gebhart/patrepeval huggingface dataset:
Brassinosteroid Signal Transduction: From Receptor Kinase Activation to Transcriptional Networks Regulating Plant Development (2011)

Brassinosteroid (BR) signal transduction research has progressed rapidly from the initial discovery of the BR receptor to a complete definition of the basic molecular components required to relay the BR signal from perception by receptor kinases at the cell surface to activation of a small family of transcription factors that regulate the expression of more than a thousand genes in a BR-dependent manner. These mechanistic advances have helped answer the intriguing question of how a single molecule, such as a hormone, can have dramatic pleiotropic effects on a broad range of diverse developmental pathways and have shed light on how BRs interact with other plant hormones and environmental cues to shape the growth of the whole plant. This review summarizes the current state of BR signal transduction research and then examines recent articles uncovering gene regulatory networks through which BR influences both vegetative and reproductive development.
Oxygen production using dense ceramic hollow fiber membrane modules with different operating modes (2007)

Abstract Oxygen production with three operating modes, i.e. high‐pressure operation, sweep‐gas operation, and vacuum operation, using dense La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3−α (LSCF) hollow fiber membrane modules has been investigated both theoretically and experimentally. The results indicate that the vacuum operation is the best and the most economical operating mode to produce oxygen from air. The sweep‐gas operation using water vapor is another choice to obtain a high capacity of oxygen production, providing that problems associated with high temperature sealing can be solved. The high‐pressure operation failed to achieve the expected oxygen production capacity. For the LSCF hollow fiber membranes, the surface exchange reaction at the downstream side plays a key role in the oxygen production at operating temperatures lower than 900°C. © 2007 American Institute of Chemical Engineers AIChE J, 2007
CD4+T Cells and Antibody Are Required for Optimal Major Outer Membrane Protein Vaccine-Induced Immunity toChlamydia muridarumGenital Infection (2010)

Despite effective antimicrobial chemotherapy, control of Chlamydia trachomatis urogenital infection will likely require a vaccine. We have assessed the protective effect of an outer membrane protein-based vaccine by using a murine model of chlamydial genital infection. Female mice were first vaccinated with Chlamydia muridarum major outer membrane protein (MOMP) plus the adjuvants CpG-1826 and Montanide ISA 720; then they were challenged with C. muridarum. Vaccinated mice shed 2 log(10) to 3 log(10) fewer inclusion-forming units (IFU) than ovalbumin-vaccinated or naïve animals, resolved infection sooner, and had a lower incidence of hydrosalpinx. To determine the relative contribution of T cells to vaccine-induced protection, mice were vaccinated, depleted of CD4(+) or CD8(+) T cells, and then challenged vaginally with C. muridarum. Depletion of CD4(+) T cells, but not depletion of CD8(+) T cells, diminished vaccine-induced protection, with CD4-depleted mice shedding 2 log(10) to 4 log(10) more IFU than CD8-depleted or nondepleted mice. The contribution of antibodies to vaccine-induced protection was demonstrated by the absence of protective immunity in vaccinated B-cell-deficient mice and by a 2 log(10) to 3 log(10) decrease in bacterial shedding by mice passively administered an anti-MOMP serum. Thus, optimal protective immunity in this model of vaccine-induced protection depends on contributions from both CD4(+) T cells and antibody.
Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria (2016)

Cyanobacteria are the ideal organisms for the production of a wide range of bioproducts as they can convert CO<sub>2</sub> directly into the desired end product using solar energy. Unfortunately, the engineering of cyanobacteria to create efficient cell factories has been impaired by the cumbersome genetic tools that are currently available for these organisms; especially when trying to accumulate multiple modifications. We sought to construct an efficient and precise tool for generating numerous markerless modifications in cyanobacteria using CRISPR technology and the alternative nuclease, Cpf1. In this study we demonstrate rapid engineering of markerless knock-ins, knock-outs and point mutations in each of three model cyanobacteria; Synechococcus, Synechocystis and Anabaena. The markerless nature of cpf1 genome editing will allow for complex genome modification that was not possible with previously existing technology while facilitating the development of cyanobacteria as highly modified biofactories.
Synthesis and Characterization of Nanometer-Size Fe3O4 and γ-Fe2O3 Particles (1996)

