gebhart/patrepeval huggingface dataset:
COVID-19 Outbreak Prediction and Analysis using Self Reported Symptoms (2021)

It is crucial for policymakers to understand the community prevalence of COVID-19 so combative resources can be effectively allocated and prioritized during the COVID-19 pandemic. Traditionally, community prevalence has been assessed through diagnostic and antibody testing data. However, despite the increasing availability of COVID-19 testing, the required level has not been met in parts of the globe, introducing a need for an alternative method for communities to determine disease prevalence. This is further complicated by the observation that COVID-19 prevalence and spread vary across different spatial, temporal, and demographic verticals. In this study, we study trends in the spread of COVID-19 by utilizing the results of self-reported COVID-19 symptoms surveys as a complement to COVID-19 testing reports. This allows us to assess community disease prevalence, even in areas with low COVID-19 testing ability. Using individually reported symptom data from various populations, our method predicts the likely percentage of the population that tested positive for COVID-19. We achieved a mean absolute error (MAE) of 1.14 and mean relative error (MRE) of 60.40% with 95% confidence interval as [60.12, 60.67]. This implies that our model predicts +/- 1140 cases than the original in a population of 1 million. In addition, we forecast the location-wise percentage of the population testing positive for the next 30 days using self-reported symptoms data from previous days. The MAE for this method is as low as 0.15 (MRE of 11.28% with 95% confidence interval [10.9, 11.6]) for New York. We present an analysis of these results, exposing various clinical attributes of interest across different demographics. Lastly, we qualitatively analyze how various policy enactments (testing, curfew) affect the prevalence of COVID-19 in a community.
Protection of Rabbits against Challenge with Rabbit Papillomaviruses by Immunization with the N Terminus of Human Papillomavirus Type 16 Minor Capsid Antigen L2 (2007)

Current L1 virus-like particle (VLP) vaccines provide type-restricted protection against a small subset of the human papillomavirus (HPV) genotypes associated with cervical cancer, necessitating continued cytologic screening of vaccinees. Cervical cancer is most problematic in countries that lack the resources for screening or highly multivalent HPV VLP vaccines, suggesting the need for a low-cost, broadly protective vaccinogen. Here, N-terminal L2 polypeptides comprising residues 1 to 88 or 11 to 200 derived from HPV16, bovine papillomavirus type 1 (BPV1), or cottontail rabbit papillomavirus (CRPV) were produced in bacteria. Rabbits were immunized with these N-terminal L2 polypeptides and concurrently challenged with CRPV and rabbit oral papillomavirus (ROPV). Vaccination with either N-terminal L2 polypeptides of CRPV effectively protected rabbits from CRPV challenge but not from papillomas induced by cutaneous challenge with CRPV genomic DNA. Furthermore, papillomas induced by CRPV genomic DNA deficient for L2 expression grew at the same rate as those induced by wild-type CRPV genomic DNA, further suggesting that the L2 polypeptide vaccines lack therapeutic activity. Neutralizing serum antibody titers of >15 correlated with protection (P < 0.001), a finding consistent with neutralizing antibody-mediated protection. Surprisingly, a remarkable degree of protection against heterologous papillomavirus types was observed after vaccination with N-terminal L2 polypeptides. Notably, vaccination with HPV16 L2 11-200 protected against cutaneous and mucosal challenge with CRPV and ROPV, respectively, papillomaviruses that are evolutionarily divergent from HPV16. Further, vaccination with HPV16 L2 11-200 generates broadly cross-neutralizing serum antibody, suggesting the potential of L2 as a second-generation preventive HPV vaccine antigen.
A Perception-based Quality Metric for Omnidirectional Images (2019)

A key component in VR systems is omnidirectional content, which provides 360-degree views of scenes. At a given time, only a portion of a content, called viewport, is displayed using head-mounted displays. In this work, we develop an objective quality metric, called Weighted Viewport PSNR (W-VPSNR), for omnidirectional content of spatially-varying quality. Through experiment results, it is found that the W-VPSNR metric well correlates with the subjective quality scores.
Thermionic detection in microcolumn liquid chromatography (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermionic detection in microcolumn liquid chromatographyV. L. McGuffin and Milos. NovotnyCite this: Anal. Chem. 1983, 55, 14, 2296–2302Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/ac00264a022https://doi.org/10.1021/ac00264a022research-articleACS PublicationsRequest reuse permissionsArticle Views58Altmetric-Citations27LEARN 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
Incorporating the Impacts of Workload-Dependent Runtime Variations into Timing Analysis (2013)

