gebhart/patrepeval huggingface dataset:
Virus-Specific Cytotoxic T Lymphocytes in Human Immunodeficiency Virus Type 1-Infected Chimpanzees (1999)

Chimpanzees have been important in studies of human immunodeficiency virus type 1 (HIV-1) pathogenesis and in evaluation of HIV-1 candidate vaccines. However, little information is available about HIV-1-specific cytotoxic T lymphocytes (CTL) in these animals. In the present study, in vitro stimulation of peripheral blood mononuclear cells (PBMC) from infected chimpanzees with HIV-1 Gag peptides was shown to be a sensitive, reproducible method of expanding HIV-1-specific CD8(+) effector CTL. Of interest, PBMC from two chimpanzees had CTL activity against Gag epitopes also recognized by major histocompatibility complex class I-restricted CTL from HIV-1-infected humans. The use of peptide stimulation will help to clarify the role of CTL in vaccine-mediated protection and HIV-1 disease progression in this important animal model.
A pilot study of genetic polymorphisms and hemodialysis vascular access thrombosis (2009)

Vascular access thrombosis (VAT) remains a significant problem worldwide. This study determined the association between VAT and 7 candidate gene polymorphisms (factor V Leiden 1691G>A, factor II 20210G>A, methylenetetrahydrofolate reductase 677C>T, angiotensin converting enzyme 287 base pair (bp) insertion/deletion, transforming growth factor-beta1 869T>C and 915G>C, NOS3 -786T>C and intron 4 27 bp tandem repeat, and endotoxin receptor CD14 -159C>T). This was a retrospective case-control pilot study conducted in 101 hemodialysis patients at a large tertiary-care, University health-science center. Sixty cases that experienced frequent VAT and 41 controls that had not experienced VAT in at least 3 years were evaluated for demographics and genotyping. These data were summarized, and univariable and multivariable regression models were constructed. Univariate VAT predictors included the NOS3 420 bp allele (P=0.03) and the presence of a central venous dialysis catheter (P<0.01). Aspirin use was protective against VAT (P=0.02). In the multivariate analysis, the dialysis access type remained a significant predictor of thrombosis (P<0.01), while aspirin use retained its protective status (P=0.01). Statin use was associated with the cases (P=0.02); however, the NOS3 420 bp allele failed to improve the model. These data confirm that central venous dialysis catheter access is associated with thrombosis, while aspirin use appears protective. The NOS3 420 bp allele may have an association with thrombosis; however, further epidemiologic data evaluating large dialysis registries are needed to confirm our observation.
Reply to “Can Limited Scientific Value of Potential Pandemic Pathogen Experiments Justify the Risks?” (2014)

We thank Dr. Lipsitch for his comments (1). Dr. Lipsitch does not argue with the notion that gain-of-function experiments are epistemologically valuable, but he does feel that their practical value is limited. Likewise, we would not argue that reasonable people cannot come to different conclusions about the relative epistemic value of any given experiment. He makes several points to which we will respond.

The first point is that the epistemic yield of influenza virus GOF experiments in ferrets is limited. Dr. Lipsitch questions the value of the experiments establishing H5N1 transmissibility in ferrets (2, 3) on the basis of underpowered experiments and the possibility that the information is limited to ferrets. That may be true for quantitative data, although arguments have been made to the contrary (4), but the experiments on H5N1 transmissibility unequivocally established that H5N1 had the biological potential to become mammalian transmissible, and that observation was a qualitative, all-or-nothing, result for which there is no need for statistical analysis: it happened. The fact that it happened is the epistemic gain, and the definitive nature of the result makes it of high epistemic value. Prior to these experiments, the question of whether highly pathogenic avian influenza viruses (HPAIV) had the biological potential for mammalian transmissibility was in doubt. Since the completion of these experiments, we know with great confidence that H5N1 can …
Interactions of Glucose Metabolism and Chronic Heart Failure (2008)