Synthesis of suspensions of nanosize particles of Fe3O4 was carried out in bulk aqueous solutions without the presence of surfactants. The Fe3O4 nanoparticles were oxidized to γ-Fe2O3 by direct aeration of the suspension at 100 °C. The shape and size distribution and crystallinity of the Fe3O4 nanoparticles were assessed by transmission electron microscopy and selected area electron diffraction. Very uniform and stable colloidal suspensions of the Fe3O4 nanoparticles in water could be synthesized. Oxidation of the colloidal system leads to γ-Fe2O3 nanoparticles of much larger size than Fe3O4.
[Light-induced retinal damage in pigmented rabbit--2. Effect of alpha-tocopherol]. (1994)

We have reported previously that xenon light exposure without long waves primarily damages the retinal pigment epithelium (RPE) of pigmented rabbits. Alpha-tocopherol, which is a free radical scavenger, was administered systemically to pigmented rabbits before light exposure in order to evaluate the protective effect against retinal light damage. In fluoresceine angiography, at 12 hours after the light exposure, diffuse and marked hyperfluorescence was seen in the lower portion of the retina adjacent to the optic disc in the untreated group, and slight hyperfluorescence in a small area was seen in the treated group. Histopathologically, the RPE became necrotic 12 hours after the light exposure in the untreated group. In the treated group, only slight damage appeared in the RPE 12 hours after the light exposure. The light-induced retinal damage, particularly in the RPE, was remarkably reduced by administration of alpha-tocopherol before the light exposure.
Restricted Ig H chain V gene usage in the human antibody response to Haemophilus influenzae type b capsular polysaccharide (1991)

The mechanisms that govern the content of the human antibody repertoire are poorly understood. To investigate the antibody response to a clinically relevant Ag, we have produced heterohybridomas secreting human antibodies directed against the capsular polysaccharide of Haemophilus influenzae type b (Hib PS). Immune lymphocytes were harvested 7 days after immunization with either of two vaccine formulations, a plain polysaccharide vaccine (Hib PS) or a polysaccharide-protein conjugate of Hib PS and diphtheria toxoid (Hib PS-D). H chain V region gene nucleic acid sequences were determined for five stable hybridomas. All use members of the VHIII gene family and are 83% to 98% homologous to two candidate germ-line sequences. A variety of D and JH segments are used. Thus the Ig H chain repertoire appears to be restricted to a limited group of VHIII family members. The previously reported expression of homologous sequences in the human fetal repertoire suggests that the inability of young children to respond to this Ag is not caused by deficiencies of these important elements early in development. The restricted use of VHIII gene segments suggests that this gene family plays a pivotal role in the immune response to this important childhood pathogen.
Inhibition of CRIPTO expression and tumorigenicity in human colon cancer cells by antisense RNA and oligodeoxynucleotides. (1994)

CRIPTO is an epidermal growth factor-related gene expressed in a majority of human colorectal tumors. To assess the role of CRIPTO in the growth control of human colon cancer, we have treated human colon carcinoma GEO and CBS cells, that possess high levels of CRIPTO, and WIDR colon cancer cells, that are negative for CRIPTO expression, with two antisense phosphorothioate oligodeoxynucleotides complementary to the 5' end of the human CRIPTO mRNA. Both antisense oligodeoxynucleotides significantly reduced endogenous CRIPTO protein levels and inhibited GEO and CBS cell growth in monolayer and in semisolid medium, whereas they did not affect WIDR cell growth. In addition, GEO, CBS and WIDR cells were infected with a recombinant retroviral vector containing the hygromycin-resistance gene and a 900 bp EcoRI-EcoRI coding fragment of the human CRIPTO cDNA oriented in the 3' to 5' direction. GEO and CBS CRIPTO antisense infectants exhibited a 60 to 70% reduction in CRIPTO protein expression, in monolayer growth and in soft agar cloning efficiency as compared to parental noninfected cells. In contrast, infection of WIDR cells with the CRIPTO antisense retrovirus did not alter their growth. Finally, GEO CRIPTO antisense infectants formed tumors in nude mice that were significantly smaller and had a larger latency period as compared to noninfected GEO cells.
Fingerprint Indexing Based on Minutia Cylinder-Code (2010)