In the nanometer era, runtime variations due to workload dependent voltage and temperature variations as well as transistor aging introduce remarkable uncertainty and unpredictability to nanoscale VLSI designs. Consideration of short-term and long-term workload-dependent runtime variations at design time and the interdependence of various parameters remain as major challenges. Here, we propose a static timing analysis framework to accurately capture the combined effects of various workload-dependent runtime variations happening at different time scales, making the link between system-level runtime effects and circuit-level design. The proposed framework is fully integrated with existing commercial EDA toolset, making it scalable for very large designs. We observe that for benchmark circuits, treating each aspect independently and ignoring their intrinsic interactions is optimistic and results in considerable underestimation of timing margin.
Whole Genome Microarray Analysis of DUSP4-Deletion Reveals A Novel Role for MAP Kinase Phosphatase-2 (MKP-2) in Macrophage Gene Expression and Function (2019)

Transcriptome profiling reveals that MKP-2 regulates macrophage development showing candidate targets from monocyte-to-macrophage differentiation and macrophage proliferation. However, it is unclear whether effects upon ERK signalling are able to explain the effects of DUSP-4 deletion on macrophage function.
Computing Tire Component Durability via Critical Plane Analysis (2019)

ABSTRACT Tire developers are responsible for designing against the possibility of crack development in each of the various components of a tire. The task requires knowledge of the fatigue behavior of each compound in the tire, as well as adequate accounting for the multiaxial stresses carried by tire materials. The analysis is illustrated here using the Endurica CL fatigue solver for the case of a 1200R20 TBR tire operating at 837 kPa under loads ranging from 66 to 170% of rated load. The fatigue behavior of the tire's materials is described from a fracture mechanical viewpoint, with care taken to specify each of the several phenomena (crack growth rate, crack precursor size, strain crystallization, fatigue threshold) that govern. The analysis of crack development is made by considering how many cycles are required to grow cracks of various potential orientations at each element of the model. The most critical plane is then identified as the plane with the shortest fatigue life. We consider each component of the tire and show that where cracks develop from precursors intrinsic to the rubber compound (sidewall, tread grooves, innerliner) the critical plane analysis provides a comprehensive view of the failure mechanics. For cases where a crack develops near a stress singularity (i.e., belt-edge separation), the critical plane analysis remains advantageous for design guidance, particularly relative to analysis approaches based upon scalar invariant theories (i.e., strain energy density) that neglect to account for crack closure effects.
Design of bidirectionally pumped fiber amplifiers generating double Rayleigh backscattering (2002)

Optimum pumping schemes for bidirectionally pumped distributed fiber amplifiers are evaluated that simultaneously minimize the beat noise between signal and amplified spontaneous emission, as well as between signal and double Rayleigh backscattering. A way of adding a constraint on signal power to describe operation in a strong Kerr fiber nonlinearity regime is included. We show that one can find an optimum Raman net gain, as well as a percentage of forward to total Raman pumping maximizing the signal-to-noise ratio at the end of a transmission line using bidirectionally Raman-pumped transmission fibers.
Dielectric SiO2Planarization Using MnO2Slurry (2012)

MnO2 slurry can polish SiO2 film faster and planarize wide feature steps (2 ×2 mm2) to a lower height than conventional silica slurry. A comparison of Gibbs free energies indicates that the MnO2 abrasive directly reacts on the SiO2 film. In post-Chemical mechanical polishing (CMP), the MnO2 abrasive can be completely removed by dipping it in mixed solutions of inorganic acids and H2O2 followed by scrubbing and dipping in HF solution. A comparison of Gibbs free energies clarifies that the MnO2 abrasive on the wafer is easily dissolved in a mixed solution of an inorganic acid and H2O2.
Characterization of the Phenol Hydroxylase from Burkholderia kururiensis KP23 Involved in Trichloroethylene Degradation by Gene Cloning and Disruption. (2003)

Burkholderia kururiensis KP23 was isolated as a trichloroethylene (TCE)-degrading bacterium. Its degrading activity was induced by phenol, suggesting that the degradation is catalyzed by a phenol hydroxylase (PH). To elucidate the involvement of the PH in the degradation of TCE, the gene cluster for the enzyme was cloned and sequenced. The structural genes (phkABCDEFG) and cognate regulatory gene (phkR) were identified in a divergent transcriptional organization. The products are homologous to those of dmpRKLMNOPQ of Pseudomonas putida CF600, sharing 30-62% identity of amino acid sequence, indicating that the PH is a multi-component enzyme. Disruption of phkD encoding a large oxygenase subunit of the enzyme completely abolished the utilization of phenol as well as degradation of TCE by strain KP23. In addition, a disruptant of phkR was not able to grow on phenol and showed no activity to degrade TCE, indicating that PhkR is an activator and controls the expression of phkABCDEFG.
Term infant formula supplemented with milk-derived oligosaccharides shifts the gut microbiota closer to that of human milk-fed infants and improves intestinal immune defense: a randomized controlled trial (2021)

