gebhart/patrepeval huggingface dataset:
Testbed evaluation of navigation and text display techniques in an information-rich virtual environment (2004)

The fundamental question for an information-rich virtual environment is how to access and display abstract information. We investigated two existing navigation techniques: hand-centered object manipulation extending ray-casting (HOMER) and go-go navigation, and two text layout techniques: within-the-world display (WWD) and heads-up display (HUD). Four search tasks were performed to measure participants' performance in a densely packed environment. HUD enabled significantly better performance than WWD and the go-go technique enabled better performance than the HOMER technique for most of the tasks. We found that using HOMER navigation combined with the WWD technique was significantly worse than other combinations for difficult naive search tasks. Users also preferred the combination of go-go and HUD for all tasks.
Host NKT Cells Can Prevent Graft-versus-Host Disease and Permit Graft Antitumor Activity after Bone Marrow Transplantation (2007)

Allogeneic bone marrow transplantation is a curative treatment for leukemia and lymphoma, but graft-vs-host disease (GVHD) remains a major complication. Using a GVHD protective nonmyeloablative conditioning regimen of total lymphoid irradiation and antithymocyte serum (TLI/ATS) in mice that has been recently adapted to clinical studies, we show that regulatory host NKT cells prevent the expansion and tissue inflammation induced by donor T cells, but allow retention of the killing activity of donor T cells against the BCL1 B cell lymphoma. Whereas wild-type hosts given transplants from wild-type donors were protected against progressive tumor growth and lethal GVHD, NKT cell-deficient CD1d-/- and Jalpha-18-/- host mice given wild-type transplants cleared the tumor cells but died of GVHD. In contrast, wild-type hosts given transplants from CD8-/- or perforin-/- donors had progressive tumor growth without GVHD. Injection of host-type NKT cells into Jalpha-18-/- host mice conditioned with TLI/ATS markedly reduced the early expansion and colon injury induced by donor T cells. In conclusion, after TLI/ATS host conditioning and allogeneic bone marrow transplantation, host NKT cells can separate the proinflammatory and tumor cytolytic functions of donor T cells.
PCR in Integrated Microfluidic Systems (2007)

Miniaturized integrated DNA analysis systems offer the potential to provide unprecedented advances in cost and speed relative to current benchtop-scale instrumentation by allowing rapid bioanalysis assays to be performed in a portable self contained device format that can be inexpensively mass-produced. The polymerase chain reaction (PCR) has been a natural focus of many of these miniaturization efforts, owing to its capability to efficiently replicate target regions of interest from small quantities template DNA. Scale-down of PCR has proven to be particularly challenging, however, due to an unfavorable combination of relatively severe temperature extremes (resulting in the need to repeatedly heat minute aqueous sample volumes to temperatures in the vicinity of 95°C with minimal evaporation) and high surface area to volume conditions imposed by nanoliter reactor geometries (often leading to inhibition of the reaction by nonspecific adsorption of reagents at the reactor walls). Despite these daunting challenges, considerable progress has been made in the development of microfluidic devices capable of performing increasingly sophisticated PCR-based bioassays. This chapter reviews the progress that has been made to date and assesses the outlook for future advances.
Possible ideal lac operator: Escherichia coli lac operator-like sequences from eukaryotic genomes lack the central G X C pair. (1984)

Five DNA fragments have been cloned from yeast, chicken, and mouse DNA that titrate lac repressor in an Escherichia coli lac+ I+Z+ wild-type strain when on a multi-copy plasmid. The five repressor-binding sequences have been identified by DNA sequence determinations and DNase cleavage-inhibition patterns. They share the 14-base-pair symmetrical consensus sequence 5' T-G-T-G-A-G-C:G-C-T-C-A-C-A 3' (the colon represents the center of symmetry), which is an inverted repeat of 7 base pairs of the left half of the E. coli lac operator. A similar perfect palindromic DNA fragment--an 11-base-pair inverted repeat of the left half of the lac operator--was synthesized. The cloned synthetic DNA 5' G-A-A-T-T-G-T-G-A-G-C:G-C-T-C-A-C-A-A-T-T-C 3' binds lac repressor 8-fold more tightly than does wild-type E. coli lac operator DNA.
Carbohydrate structure of human fibrinogen. Use of 300-MHz 1H-NMR to characterize glycosidase-treated glycopeptides. (1982)

