gebhart/patrepeval huggingface dataset:
Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo, Brazil (2009)

The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in São Paulo, Brazil. A total of 36 samples were selected from 888 adult patients residing in São Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysis Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively. All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.
An automated meniscus coating system for polymer deposition on large-area MCM-D and MCM-L substrates (2000)

Material deposition techniques can be a significant contributor to the overall electronics manufacturing costs. The present study evaluates meniscus coating as a low-cost tool for large-area polymer deposition. Meniscus coating has the following advantages over conventional spin coating: (1) minimal material waste; (2) higher throughput; (3) higher planarity; (4) minimal defect density; (5) thickness uniformity over a large area. Each of these factors help reduce the overall manufacturing costs. The objective of this effort is to develop, install, and qualify an automated, low-cost, high-throughput polymer deposition method for large area MCM-D and MCM-L substrates. A variety of polymer photoresists, dielectrics, and composites are used for thick film coating on 12 in PWB and glass substrates. For each material, the deposition process is optimized to the desired film thickness. In this paper, we report materials and process optimization for 12 in/spl times/12 in substrates that is scalable to 24 in/spl times/24 in substrates. For higher throughput and lower manufacturing cost, an automated coating workcell is designed. The proposed workcell includes a robotic material handling and convection drying of coated films with automated loading/unloading capability. Design and fabrication of the integrated workcell are also addressed.
Overcoming Low Ge Ionization and Erosion Rate Variation for Quantitative Ultralow Energy Secondary Ion Mass Spectrometry Depth Profiles of Si<sub>1–<i>x</i></sub>Ge<sub><i>x</i></sub>/Ge Quantum Well Structures (2012)

We specify the O(2)(+) probe conditions and subsequent data analysis required to obtain high depth resolution secondary ion mass spectrometry profiles from multiple Ge/Si(1-x)Ge(x) quantum well structures (0.6 ≤ x ≤ 1). Using an O(2)(+) beam at normal incidence and with energies >500 eV, we show that the measured Ge signal is not monotonic with concentration, the net result being an unrepresentative and unquantifiable depth profile. This behavior is attributed to a reduced Ge ionization rate as x approaches 1. At lower beam energies the signal behaves monotonically with Ge fraction, indicating that the Ge atoms are now ionizing more readily for the whole range of x, enabling quantitative profiles to be obtained. To establish the depth scale a point-by-point approach based on previously determined erosion rates as a function of x is shown to produce quantum well thicknesses in excellent agreement with those obtained using transmission electron microscopy. The findings presented here demonstrate that to obtain reliable quantitative depth profiles from Ge containing samples requires O(2)(+) ions below 500 eV and correct account to be taken of the erosion rate variation that exists between layers of different matrix composition.
In-air Typing Interface: Realizing 3D operation for mobile devices (2012)

In this paper, we explore the usability of the “In-air Typing Interface” that we developed to overcome the problems common with traditional mobile interfaces. We performed two studies focused on frame rate, latency, and tactile feedback. We found that reducing the latency even by several milliseconds can improve the operating efficiency, and the frame rate partly affects the efficiency. Tactile feedback significantly reduced the number of mistypes, and it is likely that vibration feedback can improve the operating efficiency further if there is a penalty for erroneous operations.
A Mesoscale Mechanism for Adaptive Mobile Manipulation (2000)

Abstract A novel, centimeter-scale crawling robot is described. Intended for military and civilian surveillance and search-and-rescue applications, the robot must be small, rugged, and lightweight with robust, reconfigurable capabilities. As a result, a dual-use design employing two arms for both manipulation and locomotion was conceived. The robot consists of two, three-degree-of-freedom arms that can stow completely inside the 75 mm diameter cylindrical body for ballistic deployment. This paper describes the mechanism and design motivation as well as three novel locomotion gaits and a fourth conventional gait. An outline for gait adaptation is suggested for future work.
Translocations involving the immunoglobulin heavy-chain locus are possible early genetic events in patients with primary systemic amyloidosis (2001)

Primary systemic amyloidosis (AL) is a plasma cell (PC) dyscrasia with clinical similarities to multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS), but its molecular basis is poorly understood. Translocations at the immunoglobulin heavy-chain (IgH) locus, 14q32, are likely early genetic events in both MM and MGUS and involve several nonrandom, recurrent, partner chromosomes such as 11q13, 16q23, and 4p16.3. Given the similarities between MM, MGUS, and AL, bone marrow clonal PCs were evaluated in 29 patients with AL using interphase fluorescence in situ hybridization (FISH) combined with immunofluorescence detection of the cytoplasmic light-chain (cIg-FISH) for the presence of 14q32 translocations and the t(11;14)(q13;q32). Of 29 patients studied, 21 (72.4%) showed results compatible with the presence of a 14q32 translocation, and 16 (76.2%) of those had translocation (11;14)(q13;q32) for an overall prevalence of the abnormality of 55%. IgH translocations are common in AL, especially the t(11;14)(q13;q32).
2469. A National Intervention to Improve Infection Prevention Efforts in Hospitals with High Rates of Clostridioides difficile infection, Central Line-Associated Bloodstream Infection, Catheter-Associated Urinary Tract Infection and/or Methicillin-Resistant Staphylococcus aureus (2019)

