gebhart/patrepeval huggingface dataset:
Distinctive Enzymes of Aromatic Amino Acid Biosynthesis That Are Highly Conserved in Land Plants Are Also Present in the Chlorophyte Alga Chlorella sorokiniana (1995)

Considerable enzymological diversity underlies the capacity for biosynthesis of aromatic amino acids in nature. For this biochemical pathway, higher plants as a group exhibit a uniform pattern of pathway steps, compartmentation, and catalytic, physical and allosteric properties of enzymes. This biochemical pattern of higher plants contains a collection of features which are completely different from photosynthetic prokaryotes such as the cyanobacteria. A unicellular representative of the chlorophyte algae, Chlorella sorokiniana, was found to be strikingly similar to higher-plant plastids in possessing the following distinctive enzymes: a Mn2+-stimulated, dithiothreitol-activated isoenzyme of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, a probable bifunctional protein competent as both dehydroquinase and shikimate dehydrogenase, an allosterically controlled isoenzyme of chorismate mutase, a highly thermotolerant species of prephenate aminotransferase, an NADP+-dependent, tyrosine-inhibited arogenate dehydrogenase, and an arogenate dehydratase. In addition an isoenzyme of DAHP synthase shown in higher plants to be cytosolic, absolutely dependent upon the presence of divalent metals, and able to substitute other sugars for erythrose-4-phosphate, was also demonstrated in this alga. A broad-specificity 3-deoxy-D-manno-octulosonate 8-phosphate synthase, recently discovered in higher plants, is also present in this Chlorella species.
Network traffic matrix: how can one learn the prior distributions from the link counts only? (2004)

The origin destination (OD) traffic matrix in a network is the volume of traffic for each OD pair. It is very useful for capacity planning, routing, operations and management, SLAs, customer reports, etc... But this matrix cannot be measured directly, it would require very costly upgrades of the existing infrastructures. On the contrary SNMP reports give a periodic account on the volume of traffic for each link. The traffic matrix must then be estimated by mathematical methods from the link counts only. This inverse problem is typically ill-posed since the number of OD pairs is much greater than the number of links. One of the existing techniques is Bayesian: it runs Markov chain Monte Carlo (MCMC) algorithms to simulate the joint distribution of the OD pairs given the link counts. It requires a prior distribution for each OD pair and, most of the time, those priors are arbitrary. A challenging issue would be to train the priors from the only available data, that is to say the link counts themselves. This is exactly what we do in this paper. We prove the validity of our approach on a network on which direct measurements of the OD counts were made available.
Synthesis of cis‐4‐methyl‐3‐phenylpyrrolidines as potential dopaminergic agonists (1988)

Abstract cis ‐3‐(3,4‐Dihydroxyprienyl)4‐methyl‐1‐( n ‐propyl)pyrrolidine ( 23 ) was synthesized and evaluated for dopaminergic activity. The synthesis of 23 involved selective 4‐acylation of the 3‐phenylpyrrolidine‐2,5‐dione 15 and cis ‐addition of hydrogen to a 4‐methyl‐3‐phenyl‐3‐pyrroline 4 . Pharmacological evaluation of 23 showed that introduction of a cis ‐4‐methyl group into the 3‐phenylpyrrolidine nucleus decreases dopaminergic activity.
Genetic screening of FecB, FecXGand FecXI mutations and their linkage with litter size in Barki and Rahmani sheep breeds (2017)

Characterization of fecundity genes offers the opportunity to improve production efficiency, and the consequent increase in litter size in livestock industry, through utilizing them in breeding programs. The main objective of this study was to detect the BMPR-IB, BMP15 and GDF9 gene mutations and to investigate whether these mutations are associated with litter size in Egyptian sheep breeds. To achieve this goal, 73 adult ewes representing Barki (n = 33) and Rahmani (n = 40) breeds were used. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) screening approach was used to detect the presence of FecB, FecX<sup>G</sup> and FecX<sup>I</sup> mutations in the two selected breeds. Results of this study showed that the three different candidate gene mutations, namely FecB, FecX<sup>G</sup> and FecX<sup>I</sup> are not present among these selected populations of the Egyptian breeds. Further studies regarding other mutations and/or other genes, which may influence ovulation rate, should be carried out to determine the type and mode of inheritance of such genes in Egyptian sheep breeds.
Data from Breast Field Cancerization: Isolation and Comparison of Telomerase-Expressing Cells in Tumor and Tumor Adjacent, Histologically Normal Breast Tissue (2023)

