gebhart/patrepeval huggingface dataset:
Using Single‐Gene Deletions to Identify Checkpoints in the Progression of Systemic Autoimmunity (2003)

Systemic lupus erythematosus is a multigenic disorder of unknown etiology. To investigate the roles that specific genes play in lupus, we have examined the disease profiles in mice with single-gene deletions. In total, some 17 genes have been studied. Absence of certain genes, such as CD40L, CD28, or Igh6, abrogated induction of autoimmunity. Other genes, such as Igh5, IL-4, or ICAM-1, had little effect on the development of disease. Intermediate effects were observed in IL-6-deficient mice, while absence of beta2-microglobulin resulted in loss of hypergammaglobulinemia and IgG1 autoantibodies, but produced little change in anti-chromatin antibodies or glomerular deposits. The most interesting observations were obtained with genes related to the expression or function of interferon-gamma (IFN-gamma). Reductions in IFN-gamma levels in murine lupus are associated with reductions in both autoantibody levels and immune-complex- mediated pathology. Genes involved in up-regulation of IFN-gamma expression, such as IL-12, STAT-4, or ICE, did not significantly influence autoimmunity, whereas absence of IFN-gamma or IFN-gamma receptor led to greatly reduced autoantibody response and immunopathology. Absence of IRF-1, a gene ex-pressed in response to IFN-gamma, resulted in selective retention of anti-chromatin antibodies but little glomerular pathology. These studies suggest that the presence of a baseline level of IFN-gamma, rather than increased expression, is important for autoimmunity. Furthermore, as the IRF-1 knockout demonstrates, specific defects in signaling pathways and gene expression subsequent to IFN-gamma/IFN-gamma receptor interaction may influence only certain disease parameters. It has not escaped our attention that IFN-gamma influences the expression and function of other immunologically relevant genes, such as IL-4, IL-6, and beta2-microglobulin. Thus, these genes may be part of the downstream events following IFN-gamma/IFN-gamma receptor interaction that promote the development of autoimmunity.
Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies (2014)

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.
The structure of a family GH25 lysozyme fromAspergillus fumigatus (2010)

Lysins are important biomolecules which cleave the bacterial cell-wall polymer peptidoglycan. They are finding increasing commercial and medical application. In order to gain an insight into the mechanism by which these enzymes operate, the X-ray structure of a CAZy family GH25 ;lysozyme' from Aspergillus fumigatus was determined. This is the first fungal structure from the family and reveals a modified alpha/beta-barrel-like fold in which an eight-stranded beta-barrel is flanked by three alpha-helices. The active site lies toward the bottom of a negatively charged pocket and its layout has much in common with other solved members of the GH25 and related GH families. A conserved active-site DXE motif may be implicated in catalysis, lending further weight to the argument that this glycoside hydrolase family operates via a ;substrate-assisted' catalytic mechanism.
Vaccines against Avian Influenza — A Race against Time (2006)

Avian influenza A (H5N1) virus poses an important pandemic threat. A study by the Congressional Budget Office estimates that the consequences of a severe pandemic could, in the United States, include 200 million people infected, 90 million clinically ill, and 2 million dead.1 The study estimates that 30 percent of all workers would become ill and 2.5 percent would die, with 30 percent of workers missing a mean of three weeks of work — resulting in a decrease in the gross domestic product of 5 percent. Furthermore, 18 million to 45 million people would require outpatient care, and economic costs . . .
Synthesis of Antihemophilic Factor Antigen by Cultured Human Endothelial Cells (1973)

Antihemophilic factor (AHF, Factor VIII) antigen has been demonstrated in cultured human endothelial cells by immunofluorescence studies using monospecific rabbit antibody to human AHF. Control studies with cultured human smooth muscle cells and human fibroblasts were negative. By radioimmunoassay it was demonstrated that cultured human endothelial cells contain AHF antigen which is released into the culture medium. Cultured smooth muscle cells and fibroblasts did not have this property. Cultured endothelial cells incorporated radioactive amino acids into high molecular weight, AHF antigen-rich protein fractions prepared from the culture media, 7% of the radioactive amino acid counts incorporated into this material were precipitated by globulin prepared from rabbit anti-AHF whereas normal rabbit globulin precipitated only 1.5% of the counts. Although cultured endothelial cells actively synthesize AHF antigen, AHF procoagulant activity was not detected in the culture medium. Studies seeking a basis for the lack of procoagulant activity have not clarified this deficiency, but they have established that exogenous AHF procoagulant activity is not inactivated by the tissue culture system.
Extracellular hsp70 levels in children with septic shock* (2005)

Extracellular hsp70 levels are significantly elevated in children with septic shock compared with controls. Given the newly described cell signaling properties of hsp70, these data suggest that extracellular hsp70 may play a role in the host response during septic shock.
A Branch and Bound Algorithm for Feature Subset Selection (1977)

