gebhart/patrepeval huggingface dataset:
Functional Olefin Copolymers:  Uniform Architectures of Propene/7-Methyl-1,6-octadiene Copolymers by ATR-FTIR Spectroscopy Control of Monomer Composition (2000)

Propene and 7-methyl-1,6-octadiene (MOD) were copolymerized with the catalyst system rac-Et[Ind]2ZrCl2/MAO in semibatch reactions and under constant comonomer concentrations using an autoclave setup that is equipped with an ATR-FTIR sensor coupled with a dosage system for the liquid MOD comonomer. The concentration of the monomer propene is regulated precisely in both types of polymerization by a gas flow controller. This setup enables to monitor the MOD concentration on-line and in real-time during the reaction by following characteristic bands arising from the double bonds. Copolymers with poorly defined incorporation data and thermal properties were obtained without control of the MOD concentration in time. This is caused by a nonuniform distribution of the MOD units over the polymer chains due to a relatively large shift of the MOD concentration during the copolymerization reaction. By means of solvent extraction fractionation experiments, these copolymers could be fractionated into three fractions with different amounts of incorporated MOD, varying from 11.5 to 7.2 mol %. Functional copolymers with uniform architectures (up to 30.5 mol % incorporated MOD) were prepared by using the on-line ATR-FTIR data to control the MOD concentration during the copolymerization reactions.
Antioxidants Prevent the Lymphocyte DNA Damage Induced by PMA-Stimulated Monocytes (2001)

Oxidative stress has been related to several degenerative diseases such as cancer and coronary heart disease. Reactive oxygen species can damage different cellular macromolecules, including DNA, which is directly responsible for mutation and carcinogenesis. In this study, monocytes that were activated by phorbol 12-myristate 13-acetate (PMA) were coincubated with lymphocytes, and the DNA damage was measured by single-cell gel electrophoresis (comet) assay. Stimulation of monocytes with PMA activates the "respiratory burst," which evokes DNA damage in lymphocytes. The extent of the damage is related to the concentration of monocytes and the exposure time. Exogenous addition of superoxide dismutase did not prevent the DNA damage, which suggests that superoxide ions are not directly responsible for the damage. Partial protection was observed when catalase was included (60% protection), which indicates that other reactive species, in addition to H2O2, are responsible for the damage. In this system, the protective activity of natural antioxidants at different concentrations was also investigated. After coincubation of PMA-activated monocytes with lymphocytes in the presence of each antioxidant for one hour at 37 degrees C, the lymphocyte DNA damage was determined. All the compounds protected the lymphocytes to a certain degree, with a maximum effect at different concentrations: 41% protection with 1 microM ascorbic acid, 55% protection with 40 microM alpha-tocopherol, 50% protection with 3 microM beta-carotene, and 56% protection with 5 microM quercetin. On the basis of these results, we maintain that this "ex vivo model," more closely related to physiological conditions, could be used to test the antioxidant activity of different compounds.
Glenohumeral Relationships during Physiologic Shoulder Motion and Stress Testing: Initial Experience with Open MR Imaging and Active Imaging-Plane Registration (1999)

Dynamic MR imaging of the glenohumeral joint is possible over a wide range of physiologic motion in vertically open systems. Use of an MR tracking coil enabled accurate tracking of the anatomy of interest. These preliminary measurements of normal glenohumeral motion patterns begin to establish normal ranges of motion and constitute a necessary first step in characterizing pathologic motion in patients with common clinical problems such as instability and impingement.
Putting the fish in the fish tank: Immersive VR for animal behavior experiments (2012)

We describe a virtual-reality framework for investigating startle-response behavior in fish. Using real-time three-dimensional tracking, we generate looming stimuli at a specific location on a computer screen, such that the shape and size of the looming stimuli change according to the fish's perspective and location in the tank. We demonstrate the effectiveness of the setup through experiments on Giant danio and compute the success rate in eliciting a response. We also estimate visual startle sensitivity by presenting the stimulus from different directions around the fish head. The aim of this work is to provide the basis for quantifying escape behavior in fish schools.
A scalable platform for biomechanical studies of tissue cutting forces (2009)