Abstract Background To strengthen state collaborative efforts and reduce common healthcare-associated infections (HAIs) in short-stay and long-term acute care hospitals, the Centers for Disease Control and Prevention (CDC) launched “States Targeting Reduction in Infections via Engagement” (STRIVE) - a national quality improvement program. Methods STRIVE consisted of a multimodal intervention implemented from November 2016 to May 2018 (Figure 1). Hospitals with excess Clostridioides difficile infection (CDI) and a high burden of at least one of the following HAIs - central line-associated bloodstream infection (CLABSI), catheter-associated urinary tract infection (CAUTI) or methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection were targeted. Monthly aggregate HAI and device utilization ratios - according to CDC National Healthcare Safety Network definitions - were measured during the pre vs. post-intervention periods. Thematic analysis of qualitative interviews with state partners was conducted to understand the influence of the intervention. Results Overall, 387 hospitals from 23 states and the District of Columbia participated. Changes in HAI rates and catheter utilization are illustrated in Figure 2. From pre- to post-intervention, substantial changes in HAI rates above temporal trends were not observed (CDI, 7.0 to 5.7 per 10000 patient-days; CLABSI, 0.88 to 0.80 per 1000 catheter days; CAUTI, 1.12 to 1.04 per 1000 catheter days; MRSA bloodstream infection, 0.075 to 0.071 per 1,000 patient-days) Similarly, catheter utilization did not differ substantially between the pre- and post-intervention periods (24.05 to 22.07 central line days per 100 patient-days; 21.46 to 19.83 urinary catheter days per 100 patient-days). Qualitative analysis of 17 interviews with state partners showed that relationships among state partners and hospitals were strengthened, potentially facilitating collaboration on future infection prevention efforts. Conclusion Though HAI reductions were observed during STRIVE, these reductions were consistent with temporal trends. Hospitals struggling with high HAI rates may require additional novel approaches. Disclosures All authors: No reported disclosures.
Genome-Wide Mutant Fitness Profiling Identifies Nutritional Requirements for Optimal Growth of Yersinia pestis in Deep Tissue (2014)

Our understanding of the functions required by bacteria to grow in deep tissues is limited, in part because most growth studies of pathogenic bacteria are conducted on laboratory media that do not reflect conditions prevailing in infected animal tissues. Improving our knowledge of this aspect of bacterial biology is important as a potential pathway to the development of novel therapeutics. Yersinia pestis, the plague bacterium, is highly virulent due to its rapid dissemination and growth in deep tissues, making it a good model for discovering bacterial adaptations that promote rapid growth during infection. Using Tn-seq, a genome-wide fitness profiling technique, we identified several functions required for fitness of Y. pestis in vivo that were not previously known to be important. Most of these functions are needed to acquire or synthesize nutrients. Interference with these critical nutrient acquisition pathways may be an effective strategy for designing novel antibiotics and vaccines.
Selective killing of Klebsiella pneumoniae by 5-trifluoromethylthioribose. Chemotherapeutic exploitation of the enzyme 5-methylthioribose kinase. (1990)

5'-Deoxy-5'-methylthioadenosine (MTA), an important intermediate in methionine recycling, can be metabolized by one of two mechanisms that appear to be mutually exclusive. In human cells, MTA is degraded in one step to adenine and 5-methylthioribose 1-phosphate (MTR-1-P) via MTA phosphorylase. In contrast, certain microbes metabolize MTA in two steps: first to 5-methylthioribose (MTR) followed by conversion to MTR-1-P. The enzymes involved in this two-step conversion are MTA nucleosidase and MTR kinase. In both cases, MTR-1-P is subsequently recycled to methionine. Because MTR kinase is "unique" to microbes (it is also found in plant tissue) and since it is essential to microbial methionine salvage, we hypothesized that MTR kinase is a promising target for chemotherapeutic exploitation. We demonstrate that 5-trifluoromethylthioribose (TFMTR), a structural analog of MTR, is a potent inhibitor of the MTR kinase-containing organism Klebsiella pneumoniae. TFMTR not only inhibits the growth of K. pneumoniae in a dose-dependent manner (50% inhibition at approximately 40 nM) but also competitively inhibits MTR kinase activity (Ki approximately 7 microM). Furthermore, TFMTR is shown to be a substrate for MTR kinase (Km = 1.7 microM), suggesting that the drug could be converted to toxic products (e.g. trifluoromethionine or carbonothionic difluoride) in enzyme-containing organisms. Structural analogs of MTR represent a new class of compounds with the potential for treating diseases caused by MTR kinase-containing microorganisms.
Gastric motor and cardiovascular effects of insulin in dorsal vagal complex of the rat (1998)

