gebhart/patrepeval huggingface dataset:
Digitizing Brings New Life to Video Collections (2008)

LET'S TAKE A LOOK AT THE OPPORTUNITIES MADE POSSIBLE THROUGH THE DIGITIZATION OF MULTIMEDIA CONTENT.
Conformational properties of molecules by ab initio quantum mechanical energy minimization. (1985)

The recent literature on the determination of minimum energy conformations by ab initio quantum mechanical techniques is reviewed. The availability of computer-coded analytical first and second derivatives of the Hartree-Fock energy makes possible calculations that will be of significant assistance in structure determination of molecules. A short review of recent progress in empirical energy minimization and molecular dynamics is provided.
Non-interleaved deferred shading of interleaved sample patterns (2006)

This paper presents a novel and fast technique to combine interleaved sampling and deferred shading on a GPU. The core idea of this paper is quite simple. Interleaved sample patterns are computed in a non-interleaved deferred shading process. The geometric buffer (G-buffer) which contains all of the pixel information is actually split into several separate and distinct sub-buffers. To achieve such a result in a fast way, a massive two-pass swizzling copy is used to convert between these two buffer organizations. Once split, the sub-buffers can then be accessed to perform any fragment operation as it is done with a standard deferred shading rendering pipeline. By combining interleaved sampling and deferred shading, real time rendering of global illumination effects can be therefore easily achieved. Instead of evaluating each light contribution on the whole geometric buffer, each shading computation is coherently restricted to a smaller subset a fragments using the sub-buffers. Therefore, each screen pixel in a regular n X m pattern will have its own small set of light contributions. Doing so, the consumed fillrate is considerably decreased and the provided rendering quality remains close to the quality obtained with a non-interleaved approach. The implementation of this rendering pipeline is finally straightforward and it can be easily integrated in any existing real-time rendering package already using deferred shading.
A mid-level representation framework for semantic sports video analysis (2003)

Sports video has been widely studied due to its tremendous commercial potentials. Despite encouraging results from various specific sports games, it is almost impossible to extend a system for a new sports game because they usually employ different sets of low-level features appropriate for the specific games and closely coupled with the use of game specific rules to detect events or highlights. There is a lack of internal representation and structure to be generic and applicable for many different sports. In this paper, we present a generic mid-level representation framework for semantic sports video analysis. The mid-level representation layer is introduced between the low-level audio-visual processing and high-level semantic analysis. It allows us to separate sports specific knowledge and rules from the low-level and mid-level feature extraction. This makes sports video analysis more efficient, effective, and less ad-hoc for various types of sports. To achieve robustness of the low-level feature analysis, a non-parametric clustering, mean shift procedure, has been successfully applied to both color and motion analysis. The proposed framework has been tested for five field-ball type sports covering duration of about 8 hours. Experiments have shown its robust performance in semantic analysis and event detection. We believe that the proposed mid-level representation framework can be used for event detection, highlight extraction, summarization and personalization of many types of sports video.
Inhibition of the Rho GTPase, Rac1, decreases estrogen receptor levels and is a novel therapeutic strategy in breast cancer (2010)

Rac1, a Rho GTPase, modulates diverse cellular processes and is hyperactive in some cancers. Estrogen receptor-alpha (ERα) in concert with intracellular signaling pathways regulates genes associated with cell proliferation, tumor development, and breast cancer cell survival. Therefore, we examined the possibility of Rac1 and ERα crosstalk in breast cancer cells. We found that Rac1 enhanced ERα transcriptional activity in breast cancer cells. Vav3, a Rho guanine nucleotide exchange factor that activates Rac1, was an upstream mediator, and P21/Cdc42/Rac1 activating kinase-1 (Pak-1) was a downstream effector of Rac1 enhancement of ERα activity. These results suggest that Rac1 may prove to be a therapeutic target. To test this hypothesis, we used a small molecule Rac inhibitor, EHT 1864, and found that EHT 1864 inhibited ERα transcriptional activity. Furthermore, EHT 1864 inhibited estrogen-induced cell proliferation in breast cancer cells and decreased tamoxifen-resistant breast cancer cell growth. EHT 1864 decreased activity of the promoter of the ERα gene resulting in down-regulation of ERα mRNA and protein levels. Therefore, ERα down-regulation by EHT 1864 is the likely mechanism of EHT 1864-mediated inhibition of ERα activity and estrogen-stimulated breast cancer cell proliferation. Since ERα plays a critical role in the pathogenesis of breast cancer and the Rac inhibitor EHT 1864 down-regulates ERα expression and breast cancer cell proliferation, further investigation of the therapeutic potential of Rac1 targeting in the treatment of breast cancer is warranted.
Failed Adoptive Immunotherapy with Tumor-Specific T Cells (2004)