A feature subset selection algorithm based on branch and bound techniques is developed to select the best subset of m features from an n-feature set. Existing procedures for feature subset selection, such as sequential selection and dynamic programming, do not guarantee optimality of the selected feature subset. Exhaustive search, on the other hand, is generally computationally unfeasible. The present algorithm is very efficient and it selects the best subset without exhaustive search. Computational aspects of the algorithm are discussed. Results of several experiments demonstrate the very substantial computational savings realized. For example, the best 12-feature set from a 24-feature set was selected with the computational effort of evaluating only 6000 subsets. Exhaustive search would require the evaluation of 2 704 156 subsets.
Multiple regulation of proenkephalin gene expression by protein kinase C. (1988)

In the present study we investigated the role of protein kinase C (Ca2+/phospholipid-dependent enzyme)-mediated processes in the regulation of proenkephalin gene expression in primary cultures of bovine adrenal chromaffin cells. Activators of protein kinase C such as 1-oleoyl-2-acetylglycerol, mezerein, and the phorbol esters phorbol 12-myristate 13-acetate (PMA) and phorbol 12,13-didecanoate induced a time-dependent increase in proenkephalin mRNA levels, whereas the inactive phorbol ester 4 alpha-phorbol 12,13-didecanoate had no effect. The increase in phorbol ester-induced proenkephalin mRNA was potentiated by low concentrations of the Ca2+ ionophore A23187, suggesting an interaction between protein kinase- and Ca2+-mediated processes in the regulation of proenkephalin mRNA. The phorbol ester-induced stimulation does not appear to be mediated by an interaction with the cAMP-generating system or increases in Ca2+ uptake. However, when proenkephalin mRNA levels were stimulated by KCl (10 mM) and the dihydropyridine BayK8644, PMA exhibited an inhibitory effect on proenkephalin mRNA, which was detectable at a 10-fold lower concentration of PMA than the stimulatory effect. This inhibitory effect appears to be mediated by an inhibition of Ca2+ entry through voltage-dependent Ca2+ channels, as suggested by 45Ca2+ uptake experiments. Thus, the net effect of PMA depends on and varies with the state of voltage-dependent Ca2+ channel activity. A third mode of action by protein kinase C to modulate proenkephalin gene expression is by interaction with the phosphatidylinositol second messenger system. Stimulation of phosphoinositide hydrolysis and proenkephalin mRNA by histaminic H1-receptor activation was inhibited by low concentrations of PMA. We suggest that protein kinase C may act as a positive and negative regulator of proenkephalin gene expression by interacting with at least three receptor-coupled second messenger systems.
Robot Task Execution with Telepresence Using Virtual Reality Technology (1998)

Robotic manipulators are widely used to replace human operators in tasks that are repetitive in nature. However, there are many tasks that are non-repetitive, unpredictable, or hazardous to the human operators. With teleoperation, or remote control, such tasks can still be performed using robotic manipulators. A suitable platform with visual and mechanical feedback is deemed necessary to simplify the operation of such system. This paper describes the design and implementation of a telepresent robot control system using virtual reality (VR) instruments. The system includes a stereo Head-Eye Module (HEM) with 3 degree-of-freedom, a highresolution stereo Head Mounted Display (HMD) for remote supervision, and a 6 degree-of-freedom articulated robotic manipulator. The motion of the operator’s head and hand are tracked using 6 degree-of-freedom magnetic trackers. Implementation of the system includes the mechanical design and fabrication of the HEM, and the overall software and hardware integration. The operation of the system was subsequently demonstrated by performing 2 specific tasks
POLICRYPS Composite Materials: Features and Applications (2011)

In recent decades, great attention has been devoted to the realization of electrically switchable holographic gratings in liquid crystalline composite materials. It has been shown, indeed, that devices based on holographic polymer dispersed liquid crystals (HPDLCs) are of low cost and can exhibit good diffraction efficiency (DE) However, application oriented utilization of these devices is limited, in general, by their strong scattering of light, due to the circumstance that the droplet size of the nematic liquid crystal (NLC) component inside the polymer matrix is comparable to the wavelength of the impinging light. In this framework, we have recently proposed a new kind of holographic grating called POLICRYPS, made of polymer slices alternated to films of regularly aligned NLC. These structures do not present those optical inhomogeneities that are due to the presence of NLC droplets in usual HPDLC samples This chapter is devoted to give an overview of the POLICRYPS as a composite material, along with a description of its main applications. After a short presentation of the structure, in terms of its fabrication process, we present the POLICRYPS as the device it was initially designed for: a switchable diffraction grating. We also demonstrate that, by suitably choosing the sample thickness and geometrical parameters, a POLICRYPS put perpendicular to the impinging light can behave as a switchable optical phase modulator, where the retardation between ordinary and extraordinary waves can undergo a fine electrical regulation. It is very interesting to show how by adding dye materials to the initial chemical mixture, necessary for obtaining POLICRYPS, can change the way we control its functionalities. In this case, such control can be obtained by using a laser beam of the right colour and power. This fact allows the realization of completely new applications like an optically controlled tunable beam splitter. www.intechopen.com Advances in Composite Materials -Analysis of Natural and Man-Made Materials 94
Licensing of myeloid cells promotes central nervous system autoimmunity and is controlled by peroxisome proliferator-activated receptor γ (2012)