Insulin-binding sites exist in the lower brain stem of the rat, raising the possibility that the circulating hormone may have cardiovascular and gastric effects at this site. Therefore, we investigated the autonomic effects of applying rat insulin to the surface of the dorsal medulla (0.3 and 3 microU/rat) or microinjecting it into the dorsal vagal complex (DVC) (0.1-10 nU/site) in anesthetized rats. Application of rat insulin to the surface (3 microU/rat) and its microinjection into the DVC (1 and 10 nU/site) both evoked marked, albeit transient, increases in intragastric pressure, pyloric and greater curvature contractile activity, and blood pressure. Much higher doses of human (100 mU) and porcine insulin (3 mU) were needed to evoke modest changes in gastric motor and cardiovascular function when applied to the surface of the dorsal medulla. In addition, a 1,000-fold higher dose of porcine insulin (10 microU) in the DVC was not enough to mimic the autonomic effects of rat insulin microinjected into the same site. The excitatory gastric motor effects of rat insulin in the lower brain stem were abolished by vagotomy, whereas spinal cord transection blocked insulin-evoked increases in blood pressure. To test whether the gastric motor effects of rat insulin in the lower brain stem were caused by potential contamination with pancreatic polypeptide, we microinjected rat pancreatic polypeptide into the DVC at a single dose of 2 pmol. Only a modest increase in intragastric pressure in response to the hormone was observed. Thus it is likely that insulin, through its action in the lower brain stem, may be implicated in the pathogenesis of gastrointestinal and cardiovascular complications in hyperinsulinemia. In addition, species variations in the amino acid sequence of insulin may affect its biological activity in the brain of different species.
Experimental Study for Revising Visual Noise Measurement of ISO 15739 (2021)

Visual noise is a metric for measuring the amount of noise perception in images taking into account the properties of the human visual system (HVS). A visual noise measurement method is specified in Annex B of ISO 15739, which has been used as a useful measurement metric over the years since its introduction. As several issues have been questioned recently, it is now being investigated for revision involving changes to the CSF, color space used for rms noise value measurements, and visual noise formula combining rms values in three color channels. To derive visual noise formula involving color noise weighting coefficients representing HVS sensitivity to noise, subjective experiments using simulated luminance and color noise images were done. The improvement of calculation stability and HVS correspondence was verified using simulation and real camera images under various conditions. Finally, subjective experiments using real camera images were performed to validate the revised method and update the color noise coefficients considering practical measurement cases.
Murine epidermal Langerhans cells and langerin-expressing dermal dendritic cells are unrelated and exhibit distinct functions (2009)

A new langerin(+) DC subset has recently been identified in murine dermis (langerin(+) dDC), but the lineage and functional relationships between these cells and langerin(+) epidermal Langerhans cells (LC) are incompletely characterized. Selective expression of the cell adhesion molecule EpCAM by LC allowed viable LC to be easily distinguished from langerin(+) dDC in skin and lymphoid tissue and ex vivo as well. Differential expression of EpCAM and langerin revealed the presence of at least 3 distinct skin DC subsets. We determined that LC and langerin(+) dDC exhibit different migratory capabilities in vitro and repopulate distinct anatomic compartments in skin at different rates after conditional depletion in vivo. Langerin(+) dDC, in contrast to LC, did not require TGFbeta1 for development. Carefully timed gene gun immunization studies designed to take advantage of the distinct repopulation kinetics of langerin(+) dDC and LC revealed that langerin(+) dDC were required for optimal production of beta-galactosidase-specific IgG2a/c and IgG2b in the acute phase. In contrast, immunization via LC-deficient skin resulted in persistent and strikingly reduced IgG1 and enhanced IgG2a Ab production. Our data support the concepts that LC and langerin(+) dDC represent distinct DC subsets that have specialized functions and that LC are important immunoregulatory cells. The presence of at least 3 functionally distinct skin DC subsets may have particular relevance for vaccines that are administered epicutaneously.
Thermal chemistry pathways of substituted anisoles (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal chemistry pathways of substituted anisolesAntti I. Vuori and Johan B-son BredenbergCite this: Ind. Eng. Chem. Res. 1987, 26, 2, 359–365Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/ie00062a031https://doi.org/10.1021/ie00062a031research-articleACS PublicationsRequest reuse permissionsArticle Views281Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
β2-Adrenergic Signalling Promotes Cell Migration by Upregulating Expression of the Metastasis-Associated Molecule LYPD3 (2020)

