gebhart/patrepeval huggingface dataset:
The impact of decreased Rubisco on photosynthesis, growth, allocation and storage in tobacco plants which have been transformed with antisense rbcS (1991)

Summary Transgenic tobacco plants tranformed with antisense to rbcS to decrease expression of ribulose‐1,5–bisphosphate carboxylase‐oxygenase (Rubisco) have been used to investigate (a) whether Rubisco is limiting for photosynthesis and plant growth and (b) whether biomass allocation and storage of carbohydrate and nitrogen are regulated in response to decreased rate of photosynthesis. The rate of photosynthesis (measured in growth conditions) and plant growth were not strongly inhibited until almost half of the Rubisco was removed. When Rubisco was decreased further there was a large decrease of photosynthesis and plant growth. When photosynthesis decreased in the ‘antisense’ plants there was an increase in the shoot/root ratio and the specific leaf area. As a result, the leaf area ratio (leaf area per g plant dry weight) increased 3–4–fold. This shows that tobacco compensates for decreased photosynthesis by maximizing leaf area. The decrease of photosynthesis also resulted in lower starch and free hexose in the leaf, but the volume of the diurnal starch turnover was largely maintained. This indicates that partitioning to starch is regulated to decrease non‐productive accumulation of starch, but still maintain a pool of transient starch for export during the night. The decrease of photosynthesis was also accompanied by a large increase of the nitrogen/ carbon balance, due to a large accumulation of nitrate in the leaf. This shows that assimilation of nitrate is inhibited in response to low availability of photo‐synthate.
Non‐angiogenic tumours unveil a new chapter in cancer biology (2014)

The term 'angiogenesis' was coined in 1787 and the role of vessels in cancer has been studied ever since. In 1971 Folkman introduced the hypothesis, until now widely accepted, that tumour growth is strictly dependent on angiogenesis. However, the discovery that tumours can also grow without angiogenesis by exploiting pre-existing vessels, both in humans and more recently in mice, has demonstrated that this is not always the case. These observations highlight a new aspect of the interaction between vessels and tumours and demonstrate the existence of a previously unrecognized group of tumours that grow without angiogenesis and whose biology is, so far, largely unknown.
Behaviour of metals in nitric acid (1944)

U. R. Evans, Trans. Faraday Soc., 1944, 40, 120 DOI: 10.1039/TF9444000120
Polyethylene Glycol Matrix Reduces the Rates of Photochemical and Thermal Release of Nitric Oxide from S-nitroso-N-acetylcysteine (2000)

S-nitrosothiols have many biological activities and may act as nitric oxide (NO) carriers and donors, prolonging NO half-life in vivo. In spite of their great potential as therapeutic agents, most S-nitrosothiols are too unstable to isolate. We have shown that the S-nitroso adduct of N-acetylcysteine (SNAC) can be synthesized directly in aqueous and polyethylene glycol (PEG) 400 matrix by using a reactive gaseous (NO/O2) mixture. Spectral monitoring of the S-N bond cleavage showed that SNAC, synthesized by this method, is relatively stable in nonbuffered aqueous solution at 25 degrees C in the dark and that its stability is greatly increased in PEG matrix, resulting in a 28-fold decrease in its initial rate of thermal decomposition. Irradiation with UV light (lambda = 333 nm) accelerated the rate of decomposition of SNAC to NO in both matrices, indicating that SNAC may find use for the photogeneration of NO. The quantum yield for SNAC decomposition decreased from 0.65 +/- 0.15 in aqueous solution to 0.047 +/- 0.005 in PEG 400 matrix. This increased stability in PEG matrix was assigned to a cage effect promoted by the PEG microenvironment that increases the rate of geminated radical pair recombination in the homolytic S-N bond cleavage process. This effect allowed for the storage of SNAC in PEG at -20 degrees C in the dark for more than 10 weeks with negligible decomposition. Such stabilization may represent a viable option for the synthesis, storage and handling of S-nitrosothiol solutions for biomedical applications.
Treatment with bovine hyperimmune colostrum of cryptosporidial diarrhea in AIDS patients (1990)

