIR). Although the sPBI display a very poor solubility in organic solvents, they are, in the ammonium salt form, soluble in polar aprotic solvents such as DMF, NMP, or DMSO. Tough and ductile membranes from solution casting method were prepared. The water uptake and the ionic conductivity were determined at 30 and 90 °C. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1732–1742, 2010
Demonstration of end-to-end cloud-DSL with a PON-based fronthaul supporting 576-Gb/s throughput with 48 eCDMA-encoded 1024-QAM discrete multi-tone signals (2015)

We experimentally demonstrate an end-to-end ultra-broadband cloud-DSL network using passive optical network (PON) based fronthaul with electronic code-division-multiple-access (eCDMA) encoding and decoding. Forty-eight signals that are compliant with the very-high-bit-rate digital subscriber line 2 (VDSL2) standard are transmitted with a record throughput of 5.76 Gb/s over a hybrid link consisting of a 20-km standard single-mode fiber and a 100-m twisted pair.
Revising the lower statistical limit of x-ray grating-based phase-contrast computed tomography (2017)

Phase-contrast x-ray computed tomography (PCCT) is currently investigated as an interesting extension of conventional CT, providing high soft-tissue contrast even if examining weakly absorbing specimen. Until now, the potential for dose reduction was thought to be limited compared to attenuation CT, since meaningful phase retrieval fails for scans with very low photon counts when using the conventional phase retrieval method via phase stepping. In this work, we examine the statistical behaviour of the reverse projection method, an alternative phase retrieval approach and compare the results to the conventional phase retrieval technique. We investigate the noise levels in the projections as well as the image quality and quantitative accuracy of the reconstructed tomographic volumes. The results of our study show that this method performs better in a low-dose scenario than the conventional phase retrieval approach, resulting in lower noise levels, enhanced image quality and more accurate quantitative values. Overall, we demonstrate that the lower statistical limit of the phase stepping procedure as proposed by recent literature does not apply to this alternative phase retrieval technique. However, further development is necessary to overcome experimental challenges posed by this method which would enable mainstream or even clinical application of PCCT.
Mechanics and Function of the Pulmonary Vasculature: Implications for Pulmonary Vascular Disease and Right Ventricular Function (2012)

The relationship between cardiac function and the afterload against which the heart muscle must work to circulate blood throughout the pulmonary circulation is defined by a complex interaction between many coupled system parameters. These parameters range broadly and incorporate system effects originating primarily from three distinct locations: input power from the heart, hydraulic impedance from the large conduit pulmonary arteries, and hydraulic resistance from the more distal microcirculation. These organ systems are not independent, but rather, form a coupled system in which a change to any individual parameter affects all other system parameters. The result is a highly nonlinear system which requires not only detailed study of each specific component and the effect of disease on their specific function, but also requires study of the interconnected relationship between the microcirculation, the conduit arteries, and the heart in response to age and disease. Here, we investigate systems-level changes associated with pulmonary hypertensive disease progression in an effort to better understand this coupled relationship.
Regulation of Airway Inflammation by G-protein Regulatory Motif Peptides of AGS3 protein (2016)

Abstract Respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), and lung infections have critical consequences on mortality and morbidity in humans. The aims of the present study were to examine the mechanisms by which CXCL12 affects MUC1 transcription and airway inflammation, which depend on activator of G-protein signaling (AGS) 3 and to identify specific molecules that suppress CXCL12-induced airway inflammation by acting on G-protein-coupled receptors. Herein, AGS3 suppresses CXCL12-mediated upregulation of MUC1 and TNFα by regulating Gα i . We found that the G-protein regulatory (GPR) motif peptide in AGS3 binds to Gα i and downregulates MUC1 expression; in contrast, this motif upregulates TNFα expression. Mutated GPR Q34A peptide increased the expression of MUC1 and TGFβ but decreased the expression of TNFα and IL-6. Moreover, CXCR4-induced dendritic extensions in 2D and 3D matrix cultures were inhibited by the GPR Q34A peptide compared with a wild-type GPR peptide. The GPR Q34A peptide also inhibited CXCL12-induced morphological changes and inflammatory cell infiltration in the mouse lung, and production of inflammatory cytokines in bronchoalveolar lavage (BAL) fluid and the lungs. Our data indicate that the GPR motif of AGS3 is critical for regulating MUC1/Muc1 expression and cytokine production in the inflammatory microenvironment.
Enhanced Anticancer Potential of Encapsulated Solid Lipid Nanoparticles of TPD: A Novel Triterpenediol from Boswellia serrata (2012)

