gebhart/patrepeval huggingface dataset:
Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. (2003)

A phylogenetically novel aerobic bacterium was isolated from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a gram-negative, rod-shaped aerobe. Cells often appeared to divide by budding replication. Strain T-27T grew at 25-35 degrees C with an optimum growth temperature of 30 degrees C, whilst no growth was observed below 20 degrees C or above 37 degrees C within 20 days incubation. The pH range for growth was 6.5-9.5, with an optimum at pH 7.0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15:0, C16:1 and C14:0. The G + C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate division BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence).
Relationship Between Auditory Function of Nonimplanted Ears and Bimodal Benefit (2012)

The SMD threshold at 1 cycle/octave has the potential to provide clinicians with information relevant to the question of whether an ear with low-frequency hearing is likely to add to the intelligibility of speech provided by a CI.
Nucleation and Crystallization of Low-Crystallinity Polypropylene Followed in Situ by Hot Stage Atomic Force Microscopy (2003)

The isothermal crystallization of the ether-soluble fraction (ES) of elastomeric stereoblock polypropylene (ePP) was investigated in situ by hot stage atomic force microscopy (AFM) at temperatures between 30 and 60 °C. Owing to the low average tacticity of 21% ([mmmm]), this material possesses a very low degree of crystallinity (≤1% as determined by differential scanning calorimetry (DSC) and wide-angle X-ray scattering (WAXS)) in fully crystallized samples. Despite this low degree of crystallinity, hot stage AFM allowed us to study the nucleation and growth processes of crystallization in thin ES films in real time with nanometer resolution. The crystallization occurs in the form of lamellar crystals that develop from stable nuclei. Both metastable and stable primary nuclei have been visualized. Many crystals can be assigned to the α-phase of isotactic polypropylene (iPP) based on the observation of crosshatching. The lamellar growth rates are <3 × 10-3 μm/min and show a maximum between 40 °C and 45 °C. These results form the basis for a better understanding of the crystallization of ultralow crystallinity polypropylenes and likely other low crystallinity polymers.
Investigation of the signal resolution of a high-T/sub c/ balanced comparator (1997)

The use of high-T/sub c/ Josephson junctions for digital applications requires a careful study of the influence of thermal noise on circuit performance. We investigated a balanced current comparator, which contains a basic component of all RSFQ circuits: two overdamped Josephson junctions connected in series. The dependence of the dc-voltage across the Josephson junctions on signal current was measured to determine the threshold uncertainty of switching of the comparator. The experimental data obtained at different sampling pulse frequencies, in a temperature range from 10 to 50 K, were compared with a theoretical model, taking into account the influence of thermal noise as well as of sampling pulse frequency.
IL‐18 and infections: Is there a role for targeted therapies? (2020)

Interleukin (IL)-18 is a pro-inflammatory cytokine belonging to the IL-1 family, first identified for its interferon-γ-inducing properties. IL-18 regulates both T helper (Th) 1 and Th2 responses. It acts synergistically with IL-12 in the Th1 paradigm, whereas with IL-2 and without IL-12 it can induce Th2 cytokine production from cluster of differentation (CD)4<sup>+</sup> T cells, natural killer (NK cells, NKT cells, as well as from Th1 cells. IL-18 also plays a role in the hemophagocytic lymphohistiocytosis, a life-threatening condition characterized by a cytokine storm that can be secondary to infections. IL-18-mediated inflammation was largely studied in animal models of bacterial, viral, parasitic, and fungal infections. These studies highlight the contribution of either IL-18 overproduction by the host or overresponsiveness of the host to IL-18 causing an exaggerated inflammatory burden and leading to tissue injury. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19). The damage in the later phase of the disease appears to be driven by a cytokine storm, including interleukin IL-1 family members and secondary cytokines like IL-6. IL-18 may participate in this hyperinflammation, as it was previously found to be able to cause injury in the lung tissue of infected animals. IL-18 blockade has become an appealing therapeutic target and has been tested in some IL-18-mediated rheumatic diseases and infantile-onset macrophage activation syndrome. Given its role in regulating the immune response to infections, IL-18 blockade might represent a therapeutic option for COVID-19, although further studies are warranted to investigate more in detail the exact role of IL-18 in SARS-CoV-2 infection.
Efficient Asymmetric Synthesis of Silanediol Precursors from 1,5-Dihydrosiloles (2007)

