gebhart/patrepeval huggingface dataset:
An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples (2022)

Importance The rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 ( PSCS-CoV2 ). Objective To evaluate an affordable and convenient test for COVID-19. Methods The collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2 ). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus. Results We show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method ( n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 &lt; 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%. Conclusion and Relevance We developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19.
Polymer‐Mediated Hierarchical and Reversible Emulsion Droplet Assembly (2009)

Abstract Reversible Strukturbildung : Stabile funktionelle Emulsionsmikrotröpfchen bauen verschiedene komplexe makroskopische Flüssigkeitsstrukturen auf (siehe Bild). Der hierarchische Organisationsprozess wird durch Wechselwirkungen zwischen Polymertensiden auf der Tröpfchenoberfläche vermittelt. Weil die Wechselwirkungen reversibel sind, können die Strukturen in den Emulsionen durch einfache pH‐Änderungen aufgelöst werden. magnified image
Time resolved optical detection for white matter lesion detection: preclinical tests on macaque brains and MRI co-registration (2015)

We conducted a preclinical assessment on young macaques aimed at detecting white matter lesions. We present the protocol we implemented to achieve the lesions detection using a bedside non-invasive optical-based Time-Resolved instrumentation we have optimized for this purpose. We validated the reconstructed 3D absorption map with co-registration of MRI data.
Result-as-a-Service (RaaS): Persistent Helper Functions in a Serverless Offering (2020)

Serverless Computing or Functions-as-a-Service (FaaS) is an execution model for cloud computing environments where the cloud provider executes a piece of code (a function) by dynamically allocating resources. When a function has not been executed for a long time or is being executed for the first time, a new container has to be created, and the execution environment has to be initialized resulting in a cold start. Cold start can result in a higher latency. We propose a new computing and execution model for cloud environments called Result-as-a-Service (RaaS), which aims to reduce the computational cost and overhead while achieving high availability. In between successive calls to a function, a persistent function can help in successive calls by precomputing the functions for different possible arguments and then distributing the results when a matching function call is found.
The Leukotriene Receptor Antagonist Montelukast Attenuates Neuroinflammation and Affects Cognition in Transgenic 5xFAD Mice (2021)

Alzheimer's disease (AD) is the most common form of dementia. In particular, neuroinflammation, mediated by microglia cells but also through CD8+ T-cells, actively contributes to disease pathology. Leukotrienes are involved in neuroinflammation and in the pathological hallmarks of AD. In consequence, leukotriene signaling-more specifically, the leukotriene receptors-has been recognized as a potential drug target to ameliorate AD pathology. Here, we analyzed the effects of the leukotriene receptor antagonist montelukast (MTK) on hippocampal gene expression in 5xFAD mice, a commonly used transgenic AD mouse model. We identified glial activation and neuroinflammation as the main pathways modulated by MTK. The treatment increased the number of Tmem119+ microglia and downregulated genes related to AD-associated microglia and to lipid droplet-accumulating microglia, suggesting that the MTK treatment targets and modulates microglia phenotypes in the disease model compared to the vehicle. MTK treatment further reduced infiltration of CD8+T-cells into the brain parenchyma. Finally, MTK treatment resulted in improved cognitive functions. In summary, we provide a proof of concept for MTK to be a potential drug candidate for AD and provide novel modes of action via modulation of microglia and CD8+ T-cells. Of note, 5xFAD females showed a more severe pathology, and in consequence, MTK treatment had a more pronounced effect in the females compared to the males. The effects on neuroinflammation, i.e., microglia and CD8+ T-cells, as well as the effects on cognitive outcome, were dose-dependent, therefore arguing for the use of higher doses of MTK in AD clinical trials compared to the approved asthma dose.
Determination of the Absolute Configuration of Flexible Molecules by ab Initio ORD Calculations:  A Case Study with Cytoxazones and Isocytoxazones (2005)

Ab initio calculations of the optical rotatory power of the natural cytokine modulator cytoxazone 1 and its trans-diastereomer 2, as well as the structural isomers cis-3 and trans-4 isocytoxazones, have been performed at four different wavelengths (589, 546, 435, and 405 nm) by Density Functional Theory. The calculation of ORD curves provides a reliable method for the assignment of absolute configuration of these conformationally flexible molecules. The absolute configurations of isocytoxazones has been established as (+)-(4R,5S)-cis-3 and (+)-(4S,5S)-trans-4.
Low Cost Absorption Sensors for Networked Applications (2011)

Evolution of the laser sources and associated measurement tools provide new opportunities for absorption-based gas sensors. This paper highlights recent work by the authors using mid-IR sources that target two emerging market segments for monitoring major atmospheric species: (1) compact, low-cost sensors for distributed networks, balloons, and unmanned air vehicles; (2) ultra-precise sensors for monitoring local small changes in background levels.
Chiral Fibers: Microformed Optical Waveguides for Polarization Control, Sensing, Coupling, Amplification, and Switching (2013)