This paper proposes a new hash-based indexing method to speed up fingerprint identification in large databases. A Locality-Sensitive Hashing (LSH) scheme has been designed relying on Minutiae Cylinder-Code (MCC), which proved to be very effective in mapping a minutiae-based representation (position/ angle only) into a set of fixed-length transformation-invariant binary vectors. A novel search algorithm has been designed thanks to the derivation of a numerical approximation for the similarity between MCC vectors. Extensive experimentations have been carried out to compare the proposed approach against 15 existing methods over all the benchmarks typically used for fingerprint indexing. In spite of the smaller set of features used (top performing methods usually combine more features), the new approach outperforms existing ones in almost all of the cases.
Fidelity of T Cell Activation Through Multistep T Cell Receptor ζ Phosphorylation (1998)

The T cell receptor (TCR) alphabeta heterodimer interacts with its ligands with high specificity, but surprisingly low affinity. The role of the zeta component of the murine TCR in contributing to the fidelity of antigen recognition was examined. With sequence-specific phosphotyrosine antibodies, it was found that zeta undergoes a series of ordered phosphorylation events upon TCR engagement. Completion of phosphorylation steps is dependent on the nature of the TCR ligand. Thus, the phosphorylation steps establish thresholds for T cell activation. This study documents the sophisticated molecular events that follow the engagement of a low-affinity receptor.
Nanoengineering of Inorganic and Hybrid Hollow Spheres by Colloidal Templating (1998)

Hollow silica and silica-polymer spheres with diameters between 720 and 1000 nanometers were fabricated by consecutively assembling silica nanoparticles and polymer onto colloids and subsequently removing the templated colloid either by calcination or decomposition upon exposure to solvents. Scanning and transmission electron microscopy images demonstrate that the wall thickness of the hollow spheres can be readily controlled by varying the number of nanoparticle-polymer deposition cycles, and the size and shape are determined by the morphology of the templating colloid. The hollow spheres produced are envisioned to have applications in areas ranging from medicine to pharmaceutics to materials science.
Aircraft instrument for simultaneous, in situ measurement of NO3 and N2O5 via pulsed cavity ring-down spectroscopy (2006)

This article describes a cavity ring-down spectrometer (CaRDS) specifically designed and constructed for installation on the NOAA WP-3D Orion (P-3) aircraft for sensitive, rapid in situ measurement of NO3 and N2O5. While similar to our previously described CaRDS instrument, this instrument has significant improvements in the signal-to-noise ratio, the time resolution, and in overall size and weight. Additionally, the instrument utilizes a custom-built, automated filter changer that was designed and constructed to meet the requirement for removal of particulate matter in the airflow while allowing fully autonomous instrument operation. The CaRDS instrument has a laboratory detection sensitivity of 4×10−11cm−1 in absorbance or 0.1pptv (pptv denotes parts per trillion volume) of NO3 in a 1s average, although the typical detection sensitivities encountered in the field were 0.5pptv for NO3 and 1pptv for N2O5. The instrument accuracy is 25% for NO3 and 20%–40% for N2O5, limited mainly by the uncertainty in the inlet transmission. The instrument has been deployed on the P-3 aircraft as part of a major field campaign in the summer of 2004 and during several ground and tower deployments near Boulder, CO.
Rotation, Scaling and Deformation Invariant Scattering for Texture Discrimination (2013)

An affine invariant representation is constructed with a cascade of invariants, which preserves information for classification. A joint translation and rotation invariant representation of image patches is calculated with a scattering transform. It is implemented with a deep convolution network, which computes successive wavelet transforms and modulus non-linearities. Invariants to scaling, shearing and small deformations are calculated with linear operators in the scattering domain. State-of-the-art classification results are obtained over texture databases with uncontrolled viewing conditions.
Increased Efficacy and Tolerability of Pegloticase in Patients With Uncontrolled Gout Co-Treated With Methotrexate: A Retrospective Study (2020)