Dihydrosiloles are easily prepared from 1,3-dienes and dichlorosilanes, even on kilogram scale. Asymmetric hydroboration of a 3-alkyl-1,5-dihydrosilole, prepared from a 2-alkyl-1,3-diene, followed by treatment with aqueous HF results in Peterson fragmentation, forming optically active 3-alkyl-4-fluorosilyl-1-butenes. The fluorosilanes are stable to moisture but very reactive toward nucleophiles. In addition, they can be converted to nucleophilic silyllithium reagents.
Use of Subcutaneous Interstitial Fluid Glucose to Estimate Blood Glucose: Revisiting Delay and Sensor Offset (2010)

The absence of any direct comparisons between existing and new algorithms for correcting ISF delay and sensor OS current is, in part, due to the difficulty in extracting relevant details from industry patents and/or extracting unfiltered sensor signals from industry products. The model simulation environment, where all aspects of the signal can be derived, may be more appropriate for developing new filtering and calibration strategies. Nevertheless, clinicians, academic researchers, and the industry would benefit from collaborating when evaluating those strategies.
Lack of a negative influence on viral growth by the nef gene of human immunodeficiency virus type 1. (1989)

Human immunodeficiency virus type 1 (HIV-1) contains an open reading frame called nef at the 3' end of its genome. The nef gene product has been reported to down-regulate viral growth by suppressing viral transcription through interaction with the long terminal repeat region. We have compared two isogenic HIV-1 (HIV-1-WI3) strains, one of which lacks nef expression, and found little difference between them in in vitro growth. We tested effects on viral entry, DNA synthesis, and RNA expression by measuring HIV-specific low molecular weight DNA and RNA after infection. The qualitative and quantitative aspects of DNA and RNA synthesis were comparable between the nef+ and nef- strains. The effects on viral growth were also examined by following changes in reverse transcriptase activity during the course of infection. The presence of the nef gene product failed to slow viral growth in several different cell types tested, including the human T-lymphocyte cell lines H9 and CEM-SS, human primary T cells enriched for CD4+ cells, and human monocytic cell lines U-937 and THP-1. On the contrary, the nef+ strain grew more efficiently in some cell types than the nef- strain. The same results were obtained with nef+ and nef- strains of a different virus, HIV-1-432, whose Nef had been reported to have a negative effect on viral growth. Our data suggest that the Nef protein does not act as a negative factor, at least in the experimental systems employed in our studies.
Synthesis of double hydrophilic block copolymers and induced assembly with oligochitosan for the preparation of polyion complex micelles (2011)

This paper reports on the polyion complex micelles (PIC micelles) formed between neutral-ionizable double hydrophilic block copolymers (DHBC), poly(ethylene oxide)-block-poly(acrylic acid) (PEO-b-PAA), and oligochitosan, a natural polyamine. The controlled synthesis of PEO-b-PAA polymers was achieved by atom transfer radical polymerization (ATRP) of tert-butyl acrylate with ω-bromide-functionalized PEO macroinitiators (Mw = 2000 and 5000 g mol−1) and the subsequent deprotection reaction under acidic conditions. A series of copolymers with a narrow molecular weight distribution (Mw/Mn ≤ 1.2) and varied PAA block lengths was synthesized. Capillary electrophoresis (CE) was shown to unambiguously prove the blocky structure of the copolymers. It also showed that about 60% of the sodium counter ions were condensed onto the polyacrylate block in the pure diblock copolymer solution, which is consistent with the formation of polyion complex micelles triggered by counter-ion release in the presence of oligochitosan. The formation of oligochitosan/PAA–PEOcore–corona micelles has been investigated by dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). A minimum length of the PAA block is necessary to ensure micelle formation. The range of pH, where PIC micelles form, critically depends on the PAA block length, which also determines the size of the micelles. Micelles can be dissociated at ionic strength above 0.4 mol L−1. Since these PIC micelles have been used as recyclable structuring agents for the formation of ordered mesoporous materials, the reversibilty of the assembling process was studied upon pH and ionic strength cyclic variations. A hysteresis of stability was observed at low pH, probably due to hydrogen bonding.
Overlay metrology simulations: analytical and experimental validations (2003)

