gebhart/patrepeval huggingface dataset:
Engineering the Mycomembrane of Live Mycobacteria with an Expanded Set of Trehalose Monomycolate Analogues (2018)

Mycobacteria and related organisms in the Corynebacterineae suborder are characterized by a distinctive outer membrane referred to as the mycomembrane. Biosynthesis of the mycomembrane occurs through an essential process called mycoloylation, which involves antigen 85 (Ag85)-catalyzed transfer of mycolic acids from the mycoloyl donor trehalose monomycolate (TMM) to acceptor carbohydrates and, in some organisms, proteins. We recently described an alkyne-modified TMM analogue (O-AlkTMM-C7) which, in conjunction with click chemistry, acted as a chemical reporter for mycoloylation in intact cells and allowed metabolic labeling of mycoloylated components of the mycomembrane. Here, we describe the synthesis and evaluation of a toolbox of TMM-based reporters bearing alkyne, azide, trans-cyclooctene, and fluorescent tags. These compounds gave further insight into the substrate tolerance of mycoloyltransferases (e.g., Ag85s) in a cellular context and they provide significantly expanded experimental versatility by allowing one- or two-step cell labeling, live cell labeling, and rapid cell labeling via tetrazine ligation. Such capabilities will facilitate research on mycomembrane composition, biosynthesis, and dynamics. Moreover, because TMM is exclusively metabolized by Corynebacterineae, the described probes may be valuable for the specific detection and cell-surface engineering of Mycobacterium tuberculosis and related pathogens. We also performed experiments to establish the dependence of probe incorporation on mycoloyltransferase activity, results from which suggested that cellular labeling is a function not only of metabolic incorporation (and likely removal) pathway(s), but also accessibility across the envelope. Thus, whole-cell labeling experiments with TMM reporters should be carefully designed and interpreted when envelope permeability may be compromised. On the other hand, this property of TMM reporters can potentially be exploited as a convenient way to probe changes in envelope integrity and permeability, facilitating drug development studies.
PipeRench: A virtualized programmable datapath in 0.18 micron technology (2003)

PipeRench is a programmable datapath that can be used to accelerate numerically intensive applications. The unique aspect of PipeRench is its ability to virtualize hardware through self-managed dynamic reconfiguration. This capability provides application portability and scalability without redesign or recompilation. This paper describes the implementation of PipeRench in a 0.18 micron process. The implementation has 3.65 million transistors and runs at 120 MHz. Performance is competitive with high-end commercial DSP architectures and more than five times faster than a commercial microprocessor. Executing at 33 MHz, an FIR filter without virtualization consumes 519 mW. When virtualization is required, the implementation consumes approximately 675 mW.
Visual Pattern Analyzers (1989)

From the light that falls on the retina, the visual system must extract meaningful information about what is where in our environment. At an early stage in this process, it analyzes the incoming sensory data along many dimensions of pattern vision. This book describes the current knowledge about this stage of visual processing, focusing both on psychophysical experiments measuring the detection and identification of near-threshold patterns and on the mathematical models used to draw inferences from such experimental results. Neurophysiological evidence is presented and compared critically to the psychophysical evidence. Orientation, spatial frequency, direction of motion, and eye of origin are among the many dimensions of spatiotemporal pattern vision for which experimental results and mathematical models are reviewed. Introductory material on psychophysical methods, signal detection theory, and the mathematics of Fourier analysis is also given. The preface gives a guide to the organization of the book and to what parts of the book can be read independently of one another. The last two chapters contain lists of references organized by dimensions of pattern vision. An appendix at the end of the book lists the assumptions used in the models both in order of appearance and in groups according to function.
Associated-particle sealed-tube neutron probe for characterization of materials (1993)