The carbohydrate composition of fibrinogen and constituent S-carboxymethylated chains was determined. All the carbohydrate on the parent molecule could be accounted for on the B beta and gamma chains. The A alpha chain was found to be devoid of carbohydrate. Glycopeptides were prepared from fibrinogen, B beta, and gamma chains by pronase digestion and subsequent chromatography on Sephadex G-50. The 300-MHz 1H-NMR spectra of glycopeptides from all three sources were consistent with biantennary type oligosaccharide chains. The glycopeptides resulting from exoglycosidase digestions were examined with 300-MHz 1H-NMR spectroscopy, and the changes in the signals caused by selective removal of sugar residues were studied. This technique enabled us to assign each anomeric proton to the corresponding monosaccharide unit independent of previous work. Our results indicate that fibrinogen glycopeptides are of the biantennary type, and are in complete agreement with the previously reported peak assignments (Vliegenthart, J. F. G., van Halbeek, H., and Dorland, L. (1981) Pure Appl. Chemn. 53, 45-77). Affinity chromatography of the glycopeptides on concanavalin A-Sepharose also showed that the glycopeptides from fibrinogen are greater than 95% biantennary oligosaccharide chains. Based on carbohydrate composition, 1H-NMR spectroscopy, sequential exoglycosidase digestion, and gas chromatography-mass spectrometry of derived partially methylated alditol acetates, we propose that fibrinogen contains four oligosaccharide chains of the structure shown below. (formula, see text)
Facioscapulohumeral dystrophy: the path to consensus on pathophysiology (2014)

Although the pathophysiology of facioscapulohumeral dystrophy (FSHD) has been controversial over the last decades, progress in recent years has led to a model that incorporates these decades of findings and is gaining general acceptance in the FSHD research community. Here we review how the contributions from many labs over many years led to an understanding of a fundamentally new mechanism of human disease. FSHD is caused by inefficient repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat array on chromosome 4, resulting in the variegated expression of the DUX4 retrogene, encoding a double-homeobox transcription factor, in skeletal muscle. Normally expressed in the testis and epigenetically repressed in somatic tissues, DUX4 expression in skeletal muscle induces expression of many germline, stem cell, and other genes that might account for the pathophysiology of FSHD. Although some disagreements regarding the details of mechanisms remain in the field, the coalescing agreement on a central model of pathophysiology represents a pivot-point in FSHD research, transitioning the field from discovery-oriented studies to translational studies aimed at developing therapies based on a sound model of disease pathophysiology.
Molecular and Cellular Effects of Heat-shock and Related Treatments of Mammalian Tissue-culture Cells (1982)

Most, if not all, organisms, from prokaryotes to the most complex eukaryotes, exhibit specific homeostatic-type responses when their environmental circumstance is perturbed. Such responses range from temporary and reversible modifications of enzyme function, by which specific metabolic pathways are redirected or arrested, to more long-term changes, which may involve altered patterns of gene expression of a more permanent nature. The subject of this paper is the induction of a particular set of genes in cultured mammalian cells in response to growth at elevated temperatures or in medium containing amino acid analogs. These treatments (as well as a variety of others) give rise to what we refer to as the stress response, and for heat shock there is evidence that the response has a protective effect on cells (Gerner et al. 1976; McAllister and Finkelstein 1980; Petersen and Mitchell 1981).
(Aminoethinyl)metallierungen, 11. Umsetzung silylierter und stannylierter Inamine mit Carbodiimiden (1983)

Abstract In der Regel reagieren die (Silylethinyl)‐ und (Stannylethinyl)amine 1 mit den Diarylcarbodiimiden 2 zu den 2,4‐Diamino‐3‐silyl‐ bzw. 2,4‐Diamino‐3‐stannylchinolinen 4 und den 3‐Amino‐propiolamidinen 6 . Diese Verzweigungsreaktion ist mechanistisch über das als gemeinsame Vorstufe fungierende Zwitterion 3 erklärbar.
A 65-nm Dual-Core Multithreaded Xeon® Processor With 16-MB L3 Cache (2007)