Insulin sensitivity and insulin secretion are impaired in CHF and biomarkers of heart failure and atherosclerotic disease correlate to glucose metabolism.
Optical ranked-order filtering using threshold decomposition (2023)

A hybrid optical/electronic system performs median filtering and related ranked-order operations using threshold decomposition to encode the image. Threshold decomposition transforms the nonlinear neighborhood ranking operation into a linear space-invariant filtering step followed by a point-to-point threshold comparison step. Spatial multiplexing allows parallel processing of all the threshold components as well as recombination by a second linear, space-invariant filtering step. An incoherent optical correlation system performs the linear filtering, using a magneto-optic spatial light modulator as the input device and a computer-generated hologram in the filter plane. Thresholding is done electronically. By adjusting the value of the threshold, the same architecture is used to perform median, minimum, and maximum filtering of images. A totally optical system is also disclosed.
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs (2021)

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.
Processing of acoustic signals in the auditory system of bony fish (1988)

In order to determine unambiguously the bearing of a sound source, a fish must be able to resolve acoustic pressure and the components of the acoustic displacement vector from the signals detected by the otolithic organs. A new hypothesis for the processing of acoustical information by bony fish is presented. It is demonstrated that much of the processing required to do this may be implicit in the structure of the ear and its associated neural innervation. Possible algorithms are presented that the central nervous system might use to further process the derived information to localize a sound source and discriminate frequency and range. The hypothesis is shown to be consistent with much of what is known of the morphology and physiology of the auditory system of bony fishes.
Beta Process Sparse Nonnegative Matrix Factorization For Music. (2013)

[TODO] Add abstract here.
Autolytic reduction of the nucleic acid content in Candida utilis (1990)

The nucleic acid content in Candida utilis was autolytically reduced only after previous lyophilization of yeast cells or pretreatment of the cells with ethyl acetate. These pretreatments provided a sufficient permeability of the cell membrane system and thus enabled a reduction of the nucleic acid content. While deep freezing of the cells (-35 degrees C) had no positive effect on the degradation of nucleic acids, lyophilization of yeast cells led to a 75% decrease of the nucleic acid content. Furthermore, a 55% reduction of the nucleic acid content was proceeded without a concomitant loss of proteins. Similar results were obtained by using ethyl acetate.
Neutralization of Haptenated Bacteriophage F2 by Anti-Hapten Antibodies: Direct Evidence for a Critical Site (1972)

Abstract The neutralization of trinitrophenyl (TNP) derivatives of the small RNA bacteriophage f2 by rabbit anti-DNP antibodies was studied by the plaque assay technique. In agreement with previous work using other hapten-bacteriophage conjugates, we found that whole antibody was much more effective in the neutralization reaction than were corresponding Fab fragments. Measurement of the association constant for whole antibody with heavily substituted phage derivatives (TNP305-f2) gave a result (Ka = 3.2 × 1010) which was 103 greater than the corresponding value for Fab fragments. This difference was, in part, reflected in a 400-fold decrease in the second order rate constant for the phage-antibody association reaction, in going from γG antibody to Fab fragment. Analysis of these results lends further support for a simple steric model of phage neutralization by antibody. The relative effectiveness of antibody in neutralizing TNP-f2 conjugates was in large measure controlled by the degree of phage modification. For example, a lightly substituted f2 derivative (TNP3-f2) remained fully viable in the presence of a large excess of antibody, providing direct evidence for the infectivity of antibody-f2 aggregates. A quantitative study of the infectivity of another lightly substituted TNP-f2 conjugate (TNP30-f2) led directly to a model of f2 neutralization, in which an antibody molecule must directly interact with a single critical site on the surface of f2 in order to inactivate the phage. A consideration of the icosahedral structure of f2 suggests that f2 neutralization occurs by attachment of a single antibody molecule at or in the vicinitv of A-protein.
Primer delivery by T7 gene 4 proteins (2010)

