gebhart/patrepeval huggingface dataset:
Rapid 3-D cone-beam reconstruction with the simultaneous algebraic reconstruction technique (SART) using 2-D texture mapping hardware (2000)

Algebraic reconstruction methods, such as the algebraic reconstruction technique (ART) and the related simultaneous ART (SART). reconstruct a two-dimensional (2-D) or three-dimensional (3-D) object from its X-ray projections. The algebraic methods have, in certain scenarios, many advantages over the more popular Filtered Backprojection approaches and have also recently been shown to perform well for 3-D cone-beam reconstruction. However, so far the slow speed of these iterative methods have prohibited their routine use in clinical applications. In this paper, we address this shortcoming and investigate the utility of widely available 2-D texture mapping graphics hardware for the purpose of accelerating the 3-D algebraic reconstruction. We find that this hardware allows 3-D cone-beam reconstructions to be obtained at almost interactive speeds, with speed-ups of over 50 with respect to implementations that only use general-purpose CPUs. However, we also find that the reconstruction quality is rather sensitive to the resolution of the framebuffer, and to address this critical issue we propose a scheme that extends the precision of a given framebuffer by 4 bits, using the color channels. With this extension, a 12-bit framebuffer delivers useful reconstructions for 0.5% tissue contrast, while an 8-bit framebuffer requires 4%. Since graphics hardware generates an entire image for each volume projection, it is most appropriately used with an algebraic reconstruction method that performs volume correction at that granularity as well, such as SART or SIRT. We chose SART for its faster convergence properties.
Role for c-myc in Activation-Induced Apoptotic Cell Death in T Cell Hybridomas (1992)

Immature T cells and some T cell hybridomas undergo apoptotic cell death when activated through the T cell receptor complex, a phenomenon that is probably related to antigen induced negative selection of developing T cells. This activation-induced apoptosis depends on active protein and RNA synthesis in the dying cells, although none of the genes required for this process have previously been identified. Antisense oligonucleotides corresponding to c-myc block the constitutive expression of c-Myc protein in T cell hybridomas and interfere with all aspects of activation-induced apoptosis without affecting lymphokine production in these cells. These data indicate that c-myc expression is a necessary component of activation-induced apoptosis.
3D Measurement of Forearm and Upper Arm during Throwing Motion using Body Mounted Sensor (2010)

The aim of this study is to propose the measurement method of three-dimensional (3D) movement of forearm and upper arm during pitching motion of baseball using inertial sensors without serious consideration of sensor installation. Although high accuracy measurement of sports motion is achieved by using optical motion capture system at present, it has some disadvantages such as the calibration of cameras and limitation of measurement place. Whereas the proposed method for 3D measurement of pitching motion using body mounted sensors provides trajectory and orientation of upper arm by the integration of acceleration and angular velocity measured on upper limb. The trajectory of forearm is derived so that the elbow joint axis of forearm corresponds to that of upper arm. Spatial relation between upper limb and sensor system is obtained by performing predetermined movements of upper limb and utilizing angular velocity and gravitational acceleration. The integration error is modified so that the estimated final position, velocity and posture of upper limb agree with the actual ones. The experimental results of the measurement of pitching motion show that trajectories of shoulder, elbow and wrist estimated by the proposed method are highly correlated to those from the motion capture system within the estimation error of about 10 [%].
Quorum sensing by peptide pheromones and two‐component signal‐transduction systems in Gram‐positive bacteria (1997)

Cell-density-dependent gene expression appears to be widely spread in bacteria. This quorum-sensing phenomenon has been well established in Gram-negative bacteria, where N-acyl homoserine lactones are the diffusible communication molecules that modulate cell-density-dependent phenotypes. Similarly, a variety of processes are known to be regulated in a cell-density- or growth-phase-dependent manner in Gram-positive bacteria. Examples of such quorum-sensing modes in Gram-positive bacteria are the development of genetic competence in Bacillus subtilis and Streptococcus pneumoniae, the virulence response in Staphylococcus aureus, and the production of antimicrobial peptides by several species of Gram-positive bacteria including lactic acid bacteria. Cell-density-dependent regulatory modes in these systems appear to follow a common theme, in which the signal molecule is a post-translationally processed peptide that is secreted by a dedicated ATP-binding-cassette exporter. This secreted peptide pheromone functions as the input signal for a specific sensor component of a two-component signal-transduction system. Moreover, genetic linkage of the common elements involved results in autoregulation of peptide-pheromone production.
Phagocytosis of bacteria by macrophages: changing the carbohydrate of lipopolysaccharide alters interaction with complement and macrophages. (1982)