Cryptosporidium parvum may cause severe, debilitating diarrhea in patients with AIDS. Recent anecdotal reports have suggested that hyperimmune bovine colostrum may be effective. We conducted a double-blind, controlled pilot study of hyperimmune bovine colostrum for diarrhea due to cryptosporidiosis in five AIDS patients. The patients were randomized to receive either hyperimmune or control colostrum by continuous nasogastric infusion for 10 days. All stools were collected, graded, and weighed, and the concentration of oocysts excreted was determined daily. One of the three patients treated with hyperimmune colostrum had a reduction in diarrhea and in the concentration of oocysts excreted. A second treated patient had a modest decrease in the concentration of oocysts excreted. Two patients who received control colostrum also had decreases in the volume of diarrhea but no change in the concentration of oocysts excreted. We conclude that hyperimmune colostrum with high titers of specific anti-Cryptosporidium antibody could be effective in treating patients with cryptosporidiosis. However, more studies of cow colostral immunoglobulin need to be performed so that the efficacy of this treatment can be assessed more thoroughly.
Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B (2015)

The bromodomain containing proteins BAZ2A/B play essential roles in chromatin remodeling and regulation of noncoding RNAs. We present the structure based discovery of a potent, selective, and cell active inhibitor 13 (BAZ2-ICR) of the BAZ2A/B bromodomains through rapid optimization of a weakly potent starting point. A key feature of the presented inhibitors is an intramolecular aromatic stacking interaction that efficiently occupies the shallow bromodomain pockets. 13 represents an excellent chemical probe for functional studies of the BAZ2 bromodomains in vitro and in vivo.
Glycosaminoglycans Mediate Cell Surface Oligomerization of Chemokines (1997)

Chemokines are 8-10 kDa proteins involved in the control of leukocyte trafficking and activation. In free solution, chemokines are monomers at physiologic concentrations, although many multimerize at higher concentrations. Cell surface heparan sulfate may sequester chemokines, increasing their local concentrations and facilitating their binding to receptors expressed on leukocytes. In competitive binding assays using immobilized heparin, a 2-3-fold increase in the bound radiolabeled chemokine was seen with increasing concentrations of unlabeled chemokine in the nanomolar range. Unlabeled chemokine concentrations between 0.25 and 50 microM were needed to compete the bound radioactivity. This biphasic competition curve was not seen for N-methyl-L25 IL-8, a variant of IL-8 which is unable to dimerize. In addition, complexes of chemokine and heparin eluted from gel filtration columns with apparent molecular masses of 33-60 kDa, suggesting that chemokine multimerization had occurred. The physiological relevance of this multimerization process was seen from studies using human endothelial cells. The endothelial cell binding sites for IL-8, RANTES, and MCP-1 were deduced to be glycosaminoglycans since competition assays showed the biphasic curves and micromolar IC50 values seen in studies with immobilized heparin, and mRNA for known chemokine receptors was not detected. Furthermore, digestion of endothelial cell monolayers with glycosaminidases decreased chemokine binding by up to 80%. Glycosaminoglycans can act as modulators of the ligand binding affinity of chemokine receptor-bearing cells. Removal of glycosaminoglycans from CHO cells expressing chemokine receptors CXCR1, CCR1, or CCR2 resulted in 40-70% decreases in the binding of RANTES, MCP-1, IL-8, and MIP-1alpha. Our data show that cell surface glycosaminoglycans induce polymerization of chemokines, increasing their local concentration and therefore enhancing their effects on high-affinity receptors within the local microenvironment.
Adsorption configurations and thermal chemistry of acetylene on the Ge(100) surface (2002)

The adsorption structures and thermal desorption behavior of C2H2 on Ge(100) were studied in ultrahigh vacuum by scanning tunneling microscopy (STM) and temperature programmed desorption (TPD). The STM investigation revealed that, at low coverage, C2H2 initially adsorbs onto the Ge(100) surface with two types of configurations: (i) a di-σ configuration on top of a single Ge–Ge dimer (on-top) and (ii) a tetra-σ configuration parallel to the dimer axes, bridging two neighboring Ge dimers (p-bridge). TPD measurements show that chemisorbed C2H2 desorbs from Ge(100) nondissociatively with two different desorption features, denoted as α (520 K) and β (560 K). In addition, it was found that the desorption of C2H2 follows first order kinetics for both states and that the desorption energies of the α (520 K) and β (560 K) states are 1.3 and 1.4 eV, respectively. STM studies of the adsorption of C2H2 at various Ge surface temperatures indicate that the α and β features correspond to the on-top and p-bridge configurations, respectively.
Authoring motion cycles (2017)