This paper describes a dual-core 64-b Xeon MP processor implemented in a 65-nm eight-metal process. The 435-mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die has 1.328-B transistors. Each core has two threads and a unified 1-MB L2 cache. The 16-MB shared, 16-way set-associative L3 cache implements both sleep and shut-off leakage reduction modes. Long channel transistors are used to reduce subthreshold leakage in cores and uncore (all portions of the die that are outside the cores) control logic. Multiple voltage and clock domains are employed to reduce power
A honeypot-driven cyber incident monitor (2015)

In recent years, the amount and the sophistication of cyber attacks has increased significantly. This creates a plethora of challenges from a security perspective. First, for the efficient monitoring of a network, the generated alerts need to be presented and summarized in a meaningful manner. Second, additional analytics are required to identify sophisticated and correlated attacks. In particular, the detection of correlated attacks requires collaboration between different monitoring points. Cyber incident monitors are platforms utilized for supporting the tasks of network administrators and provide an initial step towards coping with the aforementioned challenges.
Programa educativo para la prevención del embarazo en la adolescencia. Barrio La Victoria, Venezuela. 2008-2009. (2012)

Fundamento: En Venezuela es evidente la incidencia cada vez mayor de embarazos en mujeres entre 11 y 14 años, lo que se atribuye a la falta de educación sexual, desconocimiento sobre la sexualidad humana y al inicio temprano de la actividad sexual, que trae como consecuencia enfermedades de transmisión sexual, abortos, hijos no deseados, abandono escolar y madres solteras. Existen mitos e ignorancia referente al embarazo, parto, anticonceptivos y enfermedades de transmisión sexual. Objetivo: Diseñar un programa educativo que contribuya a la prevención del embarazo en la adolescencia, en pacientes del consultorio La Victoria, Venezuela.2008-2009. Material y Métodos: Es una investigación de desarrollo en el consultorio médico barrio adentro La Victoria, de la ciudad de Barquisimeto, Estado Lara, Venezuela durante el año 2008-2009, mediante el empleo de técnicas cuantitativas y cualitativas. Resultados: Es objetivamente necesaria la introducción de esta propuesta que asegura estrategias que permitan desarrollar una educación instructiva educativa y desarrolladora. El programa educativo a nivel comunitario e intersectorial está diseñado considerando la necesidad de aprendizaje de los adolescentes y las condiciones reales de la comunidad. Conclusiones: El programa educativo se considera válido y aplicable por el resultado de los criterios de expertos.
Hardness, softness, and the fukui function in the electronic theory of metals and catalysis. (1985)

The concepts of hardness eta = (2E/N2)nu and fukui function f(r) = [rho (r)/N]nu, which have recently been associated with the theory of chemical reactivity in molecules, are extended to the theory of metals. It is shown that at T = 0, 1/eta = g(epsilon F) and f(r) = g(epsilon F, r)/g(epsilon F), where g(epsilon F), and g(epsilon F, r) are the density of states and the local density of states, at the Fermi energy epsilon F. Softness S and local softness s(r) are defined as 1/eta and Sf(r), respectively, and it is shown that (formula; see text) where the averages are over a grand canonical ensemble. It is pointed out that the postulate that f(r) or g(epsilon F, r) determines site selectivity for metals in chemisorption and catalysis is synonymous with the recent argument by Falicov and Somorjai [Falicov, L. M. & Somorjai, G. A. (1985) Proc. Natl. Acad. Sci. USA 82, 2207-2211] that such selectivity is determined by low-energy density fluctuations.
The Imaging of Dynamic Multiphase Fluid Flow Using Synchrotron-Based X-ray Microtomography at Reservoir Conditions (2015)