Salmonella transductants and recombinants differing the O-antigenic side chain of their lipopolysaccharide are taken up at different rates by the murine macrophage-like cell line J774. Bacteria containing abequose, mannose, rhamnose, and galactose in O-antigenic side chain were taken up at the slowest rate; the one containing tyvelose instead of abequose was taken up at an intermediate rate; and the one containing mannose, N-acetylglucosamine, and glucose, instead of the above sequence, was taken up at the highest rate. These rates correlate well with the known virulence of these strains; the most virulent is the one taken up slowest, the one taken up at an intermediate rate is less virulent, and the one taken up fastest is the least virulent. The differences in ingestion rates reflect differences in affinity of the bacteria for the macrophages and not in the rate of ingestion once interaction has occurred, suggesting a receptor-mediated process. The majority of uptake is probably dependent on complement, as shown by the requirement for a serum component(s) destroyed by heating at 56 degrees C or by incubation with zymosan. Specific antibody is not required. We therefore postulate that relative virulence in vivo may reflect the relative ability of the polysaccharide of bacterial lipopolysaccharide to activate complement, thus determining the susceptibility of the bacteria to ingestion via the complement receptor of phagocytic cells.
Nonalcoholic fatty liver disease and bariatric surgery (2012)

Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease worldwide. Treatment recommendations for NAFLD are aimed towards weight reduction, thereby reducing insulin resistance. Unfortunately, lifestyle modifications have not yielded long-term success, while durable weight loss is routinely achieved with bariatric surgery. This article reviews the effects of bariatric surgery on patients with NAFLD. In these patients, postsurgical evaluations of liver histology by repeat liver biopsy are hindered by the risk of the procedure and the inherent sample variability, which makes the impact of bariatric surgery on NAFLD difficult to quantify. In longitudinal studies of NAFLD, the biopsy-based evaluations should be augmented by repeated measurements of the noninvasive biomarkers that may provide an insight into the changes in the physiological state of the liver after bariatric or other types of interventions. Nevertheless, currently available tests are not able to provide this type of in-depth outcome measures for these patients.
Domain characterization of rabbit skeletal muscle myosin light chain kinase. (1990)

Myosin light chain kinase can be divided into three distinct structural domains, an amino-terminal "tail," of unknown function, a central catalytic core and a carboxy-terminal calmodulin-binding regulatory region. We have used a combination of deletion mutagenesis and monoclonal antibody epitope mapping to define these domains more closely. A 2.95-kilobase cDNA has been isolated that includes the entire coding sequence of rabbit skeletal muscle myosin light chain kinase (607 amino acids). This cDNA, expressed in COS cells encoded a Ca2+/calmodulin-dependent myosin light chain kinase with a specific activity similar to that of the enzyme purified from rabbit skeletal muscle. Serial carboxy-terminal deletions of the regulatory and catalytic domains were constructed and expressed in COS cells. The truncated kinases had no detectable myosin light chain kinase activity. Monoclonal antibodies which inhibit the activity of the enzyme competitively with respect to myosin light chain were found to bind between residues 235-319 and 165-173, amino-terminal of the previously defined catalytic core. Thus, residues that are either involved in substrate binding or in close proximity to a light chain binding site may be located more amino-terminal than the previously defined catalytic core.
Functionally Inert HIV-Specific Cytotoxic T Lymphocytes Do Not Play a Major Role in Chronically Infected Adults and Children (2000)