Motion cycles play an important role in animation production and game development. However, creating motion cycles relies on general-purpose animation packages with complex interfaces that require expert training. Our work explores the specific challenges of motion cycle authoring and provides a system simple enough for novice animators while maintaining the flexibility of control demanded by experts. Due to their cyclic nature, we show that performance animation provides a natural interface for motion cycle specification. Our system allows the user to act several loops of motion using a variety of capture devices and automatically extracts a looping cycle from this potentially noisy input. Motion cycles for different character components can be authored in a layered fashion, or our method supports cycle extraction from higher-dimensional data for capture devices that deliver many degrees of freedom. After capture, a custom curve representation and manipulation tool allows the user to coordinate and control spatial and temporal transformations from a single viewport. Ground and other planar contacts are specified with a single sketched line that adjusts a curve's position and timing to establish non-slipping contact. We evaluate the effectiveness of our work through tests with both novice and expert users and show a variety of animated motion cycles created with our system.
T Cells with Chimeric Antigen Receptors Have Potent Antitumor Effects and Can Establish Memory in Patients with Advanced Leukemia (2011)

Tumor immunotherapy with T lymphocytes, which can recognize and destroy malignant cells, has been limited by the ability to isolate and expand T cells restricted to tumor-associated antigens. Chimeric antigen receptors (CARs) composed of antibody binding domains connected to domains that activate T cells could overcome tolerance by allowing T cells to respond to cell surface antigens; however, to date, lymphocytes engineered to express CARs have demonstrated minimal in vivo expansion and antitumor effects in clinical trials. We report that CAR T cells that target CD19 and contain a costimulatory domain from CD137 and the T cell receptor ζ chain have potent non-cross-resistant clinical activity after infusion in three of three patients treated with advanced chronic lymphocytic leukemia (CLL). The engineered T cells expanded >1000-fold in vivo, trafficked to bone marrow, and continued to express functional CARs at high levels for at least 6 months. Evidence for on-target toxicity included B cell aplasia as well as decreased numbers of plasma cells and hypogammaglobulinemia. On average, each infused CAR-expressing T cell was calculated to eradicate at least 1000 CLL cells. Furthermore, a CD19-specific immune response was demonstrated in the blood and bone marrow, accompanied by complete remission, in two of three patients. Moreover, a portion of these cells persisted as memory CAR(+) T cells and retained anti-CD19 effector functionality, indicating the potential of this major histocompatibility complex-independent approach for the effective treatment of B cell malignancies.
Role of Vacuum-Assisted Closure in the Treatment of Pediatric Lawnmower Injuries (2004)

Lawnmower injuries in children often present treatment challenges due to complex soft tissue damage. Vacuum-assisted closure (VAC), the application of controlled subatmospheric pressure to a wound surface, has been used to treat complex lacerations in many patients and has been shown to be safe and effective in children. However, VAC treatment of lawnmower injuries in children has not been reported. This study analyzes the outcomes of treatment following the use of VAC in children with lawnmower injuries and compares the results of VAC treatment to historical controls who were treated before VAC was available for wound treatment. The use of VAC demonstrated a trend toward a decrease in revision amputations and an improvement in function after treatment. There were no complications or adverse reactions related to VAC treatment. The VAC system is a safe and effective method of treating soft tissue injuries resulting from lawnmower accidents in children.
Distortion properties of gallium arsenide and silicon RF and microwave switches (2002)

An important parameter for RF and microwave system design is the prediction of distortion produced by system components. This paper presents the results of a study on the distortion produced by GaAs and Si RF and microwave switches. The results presented will provide RF and microwave circuit designers with information needed to help decide which switch to use for a specific switching application.
Quantification of Odor Quality (2000)