A neutron diagnostic probe system has been developed that can identify and image most elements having a larger atomic number than boron. It can satisfy van-mobile and fixed-portal requirements for nondestructive detection of contraband drugs, explosives, and nuclear and chemical warfare weapon materials, and for treaty verification of sealed munitions and remediation of radioactive waste. The probe is based on a nonpulsed associated-particle sealed-tube neutron generator (APSTNG) that interrogates the object with a 14-MeV neutrons and detects alpha-particle associated with each neutron. Gamma-ray spectra of resulting neutron reactions (primarily inelastic scattering) identify nuclides associated with drugs, explosives, and other contraband. Flight times determined from detection times of gamma-rays and alpha-particles yield a separate coarse tomographic image of each identified nuclide. Chemical substances are identified and imaged by comparing relative spectra fine intensities with ratios of elements in reference compounds. The High-energy neutrons in gamma-rays will penetrate large objects and dense materials. The source and emission detection systems can be on the same side, allowing measurements with access to one side only. A high signal-to-background ratio is obtained and maximum information is extracted from each detected gamma-ray, yet high-bandwidth data acquisition is not required. The APSTNG also forms the basis for a compact fast-neutron transmission imaging system. No collimators are required, and only minimal shielding is needed. The small and relatively inexpensive neutron generator tube exhibits high reliability and can be quickly replaced. The detector arrays and associated electronics can be made reliable with low maintenance cost.
Cloning of a Protein That Mediates Transcriptional Effects of Fatty Acids in Preadipocytes (1995)

Exposure of preadipocytes to long chain fatty acids induces expression of several gene markers of adipocyte differentiation. This report describes the cloning, from a preadipocyte library, of a cDNA encoding a fatty acid-activated receptor, FAAR. The cDNA had the characteristics and ligand-binding domains of nuclear hormone receptors and encoded a 440 amino acid protein related to peroxisome proliferator-activated receptors, PPAR. The deduced protein sequence was 88% homologous to that of hNUC I, isolated from human osteosarcoma cells. FAAR mRNA was abundant in adipose tissue, intestine, brain, heart, and skeletal muscles and less abundant in kidney, liver, testis, and spleen. The mRNA was undetectable in growing Ob1771 and 3T3-F442A preadipocytes, was strongly induced early during differentiation, and was increased by fatty acid. Transcription assays using hybrid receptor showed strong stimulation by fatty acid and weaker induction by fibrates. Transfection of 3T3-C2 fibroblasts, with a FAAR expression vector, conferred fatty acid inducibility of the adipocyte lipid-binding protein and the fatty acid transporter. Transcriptional induction of these genes exhibited inducer specificity identical to that described in preadipocytes. In summary, the data indicate that FAAR is likely a mediator of fatty acid transcriptional effects in preadipocytes.
Objective Eye Tracking Metrics of Vision and Autonomic Dysfunction Distinguish Adolescents With Acute Concussion and Those with Persistent Post-Concussion Symptoms from Uninjured Controls (2021)