This paper presents a novel and scalable experimental platform for biomechanical analysis of tissue cutting that exploits a triaxial force-sensitive scalpel and a high resolution vision system. Real-time measurements of cutting forces can be used simultaneously with accurate visual information in order to extract important biomechanical clues in real time that would aid the surgeon during minimally invasive intervention in preserving healthy tissues. Furthermore, the in vivo data gathered can be used for modeling the viscoelastic behavior of soft tissues, which is an important issue in surgical simulator development. Thanks to a modular approach, this platform can be scaled down, thus enabling in vivo real-time robotic applications. Several cutting experiments were conducted with soft porcine tissues (lung, liver and kidney) chosen as ideal candidates for biopsy procedures. The cutting force curves show repeated self-similar units of localized loading followed by unloading. With regards to tissue properties, the depth of cut plays a significant role in the magnitude of the cutting force acting on the blade. Image processing techniques and dedicated algorithms were used to outline the surface of the tissues and estimate the time variation of the depth of cut. The depth of cut was finally used to obtain the normalized cutting force, thus allowing comparative biomechanical analysis.
3D Graph Neural Networks for RGBD Semantic Segmentation (2017)

RGBD semantic segmentation requires joint reasoning about 2D appearance and 3D geometric information. In this paper we propose a 3D graph neural network (3DGNN) that builds a k-nearest neighbor graph on top of 3D point cloud. Each node in the graph corresponds to a set of points and is associated with a hidden representation vector initialized with an appearance feature extracted by a unary CNN from 2D images. Relying on recurrent functions, every node dynamically updates its hidden representation based on the current status and incoming messages from its neighbors. This propagation model is unrolled for a certain number of time steps and the final per-node representation is used for predicting the semantic class of each pixel. We use back-propagation through time to train the model. Extensive experiments on NYUD2 and SUN-RGBD datasets demonstrate the effectiveness of our approach.
Surface photograft polymerization on segmented polyurethane using the iniferter technique (1999)

A segmented polyurethane (SPU) film was chloromethylated and subsequently dithiocarbamated. The treated films were immersed in solutions containing poly(ethylene glycol) methacrylate (PEGMA) or N, N-dimethyl-acryl amide (DMAAm) and irradiated with ultraviolet (UV) light. The resultant surfaces were highly wettable with water. The surface chemical compositions, as determined by X-ray photoelectron spectroscopy, indicated that surface graft polymerization, initiated from surface-derivatized dithiocarbamate, had occurred and had altered the surface properties and the composition of SPU. The platelet adhesion test using platelet-rich plasma showed minimal adhesion for the poly(PEGMA)-grafted surface, followed by the poly(DMAAm)-grafted surface.
Genetic analysis of membrane protein topology by a sandwich gene fusion approach. (1990)

We describe a cloning vector that allows the construction of phoA sandwich fusions in which mature alkaline phosphatase is inserted into target proteins. In contrast to previous fusions obtained using the TnphoA transposon, the entire amino acid sequence of the target protein is present in the fusion product. We have constructed a series of sandwich fusions of alkaline phosphatase to the multispanning cytoplasmic membrane protein MalF. Despite the fact that the alkaline phosphatase was tethered to MalF at both its N and its C terminus, the enzyme exhibited high activity when it was fused to a periplasmic domain of the membrane protein. Cells harboring an alkaline phosphatase sandwich fusion to the end of the first membrane-spanning segment of MalF exhibited both MalF and alkaline phosphatase activity. When alkaline phosphatase was inserted into a cytoplasmic domain of MalF, its specific activity was very low. Our results suggest that the alkaline phosphatase activity of phoA sandwich fusions provides a more sensitive monitor than previous methods of the cellular localization of the domain of the target protein to which the enzyme is fused. Thus, the sandwich fusion approach can give a more accurate picture of membrane protein topology.
Investigating an incidental finding of lymphopenia (2014)

#### Learning points

A 55 year old man had a full blood count undertaken when he presented with fatigue. There was no significant medical history of note. He was a non-smoker who took no medications. He was noted to have a lymphopenia of 0.8×109/L (reference interval 1.5-4.0×109/L). Otherwise his results were normal, with haemoglobin of 135 g/L (130-180 g/L), white cell count 4.2×109/L (4-12×109/L), and platelet count 150×109/L (140-400×109/L). He did not return for follow-up but presented to a local hospital emergency department six months later with a short history of increasing breathlessness. He was diagnosed with a severe bacterial pneumonia, from which he recovered after prolonged therapy with intravenous antibiotics. His lymphocyte count during admission ranged between 0.5 and 1.0×109/L.