The highly sensitive quantitation of virus-specific CD8(+) T cells using major histocompatibility complex-peptide tetramer assays has revealed higher levels of cytotoxic T lymphocytes (CTLs) in acute and chronic virus infections than were recognized previously. However, studies in lymphocytic choriomeningitis virus infection have shown that tetramer assays may include measurement of a substantial number of tetramer-binding cells that are functionally inert. Such phenotypically silent CTLs, which lack cytolytic function and do not produce interferon (IFN)-gamma, have been hypothesized to explain the persistence of virus in the face of a quantitatively large immune response, particularly when CD4 help is impaired. In this study, we examined the role of functionally inert CTLs in chronic HIV infection. Subjects studied included children and adults (n = 42) whose viral loads ranged from <50 to >100,000 RNA copies/ml plasma. Tetramer assays were compared with three functional assays: enzyme-linked immunospot (Elispot), intracellular cytokine staining, and precursor frequency (limiting dilution assay [LDA]) cytotoxicity assays. Strong positive associations were observed between cell numbers derived by the Elispot and the tetramer assay (r = 0.90). An even stronger association between tetramer-derived numbers and intracellular cytokine staining for IFN-gamma was present (r = 0.97). The majority (median 76%) of tetramer-binding cells were consistently detectable via intracellular IFN-gamma cytokine staining. Furthermore, modifications to the LDA, using a low input cell number into each well, enabled LDAs to reach equivalence with the other methods of CTL enumeration. These data together show that functionally inert CTLs do not play a significant role in chronic pediatric or adult HIV infection.
Understanding Black-box Predictions via Influence Functions (2017)

How can we explain the predictions of a black-box model? In this paper, we use influence functions -- a classic technique from robust statistics -- to trace a model's prediction through the learning algorithm and back to its training data, thereby identifying training points most responsible for a given prediction. To scale up influence functions to modern machine learning settings, we develop a simple, efficient implementation that requires only oracle access to gradients and Hessian-vector products. We show that even on non-convex and non-differentiable models where the theory breaks down, approximations to influence functions can still provide valuable information. On linear models and convolutional neural networks, we demonstrate that influence functions are useful for multiple purposes: understanding model behavior, debugging models, detecting dataset errors, and even creating visually-indistinguishable training-set attacks.
Comparison of Stem Cell Properties in Cell Populations Isolated From Human Central and Limbal Corneal Epithelium (2011)

Both limbal and central epithelial cells are capable of forming spheres in cultures that have stem cell properties. Central and limbal epithelial cells cannot be differentiated using FACS, but younger donor tissues give rise to greater numbers of large cells with high dye efflux. Therefore, results indicate that human central corneal epithelium contains cells with stem/progenitor properties, and these stem properties decline with age.
An overlapped block motion compensation for high quality motion picture coding (2003)

An overlapped block motion compensation scheme, which is especially suitable for hybrid coding schemes combine with overlapped transforms, is described. Motion compensation is achieved using enlarged and overlapped blocks. When motion estimation is executed, a window function operates on the prediction error signals. The power of the resulting signal is calculated and used for motion vector evaluation. When motion-compensated prediction is executed, the same window function operates on the prediction signals. The total prediction signal is generated by summing up all the block signals obtained. With this scheme, prediction signals without blocking edges are obtained. The mean square error (MSE) of the prediction error signal is reduced about 19%, and FFT analysis results show that the coefficient power in the frequency domain is concentrated in the lower frequency part. This indicates higher coding efficiency for the overlapped transforms, and for conventional block based transforms as well.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intelligent Anticipated Exploration of Web Sites (2001)

In this paper we describe a web search agent, called Global Search Agent (hereafter GSA for short). GSA integrates and enhances several search techniques in order to achieve significant improvements in the user-perceived quality of delivered information as compared to usual web search engines. GSA features intelligent merging of relevant documents from different search engines, anticipated selective exploration and evaluation of links from the current resuk set, automated derivation of refined queries based on user relevance feedback. System architecture as well as experimental accounts are also illustrated.
Smart cards inside (2005)

Today's smartcard- and security-ICs are no longer just phone cards, they are now embedded cryptographic security processors and have to face special challenges concerning architecture, design methodology and technology. The requirements for power consumption and performance are quite contradictory. On the one hand, embedded Java capability needs the high computing power of a 16 bit or even 32 bit CPU core. On the other hand, the contactless mode of operation requires lowest power ability. Smartcard ICs have specific coprocessors for efficient execution of several cryptographic algorithms and a set of peripherals to enable a flexible use of the controller for many kinds of applications. The most important challenge of security ICs is their resistance against attacks. An overview of invasive and noninvasive attacks and examples for appropriate countermeasures in system and circuit design is given.
Design of polydactyl zinc-finger proteins for unique addressing within complex genomes (1997)