A pentacyclic triterpenediol (TPD) from Boswellia serrata has significant cytotoxic and apoptotic potential in a large number of human cancer cell lines. To enhance its anticancer potential, it was successfully formulated into solid lipid nanoparticles (SLNs) by the microemulsion method with 75% drug entrapment efficiency. SEM and TEM studies indicated that TPD-SLNs were regular, solid, and spherical particles in the range of 100-200 nm, and the system indicated that they were more or less stable upon storing up to six months. TPD loaded SLNs showed significantly higher cytotoxic/antitumor potential than the parent drug. TPD-SLNs have 40-60% higher cytotoxic and apoptotic potential than the parent drug in terms of IC(50), extent of apoptosis, DNA damage, and expression of pro-apoptotic proteins like TNF-R1, cytochrome-c, and PARP cleavage in HL-60 cells. Moreover, blank SLNs did not have any cytotoxic effect on the cancer as well as in normal mouse peritoneal macrophages. The in vivo antitumor potential of TPD-SLNs was significantly higher than that of TPD alone in Sarcoma-180 solid tumor bearing mice. Therefore, SLNs of TPD successfully increased the apoptotic and anticancer potential of TPD at comparable doses (both in vitro and in vivo). This work provides new insight into improvising the therapeutic efficacy of TPD by adopting novel delivery strategies such as solid lipid nanoparticles.
Optical constants of SiO2 from 196 to 1688 nm (0.735–6.33 eV) from 20, 40, and 60 nm films of reactively sputtered SiO2 on Eagle XG® glass by spectroscopic ellipsometry (2017)

Three thicknesses of reactively sputtered SiO2, nominally 20, 40, and 60 nm, deposited on Corning Eagle XG® (EXG), an important display glass, were analyzed by spectroscopic ellipsometry. Reflection ellipsometry data from the samples were analyzed from 196 to 1688 nm at angles of 55°–60°, inclusive, in 1° increments. These angles were chosen because they bracket the Brewster angles of both EXG glass and SiO2. The backsides of the samples were roughened by sand blasting to suppress backside reflections from the substrates. A total of nine datasets were collected from nine different samples (three for each nominal thickness of SiO2), each at six different angles of incidence (54 spectra). The optical constants for each thickness of SiO2 was determined, as well as a set of constants for all the films (the material in general) via a multisample analysis (MSA). The optical constants of the SiO2 films were modeled using two poles with transparency assumed over the entire spectral range (a Sellmeier model). A Bruggeman effective medium approximation (BEMA) roughness layer was included in the model, which assumed 50/50 volume fractions that corresponded to the modeled SiO2 optical constants and void. The fit did not substantially improve when an interface layer between the Eagle XG® and the sputtered film was included, so it was omitted. Three sets of previously reported optical constants for the substrate over two wavelength ranges were considered in the modeling. The thin SiO2 films analyzed herein have very similar optical properties to those of their EXG substrate—this is a challenging analytical problem involving a transparent film on a transparent substrate. Accordingly, analysis of multiple samples, an MSA that included multiple film thicknesses analyzed at multiple angles, and an exploration of multiple modeling approaches helped ensure that the optical constants reported herein are accurate and the modeling robust. In particular, these measures helped avoid correlation between the optical constants, the layer thicknesses, and the thicknesses of the BEMA layers. Atomic force microscopy roughness measurements were made on the SiO2 films and compared to the roughness values obtained by spectroscopic ellipsometry. In summary, the authors provide here the optical constants and some accompanying physical characterization of sputtered 20–60 nm SiO2 films from 196 to 1688 nm.
Expression of N-Methyl-D-Aspartate receptor subunit mRNA in the human brain: Mesencephalic dopaminergic neurons (1998)

Evidence is accumulating that glutamate-mediated excitotoxicity plays an important role in neuronal degeneration in Parkinson's disease (PD). In addition, alterations in excitatory amino acid neurotransmission in the basal ganglia contribute to the clinical manifestations of motor dysfunction. However, detailed knowledge of the anatomical distribution and subtype specificity of glutamate receptors in the dopamine neurons of human substantia nigra (SN) has been lacking. In order to test the hypothesis that selective expression of particular N-methyl-D-aspartate receptor (NR) subunit mRNA contributes to the differential vulnerability of specific neuronal populations to excitotoxic injury in PD, we have used a quantitative dual label, in situ hybridization technique with ribonucleotide probes to examine the cellular distribution of NR subunit mRNA in postmortem human mesencephalic dopaminergic neurons from subjects with no known neurological disorder. Analysis of both film autoradiograms and emulsion-dipped sections demonstrated significant labeling of nigral neurons for each NR subunit. Neuronal labeling was most intense for the NR1 and NR2D subunits, with low level labeling for the remaining subunits. In addition, we examined four subregions of the ventral mesencephalon for differential expression of NR subunit mRNA. For all NR subunits, the pars lateralis (PL) exhibited the most intense signal, while neurons of the ventral tier substantia nigra pars compacta (SNpc) failed to demonstrate a preponderance of a particular subunit. These results demonstrate that NRs are expressed to a significant degree in dopaminergic neurons of the SN and that their distribution does not correlate with the characteristic pattern of neuronal degeneration in PD.
The Utility of Semi-Automating Multiplexed Assays for ADME/Tox Applications (2011)