Gene 4 protein (gp4) encoded by bacteriophage T7 contains a C‐terminal helicase domain and a N‐terminal primase domain. After synthesis of the tetraribonucleotide primers gp4 must then transfer them to the polymerase for use as primers to initiate DNA synthesis. A truncated version of the full‐length 63‐kDa gp4, the 56‐kDa gp4, lacks the N‐terminal Cys 4 zinc‐binding motif that is important in the recognition of primase sites in the DNA. We find that the 56‐kDa gp4 is defective in primer synthesis but delivers a wider range of primers to initiate DNA synthesis compared to the 63‐kDa gp4. This property of the 56‐kDa gp4 is potentially significant in the initiation of T7 DNA replication. We have identified DNA primases that are defective in primer delivery by screening 56‐kDa gp4s containing mutations for their ability to support the growth of T7 phage lacking gene 4 but containing a suppressor that allows it to grow in the presence of the 56‐kDa gp4. We find that Trp69 of the 56‐kDa gp4 is critical for primer delivery. Substitution of lysine for Trp69 yields 56‐kDa gp4‐W69K and 63‐kDa gp4‐W69K that are defective in primer delivery to the polymerase with other functions unaffected. DNA primase harboring lysine at position 69 fails to stabilize the primer on DNA as analyzed by surface plasmon resonance.
Quanta image sensors: Photon-number-resolving megapixel image sensors at room temperature without avalanche gain (2018)

This paper reports on the state of the art of the Quanta Image Sensor (QIS) being developed by Dartmouth. The QIS is a photon-counting image sensor. Experimental 1Mpixel devices have been implemented in a modified backside-illuminated stacked CMOS image sensor process. Without the use of avalanche multiplicative gain, the sensors have achieved room temperature average read noise of 0.22e- rms (analog readout) permitting photon counting, and over 1000fps readout at under 20mW total power dissipation including pads (single-bit digital readout).
Extracellular Matrix-mediated Signaling by Dentin Phosphophoryn Involves Activation of the Smad Pathway Independent of Bone Morphogenetic Protein (2005)

Cells have ingenious mechanisms for interpreting complex signals from their external microenvironment. Previously, we have shown that phosphophoryn (PP) regulates the expression of bone/dentin marker genes via the integrin/MAPK signaling pathway (Jadlowiec, J., Koch, H., Zhang, X., Campbell, P. G., Seyedain, M., and Sfeir, C. (2004) J. Biol. Chem. 279, 53323-53330). We hypothesize that other signaling pathways important for mineralized tissue morphogenesis such as the Smad pathway could be involved in PP signaling. We determined activation of the Smad pathway in human adult mesenchymal stem cells following treatment with recombinant PP (rPP). We observed that PP enhanced phosphorylation of Smad1 within 30 min and Smad1 translocation to the nucleus within 1 h. PP up-regulated the expression of Smad1 target genes, Smad6, Dlx5, and Runx2. The timing of PP activation of Smad1 implies this is a direct effect; however, we also investigated the possible involvement of bone morphogenetic proteins in PP stimulation of the Smad pathway. PP was shown to up-regulate Bmp-2 gene expression 12 h post-treatment with PP, which is much later than initial detection of Smad1 phosphorylation at 30 min. Furthermore, addition of Noggin did not block Smad1 phosphorylation by PP. We propose that PP could signal via the Smad pathway by either directly stimulating the phosphorylation of Smad1 via integrins or other mechanisms. These might include integrin/bone morphogenetic protein receptor interactions or involvement of PP with other growth factors leading to the modulation of intracellular signaling. It is noteworthy that a non-transforming growth factor-beta family member activates the Smad pathway. The role of PP in regulating the Smad pathway raises very interesting questions regarding the role of PP during bone and tooth development.
Reproducibility of histological assessments of disease activity in UC (2014)