Infant formula with MOS shifts the gut microbiota and metabolic signature closer to that of HFI, has a strong bifidogenic effect, reduces fecal pathogens, and improves the intestinal immune response.
A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism (2016)

The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.
Norfloxacin-releasing urethral catheter for long-term catheterization (2003)

Norfloxacin-releasing urethral catheters were prepared for the purpose of preventing urinary tract infections during long-term catheterization. The outer and inner surfaces of the catheters were coated with poly(ethylene-co-vinyl acetate) (EVA) and an amphiphilic multiblock co-polymer (PEO2kPDMS), composed of poly(ethylene oxide) and poly(dimethyl siloxane). Norfloxacin, a fluoroquinolone synthetic antibiotic, was impregnated into a coating layer. The in vitro drug release behavior was monitored for 30 days, the surface topography was investigated using scanning electron microscopy (SEM) and the antibacterial activity against different bacteria implicated in urinary tract infection was evaluated by the in vitro inhibition zone test. All the coated catheters showed continuous delivery of norfloxacin for up to 30 days owing to hydrophobic natures of norfloxacin and EVA. PEO2kPDMS incorporated in a coating layer produced a smooth and uniform surface. The coated catheters created considerable inhibition zones for 10 days against Escherichia coli. Klebsiella pneumoniae and Proteus vulgaris, indicating the continuous release of norfloxacin. Overall, it was evident that the catheters coated with EVA/PEO2kPDMS blends containing norfloxacin have a promising potential for the clinical use in patients undergoing long-term catheterization.
Charge-Transfer Complexes for Solid-State Li+ Conduction (2020)

Contradictory to the conventional understanding of solid-state ionics, we find that some organic crystals are highly ion conducting (>10–4 S/cm at room temperature). Through the microparticles of charge-transfer (CT) complexes, dissociated lithium ions move readily. Fast conduction is observed for a wide variety of compounds that form CT complexes, irrespective of the functional groups. Automatic relationship analysis via machine learning indicates the importance of polarization of the CT complexes for the ionic conduction. The decoupling system, where ion transport is not dominated by the segmental motion of media molecules, paves the way for achieving superionic properties in organic monomeric and polymeric conductors.
Clinical Proteomics and Biomarker Discovery (2004)

Early detection of disease generally provides much-improved outcomes by a definitive medical procedure or through lifestyle modification along with specific medical management strategies. For serum biomarkers, which are central to the diagnosis of many diseases, to become truly useful sentinels of pathogenesis, their sensitivity and specificity in both early detection and recurrence monitoring must be improved. Currently, the detection and monitoring of disease markers is based on solitary proteins, and this approach is not always reliable. New classes of biomarkers derived from mass spectroscopy analysis of the low molecular weight proteome have shown improved abilities in the early detection of disease and hence in patient risk stratification and outcome. The development of a modular platform technology with sufficient flexibility and design abstractions allowing for concurrent experimentation, test, and refinement will help speed the progress of mass spectroscopy-derived proteomic pattern-based diagnostics from the scientific laboratory to the medical clinic. For acceptance by scientists, physicians, and regulatory personnel, new bioinformatic tools are essential system components for data management, analysis, and intuitive display of these new and complex data. Clinically engineered mass spectroscopy systems are essential for the further development and validation of multiplexed biomarkers that have shown tremendous promise for the early detection of disease.
Oral candidiasis of HIV-infected children undergoing sequential HIV therapies (2008)

Candida oral flora from 52 Brazilian HIV-infected children was characterized while they received antiviral monotherapy therapy and subsequently, HAART with the use of protease inhibitor. There was a significant increase in non-C. albicans Candida isolates from 9.6-28.8% (P=0.005) after the children were placed on protease inhibitor therapy. Although Candida albicans still remained the most commonly isolated species, relative presence of C. tropicalis (n=9) followed by C. parapsilosis (n=8) markedly increased in association with protease inhibitor therapy. Furthermore, rare Candida species including C. dubliniensis, C. norvegensis, C. humicula and C. rugosa also appeared after the onset of protease inhibitor therapy. Subsequent investigation of the antifungal sensitivity of these diverse isolates, derived during protease inhibitor therapy, demonstrated some variation in antifungal sensitivity. With notable exceptions, the majority were sensitive to amphotericin B while most C. albicans and non-C. albicans Candida isolates were also susceptible to fluconazole, itraconazole and ketoconazole. Amongst exceptions was a single C. tropicalis isolates which was resistant to fluconazole (MIC>64 microl/ml) and one C. albicans-B isolate which showed cross-resistance to all azoles and amphotericin.
Manganese-Enriched Gradient Lithium-Ion Battery Cathodes from Carbonate Precursors (2011)