We have previously reported on an overlay metrology simulation platform, used for modeling both the effects of overlay metrology tool behavior and the impact of target design on the ultimate metrology performance. Since our last report, the simulation platform has been further enhanced, consisting now of eleven PCs and running commercial software both for lithography (PROLITH) and rigorous Maxwell calculations (EM-Suite). In this paper we report on the validation of the metrology simulations by comparing them to both analytical calculations and to experimental results. The analytical validation is based on the classical calculation of the diffraction of a polarized plane wave from a perfectly conducting half plane. For the experimental validation, we chose an etched silicon wafer manufactured by International SEMATECH (ISMT) and characterized at National Institute of Science and Technology (NIST). The advantages of this wafer are its well known topography and its suite of different metrology targets. A good fit to both analytical and experimental results is demonstrated, attesting to the capabilities of our enhanced simulation platform. The results for both the analytical and experimental validations are presented.
Orienteering Algorithms for Generating Travel Itineraries (2018)

We study the problem of automatically and efficiently generating itineraries for users who are on vacation. We focus on the common case, wherein the trip duration is more than a single day. Previous efficient algorithms based on greedy heuristics suffer from two problems. First, the itineraries are often unbalanced, with excellent days visiting top attractions followed by days of exclusively lower-quality alternatives. Second, the trips often re-visit neighborhoods repeatedly in order to cover increasingly low-tier points of interest. Our primary technical contribution is an algorithm that addresses both these problems by maximizing the quality of the worst day. We give theoretical results showing that this algorithm»s competitive factor is within a factor two of the guarantee of the best available algorithm for a single day, across many variations of the problem. We also give detailed empirical evaluations using two distinct datasets:(a) anonymized Google historical visit data and(b) Foursquare public check-in data. We show first that the overall utility of our itineraries is almost identical to that of algorithms specifically designed to maximize total utility, while the utility of the worst day of our itineraries is roughly twice that obtained from other approaches. We then turn to evaluation based on human raters who score our itineraries only slightly below the itineraries created by human travel experts with deep knowledge of the area.
Colorectal cancer detection in the practice setting. Impact of fecal blood testing (1990)

To assess the contribution of fecal blood testing to cancer detection in a clinical practice setting, we studied records from 160 patients with both a new tissue diagnosis of colorectal adenocarcinoma and a preceding stool blood test (HemoQuant, Mayo Medical Laboratories, Rochester, Minn) determination. In this group, 71% had suggestive colorectal symptoms (particularly stool changes, overt bleeding, and abdominal pain) or anemia at presentation, and 29% were asymptomatic. Fecal blood levels remained normal in more than 40% of both symptomatic and asymptomatic patients. In only 26 patients (16% overall) was an abnormal fecal blood level the sole heralding feature, but this subset of patients had a more favorable stage. Fecal blood levels were higher with advanced, larger, and more proximal tumors and with stools collected before purgation. We conclude that, in the practice setting, fecal blood level elevation alone is an uncommon but important manner of colorectal cancer presentation, most cancers present with symptoms, and fecal blood levels are often normal in both symptomatic and asymptomatic patients.
Special Section Guest Editorial: Optical Diagnostic and Biophotonic Methods from Bench to Bedside (2010)

The <i>Journal of Biomedical Optics</i> (JBO) is a Gold Open Access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Estimation of TDMA and CDMA capacities for an air-to-ground communication system (1997)