Although 'substantial' to 'almost perfect' ICCs for intrarater agreement were found in the assessment of HA in UC, ICCs for inter-rater agreement were considerably lower. According to the consensus process results, standardisation of item definitions and modification of the existing indices is required to create an optimal UC histological instrument.
Successful Targeted Ablation of the Pathway Potential in the Noncoronary Cusp of the Aortic Valve in an Infant with Incessant Orthodromic Atrioventricular Reentrant Tachycardia (2008)

Myocardial fibers above the aortic valve cusps may constitute the atrioventricular bypass connection and can be identified and targeted for successful ablation even in infants.
Current Status of the EUV Engineering Test Stand. (2002)

The EUV Engineering Test Stand (ETS) has demonstrated the printing of static and scanned 100nm dense features. This milestone was first achieved in 2001 with a developmental set of projection optics (P0 Box 1) and with a low power LPP source (40W drive laser). Since that time, the source has been upgraded to a 1500W (3 chains, 500W per chain) TRW drive laser. Operating with one chain (500W), the printed static images for 100nm features are comparable to those obtained with the low power source, while exposure time was decreased by a factor of 15 to 30. One hundred nanometer dense features printed in step-and-scan mode are of the same image quality as those obtained in static imaging. The stages have demonstrated combined x any y j fitter values of 2 to 4nm RMS over most of the wafer stage travel range, at the designed scanned speed of 10mm/s at the wafer. This value is less than half of the designed value and provides sufficient stability to support printing of 70nm features. EUV specific sensors at the wafer and reticle planes have been demonstrated with the TRW laser and integration will be completed later this year. The developmental projection optics (P0 Box 1) will be replaced later this year with an improved projection optics system (PO Box 2) capable of printing 70nm dense features.
Nearly Planar Low Threshold Vertical-Cavity Surface-Emitting Lasers Using High Contrast Mirrors and Native Oxidation (1994)

Data will be presented characterizing a device structure for the vertical-cavity surface-emitting laser (VCSEL) which has achieved low threshold operation. An advantage of the laser structure is nearly planar processing. In initial results we have achieved a room-temperature continuous-wave threshold current of 225μA in an 8μm square device. To our knowledge, this is the lowest threshold current yet achieved in a vertical-cavity laser. Since the threshold current density is only 350A/cm2, this also represents to our knowledge the lowest threshold current density in a VCSEL of any diameter. The threshold voltage drive is 1.9V, with a drive voltage of 2.9V at four times threshold.
Histidine 21 Is at the NAD+ Binding Site of Diphtheria Toxin (1989)

Treatment of fragment A chain of diphtheria toxin (DT-A) with diethylpyrocarbonate modifies His-21, the single histidine residue present in the chain, without alteration of other residues. Parallel to histidine modification, NAD+ binding and the NAD-glycohydrolase and ADP-ribosyltransferase activities of DT-A are lost. Both NAD+ and adenosine are very effective in protecting DT-A from histidine modification and in preserving its biological properties, while adenine is ineffective. Reversal of histidine modification with hydroxylamine restores both NAD+ binding and enzymatic activities of the toxin. The possible role of His-21 in the activity of diphtheria toxin is discussed in relation to the available three-dimensional structure of the related toxin produced by Pseudomonas aeruginosa.
The rise and fall of prostate brachytherapy: Use of brachytherapy for the treatment of localized prostate cancer in the National Cancer Data Base (2014)

For patients with localized prostate cancer who are treated at National Cancer Data Base institutions, there has been a steady decline in brachytherapy use since 2003. For low-risk patients, the declining use of brachytherapy monotherapy compared with more costly emerging therapies has significant health policy implications.
Genetic and sequence analyses of a Pseudomonas denitrificans DNA fragment containing two cob genes (1991)