Abstract not Available.
Data from A Very Long-acting Exatecan and Its Synergism with DNA Damage Response Inhibitors (2023)

&lt;div&gt;&lt;p&gt;Exatecan (Exa) is a very potent inhibitor of topoisomerase I and anticancer agent. It has been intensively studied as a single agent, a large macromolecular conjugate and as the payload component of antigen-dependent antibody–drug conjugates. The current work describes an antigen-independent conjugate of Exa with polyethylene glycol (PEG) that slowly releases free Exa. Exa was conjugated to a 4-arm 40 kDa PEG through a β-eliminative cleavable linker. Pharmacokinetic studies in mice showed that the conjugate has an apparent circulating half-life of 12 hours, which reflects a composite of both the rate of renal elimination (half-life ∼18 hours) and release of Exa (half-life ∼40 hours). Remarkably, a single low dose of 10 μmol/kg PEG-Exa—only approximately 0.2 μmol/mouse—caused complete suppression of tumor growth of BRCA1-deficient MX-1 xenografts lasting over 40 days. A single low dose of 2.5 μmol/kg PEG-Exa administered with low but efficacious doses of the PARP inhibitor talazoparib showed strong synergy and caused significant tumor regression. Furthermore, the same low, single dose of PEG-Exa administered with the ATR inhibitor VX970 at doses of the DNA damage response inhibitor that do not affect tumor growth show high tumor regression, strong synergy, and synthetic lethality.&lt;/p&gt;Significance:&lt;p&gt;A circulating conjugate that slowly releases Exa is described. It is efficacious after a single dose and synergistic with ATR and PARP inhibitors.&lt;/p&gt;&lt;/div&gt;
DEVELOPMENT OF PROSTATE-SPECIFIC ANTIGEN PROMOTER-BASED GENE THERAPY FOR ANDROGEN-INDEPENDENT HUMAN PROSTATE CANCER (1998)

The 5837 bp long PSA promoter was active in the androgen free environment and could be used to target both androgen-dependent and independent PSA-producing prostate cancer cells in vitro, and prostate tumors in castrated hosts.
Faculty Opinions recommendation of Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. (2005)

Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8 A. The enzyme is a trimer with an alpha3beta3gamma3 polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles cytochrome c oxidase subunit II. A third metal centre, occupied by zinc in the crystal, is located within the membrane. The structure provides new insight into the molecular details of biological methane oxidation. PMID: 15674245
Simulation of Cyclic Displacement by Counterpoised Shape Memory Elements (1999)

The most common shape memory actuation procedure involves a shape memory element that works against a conventional elastic biasing element. Actuation is provided by the movement of the contact interface separating the two elements. The interface then occupies one location at high temperature and another location at low temperature. Certain applications call for switching between two separate interface locations, both of which are stable at a common ambient temperature. A shape memory element working against a conventional elastic biasing element cannot generally give such capability. However, two shape memory elements working against each other does give this capability, provided that the ambient temperature supports stress-free martensite, and provided as well that the contact interface thermally isolates the elements during short duration heating spikes which trigger such a switch. There is an obvious operational benchmark involving one element with fully oriented martensite and the other element with random martensite. The benchmark operation exchanges these states between the two elements, in which case the device stroke follows immediately from the material’s transformation strain. This benchmark behavior is not achievable due to elastic strain effects. Here we analyze the achievable behavior of such a device using a recent model for shape memory behavior. This model tracks the state of the shape memory material in terms of austenite and two variant martensite. This enables the determination of the device’s shakedown behavior in terms of repeatable per-stroke strain delivery, and also gives the temperature excursions necessary for the associated full displacement.
PDL1 Signals through Conserved Sequence Motifs to Overcome Interferon-Mediated Cytotoxicity (2017)

PDL1 blockade produces remarkable clinical responses, thought to occur by T cell reactivation through prevention of PDL1-PD1 T cell inhibitory interactions. Here, we find that PDL1 cell-intrinsic signaling protects cancer cells from interferon (IFN) cytotoxicity and accelerates tumor progression. PDL1 inhibited IFN signal transduction through a conserved class of sequence motifs that mediate crosstalk with IFN signaling. Abrogation of PDL1 expression or antibody-mediated PDL1 blockade strongly sensitized cancer cells to IFN cytotoxicity through a STAT3/caspase-7-dependent pathway. Moreover, somatic mutations found in human carcinomas within these PDL1 sequence motifs disrupted motif regulation, resulting in PDL1 molecules with enhanced protective activities from type I and type II IFN cytotoxicity. Overall, our results reveal a mode of action of PDL1 in cancer cells as a first line of defense against IFN cytotoxicity.