### Lymphopenia and its causes

T lymphocytes make up most (60-80%) of the total peripheral …
On the issue of camera calibration with narrow angular field of view (2009)

This paper considers the issue of calibrating a camera with narrow angular field of view using standard, perspective methods in computer vision. In doing so, the significance of perspective distortion both for camera calibration and for pose estimation is revealed. Since narrow angular field of view cameras make it difficult to obtain rich images in terms of perspectivity, the accuracy of the calibration results is expectedly low. From this, we propose an alternative method that compensates for this loss by utilizing the pose readings of a robotic manipulator. It facilitates accurate pose estimation by nonlinear optimization, minimizing reprojection errors and errors in the manipulator transformations at the same time. Accurate pose estimation in turn enables accurate parametrization of a perspective camera.
Autoantibodies in Nonobese Diabetic Mice Immunoprecipitate 64,000-Mr Islet Antigen (1988)

In insulin-dependent diabetes mellitus (IDDM) in humans and BB rats, islet cell autoimmunities associated with autoantibodies to a beta-cell protein of 64,000 Mr (64K) have been described. We report that sera from newly diagnosed nonobese diabetic (NOD) mice similarly contain an autoantibody that immunoprecipitates 64K autoantigen from detergent lysates of [35S]methionine-labeled murine islet cells. The autoantibody was detectable by weaning; it disappeared within weeks after diabetes onset and was absent in older nondiabetic NOD mice as well as all of three non-diabetes-prone control strains tested. The 64K beta-cell autoantigen may be a critical target in the immunopathogenesis of IDDM.
Homothallic mating type switching generates lethal chromosome breaks in rad52 strains of Saccharomyces cerevisiae. (1981)

In homothallic cells of Saccharomyces cerevisiae, a or alpha mating type information at the mating type locus (MAT) is replaced by the transposition of the opposite mating type allele from HML alpha or HMRa. The rad52-1 mutation, which reduces mitotic and abolishes meiotic recombination, also affects homothallic switching (Malone and Esposito, Proc. Natl. Acad. Sci. U.S.A. 77:503-507, 1980). We have found that both HO rad52 MATa and HO rad52 MAT alpha cells die. This lethality is suppressed by mutations that substantially reduce but do not eliminate homothallic conversions. These mutations map at or near the MAT locus (MAT alpha inc, MATa-inc, MATa stk1) or are unlinked to MAT (HO-1 and swi1). These results suggest that the switching event itself is involved in the lethality. With the exception of swi1, HO rad52 strains carrying one of the above mutations cannot convert mating type at all. MAT alpha rad52 HO swi1 strains apparently can switch MAT alpha to MATa. However, when we analyzed these a maters, we found that few, if any, of them were bona fide MATa cells. These a-like cells were instead either deleted for part of chromosome III distal to and including MAT or had lost the entire third chromosome. Approximately 30% of the time, an a-like cell could be repaired to a normal MATa genotype if the cell was mated to a RAD52 MAT alpha-inc strain. The effects of rad52 were also studied in mata/MAT alpha-inc rad52/rad52 ho/HO diploids. When this diploid attempted to switch mata to MATa, an unstable broken chromosome was generated in nearly every cell. These studies suggest that homothallic switching involves the formation of a double-stranded deoxyribonucleic acid break or a structure which is labile in rad52 cells and results in a broken chromosome. We propose that the production of a double-stranded deoxyribonucleic acid break is the lethal event in rad52 HO cells.
High Performance Code Generation for Stencil Computation on Heterogeneous Multi-device Architectures (2013)