Microformed optical waveguides, made by tapering and/or twisting fibers as they are passed through a miniature heat zone, possess unique properties that may be exploited for polarization control, harsh-environment sensing, dense multichannel coupling, spatial division multiplexing, amplification, and optical switching.
Host-microbe interactions mediating antitumorigenic effects of MRX0518, a gut microbiota-derived bacterial strain, in breast, renal and lung carcinoma. (2018)

e15006 Background: The gut microbiota is a key player in therapeutic response to cancer treatment and is linked to the efficacy of checkpoint inhibitors. Proposed antitumorigenic mechanisms of commensal bacteria include expansion of (tumor-specific) T cells, activation of dendritic cells and modulation of the gut microbiota. We examined the antitumor effects of the commensal isolate MRx0518, Enterococcus gallinarum, and analyzed its active compounds and immunotherapy targets. Methods: MRx0518 efficacy on tumor growth was assessed in syngeneic mouse models of breast, renal and lung carcinoma. Tumor flow cytometry, cytokine profiling, transcriptomics, immunohistochemistry and microbiota analysis was performed. MRx0518-induced cytokine production and activation of immunotherapy-relevant cell types was investigated in vitro. Intra-species comparative genomics of MRx0518 was performed, and the transcriptional and proteomic signature associated with host cell activation was assessed. A mono-colonized mouse model was used to study host-microbe interactions in vivo. Results: MRx0518 monotherapy reduced tumor size between 35-51% compared to controls. Tumor reduction corresponded to an increased CD8+ T cells:Tregs ratio and decreased Ki67+ cells. 16S gut microbiota profiling showed a significantly increased diversity for Observed Species. MRx0518 antitumor activity was linked to a strong in vitro immuno-stimulatory phenotype characterized by a distinct transcriptomic signature and induction of inflammatory mediators (IL-8, TNF-α, IL-1ß, IL-6, IL-23, CXCL9, CXCL10). The relative proliferation and activation of CD4+, CD8+ and regulatory T cells was also measured. The MRx0518 genome contained strain-specific regions, and putative immunomodulatory effectors were identified. Mono-colonization studies in germfree mice showed interactions between MRx0518 and activated gut immune cell populations. Conclusions: The gut microbiota-derived strain MRx0518 displays strong antitumor efficacy, and active microbial signaling compounds have been identified. Clinical studies in a variety of solid tumors are planned to commence shortly.
Reduced Poisoning of Platinum Fuel-Cell Electrocatalysts Supported on Desulfurized Carbon (1999)

The vulcanized carbon (VC) used to support nanoscale catalysts in fuel cells contains organosulfur that poisons the upon heating in the absence of water. We have previously shown that in the art of making fuel‐cell electrodes (which includes water and heat), surface‐sited organosulfur in the VC is catalytically oxidized to innocuous sulfate when it contacts . When the carbon surface is desulfurized, electroactive electrodes can be fabricated without water and at temperatures that would otherwise poison when mixed with standard VC. The subsurface organosulfur in VC does not migrate over time to the desulfurized carbon surface under ambient conditions to deactivate supported . Electroactive sulfur‐content carbon electrodes can now be made using nonaqueous protocols. Low‐sulfur‐content carbon supports should reduce performance losses in fuel cells. ©2000 The Electrochemical Society
Spatially Adaptive Bayesian P-Splines with Heteroscedastic Errors (2004)

An increasingly popular tool for nonparametric smoothing are penalized splines (P-splines) which use low-rank spline bases to make computations tractable while maintaining accuracy as good as smoothing splines. This paper extends penalized spline methodology by both modeling the variance function nonparametrically and using a spatially adaptive smoothing parameter. These extensions have been studied before, but never together and never in the multivariate case. This combination is needed for satisfactory inference and can be implemented effectively by Bayesian \\mbox{MCMC}. The variance process controlling the spatially-adaptive shrinkage of the mean and the variance of the heteroscedastic error process are modeled as log-penalized splines. We discuss the choice of priors and extensions of the methodology,in particular, to multivariate smoothing using low-rank thin plate splines. A fully Bayesian approach provides the joint posterior distribution of all parameters, in particular, of the error standard deviation and penalty functions. In the multivariate case we produce maps of the standard deviation and penalty functions. Our methodology can be implemented using the Bayesian software WinBUGS.
Cooperative Load Transport: A Formation-Control Perspective (2010)