Adoptive immunotherapy with tumor-specific T cells has emerged as a valid approach for prevention or treatment of diseases, such as melanoma and EBV-associated lymphoma. As interleukin (IL) 15 promotes survival of CD8(+) memory CTLs, we hypothesized that it could be used to enhance antitumor immunity in vivo through the maintenance of adoptively transferred memory CTL. To test this, we treated mice bearing P1A(+) tumors with adoptively transferred T cells possessing a transgenic Valpha8(+) T-cell receptor specific for the P1A tumor antigen (called P1CTL). Mice were then randomized to receive daily low-dose IL-15 (0.5 microg/day) or PBS. Mice receiving the transgenic P1CTL and IL-15 experienced a significantly delayed tumor relapse or complete tumor regression (P < 0.002 compared with PBS), with a striking persistence of the CD8(+) Valpha8(+) P1CTL compared with mice receiving the CD8(+) Valpha8(+) P1CTL and PBS vehicle (26.3 versus 5.1% P < 10(-5)). Animals exhibiting complete tumor regression had a significant population of CD8(+) Valpha8(+) P1CTL (46%) that persisted with IL-15 treatment until 140 days after adoptive transfer and successfully defended them against tumor rechallenge without IL-15. Low-dose IL-2 afforded no protection over vehicle and resulted in lower percentages of T cells with an activated memory phenotype, lower Bcl-2 expression, and lower ex vivo antitumor cytotoxicity compared with mice treated with IL-15. Collectively, the data support the notion that exogenous low-dose IL-15 therapy can enhance and even reverse the limited efficacy of adoptively transferred tumor-specific T-cell therapy and may do so in a fashion that is superior and distinct from exogenous IL-2 therapy.
Integration of minisolenoids in microfluidic device for magnetic bead–based immunoassays (2007)

Microfluidic devices with integrated minisolenoids, microvalves, and channels have been fabricated for fast and low-volume immunoassay using superparamagnetic beads and well-known surface bioengineering protocols. A magnetic reaction area can be formed in the microchannel, featuring a high surface-to-volume ratio and low diffusion distances for the reagents to the bead surface. Such a method has the obvious advantage of easy implementation at low cost. Moreover, the minisolenoids can be switched on or off and the magnetic field intensity can be tuned on demand. Fluids can be manipulated by controlling the integrated air-pressure-actuated microvalves. Accordingly, magnetic bead–based immunoassay, as a typical example of biochemical detection and analysis, has been successfully performed on the integrated microfluidic device automatically in longitudinal mode. With a sample consumption of 0.5μl and a total assay time of less than 15min, goat immunoglobulin G was detected and the method exhibited a detection limit of 4.7ng∕ml.
A single camera eye-gaze tracking system with free head motion (2006)

Eye-gaze as a form of human machine interface holds great promise for improving the way we interact with machines. Eye-gaze tracking devices that are non-contact, non-restrictive, accurate and easy to use will increase the appeal for including eye-gaze information in future applications. The system we have developed and which we describe in this paper achieves these goals using a single high resolution camera with a fixed field of view. The single camera system has no moving parts which results in rapid reacquisition of the eye after loss of tracking. Free head motion is achieved using multiple glints and 3D modeling techniques. Accuracies of under 1° of visual angle are achieved over a field of view of 14x12x20 cm and over various hardware configurations, camera resolutions and frame rates.
Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array (2016)