Metastasis is associated with poor prognosis in breast cancer. Although some studies suggest beta-blockers increase survival by delaying metastasis, others have been discordant. This study provides both insights into the anomalous findings and identifies potential biomarkers that may be treatment targets. Cell line models of basal-type and oestrogen receptor-positive breast cancer were profiled for basal levels of adrenoceptor gene/protein expression, and β2-adrenoceptor mediated cell behaviour including migration, invasion, adhesion, and survival in response to adrenoceptor agonist/antagonist treatment. Protein profiling and histology identified biomarkers and drug targets. Baseline levels of adrenoceptor gene expression are higher in basal-type rather than oestrogen receptor-positive cancer cells. Norepinephrine (NE) treatment increased invasive capacity in all cell lines but did not increase proliferation/survival. Protein profiling revealed the upregulation of the pro-metastatic gene Ly6/PLAUR Domain-Containing Protein 3 (LYPD3) in norepinephrine-treated MDA-MB-468 cells. Histology confirmed selective LYPD3 expression in primary and metastatic breast tumour samples. These findings demonstrate that basal-type cancer cells show a more aggressive adrenoceptor-β2-activated phenotype in the resting and stimulated state, which is attenuated by adrenoceptor-β2 inhibition. This study also highlights the first association between ADRβ2 signalling and LYPD3; its knockdown significantly reduced the basal and norepinephrine-induced activity of MCF-7 cells in vitro. The regulation of ADRβ2 signalling by LYPD3 and its metastasis promoting activities, reveal LYPD3 as a promising therapeutic target in the treatment of breast and other cancers.
Dynamical interrogation of interferometric sensor arrays by a simple polarimetric setup (2011)

Numerous methods have been proposed for multiplexing interferometric sensors into large scale arrays. Previously we described a low loss polarimetric sensor array based on a concatenation of high-birefringence fiber. It was interrogated by a wavelength scanning laser and its output was measured by a polarization analyzer. Here we demonstrate how the same source and detection system can be used to interrogate a different sensor array with increased sensitivity: a cascade of fiber-optic Fabry-Perot interferometers. The auxiliary interferometer, needed for obtaining a synchronized linear frequency grid, is implemented "in-line" and does not require an additional detection and digitizing circuitry. The proposed approach, therefore, constitutes a simple and modular sensor array interrogation scheme in which different arrays of sensors with significantly different sensitivities can be interchanged according to circumstances.
Transcriptional regulation of human retinoic acid receptor-alpha (RAR-{alpha}) by Wilms` tumour gene product (1994)

The Wilms` tumor gene encodes a 47-49 kDa transcription factor expressed in kidney, gonads and mesothelium during embryogenesis. Inherited mutations of WT1 lead to aberrant urogenital development and Wilms` tumor, but the role of WT1 in development is not fully understood. Since the human RAR-{alpha} gene contains a potential WT1 binding site at its 5{prime} end, we studied the effect of WT1 co-transfection on expression of an RAR-{alpha} promoter/CAT reporter construct in COS cells. COS cells were plated at 5X10{sup 5} cells/dish in DMEM with 10% FBS and transfected by the Ca/PO4 method with an expression plasmid containing the full-length WT1 (-/-) cDNA under the control of the CMV promoter, plasmid containing the RAR-{alpha} promoter (-519 to +36)/CAT reporter and TK/growth hormone plasmid to control for efficiency of transfection. CAT/GH activity at 48 hours was inhibited by co-transfection with increasing amounts of WT1 (-/-); maximum inhibition = 5% of control. WT1 co-transfection did not affect expression of TKGH, nor of a CMV-CAT vector. Expression of WT1 protein in tranfected COS cells was demonstrated by Western blotting. Minimal inhibiton of RAR-{alpha}/CAT activity was seen when cells were co-transfected with vectors containing WT1 deletion mutants, alternate WT1 splicing variants, or WT1 (-/-)more » cDNA bearing a mutation identified in a patient with Drash syndrome. Gel shift assays indicated binding of WT1 to RAR-{alpha} cDNA but not to an RAR-{alpha} deletion mutant lacking the GCGGGGGGCG site. These observations suggest that WT1 may function to regulate RAR-{alpha} expression during normal development.« less