Methotrexate/pegloticase co-therapy resulted in a higher responder rate than the established 42% with pegloticase alone. Therefore, methotrexate/pegloticase co-therapy may safely allow more patients to benefit from a full treatment course, likely through ADA attenuation.
C-Reactive Protein as a Marker for Inflammatory Bowel Disease (2004)

The production of CRP occurs almost exclusively in the liver by the hepatocytes as part of the acute phase response upon stimulation by IL-6, TNF-alphaand IL-1-betaoriginating at the site of inflammation. Its short half-life makes CRP a valuable marker to detect and follow up disease activity in Crohn's disease (CD). In contrast, ulcerative colitis has only a modest to absent CRP response despite active inflammation, and the reason for this is unknown. In CD, serum levels of CRP correlate well with disease activity and with other markers of inflammation as the CDAI, serum amyloid, IL-6 and faecal calprotectin. CRP is a valuable marker for predicting the outcome of certain diseases as coronary heart disease and haematological malignancies. An increased CRP (>45 mg/L) in patients with IBD predicts with a high certainty the need for colectomy and this by reflecting severe ongoing and uncontrollable inflammation in the gut. Finally, trials with anti-TNF and anti-adhesion molecules have shown that a high CRP predicts better response to these drugs. However, whether we need to include CRP as an inclusion criterion for future trials with biologicals is still a matter of debate.
Biological Activities of Novel Zaragozic Acids, the Potent Inhibitors of Squalene Synthase, Produced by the Fungus, Mollisia sp. SANK 10294. (1997)

Four novel zaragozic acids, F-10863A, B, C and D, were isolated from a culture broth of the fungus Mollisia sp. SANK 10294. F-10863 compounds contain a 4,6,7-trihydroxy-2,8-dioxyobicyclo-[3.2.1]octane-3,4,5-tricarboxyl ic acid core like previously reported zaragozic acids, but the structures of the side chains are different. Recently, it was found that F-10863A is identical to zaragozic acid D3, while the other three are novel compounds. F-10863 compounds are potent inhibitors of squalene synthase like previously reported zaragozic acids, and, furthermore, they exhibit serum cholesterol-lowering activity in vivo.
Benchmarking GPUs to tune dense linear algebra (2008)

We present performance results for dense linear algebra using recent NVIDIA GPUs. Our matrix-matrix multiply routine (GEMM) runs up to 60% faster than the vendor's implementation and approaches the peak of hardware capabilities. Our LU, QR and Cholesky factorizations achieve up to 80--90% of the peak GEMM rate. Our parallel LU running on two GPUs achieves up to ~540 Gflop/s. These results are accomplished by challenging the accepted view of the GPU architecture and programming guidelines. We argue that modern GPUs should be viewed as multithreaded multicore vector units. We exploit blocking similarly to vector computers and heterogeneity of the system by computing both on GPU and CPU. This study includes detailed benchmarking of the GPU memory system that reveals sizes and latencies of caches and TLB. We present a couple of algorithmic optimizations aimed at increasing parallelism and regularity in the problem that provide us with slightly higher performance.
Small Molecule Gated Split-Tyrosine Phosphatases and Orthogonal Split-Tyrosine Kinases (2014)

Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
Microgram-Scale Testing of Reaction Conditions in Solution Using Nanoliter Plugs in Microfluidics with Detection by MALDI-MS (2006)

This paper describes a microfluidic system to screen and optimize organic reaction conditions on a submicrogram scale. The system uses discrete droplets (plugs) as microreactors separated and transported by a continuous phase of a fluorinated carrier fluid. Previously, we demonstrated the use of a microfabricated PDMS plug-based microfluidic system to perform assays and crystallization experiments in aqueous solutions with optical detection. Here, we developed an approach that does not require microfabrication of microfluidic devices, is applicable to synthetic reactions in organic solvents, and uses detection by MALDI-MS. As a demonstration, conditions for selective deacetylation of ouabain hexaacetate were tested, and the optimum conditions for mono-, bis-, or trisdeacetylation have been identified. These conditions were validated by scale-up reactions and isolating these potentially neurotoxic products. Mono- and bisdeacetylated products are unstable intermediates in the deacetylation and were isolated for the first time. This system enables no-loss handling of submicroliter volumes containing a few micrograms of a compound of interest. It could become valuable for investigating or optimizing reactions of precious substrates (e.g., products of long synthetic sequences and natural products that can be isolated only in small quantities).
Extracellular matrix of cultured bovine aortic endothelial cells contains functionally active type 1 plasminogen activator inhibitor (1987)