We consider a group of agents collaboratively transporting a flexible payload. The contact forces between the agents and the payload are modeled as gradients of nonlinear potentials that describe the deformations of the payload. The load-transport problem is then treated in a similar fashion to the formation-control problem. Decentralized control laws are developed such that without explicit communication, the agents and the payload converge to the same constant velocity; meanwhile, the contact forces are regulated. Experimental results illustrate the effectiveness of our designs.
Underdocumentation of Obesity by Medical Residents Highlights Challenges to Effective Obesity Care (2018)

Though residents recognize obesity and its clinical implications, it is underreported in the assessment of inpatients. This low level of documenting obesity and its impact on clinical care planning underscores a missed opportunity to establish appropriate referrals and initiate treatment at a clinically opportune time.
Thoracic Vertebrectomy and Reconstruction Using a Microsurgical Thoracoscopic Approach (1996)

A video-assisted thoracoscopic microsurgical approach was developed in the laboratory and subsequently used clinically to resect abnormalities of the thoracic vertebrae, to decompress the thoracic spinal cord, and to reconstruct the thoracic vertebral bodies. This report describes the development of the clinical operative techniques for microsurgical thoracoscopic vertebrectomy, neural decompression, and spinal reconstruction. This minimally incisional approach was clinically used in 17 patients to treat vertebral osteomyelitis, tumors, and compression fractures. Microsurgical thoracoscopic techniques were performed using several narrow, flexible, working portals placed in small incisions in the intercostal spaces. Access to the thoracic spine was achieved through the pleural cavity after temporary deflation of one lung using a double-lumen endotracheal tube. The parietal pleura, segmental vessels, and rib heads were dissected off the surfaces of the involved vertebrae to expose the region of interest. Long narrow spine dissection tools were used to perform the spinal decommpression and reconstruction. This technique achieved the same amount of spinal dissection as that achieved with conventional open spinal procedures and used microsurgical visualization techniques. The small incisions with reduced soft tissue dissection may reduce postoperative pain, shorten the length of hospitalization, and have cosmetic and functional advantages. Thoracoscopic vertebrectomies and reconstruction of the spine were technically feasilble procedures that were performed with excellent clinical results. This minimally incisional technique provides a viable alternative to thoracotomy or to posterolateral approaches for thoracic vertebrectomy and vertebral body reconstruction.
Continuous Thermal Oxidation of Alkenes with Nitrous Oxide in a Packed Bed Reactor (2014)

The reaction of nitrous oxide with internal olefins is investigated in a flow reactor. When using a mixture of dodecene isomers, ketones are formed as the primary product with conversions up to 77% and yields up to 45%. The multiphase system is studied experimentally and computationally to gain understanding of the residence time distribution and phase composition. Significant volatility of the dodecenes and solubility of the nitrous oxide result in a system where reaction occurs in both the vapor and liquid at elevated temperatures. The rate constant for oxidation with nitrous oxide is determined by considering both phases and the material transfer between them using 16 different physical parameters through nonlinear optimization. The determined rate constant is in good agreement with parameters estimated by quantum chemistry calculations.
SEMOPS: Paying with Mobile Devices. (2004)

Long noncoding RNAs (lncRNAs) have emerged as an important class of molecules that have been associated with brain function and neurological disease, but the expression profiles of lncRNAs after intracerebral hemorrhage (ICH) remain to be elucidated. In this study, we determined the expression pattern of nuclear factor-k-gene binding (NF-kB) interacting lncRNA (NKILA) after ICH and examined its respective effects on the endoplasmic reticulum stress (ERS)/autophagy pathway, hippocampal neuron loss, and the NF-kB pathway after type VII collagenase-induced ICH in rats. The regulatory mechanisms of NKILA were investigated by an intraperitoneal injection of small interfering (siRNA) against NKILA into rats after ICH. NKILA inhibition mediated by siRNA against NKILA was shown to significantly reduce ERS and autophagy, activate the NF-kB pathway, decrease neurological deficits, brain edema, and injury, and induce blood-brain barrier breakdown, further leading to hippocampal neuron loss and the production of inflammation cytokines. Taken together, the demonstration that NKILA induces the ERS/autophagy pathway and inhibits the NF-kB pathway after ICH supports the concept that NKILA functions as a novel target that is required for the attenuation of brain injuries after ICH.
Calyculin E and F, Novel Insecticidal Metabolites, from the Marine Sponge, Discodermia sp. (1991)

Two novel insecticidal metabolites, calyculin E (1) and F (2), which had insecticial activity against the Germancockroach and mosquito larvae, were isolated from a Japanese marine sponge, Discodermia sp. By an extensive examination of the NMRspectra, the isolates were elucidated to be stereoisomers of calyculin A (3) and B (4), respectively. The molecular shape of calyculin E in solution was deduced to be in a folded conformation by using NMRparameters such as NOEvalues and coupling constants in conjunction with NOE-restricted energy minimization and computer-assisted molecular modeling.
P‐13: High Performance a ‐IGZO Thin‐Film Transistors Grown by Atomic Layer Deposition: Cation Combinatorial Approach (2019)