Heterogeneous archioectures have been widely used in the domain of high performance computing. On one hand, it allows a designer to use multiple types of computing units and each able to execute the tasks that it is best suited for to increase performance, on the other hand, it brings many challenges in programming for novice users, especially for heterogeneous systems with multi-devices. In this paper, we propose the code generator STEPOCL that generates OpenCL host program for heterogeneous multi-device architecture. In order to simplify the analyzing process, we ask user to provide the description of input and kernel parameters in an XML file, then our generator analyzes the description and generates automatically the host program. Due to the data partition and data exchange strategies, the generated host program can be executed on multi-devices without changing any kernel code. The experiment of iterative stencil loop code (ISL) shows that our tool is efficient. It guarantees the minimum data exchanges and achieves high performance on heterogeneous multi-device architecture.
Continuous Autonomic Assessment in Patients With Symptomatic Heart Failure (2004)

This study demonstrates that SDAAM continuously measured from an implanted cardiac resynchronization device is lower in patients at high mortality and hospitalization risk. SDAAM declines as patient status decompensates. Continuous long-term SDAAM may be a useful tool in the clinical management of patients with chronic heart failure.
Argos: Practical Base Stations for Large-scale Beamforming (2012)

MU-MIMO theory predicts manyfold capacity gains by leveraging many antennas (e.g. M &gt;&gt; 10) on wireless base stations to serve many users simultaneously through multi-user beamforming (MUBF). However, realizing such a large-scale design is nontrivial, and has yet to be achieved in the real world. We present the design, realization, and evaluation of Argos, the first reported large-scale base station that is capable of serving many (e.g., 10s of) terminals simultaneously through MUBF. Designed with extreme flexibility and scalability in mind, Argos exploits hierarchical and modular design principles, properly partitions baseband processing, and holistically considers real-time requirements of MUBF. To achieve unprecedented scalability, we devise a novel, completely distributed, beamforming technique, as well as an internal calibration procedure to enable implicit beamforming across large arrays. We implement a prototype with 64 antennas, and demonstrate that it can achieve up to 6.7 fold capacity gains while using a mere 1/64th the transmission power.
Redox control of catalysis in ATP‐citrate lyase from rat liver (1992)

In thiol redox buffers at pH 8.0, rat liver ATP-citrate lyase is in equilibrium between an oxidised inactive form and a reduced active form. The reduced enzyme is inactivated by oxidised glutathione (GSSG) at a rate of 45 min-1.M-1 and the oxidised enzyme is activated by reduced glutathione (GSH) at a rate of 3.2 min-1.M-1. At redox equilibrium, the enzyme activity depends on the ratio [GSH]2/[GSSG]. The inactivation involves formation of a protein-protein disulphide rather than a protein-glutathione complex. This reaction has Keq = 78 +/- 7 mM for the oxidative reaction. Activity can therefore be controlled by the redox state of the cell, being more active in the fed state than in the oxidatively stressed state. This redox process is also important in the in vitro enzyme assay, where ATP-citrate lyase is in redox equilibrium with oxygen and either dithiothreitol or 2-mercaptoethanol. Reduction is a two-step process, requiring high concentrations of reductant for full activation (30 mM dithiothreitol or 200 mM 2-mercaptoethanol). The enzyme inhibitor, Medica-16 raises the redox equilibrium constant to greater than 400 mM. It binds more tightly to the oxidised form of the enzyme, with Ki less than 40 microM compared to 180 microM for the reduced form.
Differential interaction of the tSXV motifs of the NR1 and NR2A NMDA receptor subunits with PSD‐95 and SAP97 (1999)