Zinc-finger proteins of the Cys2-His2 type represent a class of malleable DNA-binding proteins that may be selected to bind diverse sequences. Typically, zinc-finger proteins containing three zinc-finger domains, like the murine transcription factor Zif268 and the human transcription factor Sp1, bind nine contiguous base pairs. To create a class of proteins that would be generally applicable to target unique sites within complex genomes, we have utilized structure-based modeling to design a polypeptide linker that fuses two three-finger proteins. Two six-fingered proteins were created and demonstrated to bind 18 contiguous bp of DNA in a sequence-specific fashion. Expression of these proteins as fusions to activation or repression domains allows transcription to be specifically up- or down-modulated within human cells. Polydactyl zinc-finger proteins should be broadly applicable as genome-specific transcriptional switches in gene therapy strategies and the development of novel transgenic plants and animals.
Browsing digital video (2000)

Video in digital format played on programmable devices presents opportunities for significantly enhancing the user's viewing experience. For example, time compression and pause removal can shorten the viewing time for a video, textual and visual indices can allow personalized navigation through the content, and random-access digital storage allows instantaneous seeks into the content. To understand user behavior when such capabilities are available, we built a software video browsing application that combines many such features. We present results from a user study where users browsed video in six different categories: classroom lectures, conference presentations, entertainment shows, news, sports, and travel. Our results show that the most frequently used features were time compression, pause removal, and navigation using shot boundaries. Also, the behavior was different depending on the content type, and we present a classification. Finally, the users found the browser to be very useful. Two main reasons were: i) the ability to save time and ii) the feeling of control over what content they watched.
Effect of Magnetic Fields on Surface Plasma Discharges at Mach 5 (2006)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
XRP6258‐induced gene expression patterns in head and neck cancer carcinoma (2010)

XRP6258 appeared to have a similar mechanism of action as docetaxel in the two HNSCC cell lines studied. XRP6258 induced cell cycle arrest, growth suppression, and apoptosis by altering gene expression patterns similar to that induced by docetaxel. These preclinical experiments suggest that XRP6258 may be useful in treating HNSCC, and the aforementioned genes can potentially be used as surrogate endpoint biomarkers.
Nonlinear optical collagen cross-linking and mechanical stiffening: a possible photodynamic therapeutic approach to treating corneal ectasia (2013)

In this study we test the hypothesis that nonlinear optical (NLO) multiphoton photoactivation of riboflavin using a focused femtosecond (FS) laser light can be used to induce cross-linking (CXL) and mechanically stiffen collagen as a potential clinical therapy for the treatment of keratoconus and corneal ectasia. Riboflavin-soaked, compressed collagen hydrogels are cross-linked using a FS laser tuned to 760 nm and set to either 100 mW (NLO CXL I) or 150 mW (NLO CXL II) of laser power. FS pulses are focused into the hydrogel using a 0.75 NA objective lens, and the hydrogel is three-dimensionally scanned. Measurement of hydrogel stiffness by indentation testing show that the calculated elastic modulus (E) values are significantly increased over twofold following NLO CXL I and II compared with baseline values (P<0.05). Additionally, no significant differences are detected between NLO CXL and single photon, UVA CXL (P>0.05). This data suggests that NLO CXL has a comparable effect to conventional UVA CXL in mechanically stiffening collagen and may provide a safe and effective approach to localize CXL at different regions and depths within the cornea.
Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria (2008)

An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 - 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes.
3GPP TFT Reference for Flow Binding (2010)

This memo describes a reference to third generation partner ship
project (3GPP) defined traffic flow template (TFT) as a traffic
selector in the flow based routing mechanism described in the flow
binding draft [1]. This memo, further specifies a new traffic selector
sub-option format to be used with the flow binding mobility option
defined in draft [1], in order to transport the TFT reference from the
mobile node to its home agent in a 3GPP SAE (service architecture
evolution) scenario.
A simple, combinatorial algorithm for solving SDD systems in nearly-linear time (2013)

In this paper, we present a simple combinatorial algorithm that solves symmetric diagonally dominant (SDD) linear systems in nearly-linear time. It uses little of the machinery that previously appeared to be necessary for a such an algorithm. It does not require recursive preconditioning, spectral sparsification, or even the Chebyshev Method or Conjugate Gradient. After constructing a "nice" spanning tree of a graph associated with the linear system, the entire algorithm consists of the repeated application of a simple update rule, which it implements using a lightweight data structure. The algorithm is numerically stable and can be implemented without the increased bit-precision required by previous solvers. As such, the algorithm has the fastest known running time under the standard unit-cost RAM model. We hope the simplicity of the algorithm and the insights yielded by its analysis will be useful in both theory and practice.