<h3>Objective</h3> To explore the utility of an eye-tracking assessment in distinguishing binocular alignment, saccadic movement, and pupillary dynamics among uninjured adolescents, acute cases (= 28 days since concussion), and persistent cases (&gt;28 days since concussion). <h3>Background</h3> Visual and autonomic system disturbances are common sequelae of concussion. Quantification of visual and autonomic dysfunction via an eye tracking device could provide an objective method of acute diagnosis and subacute identification of ongoing injury. <h3>Design/Methods</h3> We compared 347 eye tracking metrics, derived from a 220 seconds eye-tracking assessment, among 132 uninjured adolescents (mean age: 15.3, 56.2% female), 110 acute cases (mean days since injury: 12.5, mean age: 15.4, 46.4% female), and 95 persistent cases (mean days since injury: 53.6, mean age: 15.4, 70.2% female) using Kruskal-Wallis tests with Bonferroni corrections to account for multiple comparisons. <h3>Results</h3> Nine eye-tracking metrics were significantly associated with injury status. One measure of binocular alignment (acute v. control: <i>p</i> = 0.003, persistent v. control: <i>p</i> = 0.001) and one measure of saccadic movement (acute v. persistent: <i>p</i> = 0.03, acute v. control: <i>p</i> = 0.03, persistent v. control: <i>p</i> &lt; 0.001) were worse in cases. Cases had larger left and right mean and median pupil size than uninjured adolescents (acute v. control, <i>p</i> &lt; 0.001; persistent v. control, <i>p</i> &lt; 0.001). Cases had greater differences in mean (acute v. control: <i>p</i> &lt; 0.001, persistent v. control: <i>p</i> &lt; 0.001), median (acute v. control, <i>p</i> &lt; 0.001, persistent v. control, <i>p</i> = 0.003), and variance of (acute v. control: <i>p</i> &lt; 0.001, persistent v. control: <i>p</i> &lt; 0.001) left and right pupil size. Eight of these metrics distinguished female cases from uninjured adolescents, but similar differences were not observed in male participants. <h3>Conclusions</h3> Objective eye tracking technology can identify vision and pupillary disturbances after concussion. These metrics could be integrated into clinical practice to monitor recovery in a heterogeneous adolescent concussion population and may identify sex-specific differences in autonomic dysfunction.
Fast high-temperature (250 &#x00B0;C / 500 &#x00B0;F) isolated dc and ac current measurement: Bidirectionally saturated current transformer (2012)

In an increasing number of application areas and industry sectors, such as the automotive, aerospace, military or oil and gas industry, a trend towards higher ambient temperature rating from 85 °C upward for electrical machines and power electronic converters can be observed. To reduce the impact of high ambient temperatures on the power density, the interest in power electronic converters with SiC power semiconductors operated up to a junction temperature of 250 °C rises. The control of power electronic converters typically requires a precise, fast and robust current measurement. Analyzing current measurement concepts from the literature reveals that there is a lack of a current measurement systems, that are galvanically isolated and are able to measure dc and ac fast at high ambient temperatures of 250 °C. In this paper, a current measurement concept of a bidirectionally saturated current transformer is presented, that is able to measure dc and sinusoidal ac up to 1 kHz and 50A at an ambient temperature of 250 °C with an relative error of 2.6% and less than 0.5% after initial calibration. Furthermore, a prototype is designed, built and used for experimental verification of the concept.
Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma (2019)

Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.
A time series 3D hierarchy for real-time dynamic point cloud interaction (2012)

Point-based scanning is commonly used for 3D data acquisition. Applications can simply adopt a point cloud representation avoiding the computational complexity of connectivity construction. Despite many state-of-the-art algorithms discussing point cloud representation and rendering, research on dynamic point cloud visualization and interaction still lacks sufficient attention. We propose a time series hierarchy for interactive rendering of dynamic point-based 3D models. The synchronization of spatio-temporal attributes in the hierarchy makes this structure novel. A balanced hierarchy together with a compact quantization encoding scheme, results in higher precision, efficient memory usage and responsive user interaction. This representation provides smooth visualization of dense dynamic point-based models, in long sequences of 3D frames, at interactive frame rates and quality rendering, which can be displayed on regular desktops or mobile devices in either single-view or multi-view mode. A prototype system is implemented to validate the feasibility of our approach.
<p>The SinuSonic: reducing nasal congestion with acoustic vibration and oscillating expiratory pressure</p> (2019)

Overall, outcomes were encouraging from this small pilot study with effect sizes in the moderate to large range and no reports of discomfort. It is probable that this device will provide acute, and possibly chronic, relief of nasal congestion with minimal side-effects.
Using Alcohol for Hand Antisepsis: Dispelling Old Myths (2000)

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Tumor Cell-Surface Binding of Immune Stimulating Polymeric Glyco-Adjuvant via Cysteine-Reactive Pyridyl Disulfide Promotes Antitumor Immunity (2022)