The relationship between odor quality and molecular properties is arguably the most important issue in olfaction. Despite sophistication in the chemical characterization of molecules, accompanying perceptual characterization has had little quantitative usefulness, relying mostly on enumerative description. As a result of weak interest in the topic outside industry and little agreement regarding how to measure quality, the field of olfactory psychophysics has failed to develop a substantial database for odor quality and has offered little help to other researchers, e.g. neurobiologists, in choice of stimuli, interpretation of outcome or testable hypotheses. This review scrutinizes how psychophysicists and others have measured quality and offers criteria for useful techniques. Most measures have had a subjective component that makes them anachronistic with modern methodology in experimental behavioral science, indeterminate regarding the extent of individual differences, unusable with infrahumans and of unproved ability to discern small differences. Techniques based upon performance, rather than on the more common reporting of mental content, offer firmer possibilities for growth. These techniques inevitably tap the discriminative basis of perception. The nonsubjective techniques have high sensitivity, can have counterparts in infrahuman research, are suitable to examine individual differences and yield non-negotiable answers with potential archival value. Discriminative techniques have their limitations, too-principally excess sensitivity that abridges their use to comparisons between similar-smelling stimuli. Research has begun to extend that range and may overcome the limitation. Application of discriminative methods may have the side-effect of shifting focus in structure-activity research from searches for molecular least common denominators that underlie often vague similarity to the search for molecular properties of importance in discrimination of small differences.
Chemokines and Cell Migration in Secondary Lymphoid Organs (1999)

As few as one in 100,000 B and T lymphocytes are specific for a single protein antigen, such as tetanus toxin, yet these cells must come together if an antibody response is to occur. Bringing antigen-presenting cells and rare antigen-specific B and T lymphocytes into physical contact is a principal function of secondary lymphoid organs. In the last few years, details have begun to emerge on the cues that guide cell movements inside lymphoid organs, and a central role for the chemokine family of molecules has been uncovered. Here, current understanding of the roles played by chemokines in the functional biology of secondary lymphoid organs will be reviewed.
Hydrogen Balmer alpha line shapes for hydrogen-argon mixtures in a low-pressure rf discharge (1993)

The spectral and spatial profiles of atomic hydrogen emission (the Balmer lines Hα and Hβ) from a low-pressure rf (13.56 MHz) discharge in H2+Ar mixtures have been studied. The plasma emission was observed in a direction normal to the applied electric field. The Hα profiles exhibit central narrow components and wide components which are due to Doppler broadening. Comparisons of the Hα profiles in a pure hydrogen plasma with those in H2+Ar mixtures show that collisions of molecular hydrogen ions and hydrogen atoms with argon atoms play a significant role in the production of the Hα profile shapes.
Usilng Machine Learning Technliques to Identify Botnet Traffic (2006)

To date, techniques to counter cyber-attacks have predominantly been reactive; they focus on monitoring network traffic, detecting anomalies and cyber-attack traffic patterns, and, a posteriori, combating the cyber-attacks and mitigating their effects. Contrary to such approaches, we advocate proactively detecting and identifying botnets prior to their being used as part of a cyber-attack (Strayer et al., 2006). In this paper, we present our work on using machine learning-based classification techniques to identify the command and control (C2) traffic of IRC-based botnets - compromised hosts that are collectively commanded using Internet relay chat (IRC). We split this task into two stages: (I) distinguishing between IRC and non-IRC traffic, and (II) distinguishing between botnet and real IRC traffic. For stage I, we compare the performance of J48, naive Bayes, and Bayesian network classifiers, identify the features that achieve good overall classification accuracy, and determine the classification sensitivity to the training set size. While sensitive to the training data and the attributes used to characterize communication flows, machine learning-based classifiers show promise in identifying IRC traffic. Using classification in stage II is trickier, since accurately labeling IRC traffic as botnet and non-botnet is challenging. We are currently exploring labeling flows as suspicious and non-suspicious based on telltales of hosts being compromised
Convergent synthesis, chiral HPLC, and vitamin D receptor affinity of analogs of 1,25-dihydroxycholecalciferol (1999)