We estimate capacities of code-division multiple access (CDMA) and time-division multiple access (TDMA) systems when applied to an air-to-ground/ground-to-air (AG/GA) environment. Our analysis is based upon a regular cellular arrangement of ground stations (bases), as in the land-mobile environment, and uses waveforms based upon current cellular standards. Two of the most crucial parameters for capacity estimation, unique for the air-to-ground environment, are the outside-cell interference factor for CDMA and the frequency re-use factor for TDMA. These are computed, using a quasi-two-dimensional (2D) analysis, for average and worst-case conditions, taking into account radio propagation effects at VHF/UHF. We also investigate variations from conventional system operational modes: half-duplex for TDMA, and 1/3 frequency re-use for CDMA. We provide capacity estimates vs. cell size, and show that (as in the cellular case), capacity depends upon the many available system parameters, in addition to cell size.
Small RFID tag antenna with bandwidth-enhanced characteristic (2006)

In this paper, a small RFID tag antenna in UHF band which has bandwidth-enhanced characteristic is proposed. The shape of the proposed antenna is a meander antenna to reduce size, and the antenna consists of two radiators which make dual resonance in adjacent frequencies to enhance bandwidth. By adjusting length and location of each radiator, the proposed antenna can easily make dual resonance at arbitrary location on the Smith chart, which is able to make impedance matching with RFID tag chip in wide frequency range.
Lecithin Inverse Microemulsions for the Pulmonary Delivery of Polar Compounds Utilizing Dimethylether and Propane as Propellants (2000)

Lecithin inverse microemulsions were investigated as a means of pulmonary drug delivery, utilizing dimethylethyleneglycol (DMEG) and hexane as models for dimethyl ether (DME) and propane, respectively. Addition of lecithin to the model propellant mixtures increased the solubility of water in a nonlinear, solvent-dependent manner. The concentration of water necessary to fully hydrate cobalt(II) decreased as the solvent composition was varied from DMEG to hexane. Water proton chemical shift increased in the presence of lecithin, with the largest increases in high hexane content samples. Equilibrium dialysis and component diffusion rate determination (by pulsed-field gradient [PFG]-NMR) indicated the quantity of water associated with the dispersed phase. Collectively, these methods demonstrated that a greater fraction of water was associated with the microemulsion-dispersed phase as the solvent was varied from DMEG to hexane. Iodine solubilization indicated microemulsion formation (operational critical micelle concentration [cmc], 10 moles water per mole lecithin) at approximately 10(-4)-10(-5) molal lecithin. NMR data (trimethylammonium proton chemical shift, water, and lecithin T1) were consistent with microemulsion formation. Water-soluble compounds dissolved in lecithin inverse microemulsions in a lecithin- and water-dependent manner. Experiments with DME/lecithin demonstrated microemulsion characteristics similar to those in the model propellant. DME/lecithin metered-dose inhalers (MDIs) produced a particle size and a fine particle fraction (36% by twin impinger method) suitable for pulmonary drug delivery.
Second-harmonic generation in a sound beam reflected and transmitted at a curved interface (2000)

This article presents a model for second-harmonic generation in a sound beam that is reflected from or transmitted through a curved interface. Propagation in homogeneous fluids is assumed. Simple analytic solutions are derived for the case of focused Gaussian beams. The solutions are used to illustrate the effects of focusing or defocusing due to curvature of the interface, in combination with impedance change at the interface, on energy transfer from the fundamental to the second harmonic.
Cross‐sectional analysis of germline BRCA1 and BRCA2 mutations in Japanese patients suspected to have hereditary breast/ovarian cancer (2008)