The NR1 and NR2 subunits of the N-methyl-D-aspartate (NMDA) receptor are encoded by distinct genes. In the rat brain, four C-terminal variants of the NR1 subunit (NR1-1 to NR1-4) are encoded by a single gene, and are generated by alternative splicing of the C1 and C2 exon cassettes, while four different genes encode the NR2 subunits (NR2 A-D). Functional NMDA receptors result from the heteromultimeric assembly of NR1 variants with distinct NR2 subunits. The NR2B subunit interacts with post-synaptic density protein 95 (PSD-95), SAP97 and members of the membrane-associated guanylate-like kinase (MAGUK) family of proteins. This interaction occurs through the binding of the C-terminal tSXV intracellular motif of the NR2B subunit to the N-terminal PDZ (PSD-95, discs-large, ZO-1) domains of the PSD-95 and SAP97 proteins. Both NR1-3 and NR1-4 also display a consensus C-terminal tSXV motif. Using the two-hybrid genetic system in yeast and site-directed mutagenesis, we compared the binding of the NR2A, NR1-3 and NR1-4 tSXV motifs with the PDZ domains of PSD-95 and SAP97. The main conclusions of the present report are that: (i) while NR2A displays a strong interaction with PSD-95 and SAP97, the NR1-3 and NR1-4 NMDA receptor subunits do not display any interaction despite the presence of tSXV motifs; (ii) the C-terminal tSXV motif of the NR2A subunit is mandatory but not sufficient for efficient interaction with the PSD-95 and SAP97 proteins; (iii) as yet unidentified upstream sequences of the receptor subunits determine whether the tSXV motifs will bind to the PSD-95 and SAP97 PDZ domains; (iv) different tSXV motifs elicit interactions of variable strengths; and (v) residues in positions -3 and -4 modulate the binding affinity of the C-terminal tSXV motifs. Using immunohistochemistry, we also compared the distribution of the PSD-95, NR2A and SAP97 proteins in adult rat brain, and we show that in the cortex, hippocampus and cerebellum, there is evidence for colocalization of these proteins.
Chronic pain. Clinical management of common causes of geriatric pain. (2002)

Effective management of chronic pain in older persons is attainable, although unnecessarily elusive. A host of factors can impede assessment and drug management, including impaired cognitive function, multiple potential causes of pain, pharmacokinetics and pharmacodynamics unique to the geriatric population, and clinician anxiety regarding analgesic addiction. In the geriatric population, some of the most prevalent chronic pain management cases involve osteoarthritis, low back pain, and neuropathy. Effective pain management is achieved with analgesics (acetaminophen and nonsteroidal anti-inflammatory drugs), opioids, non-opioid agents (e.g., tricyclic antidepressants, anticonvulsants) and invasive techniques (corticosteroid epidural injections/nerve blocks).
Donor leukocyte transfusions for treatment of recurrent chronic myelogenous leukemia in marrow transplant patients (1990)

Three patients with hematologic relapse after bone marrow transplantation for chronic myelogenous leukemia were treated with interferon alpha and transfusion of viable donor buffy coat. All had complete hematologic and cytogenetic remission, which persisted 32 to 91 weeks after treatment. In two patients graft-versus-host disease developed and was treated by immunosuppression. These results are an example of adoptive immunotherapy without cytoreductive chemotherapy or radiotherapy in human chimeras.
Antigenic Variation of Anaplasma Marginale : Major Surface Protein 2 Diversity during Cyclic Transmission between Ticks and Cattle (2001)

The rickettsial pathogen Anaplasma marginale expresses a variable immunodominant outer membrane protein, major surface protein 2 (MSP2), involved in antigenic variation and long-term persistence of the organism in carrier animals. MSP2 contains a central hypervariable region of about 100 amino acids that encodes immunogenic B-cell epitopes that induce variant-specific antibodies during infection. Previously, we have shown that MSP2 is encoded on a polycistronic mRNA transcript in erythrocyte stages of A. marginale and defined the structure of the genomic expression site for this transcript. In this study, we show that the same expression site is utilized in stages of A. marginale infecting tick salivary glands. We also analyzed the variability of this genomic expression site in Oklahoma strain A. marginale transmitted from in vitro cultures to cattle and between cattle and ticks. The structure of the expression site and flanking regions was conserved except for sequence that encoded the MSP2 hypervariable region. At least three different MSP2 variants were encoded in each A. marginale population. The major sequence variants did not change on passage of A. marginale between culture, acute erythrocyte stage infections, and tick salivary glands but did change during persistent infections of cattle. The variant types found in tick salivary glands most closely resembled those present in bovine blood at the time of acquisition of infection, whether infection was acquired from an acute or from a persistent rickettsemia. These variations in structure of an expression site for a major, immunoprotective outer membrane protein have important implications for vaccine development and for obtaining an improved understanding of the mechanisms of persistence of ehrlichial infections in humans, domestic animals, and reservoir hosts.