A series of analogs of 1,25-dihydroxycholecalciferol was obtained with an additional chiral center at the terminus of the aliphatic side chain (C-25). The analogs were obtained from (+)-(R)- and (-)-(S)-2-methylglycidols, by opening of the oxirane ring with the carbanions derived from vitamin D C23a,24- or C22-sulfones. The diastereomeric purity of the analogs was determined by high-performance liquid chromatography on a chiral stationary phase. The binding affinity of analogs for the calf thymus intracellular vitamin D receptor (VDR) was two orders of magnitude lower than that of the lead compound of this group, 24a,24b-dihomo-1,25-dihydroxycholecalciferol, and it was comparable to the affinity of analogs of 24-nor-1,25-dihydroxycholecalciferol. However, a twofold difference was observed for analogs diastereomeric at C-25 in their affinity for VDR. The diastereodifferentiation of the binding affinity was found to be specific for vitamin D vicinal 25,26-diols as it disappears for analogs where 26-hydroxyl, neighboring the C-25 chiral center, is replaced with methyl.
Lithium ionic conduction and relaxation dynamics of spark plasma sintered Li5La3Ta2O12 garnet nanoceramics (2015)

In the present work, nanoceramics of Li5La3Ta2O12 (LLT) lithium ion conductors with the garnet-like structure are fabricated by spark plasma sintering (SPS) technique at different temperatures of 850°C, 875°C, and 900°C (SPS-850, SPS-875, and SPS-900). The grain size of the SPS nanoceramics is in the 50 to 100 nm range, indicating minimal grain growth during the SPS experiments. The ionic conduction and relaxation properties of the current garnets are studied by impedance spectroscopy (IS) measurements. The SPS-875 garnets exhibit the highest total Li ionic conductivity of 1.25 × 10(-6) S/cm at RT, which is in the same range as the LLT garnets prepared by conventional sintering technique. The high conductivity of SPS-875 sample is due to the enhanced mobility of Li ions by one order of magnitude compared to SPS-850 and SPS-900 ceramics. The concentration of mobile Li(+) ions, n c, and their mobility are estimated from the analysis of the conductivity spectra at different temperatures. n c is found to be independent of temperature for the SPS nanoceramics, which implies that the conduction process is controlled by the Li(+) mobility. Interestingly, we found that only a small fraction of lithium ions of 3.9% out of the total lithium content are mobile and contribute to the conduction process. Moreover, the relaxation dynamics in the investigated materials have been studied through the electric modulus formalism.
High-affinity binding of the regulatory subunit (RII) of cAMP-dependent protein kinase to microtubule-associated and other cellular proteins. (1984)

Interaction of the regulatory subunit of the type II cAMP-dependent protein kinase (RII) with tissue-specific cellular binding proteins has been demonstrated by two independent methods. Complexes of RII and its binding proteins were isolated on a cAMP analog-Sepharose affinity column, eluted from the column, and analyzed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Alternatively, nitrocellulose blots made from polyacrylamide gels containing samples of tissue extracts or affinity column eluates were treated with sequential overlays of RII, monospecific antibody, and radioiodinated protein A. In bovine cerebrum, specific high-affinity interactions between RII and several binding proteins, including major proteins of 300, 80, and 68 kDa, were recognized by the two methods. The 300-kDa and 68-kDa proteins were identified as microtubule-associated protein 2 (300 kDa) and a protein of lower molecular weight (68 kDa) that copurifies with it. The additional major binding protein of 80 kDa requires further characterization. In addition, several binding proteins distinct from those observed in bovine cerebrum were found in bovine heart. Many of the RII binding proteins from brain and heart served to differing extents as substrates for the purified catalytic subunit of cAMP-dependent protein kinase. One hypothesis of the significance of the protein kinase regulatory subunit interaction with cellular binding proteins is that this may control the protein kinase holoenzyme localization and, thereby, define the substrate targets most accessible for phosphorylation by the activated protein kinase catalytic subunit. Alternatively, RII binding to a variety of cellular proteins might regulate their function--i.e., RII could be a regulator for multiple proteins in addition to the catalytic subunit of the cAMP-dependent protein kinase.