The prevalence of BRCA1/2 germline mutations in Japanese patients suspected to have hereditary breast/ovarian cancer was examined by a multi-institutional study, aiming at the clinical application of total sequencing analysis and validation of assay sensitivity in Japanese people using a cross-sectional approach based on genetic factors estimated from personal and family histories. One hundred and thirty-five subjects were referred to the genetic counseling clinics and enrolled in the study. Full sequencing analysis of the BRCA1/2 gene showed 28 types of deleterious mutations in 36 subjects (26.7%), including 13 types of BRCA1 mutations in 17 subjects (12.6%) and 15 types of BRCA2 mutations in 19 subjects (14.1%). Subjects were classified into five groups and 22 subgroups according to their personal and family history of breast and/or ovarian cancer, and the prevalence of deleterious mutations was compared with previously reported data in non-Ashkenazi individuals. Statistical analysis using the Mantel-Haenszel test for groups I through IV revealed that the prevalence of Japanese subjects was significantly higher than that of non-Ashkenazi individuals (P = 0.005, odds ratio 1.87, 95% confidence interval 1.22-2.88). Family history of the probands suffering from breast cancer indicated risk factors for the presence of deleterious mutations of BRCA1/2 as follows: (1) families with breast cancer before age 40 within second degree relatives (P = 0.0265, odds ratio 2.833, 95% confidence interval 1.165-7.136) and (2) families with bilateral breast cancer and/or ovarian cancer within second degree relatives (P = 0.0151, odds ratio 2.88, 95% confidence interval 1.25-6.64).
EFFICIENT REMOVAL OF SMALL MOLECULAR WEIGHT PROTEINS (SMWP) WITH A BROAD-SPECTRUM HEMOADSORPTION DEVICE (BetaSorbTM) COMBINED WITH HIGH-FLUX DIALYSIS (HFD) IN ESRD SUBJECTS (2003)

Excessive mortality and morbidity in ESRD is associated with retention of SMWP and inflammatory cytokines not well removed by HFD. 12 ESRD subjects (8M, 4F, age 48±9) were enrolled in a study comparing 1 week of HFD (Fresenius F70NR) with 1 week HFD combined (CRx) with a new model of an adsorption column that removes SMWP from blood (BetaSorbTM, Renal Tech). SMWP (MW 11.8–21 kDa), beta2 microglobulin (β2m), angiogenin, leptin, retinol binding protein (rbp), and interleukin-18 (IL18), were measured pre- and post- treatment and % reduction calculated. Average β2m clearance (ACβ2m) and total removal (Tβ2m) were measured during 1 HFD and 1 CRx. Dialysis parameters were constant (BFR 300–400 ml/min, DFR 800 ml/min) and all measured plasma values were corrected for UF.TableClinically insignificant changes in leukocytes, platelets and albumin were observed with CRx. Significant reductions in SMWP relevant to ESRD were achieved. Addition of the BetaSorbTM offers potentially significant benefits not afforded by HFD.
Prognostic factors of pulmonary metastasectomy for osteosarcomas of the extremities (2008)

Current practice of pulmonary metastasectomy for osteosarcomas in our institution was well justified. The number of pulmonary metastases more than five and the advent of pulmonary metastases during pre- and postoperative chemotherapy seemed relevant to a worse prognosis.
Aggregation behaviour of carbon nanotubes in aqueous and physiological media and its influence on toxicity (2013)

Extensive use of carbon nanotubes (CNTs) in industry and in the consumer market including drug delivery will increase the likelihood of human exposure and the contamination of the ecosystems. The aggregation state of CNTs has a strong influence on their fate and transport in the environment, as well as their bioavailability. Studies on their colloidal behaviour suggest that they can be relatively stable in aqueous and biological medium, and the presence of surfactants and macromolecules may enhance their dispersibility and persistence. This paper is a review of the aggregation behaviour of CNTs as well as their functional analogues, and the possible role of the dispersal state on toxicity.
Supplementary methods from Intratumoral Plasmid IL12 Expands CD8<sup>+</sup> T Cells and Induces a CXCR3 Gene Signature in Triple-negative Breast Tumors that Sensitizes Patients to Anti–PD-1 Therapy (2023)

&lt;p&gt;Supplementary methods&lt;/p&gt;