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin-polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.
Amazing IL-9: revealing a new function for an “old” cytokine (2012)

The incidence of melanoma - the most aggressive form of skin cancer - is dramatically increasing, while the development of innovative therapeutic strategies continues to be challenging, especially due to a lack of knowledge about the molecular mechanisms underlying melanoma progression as well as antitumor immunity. In this issue of the JCI, Yong Lu and colleagues report a central role for Th9 cells in antitumor immunity.
A novel Escherichia coli lipid A mutant that produces an antiinflammatory lipopolysaccharide. (1996)

A unique screen was used to identify mutations in Escherichia coli lipid A biosynthesis that result in a decreased ability to stimulate E-selectin expression by human endothelial cells. A mutation was identified in the msbB gene of E. coli that resulted in lipopolysaccharide (LPS) that lacks the myristoyl fatty acid moiety of the lipid A. Unlike all previously reported lipid A mutants, the msbB mutant was not conditionally lethal for growth. Viable cells or purified LPS from an msbB mutant had a 1000-10,000-fold reduction in the ability to stimulate E-selectin production by human endothelial cells and TNF alpha production by adherent monocytes. The cloned msbB gene was able to functionally complement the msbB mutant, restoring both the LPS to its native composition and the ability of the strain to stimulate immune cells. Nonmyristoylated LPS acted as an antagonist for E-selectin expression when mixed with LPS obtained from the parental strain. These studies demonstrate a significant role for the myristate component of LPS in immune cell activation and antagonism. In addition, the msbB mutant allowed us to directly examine the crucial role that the lipid A structure plays when viable bacteria are presented to host defense cells.
Alleles at D6S265 and D6S105 define a haemochromatosis‐specific genotype (1994)

Hereditary haemochromatosis is an HLA-linked, recessive disorder with HLA-A3 a strong marker for the gene. We have identified molecular markers for two serologically indistinguishable subtypes of HLA-A3 and examined these in 42 patients with haemochromatosis. The common HLA-A3 subtype HLA-A*0301 (highly correlated with allele 1 of D6S265) was a slightly better marker for haemochromatosis (RR = 10.1, Chi2 = 30) than the serologically recognized A3 antigen (RR = 9.1; Chi2 = 27.3). Allele 8 of the more telomeric locus D6S105 was also strongly associated with haemochromatosis (RR = 13.0; Chi2 = 21.1) but alleles at this locus were not in strong linkage disequilibrium with HLA-A alleles in the control subjects. The co-occurrence of D6S265-1 and D6S105-8 alleles yielded a higher risk (RR = 16.9; Chi2 = 44). Homozygosity for the haplotype including these markers was specific for haemochromatosis, i.e. did not occur in 376 healthy subjects but was observed in 21.4% of patients. These results refine the HLA-A3 association with haemochromatosis, suggest that the haemochromatosis gene is located on the telomeric side of HLA-A and define a possible haplotype in which the first mutation may have occurred.
Nucleotide sequence of adenovirus 2 DNA fragment encoding for the carboxylic region of the fiber protein and the entire E4 region (1981)

The entire nucleotide sequence between coordinates 89.5 and 100% of the Ad 2 DNA genome has been determined using the Maxam and Gilbert method. This sequence of 3766 bp contains information relative to the carboxylic end of the fiber protein and to the entire E4 region. The position within the nucleotide sequence of various open reading frames and of several consensus splicing sequences was correlated with the location by EM and Sl digestion of the E4 mRNA. This correlation allows to suggest an additional splicing event in the maturation process of i or f mRNA and to deduce the structure of most E4 mRNA. The aminoacid sequences of the corresponding proteins are deduced allowing the location of several glycosylation sites. The presence of several open reading frames with a substantial coding capacity permits to postulate on the existence of additional genes located at the 3' end of the fiber gene and the 3' end of the E4 region. The existence of these putative additional genes might explain that termination of transcription is several hundred nucleotides beyond the main known poly A addition sites of the L5 and E4 regions.
Hepatic to pancreatic switch defines a role for hemostatic factors in cellular plasticity in mice (2005)