The extracellular matrix (ECM) of cultured bovine aortic endothelial cells (BAEs) was analyzed by immunoblotting and reverse fibrin autography and shown to contain type 1 plasminogen activator inhibitor (PAI-1). Most PAI-1 in the ECM formed complexes with exogenously added tissue-type plasminogen activator (tPA), demonstrating that this PAI-1 was functionally active. The resulting tPA/PAI-1 complexes were recovered in the reaction solution, indicating that the PAI-1 in such complexes no longer bound to ECM. The PAI-1 could not be removed by incubating ECM in high salt (2 mol/L NaCl), sugars (1 mol/L galactose, 1 mol/L mannose), glycosaminoglycans (10 mmol/L heparin, 10 mmol/L dermatan sulfate), or epsilon-aminocaproic acid (0.1 mol/L). However, PAI-1 could be extracted from ECM by treatment with either arginine (0.5 mol/L) or potassium thiocyanate (2 mol/L), or by incubation under acidic conditions (pH 2.5). ECM depleted of PAI-1 by acid extraction was able to bind both the active and latent forms of PAI-1. In this instance, most of the bound PAI-1 did not form complexes with tPA, indicating that the latent form was not activated as a consequence of binding to ECM. Although the PAI-1 activity in conditioned medium decayed with a half-life (t 1/2) of less than 3 hours, the t 1/2 of ECM- associated PAI-1 was greater than 24 hours. These data suggest that PAI- 1 is produced by cultured BAEs in an active form and is then either released into the medium where it is rapidly inactivated or into the subendothelium where it binds to ECM. The specific binding of PAI-1 to ECM protects it from this inactivation.
Characterization of a novel EGFP reporter mouse to monitor Cre recombination as demonstrated by a Tie2 Cre mouse line (2001)

The use of the Cre/loxP system has greatly empowered the field of gene targeting. Here we describe the successful establishment of a novel knock-in EGFP reporter mouse line to monitor Cre-induced recombination in the vast majority of cell types. The value of this reporter mouse line is demonstrated by the use of a novel Tie2Cre transgenic mouse line that facilitates gene targeting in endothelial and hematopoietic cells. High efficiency of recombination was found in all endothelial cells and in the majority of hematopoietic cells but was absent in other tissues. Furthermore, in the second generation, the Tie2Cre mouse can be used to get 100% recombination of one allele, whilst allowing tissue specific in the second, therefore offering excellent efficiency.
Benign multiple sclerosis (1999)

The ability to predict the development of disability in a disease as variable as multiple sclerosis is one of the major challenges facing researchers and clinicians alike. It focuses researchers on the mechanisms underlying irreversible deficit, while challenging clinicians to define criteria for the use of partially effective treatments with a not inconsequential side effect profile and cost. The concept of benign multiple sclerosis is of particular relevance to both these issues. However, although, as has been pointed out by Hawkins and McDonnell (pp 148–52, this issue) it has been recognised for over 40 years, the precise definition is extremely vague and would probably best be met by an index of progression rather than an arbitrary disease duration/Kurtze expanded disability …
Synaptic vesicle biogenesis, docking, and fusion: a molecular description (1996)

Secretion of neurotransmitter is the primary means of intercellular communication within the nervous system. This process is regulated by a highly orchestrated cycle of membrane trafficking within the presynaptic nerve terminal. Characterization of proteins localized to the synaptic vesicle and the subsequent studies of their properties have led to a model for the biochemical pathway that underlies vesicle docking, activation, and fusion. The proteins found to function in the synapse are related to those in yeast and other organisms, demonstrating that the mechanisms that mediate vesicle trafficking are conserved in all eukaryotic species.