Fast synchrotron-based X-ray microtomography was used to image the injection of super-critical CO 2 under subsurface conditions into a brine-saturated carbonate sample at the pore-scale with a voxel size of 3.64 m and a temporal resolution of 45 s. Capillary pressure was measured from the images by finding the curvature of terminal menisci of both connected and disconnected CO 2 clusters. We provide an analysis of three individual dynamic drainage events at elevated temperatures and pressures on the tens of seconds timescale, showing nonlocal interface recession due to capillary pressure change, and both local and distal (non-local) snap-off. The measured capillary pressure change is not sufficient to explain snap-off in this system, as the disconnected CO 2 has a much lower capillary pressure than the connected CO 2 both before and after the event. Disconnected regions instead preserve extremely low dynamic capillary pressures generated during the event. Snap-off due to these dynamic effects is not only controlled by the pore topography and throat radius, but also by the local fluid arrangement. Whereas disconnected fluid configurations produced by local snap-off were rapidly reconnected with the connected CO 2 region, distal snap-off produced much more long-lasting fluid configurations, showing that dynamic forces can have a persistent impact on the pattern and sequence of drainage events.
Difference in susceptibility to CC chemokines among HIV 1 isolates (1998)

In this study, we examined the difference in susceptibility to anti-HIV activity of the CC-chemokines (RANTES, MIP-1 alpha and MIP-1 beta) among HIV-1 isolates and analysed its relation with phenotype (syncytium inducibility) and V3 domain of gp120 of the HIV-1 isolates. Of 11 cases tested in endogenous assay, at a concentration of 200 ng/ml, RANTES, MIP-1 alpha, and MIP-1 beta showed more than 80% suppression of HIV-1 replication in 10, 8, and 7 cases, respectively. HIV-1 isolates sensitive to more than one CC-chemokine showed non-syncytium-inducing phenotype, whereas HIV-1 isolates resistant to all of the 3 CC-chemokines showed syncytium-inducing phenotype. HIV-1 isolates resistant to all of the 3 CC-chemokines contained more positively charged amino acid residues in the V3 domain of the gp120. These results indicated that utilization of the CC-chemokine receptors as co-receptors for virus entry could vary among HIV-1 isolates.
Effect of 5-Aminosalicylic Acid and Analogous Substances on Superoxide Generation and Intracellular Free Calcium in Human Neutrophilic Granulocytes (1993)

Activated polymorphonuclear leukocytes (PMNs), which are found in the inflammatory lesions of chronic inflammatory bowel disease, produce tissue-destructive oxygen-derived free radicals. The influence of 5-aminosalicylic acid (5-ASA), its acetylated metabolite (Ac-5-ASA), sulfasalazine (SAZ), and olsalazine (OLZ) (5-ASA dimer linked by an azo group) in pharmacologically relevant concentrations (0.1-10 mM) were tested on PMN superoxide production with either the receptor-specific agent formyl-methionyl-leucyl-phenylalanine (fMLP) or the protein kinase C activator phorbol myristate acetate (PMA). Inhibition of receptor-specific superoxide production occurred at 0.07, 0.32, and 0.63 mM (IC50 values) for 5-ASA, SAZ, and OLZ, respectively. No inhibitory effects of SAZ and OLZ were observed when PMA was applied as stimulus for PMN superoxide production. The results indicate that the signal to which PMNs respond by generating superoxide is primarily due to calcium release from intracellular stores. They further suggest that SAZ and OLZ may affect the oxygen-derived free radical production in human PMNs by unspecific cytotoxicity or by interference with the nicotinamide adenine dinucleotide phosphate, reduced (NADPH) oxidase system, whereas 5-ASA itself is a free radical scavenger.
Adaptations of visual pigments to the photic environment of the deep sea (1990)

This is a summary of studies that bear on the problems of the adaptation of visual pigments to the photic environment of the deep sea. The results suggest that the spectral absorption of these retinal pigments is shifted toward the blue in order to match the dim, blue-green downwelling light and/or the bioluminescence of organisms that are critical to the life of the species. Through such a spectral match, greater visual sensitivity is achieved for life in the special photic condition of their habitat. This adaptation has been found for chimaerid fishes, for elasmobranchs, for teleosts, for mammals, and for certain crustaceans and cephalopods. The most convincing evidence for such an adaptive match has been found in teleosts that have red-emitting photophores. In these fishes a photopigment with absorbance shifted toward the red has been found by extraction and microspectrophotometry. A few exceptions to this idea of an adaptive match have appeared in the literature, the cone pigments, especially, being examples of such offset pigments. The malacosteid fishes have been shown to have a red-shifted retinal pigment with 11-cis-3-dehydroretinal as the chromophore and some invertebrates have also adopted this molecule to adjust the spectral absorption to the photic environment or to the bioluminescence. These studies are beginning to reveal that visual biochemistry is basically the same in vertebrates and invertebrates and that the visual pigment protein arose early in phylogeny and has been retained, with appropraite modifications, to the present.
Farnesoid X Receptor Activates Transcription of the Phospholipid Pump MDR3 (2003)