During central nervous system autoimmunity, interactions between infiltrating immune cells and brain-resident cells are critical for disease progression and ultimately organ damage. Here, we demonstrate that local cross-talk between invading autoreactive T cells and auto-antigen-presenting myeloid cells within the central nervous system results in myeloid cell activation, which is crucial for disease progression during experimental autoimmune encephalomyelitis, the animal model of multiple sclerosis. This T cell-mediated licensing of central nervous system myeloid cells triggered astrocytic CCL2-release and promoted recruitment of inflammatory CCR2(+)-monocytes, which are the main effectors of disease progression. By employing a cell-specific knockout model, we identify the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) in myeloid cells as key regulator of their disease-determining interactions with autoreactive T cells and brain-resident cells, respectively. LysM-PPARγ(KO) mice exhibited disease exacerbation during the effector phase of experimental autoimmune encephalomyelitis characterized by enhanced activation of central nervous system myeloid cells accompanied by pronounced local CCL2 production and inflammatory monocyte invasion, which finally resulted in increased demyelination and neuronal damage. Pharmacological PPARγ activation decreased antigen-specific T cell-mediated licensing of central nervous system myeloid cells, reduced myeloid cell-mediated neurotoxicity and hence dampened central nervous system autoimmunity. Importantly, human monocytes derived from patients with multiple sclerosis clearly responded to PPARγ-mediated control of proinflammatory activation and production of neurotoxic mediators. Furthermore, PPARγ in human monocytes restricted their capacity to activate human astrocytes leading to dampened astrocytic CCL2 production. Together, interference with the disease-promoting cross-talk between central nervous system myeloid cells, autoreactive T cells and brain-resident cells represents a novel therapeutic approach that limits disease progression and lesion development during ongoing central nervous system autoimmunity.
New analytical scattering-factor functions for free atoms and ions (1995)

New analytical X-ray scattering-factor representations valid for the full range of sin Θ/λ from 0.0 to 6.0 Å−1 have been developed from fits of a linear combination of five Gaussians to the values of the scattering factors tabulated in International Tables for Crystallography (1992) [Vol. C. Dordrecht: Kluwer Academic Publishers]. The resulting functions for both neutral atoms and ions are compared with the existing parametrizations, which are applicable for 0.0–2.0 Å−1 and 2.0–6.0 Å−1, respectively. The quality of the new parametrization involving 11 parameters per atom (ion) compares well with the previous work or is even superior. Examples are discussed, some errors in International Tables for Crystallography, Vol. C are indicated and a warning is given that most of the previously published four Gaussian expansions for ions are inadequate for calculations involving sin Θ/λ ≥ 2.0 Å−1.
우선순위규칙을 이용한 두 대의 기계의 플로우샵 일정계획에 관한 연구 (1998)

This study focuses on the use of priority rule for scheduling in the two-machine flowshop. We examines the performances of seven priority rules for the two performance criterion: total weighted tardiness and work-in-process inventory. The study has a res
Adaptive two-level thread management for fast MPI execution on shared memory machines (1999)

Article Free Access Share on Adaptive two-level thread management for fast MPI execution on shared memory machines Authors: Kai Shen Department of Computer Science, University of California, Santa Barbara, CA Department of Computer Science, University of California, Santa Barbara, CAView Profile , Hong Tang Department of Computer Science, University of California, Santa Barbara, CA Department of Computer Science, University of California, Santa Barbara, CAView Profile , Tao Yang Department of Computer Science, University of California, Santa Barbara, CA Department of Computer Science, University of California, Santa Barbara, CAView Profile Authors Info & Claims SC '99: Proceedings of the 1999 ACM/IEEE conference on SupercomputingJanuary 1999 Pages 49–eshttps://doi.org/10.1145/331532.331581Published:01 January 1999Publication History 14citation471DownloadsMetricsTotal Citations14Total Downloads471Last 12 Months9Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Automatic atrial antitachycardia pacing (ATP) for the termination of atrial flutter: Clinical experience with a novel DDDRP-pacemaker device (2001)