Immune stimulating agents like Toll-like receptor 7 (TLR7) agonists induce potent antitumor immunity but are limited in their therapeutic window due to off-target immune activation. Here, we developed a polymeric delivery platform that binds excess unpaired cysteines on tumor cell surfaces and debris to adjuvant tumor neoantigens as an <i>in situ</i> vaccine. The metabolic and enzymatic dysregulation in the tumor microenvironment produces these exofacial free thiols, which can undergo efficient disulfide exchange with thiol-reactive pyridyl disulfide moieties upon intratumoral injection. These functional monomers are incorporated into a copolymer with pendant mannose groups and TLR7 agonists to target both antigen and adjuvant to antigen presenting cells. When tethered in the tumor, the polymeric glyco-adjuvant induces a robust antitumor response and prolongs survival of tumor-bearing mice, including in checkpoint-resistant B16F10 melanoma. The construct additionally reduces systemic toxicity associated with clinically relevant small molecule TLR7 agonists.
A Magnesium-Based Diastereoselective Preparation of Pyridylic 1,3-Amino Alcohols Using the tert-Butyl Sulfinamide Auxiliary (2015)

1,3-Amino alcohols were prepared by using a two-step approach and an interesting reversal in diastereoselectivity is discussed.
Plastic Working of Metallic Glass Bolts by Cold Thread Rolling (2011)

Bolts are commonly employed machine elements used for joining and fastening, and their performance and reliability influence the overall performance of machines. In this study, we have plastically worked and formed bolts using metallic glass (MG) that exhibits unique mechanical properties such as high tensile strength, low Young’s modulus, and large elastic limit. The large elastic limit increases the permissible elongation range of the bolt and helps avoid bolt loosening, while the low Young’s modulus effectively resists screwed-in bolt loosening by increasing the frictional forces on both bolt-nut contact area and bearing surface. We employed a zirconium-based MG Zr55Al10Cu30Ni5 for our experimental investigations. A pre-form of a hexagon socket head cap screw (bolt) was fabricated by squeeze casting. Cold and warm thread rolling were performed to form a metric screw thread M3×0.5 (class 6g (ISO)) below the glass transition temperature (Tg) using a flat rolling machine. Despite the extremely poor ductility of MG at room temperature, thread rolling was successfully performed. Straining behavior analysis by a three-dimensional finite element method demonstrated that these remarkable results are due to the compressive stress distribution induced during the thread rolling process. In addition, thread rolling is fundamentally an incremental process, and it enhances the deformability of MG by gradually improving ductility in the deformed region. The tensile strength of the thread-rolled bolt was approximately 1600 MPa, which is considerably higher than that of conventional heat-treated high strength steel bolts. MG was thus successfully employed to manufacture improved bolts.
PressION: An All-Fabric Piezoionic Pressure Sensor for Extracting Physiological Metrics in Both Static and Dynamic Contexts (2021)

The strategy of detecting physiological signals and body movements using fabric-based pressure sensors offers the opportunity to unobtrusively collect multimodal health metrics using loose-fitting, familiar garments in natural environments. (A. Kiaghadi, S. Z. Homayounfar, J. Gummeson, T. Andrew, and D. Ganesan, Proc. ACM Interact. Mob. Wearable Ubiquitous Technol ., 3 , 1–29 (2019)). However, many sensing scenarios, such as sleep and posture monitoring, involve an added static pressure from exerted body weight, which overpowers weaker pressure signals originating from heartbeats, respiration and pulse and phonation. Here, we introduce an all-fabric piezoionic pressure sensor (PressION) that, on account of its ionic conductivity, functions over a wide range of static and dynamic applied pressures (from subtle ballistic heartbeats and pulse waveforms, to larger-scale body movements). This piezoionic sensor also maintains its pressure responsivity in the presence of an added background pressure and upon integration into loose-fitting garments. The broad ability of PressION to record a wide variety of physiological signals in realistic environments was confirmed by acquiring heartbeat, pulse, joint motion, phonation and step data from different body locations. PressION’s sensitivity, along with its low-cost fabrication process, qualifies it as a uniquely useful sensing element in wearable health monitoring systems.
Photovoltaic system performance monitoring for manufacturing quality assurance (2015)