In multiple systems, impaired proteolysis associated with the loss of the hemostatic factor plasminogen (Plg) results in fibrin-dependent defects in tissue repair. However, repair within the liver is known to be defective in Plg-deficient (Plg(o)) mice independent of fibrin clearance and appears to be compromised in part by the poor clearance of necrotic cells. Based on these findings, we examined the hepatic transcriptome after injury in search of transcriptional programs that are sensitive to the Plg/fibrinogen system. To this end, we generated biotinylated cRNA pools from livers of Plg(o) mice and controls before and after a single dose of the hepatotoxin carbon tetrachloride and hybridized them against high-density oligonucleotide arrays. Analysis of the gene expression platform identified an unexpected transcriptional signature within challenged livers of Plg(o) mice for pancreatic gene products, including trypsinogen-2, amylase-2, elastase-1, elastase-2, and cholesteryl-ester lipase. Validation studies found that this transcriptional program also contained products of the endocrine pancreas (Reg-1 and insulin genes) and the expression of the pancreatic transcription factors p48 and PDX-1. By using a LacZ transgene to trace the cellular source of pancreatic gene expression, we found that PDX-1 was expressed in albumin-positive cells that were morphologically indistinguishable from hepatocytes, and in albumin-negative epithelioid cells within zones of pericentral injury. More detailed studies revealed that the mechanisms of heterotopic gene expression in Plg(o) mice required fibrin(ogen). Collectively, these data reveal a regulatory role for the hemostatic factors plasmin(ogen) and fibrin(ogen) in cellular plasticity within adult tissues of the digestive system.
Catheter‐Based Renal Sympathetic Denervation Improves Central Hemodynamics and Arterial Stiffness: A Pilot Study (2012)

Renal sympathetic denervation (RDN) is a novel treatment strategy for patients with resistant arterial hypertension. Recently, the Symplicity trials demonstrated significant peripheral blood pressure (BP) reduction. The present study aimed at measuring central aortic pressures and arterial stiffness as better predictors for cardiovascular risk in patients undergoing RDN. RDN was performed in 21 patients (systolic peripheral BP ≥150 mm Hg) with an Ardian/Medtronic (Mountain View, CA) ablation system. Data were recorded with an Arteriograph. After 6 months, peripheral systolic BP was reduced by 6.1% (P<.05) while central systolic pressure was reduced by 7.0% (P<.05). Subgroup analysis showed that in responders, peripheral systolic BP was reduced by 16.1% (P<.01) while central systolic pressure was reduced by 18.3% (P<.01). Arterial stiffness improved significantly. Aortic augmentation index (AIx) improved by 9.5% (P<.05). In responders, AIx improved by 19.2% (P<.02). Pulse wave velocity (PWV) was high at baseline (10.8 m/s) and improved by 10.4% (P<.05). In responders, PWV improved by 13.7% (P<.05). Multivariate analysis showed that short-term effects on PWV were BP-related, whereas during follow-up, improvement of PWV becomes BP-unrelated. RDN improves peripheral and central blood pressure as well as arterial stiffness and, thus, may improve cardiovascular outcome.
Impact of surface chemistry (2010)

The applications of molecular surface chemistry in heterogeneous catalyst technology, semiconductor-based technology, medical technology, anticorrosion and lubricant technology, and nanotechnology are highlighted in this perspective. The evolution of surface chemistry at the molecular level is reviewed, and the key roles of surface instrumentation developments for in situ studies of the gas-solid, liquid-solid, and solid-solid interfaces under reaction conditions are emphasized.
Susceptibility of Campylobacter Isolates to the Bactericidal Activity of Human Serum (1985)