We report the effect of the cation composition on the electrical performance of amorphous indium gallium zinc oxide (a‐IGZO) thin‐film transistors (TFTs) which was deposited by atomic layer deposition (ALD). The In/In+Ga ratio of a‐IGZO TFT was increased, enhancement of the field‐effect mobility (µ FE ) value was observed. The device with a higher In/In+Ga ratio: the In 0.45 Ga 0.15 Zn 0.40 O transistor showed a higher µ FE value of 48.3 cm 2 /Vs, V TH of −4.06 V, SS of 0.45 V/decade, and I ON/OFF ratio of &gt; 107. Simultaneously, Density of States (DOSs) profile in a forbidden band gap of the a‐IGZO semiconductor were extracted based on the Meyer‐Neldel rule (MN rule) to obtain an insight into the cation composition dependent performance of a‐IGZO TFTs.
A compiler for 3D machine knitting (2016)

Industrial knitting machines can produce finely detailed, seamless, 3D surfaces quickly and without human intervention. However, the tools used to program them require detailed manipulation and understanding of low-level knitting operations. We present a compiler that can automatically turn assemblies of high-level shape primitives (tubes, sheets) into low-level machine instructions. These high-level shape primitives allow knit objects to be scheduled, scaled, and otherwise shaped in ways that require thousands of edits to low-level instructions. At the core of our compiler is a heuristic transfer planning algorithm for knit cycles, which we prove is both sound and complete. This algorithm enables the translation of high-level shaping and scheduling operations into needle-level operations. We show a wide range of examples produced with our compiler and demonstrate a basic visual design interface that uses our compiler as a backend.
Supplementary Table 1 from Quantitative Detection of Promoter Hypermethylation of Multiple Genes in the Tumor, Urine, and Serum DNA of Patients with Renal Cancer (2023)

Supplementary Table 1 from Quantitative Detection of Promoter Hypermethylation of Multiple Genes in the Tumor, Urine, and Serum DNA of Patients with Renal Cancer
Multiscale recurrent pattern matching approach for depth map coding (2010)

In this article we propose to compress depth maps using a coding scheme based on multiscale recurrent pattern matching and evaluate its impact on depth image based rendering (DIBR). Depth maps are usually converted into gray scale images and compressed like a conventional luminance signal. However, using traditional transform-based encoders to compress depth maps may result in undesired artifacts at sharp edges due to the quantization of high frequency coefficients. The Multidimensional Multiscale Parser (MMP) is a pattern matching-based encoder, that is able to preserve and efficiently encode high frequency patterns, such as edge information. This ability is critical for encoding depth map images. Experimental results for encoding depth maps show that MMP is much more efficient in a rate-distortion sense than standard image compression techniques such as JPEG2000 or H.264/AVC. In addition, the depth maps compressed with MMP generate reconstructed views with a higher quality than all other tested compression algorithms.
Three‐year effectiveness and safety of the XEN gel stent as a solo procedure or in combination with phacoemulsification in open‐angle glaucoma: a multicentre study (2021)

The gel stent effectively lowered IOP and IOP-lowering medication count over 3 years, with a predictable and acceptable safety profile, when implanted via the traditional ab-interno technique.
Activated Carbons from Fast Pyrolysis Biochar as Novel Catalysts for the Post-Treatment of Pyrolysis Vapors, Studied by Analytical Pyrolysis (2020)

Biochars are attractive materials for carbon catalysts since their carbon content and surface area are relatively high and minerals present in biochar can act as active sites for catalytic reactions. In this study, biochars from the fast pyrolysis of birch, pine, and unbarked willow were activated and acid washed. These materials were tested as catalysts for a post-treatment of pine wood pyrolysis vapors, aiming at stabilizing the vapors before their condensation. All the unmodified biochars had high content of minerals, those being highest in willow due to the bark. After the activation treatments, the surface areas and pore volumes of all biochars significantly increased. All studied biochars and activated carbon catalysts reduced the oxygen content of the pyrolysis degradation products. This effect was more pronounced for compounds derived from polysaccharides vs. lignin. The most promising catalyst for vapor upgrading was unwashed activated carbon from willow, having high surface areas and pore volumes together with high mineral contents. These properties together promoted the high conversion of polysaccharide-derived products (anhydrosugars, acids, and pyrans) into CO2. Release of highly oxidized degradation products may indicate that reductive stabilization takes place via hydrogen migration from the polysaccharide-derivatives to lignin derivatives, mediated by the carbon catalyst.