Photovoltaic Reliability Group is being initiated in USA and India to assist owners of small PV systems. FSEC and Pune University have experience in monitoring performance of PV systems and household energy devices. Small PV system owners are being encouraged to participate. The scope is expected to increase because the Indian Government has decided to boost the national solar target to 100 GW by 2022. Student, teacher and engineer volunteers are sought from technical societies such as IEEE, AVS, SPIE, etc. PV parameters such as open-circuit voltage, short-circuit current, power, energy yield are measured and monitored remotely. Other parameters related to the state of the connections, switches, wire coatings, stability of mounts as a function of time also need to be monitored over the useful life. Careful analysis of this classified data will allow us to understand the ageing processes in the system. This analysis is expected to provide guidelines to devise accelerated tests for achieving longer life compatible with the warranty.
Activin A as a Mediator of NK–Dendritic Cell Functional Interactions (2014)

The interaction of NK cells with dendritic cells (DCs) results in reciprocal cell activation through the interaction of membrane proteins and the release of soluble factors. In this article, we report that in NK-DC cocultures, among a set of 84 cytokines investigated, activin A was the second highest induced gene, with CXCL8 being the most upregulated one. Activin A is a member of the TGF-β superfamily and was previously shown to possess both proinflammatory and anti-inflammatory activities. In NK-DC cocultures, the induction of activin A required cell contact and was dependent on the presence of proinflammatory cytokines (i.e., IFN-γ, TNF-α, and GM-CSF), as well as on NK cell-mediated DC killing. CD1(+) DCs were the main activin A producer cells among myeloid blood DC subsets. In NK-DC cocultures, inhibition of activin A by follistatin, a natural inhibitory protein, or by a specific blocking Ab, resulted in the upregulation of proinflammatory cytokine release (i.e., IL-6, IL-8, TNF-α) by DCs and in the increase of DC maturation. In conclusion, our study reports that activin A, produced during NK-DC interactions, represents a relevant negative feedback mechanism that might function to prevent excessive immune activation by DCs.
Pitfalls of HIV genotypic tropism testing after treatment interruption (2012)

We have shown that the redistribution of the HIV population caused by TI could potentially result in X4 viruses becoming undetected and inappropriate prescription of a CCR5 receptor antagonist. Therefore, genotypic tropism results should be interpreted with caution in such a context.
Digital enhancement of torque magnetometer signals (1976)

Torque signals from a metal single crystal in a rotating magnetic field and the corresponding angular position of the rotating magnet, for both directions of rotation, were digitally recorded on magnetic tape at equal time intervals, with a maximum recording frequency of 18.8 data pairs per degree of rotation. The signals included induced, background, and de Haas–van Alphen effect torques. Only the induced torque is an odd function of rotation direction, and enhancement of the induced torque signals is achieved by subtracting the data obtained for one rotation direction from that for the other rotation direction. Computer analysis of recorded data yielded enhancement only if prior correction of each angular reading was performed to take into account the finite compliance of the torque magnetometer. The resulting enhanced rotation diagrams were plotted on a Calcomp plotter. The technique is also useful for continuous recording of anisotropy torque data from weakly magnetic samples, since the induced-torque signals can be cancelled by adding the data from one rotation direction to those obtained from the other direction.
Serum fibrinogen alpha C‐chain 5.9 kDa fragment as a biomarker for early detection of hepatic fibrosis related to hepatitis C virus (2013)

The serum FIC 5.9 level may be an early indicator of hepatic fibrosis in HCV-related chronic liver diseases. This study provides an example of a pipeline from biomarker discovery by proteome analysis to assay optimization and preliminary clinical validation.