ADME-Tox testing examines the effects of an organism, tissue or cell on a compound, as well as the effects that the compound has on an organism, tissue or cell, and has gained in importance in the overall drug discovery process over the past twenty years. This is due to the rising percentage of drug candidate attrition in the 1990s and early 2000s due to adverse ADME/Tox profiles. The increased importance placed upon ADME/Tox testing has brought about new types of in-vitro assay technologies utilizing microplates to deliver the most pharmacologically relevant data. These tests, however, have typically been performed sequentially, where multiple assays over multiple microplates are used. This typically leads to increased time and cost required to generate the required information, and can sacrifice data quality. Multiplexed assays, however, where more than one piece of data can be attained from a single well or a single microplate, performed using appropriate liquid handling and detection instrumentation, can improve data quality and reduce the time and expense required to attain this information.
ABI-auditory brainstem implant (2021)

The Auditory Brainstem Implant (ABI) is based on the classic cochlear implant (CI) but uses a different stimulation electrode. At MED-EL, the early development activities on ABI started in the year 1994, with the suggestion coming from J. Helms and J. Müller from Würzburg, Germany in collaboration with the Univ. of Innsbruck Austria. The first ABI surgery in a neuro-fibromatosis (NF2) patient with the MED-EL device took place in the year 1997. Later, the indication of ABI was expanded to non-NF2 patients with severe inner-ear malformation, for whom a regular CI will not be beneficial. Key translational research activities at MED-EL in collaboration with numerous clinics investigating the factors that affect the hearing performance amongst ABI patients, importance of early ABI implantation in children, tools in pre-operative assessment of ABI candidates and new concepts that were pursued with the MED-EL ABI device. The CE-mark for the MED-EL ABI to be used in adults and children down to the age of 12 months without NF-2 was granted in 2017 mainly based on two long-term clinical studies in the pediatric population. This article covers the milestones of translational research from the first concept to the widespread clinical use of ABI in association with MED-EL.
Targeting oncoproteins with a positive selection assay for protein degraders (2021)

Most intracellular proteins lack hydrophobic pockets suitable for altering their function with drug-like small molecules. Recent studies indicate that some undruggable proteins can be targeted by compounds that can degrade them. For example, thalidomide-like drugs (IMiDs) degrade the critical multiple myeloma transcription factors IKZF1 and IKZF3 by recruiting them to the cereblon E3 ubiquitin ligase. Current loss of signal ("down") assays for identifying degraders often exhibit poor signal-to-noise ratios, narrow dynamic ranges, and false positives from compounds that nonspecifically suppress transcription or translation. Here, we describe a gain of signal ("up") assay for degraders. In arrayed chemical screens, we identified novel IMiD-like IKZF1 degraders and Spautin-1, which, unlike the IMiDs, degrades IKZF1 in a cereblon-independent manner. In a pooled CRISPR-Cas9-based screen, we found that CDK2 regulates the abundance of the ASCL1 oncogenic transcription factor. This methodology should facilitate the identification of drugs that directly or indirectly degrade undruggable proteins.
A seroprevalence study of herpes virus type 2 infection in Israeli women: implications for routine screening. (1994)

The aim of the study was to obtain data on the prevalence of herpes simplex virus type 2 (HSV-2) in selected populations of women and to identify groups that might benefit from routine prenatal screening. The prospective seroprevalence study was performed in 1,921 women in Israel during the period 1986-90. Four different population groups of women 17-60 years old were included. Groups 1 and 2 comprised 1,214 healthy female government employees and kibbutz and moshav residents, and Groups 3 and 4 comprised 707 Jewish and non-Jewish women with gynecological complaints. HSV-2 antibody in the sera were studied by the microneutralization method. In the healthy women (groups 1 and 2), the prevalence of antibodies to HSV-2 was 2-3%. Genital HSV-2 asymptomatic shedding was 1%. In the women with gynecological complaints (groups 3 and 4) the prevalence of antibodies to HSV-2 was 10% in Jewish and 16% in non-Jewish women. These data support the conclusion that there is no justification for routine prenatal HSV-2 screening in Israel in a healthy female population.