The human multidrug resistance gene MDR3 encodes a P-glycoprotein that belongs to the ATP-binding cassette transporter family (ABCB4). MDR3 is a critical trans-locator for phospholipids across canalicular membranes of hepatocytes, evidenced by the fact that human MDR3 deficiencies result in progressive familial intrahepatic cholestasis type III. It has been reported previously that MDR3 expression is modulated by hormones, cellular stress, and xenobiotics. Here we show that the MDR3 gene is trans-activated by the farnesoid X receptor (FXR) via a direct binding of FXR/retinoid X receptor alpha heterodimers to a highly conserved inverted repeat element (a FXR response element) at the distal promoter (-1970 to -1958). In FXR trans-activation assays, both the endogenous FXR agonist chenodeoxycholate and the synthetic agonist GW4064 activated the MDR3 promoter. Deletion or mutation of this inverted repeat element abolished FXR-mediated MDR3 promoter activation. Consistent with these data, MDR3 mRNA was significantly induced by both chenodeoxycholate and GW4064 in primary human hepatocytes in time- and dose-dependent fashions. In conclusion, we demonstrate that MDR3 expression is directly up-regulated by FXR. These results, together with the previous report that the bile salt export pump is a direct FXR target, suggest that FXR coordinately controls secretion of bile salts and phospholipids. Results of this study further support the notion that FXR is a master regulator of lipid metabolism.
The human cell-surface glycoproteins HuLy-m5, membrane co-factor protein (MCP) of the complement system, and trophoblast leucocyte-common (TLX) antigen, are CD46. (1990)

The non-lineage restricted human CD46 antigen, with two glycoproteins of 56,000 molecular weight (MW) and 66,000 MW, was defined using a panel of monoclonal antibodies (mAb) that included the E4.3 mAb to the HuLy-m5 antigen. Here the E4.3 mAb is used to show that two other human cell-surface molecules, membrane co-factor protein (MCP) of the complement system and trophoblast leucocyte-common antigen (TLX), are the same as HuLy-m5; thus, these three independently identified molecules are equivalently CD46. A mouse mAb to TLX (H316) and a specific rabbit antiserum to purified MCP (RA-MCP) blocked the binding of FITC-labelled E4.3 to the surface of human peripheral blood leucocytes (PBL). In sequential immunoprecipitation studies, E4.3 cleared all molecules detected by H316 and the RA-MCP antiserum. Immunoprecipitation from Chinese hamster ovary cells expressing transfected MCP cDNA showed that E4.3 detects both the mature 66,000 higher MW form of MCP and its 48,000 MW pro-MCP precursor, which lacks O-linked carbohydrate and bears only simple high-mannose-type N-linked carbohydrate. The IgG fraction of a polyclonal antiserum to purified MCP blocked factor I-mediated cleavage of C3b, whereas the E4.3 mAb did not. These data establish that three independently identified antigen systems are indeed the same: HuLy-m5, which shares a cross-reactive epitope with some primate retroviral gp 70 molecules and can be physically associated with class I major histocompatibility complex (MHC) chains in the cell membrane; MCP, of interest as a member of the regulators of complement activation gene family thought to protect autologous cells from complement activation; and TLX, a polymorphic molecule of interest for its potential role at the foeto-maternal tissue interface during pregnancy. Thus, the human CD46 antigen amalgamates the HuLy-m5, MCP and TLX cell-membrane glycoproteins.
Structure of Complement C5 in Complex with small molecule inhibitor and CVF (2018)

The complement pathway is an important part of the immune system, and uncontrolled activation is implicated in many diseases. The human complement component 5 protein (C5) is a validated drug target within the complement pathway, as an anti-C5 antibody (Soliris) is an approved therapy for paroxysmal nocturnal hemoglobinuria. Here, we report the identification, optimization and mechanism of action for the first small-molecule inhibitor of C5 complement protein.