Although Campylobacter jejuni and related thermophilic organisms are more common human pathogens than are Campylobacter fetus, most bloodstream or systemic isolates are C. fetus. To understand the pathophysiology related to this observation, the authors studied susceptibility to the bactericidal activity of normal human serum of Campylobacter coli, C. jejuni, and C. fetus isolates from feces and blood. In standardized assays, 10 of 15 C. jejuni and related isolates showed 90% kill (mean, 90.6% +/- 5.9); under more stringent conditions, the relatively resistant strains were completely killed. In contrast, all C. fetus strains were highly serum resistant under both standard and stringent conditions. Killing of C. jejuni was ablated by heating serum to 56 C but restored by addition of complement. Both classical and alternative complement pathways may contribute to killing, and adsorption studies demonstrated antibody dependence. Serum resistance may permit systemic infection by C. fetus, whereas complement- and antibody-mediated serum sensitivity of C. jejuni may account for the relative infrequency of systemic invasion.
Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library (2014)

The essential gene data described in this investigation provides a valuable resource to study gene function and pathways involved in B. fragilis survival. Thorough examination of the B. fragilis-specific essential genes and genes that are shared between divergent organisms opens new research avenues that will lead to enhanced understanding of survival strategies used by bacteria in different microniches and under different stress situations.
Compact, broad-bandwidth fiber laser for sub-2-µm axial resolution optical coherence tomography in the 1300-nm wavelength region (2003)

A novel, compact, user friendly fiber laser with a broad emission bandwidth (MenloSystems, lambdac = 1375 nm, deltalambda = 470 nm, Pout = 4 mW) was used to achieve unprecedented sub-2-microm axial resolution optical coherence tomography (OCT) in nontransparent biological tissue in the 1300-nm wavelength region. Fresh human skin and arterial biopsies were imaged ex vivo with approximately 1.4-microm axial and approximately 3-microm lateral resolution and 95-dB sensitivity, demonstrating the great potential for clinical OCT applications of this stable, low-cost, and turn-on-key fiber laser.
Photothermal nanodrugs: potential of TNF-gold nanospheres for cancer theranostics (2013)

Nanotechnology has been extensively explored for drug delivery. Here, we introduce the concept of a nanodrug based on synergy of photothermally-activated physical and biological effects in nanoparticle-drug conjugates. To prove this concept, we utilized tumor necrosis factor-alpha coated gold nanospheres (Au-TNF) heated by laser pulses. To enhance photothermal efficiency in near-infrared window of tissue transparency we explored slightly ellipsoidal nanoparticles, its clustering, and laser-induced nonlinear dynamic phenomena leading to amplification and spectral sharpening of photothermal and photoacoustic resonances red-shifted relatively to linear plasmonic resonances. Using a murine carcinoma model, we demonstrated higher therapy efficacy of Au-TNF conjugates compared to laser and Au-TNF alone or laser with TNF-free gold nanospheres. The photothermal activation of low toxicity Au-TNF conjugates, which are in phase II trials in humans, with a laser approved for medical applications opens new avenues in the development of clinically relevant nanodrugs with synergistic antitumor theranostic action.
Foldamers with helical cavities for binding complementary guests (2009)

This tutorial review provides a summary of the binding of neutral molecules, cations and anions within helical cavities formed specifically by the folding of unnatural oligomers, called foldamers. Foldamers are emerging as a new class of synthetic receptors whose binding sites are not formed by preorganization of covalent bonds, but rather through the combination of various noncovalent interactions that induce folding and subsequent arrangement of functional groups within a helical cavity. The function of foldamers as synthetic receptors can be tuned by careful selection of modular building blocks displaying the appropriate functionality required for guest complexation. As the molecular toolbox expands to create well-defined helical structures, new and interesting functions emerge. It is the purpose of this review to provide the reader with an introduction to helical cavities formed specifically by foldamers and their subsequent function as molecular and ionic receptors. It will interest the supramolecular, organic and bioorganic communities.