A genetic analysis of a 12-kb DNA fragment containing Pseudomonas denitrificans cob genes was performed by transposon-mediated insertional mutagenesis. The nucleotide sequence and genetic analysis have shown that a 4.8-kb DNA subfragment carried two cob genes (cobS and cobT). Biochemical data concerning the complemented cobS and cobT mutants suggested that the cobS product was involved in cobalt insertion-mediating reactions and that the cobT product was involved in the transformation of precorrin-3 into cobyrinic acid.
Opportunities of Immobilized Homogeneous Metathesis Complexes as Prominent Heterogeneous Catalysts (2016)

Abstract A plethora of strategies for immobilizing well‐defined metathesis catalysts on solid supports have been developed over the past decades. Whereas most reviews on classical heterogeneous metathesis catalyst designs mainly discuss covalent binding approaches, we here extended this topic with non‐covalent surface science methods, a research area that gained interest recently. Within this context, the main focus was set on the immobilization of ruthenium alkylidenes or so‐called Grubbs complexes, as these catalysts are known for their high activity, stability and commercial viability. Besides giving an overview of different immobilization strategies, the wide diversity of supported Grubbs catalysts also allows for discussing implications of attaching Grubbs catalysts that go beyond the traditional benefits of heterogeneous catalysis, such as easy catalyst separation. More specifically, this Review will summarize several unique opportunities of immobilized homogeneous catalysts in liquid‐phase metathesis transformations in terms of impact on activity, stability, and product selectivity, as to highlight the economic potential, but without ignoring possible shortcomings and limitations.
Meet AR-bot (2018)

Many kinds of preparations are needed when meeting. For example, projector, laptop, cables and ETC. As such, this video have constructed Meet AR-bot, which helps users to keep meeting going smoothly, based on the projection of Augmented Reality(AR). Our system can easily provide meeting room environment through the movable setting via wheel-based stand. Users do not need to carry a personal laptop and connect them to the projector. Robot reconstructs the 3D geometry information through pan-tilt system and compute projection areas to project information in the space. Users can also control through mobile devices. We offer presentation, table interaction, file sharing and virtual object registration by mobile device.
Rendering and Visualization in Parallel Environments (2001)

The continuing commoditization of the computer market has precipitated a qualitative change. Increasingly powerful processors, large memories, big harddisk, high-speed networks, and fast 3D rendering hardware are now affordable without a large capital outlay. Clusters of workstations and SMP-servers are utilizing these technologies to drive interactive applications like large graphical display walls (i.e., Powerwall or CAVE systems). In this tutorial, attendees will learn how to understand and leverage (technical and personal) workstation- and serverbased systems as components for parallel rendering. The goal of the tutorial is twofold: Attendees will thoroughly understand the important characteristics workstations architectures. We will present an overview of different workstation (Intel-based and others) and server architectures (including graphics hardware), addressing both single-processors as well as SMP architectures. We will also introduce important methods of programming in parallel environment with special attention how such techniques apply to developing cluster-based parallel renderers. Attendees will learn about different approaches to implement parallel renderers. The tutorial will cover parallel polygon and volume rendering. We will explain the underlying concepts of workload characterization, workload partitioning, and static, dynamic, and adaptive load balancing. We will then apply these concepts to characterize various parallelization strategies reported in the literature for polygon and volume rendering. We abstract from the actual implementation of these strategies and instead focus on a comparison of their benefits and drawbacks. Case studies will provide additional material to explain the use of these techniques. The tutorial will be structured into three main sections: We will first discuss the fundamentals of parallel programming and parallel machine architectures. Topics include message passing vs. shared memory, thread programming, a review of different SMP architectures, clustering techniques, PC architectures for personal workstations, and graphics hardware architectures. The second section builds on this foundation to describe key concepts and particular algorithms for parallel polygon and volume rendering. These concepts are supplemented with concrete parallel rendering implementations
Fabrication and Tolerances of Optics for High Concentration Photovoltaics (2014)

High Concentration Photovoltaics (HCPV) require an optical system with high efficiency, low cost and large tolerance. We describe the particularities of the HCPV applications, which constrain the optics design and the manufacturing techonologies.