Objective: To evaluate, whether frequency and duration of atrial tachyarrhythmia (AT) episodes (eps.) in patients (pts.) with a novel DDDRP pacemaker are influenced by the activation of preventive atrial pacing algorithms (alg.) and automatic atrial anti-tachycardia pacing (ATP). Methods: In 23 pts. with conventional pacing indication and documented history of AT, a novel DDDRP device (AT500, model 7253, Medtronic) was implanted. DDDR pacing (60-1201min.) and AT detection (atrial cycle length <360ms) was activated in all pts. One month after implant (1M), stored data including amount and duration of AT eps. were retrieved and alg. (atrial pacing preference, atrial rate stabilisation, post mode switch overdrive pacing) and ATP therapies (Ramp, Burst+) activated. ATP was delivered for AT eps. lasting >lmin and classified as atrial flutter (cycle length 220-360ms, variability <25%). Two months (1-3M) after activation of alg. and ATP, stored data were retrieved a~lain. Results: AT frequency (0-ATepisodes 1M 1-3M 25.9 eps./day) decreased in 4 per day and patient 2.81.4 2.5_+1.1+ ano increased in 7 pts. Anti-Total 1532 2780 arrhythmic medication (17/23 <24h 1526 2767 pts.) remained unchanged, duration [min.] 33.6+15+2 11.5_+5.5 # Cardioversion for persistent >1min.<24h 662 1497 AT was necessary in 4 pts. (+ATP-delivery 661) before and in 2 pts. after duration [rain.] 43.619.3 16.2_+7.2" activation of therapies at 1M. *p>0.1, #p=0.1, *p=O.09 Conclusions: Mean AT eps. frequency (per day and patient) and mean AT eps. duration decreased after activation of preventive pacing alg. and automatic atrial ATP, but not significantly.
An effective camera calibration method (2002)

Proposes a method for camera calibration that could be used in stereo systems subject to slight change in any camera parameter, as well as in stereo head navigation. A pinhole camera model plus linear and radial distortion is considered. An extended Kalman filter (EKF) is used to recover pinhole parameters and a Newton Raphson (NR) algorithm is used to obtain distortion terms. With the pinhole model the position and orientation of the camera is immediately recovered because the extrinsic and intrinsic parameters have been explicitly calculated, this is necessary for the modeling of the camera in a 3D environment. The only strong requirement for the proper convergence of the calibration algorithm is a good initial approximation to the solution. The method allows us to recalibrate the system easily if a small change has taken place. In that case, the initial approximation required for the EKF is supplied by the old parameters of the camera, after which the convergence is very quickly achieved. The on-going work is related to the application of this algorithm to the calibration of the cameras for stereo head navigation, allowing a 3D description of the environment surrounding the camera movements. The algorithm has been tested in the 3D reconstruction of real objects through a path described by a stereo camera system. Numerical results have been compared with a classical least square error algorithm. Reported errors by EKF are similar of those by LSE.
Metal-Catalyzed C–C Bond Cleavage in Alkanes: Effects of Methyl Substitution on Transition-State Structures and Stability (2014)

Methyl substituents at C-C bonds influence hydrogenolysis rates and selectivities of acyclic and cyclic C2-C8 alkanes on Ir, Rh, Ru, and Pt catalysts. C-C cleavage transition states form via equilibrated dehydrogenation steps that replace several C-H bonds with C-metal bonds, desorb H atoms (H*) from saturated surfaces, and form λ H2(g) molecules. Activation enthalpies (ΔH(‡)) and entropies (ΔS(‡)) and λ values for (3)C-(x)C cleavage are larger than for (2)C-(2)C or (2)C-(1)C bonds, irrespective of the composition of metal clusters or the cyclic/acyclic structure of the reactants. (3)C-(x)C bonds cleave through α,β,γ- or α,β,γ,δ-bound transition states, as indicated by the agreement between measured activation entropies and those estimated for such structures using statistical mechanics. In contrast, less substituted C-C bonds involve α,β-bound species with each C atom bound to several surface atoms. These α,β configurations weaken C-C bonds through back-donation to antibonding orbitals, but such configurations cannot form with (3)C atoms, which have one C-H bond and thus can form only one C-M bond. (3)C-(x)C cleavage involves attachment of other C atoms, which requires endothermic C-H activation and H* desorption steps that lead to larger ΔH(‡) values but also larger ΔS(‡) values (by forming more H2(g)) than for (2)C-(2)C and (2)C-(1)C bonds, irrespective of alkane size (C2-C8) or cyclic/acyclic structure. These data and their mechanistic interpretation indicate that low temperatures and high H2 pressures favor cleavage of less substituted C-C bonds and form more highly branched products from cyclic and acyclic alkanes. Such interpretations and catalytic consequences of substitution seem also relevant to C-X cleavage (X = S, N, O) in desulfurization, denitrogenation, and deoxygenation reactions.