&lt;div&gt;Abstract&lt;p&gt;Telomerase stabilizes chromosomes by maintaining telomere length, immortalizes mammalian cells, and is expressed in more than 90% of human tumors. However, the expression of human telomerase reverse transcriptase (&lt;i&gt;hTERT&lt;/i&gt;) is not restricted to tumor cells. We have previously shown that a subpopulation of human mammary epithelial cells (HMEC) in tumor-adjacent, histologically normal (TAHN) breast tissues expresses &lt;i&gt;hTERT&lt;/i&gt; mRNA at levels comparable with levels in breast tumors. In the current study, we first validated a reporter for measuring levels of &lt;i&gt;hTERT&lt;/i&gt; promoter activity in early-passage HMECs and then used this reporter to compare &lt;i&gt;hTERT&lt;/i&gt; promoter activity in HMECs derived from tumor and paired TAHN tissues 1, 3, and 5 cm from the tumor (TAHN-1, TAHN-3, and TAHN-5, respectively). Cell sorting, quantitative real-time PCR, and microarray analyses showed that the 10% of HMECs with the highest &lt;i&gt;hTERT&lt;/i&gt; promoter activity in both tumor and TAHN-1 tissues contain more than 95% of &lt;i&gt;hTERT&lt;/i&gt; mRNA and overexpress many genes involved in cell cycle and mitosis. The percentage of HMECs within this subpopulation showing high &lt;i&gt;hTERT&lt;/i&gt; promoter activity was significantly reduced or absent in TAHN-3 and TAHN-5 tissues. We conclude that the field of “normal tissue” proximal to the breast tumors contains a population of HMECs similar in &lt;i&gt;hTERT&lt;/i&gt; expression levels and in gene expression to the HMECs within the tumor mass and that this population is significantly reduced in tissues more distal to the tumor. &lt;i&gt;Mol Cancer Res; 9(9); 1209–21. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Active liquid-crystal deflector and lens with Fresnel structure (2017)

A new type of tunable Fresnel deflector and lens composed of liquid crystal was developed. Combined structure of multiple interdigitated electrodes and the high-resistivity (HR) layer implements the saw-tooth distribution of electrical potential with only the planar surfaces of the transparent substrates. According to the numerical calculation and design, experimental devices were manufactured with the liquid crystal (LC) material sealed into the sandwiched flat glass plates of 0.7 mm thickness with rubbed alignment layers set to an anti-parallel configuration. Fabricated beam deflector with no moving parts shows the maximum tilt angle of &plusmn;1.3 deg which can apply for optical image stabilizer (OIS) of micro camera. We also discussed and verified their lens characteristics to be extended more advanced applications. Transparent interdigitated electrodes were concentrically aligned on the lens aperture with the insulator gaps under their boundary area. The diameter of the lens aperture was 30 mm and the total number of Fresnel zone was 100. Phase retardation of the beam wavefront irradiated from the LC lens device can be evaluated by polarizing microscope images with a monochromatic filter. Radial positions of each observed fringe are plotted and fitted with 2nd degree polynomial approximation. The number of appeared fringes is over 600 in whole lens aperture area and the correlation coefficients of all approximations are over 0.993 that seems enough ideal optical wavefront. The obtained maximum lens powers from the approximations are about &plusmn;4 m<sup>-1</sup> which was satisfied both convex and concave lens characteristics; and their practical use for the tunable lens grade eyeglasses became more prospective.
Alfalfa Mosaic Virus Replicase Proteins P1 and P2 Interact and Colocalize at the Vacuolar Membrane (2001)

Replication of Alfalfa mosaic virus (AMV) RNAs depends on the virus-encoded proteins P1 and P2. P1 contains methyltransferase- and helicase-like domains, and P2 contains a polymerase-like domain. Coimmunoprecipitation experiments revealed an interaction between in vitro translated-P1 and P2 and showed that these proteins are present together in fractions with RNA-dependent RNA polymerase activity. A deletion analysis in the yeast two-hybrid system showed that in P1 the C-terminal sequence of 509 amino acids with the helicase domain was necessary for the interaction. In P2, the sequence of the N-terminal 241 aa was required for the interaction. In infected protoplasts, P1 and P2 colocalized at a membrane structure that was identified as the tonoplast (i.e., the membrane that surrounds the vacuoles) by using a tonoplast intrinsic protein as a marker in immunofluorescence studies. While P1 was exclusively localized on the tonoplast, P2 was found both at the tonoplast and at other locations in the cell. As Brome mosaic virus replication complexes have been found to be associated with the endoplasmic reticulum (M. A. Restrepo-Hartwig and P. Ahlquist, J. Virol. 70:8908-8916, 1996), viruses in the family Bromoviridae apparently select different cellular membranes for the assembly of their replication complexes.
γ‐Di‐ n ‐Butylaminopropylamine (2003)

Abstract γ‐di‐ n ‐butylaminopropylamine reactant: 107 g. (0.40 mole) of γ‐bromopropylphthalimide product: γ‐di‐ n ‐butylaminopropylamine product: γ‐diethylaminopropylamine product: γ‐di‐ n ‐propylaminopropylamine
A new integrated optic technique for time delays in wideband phased arrays (1991)

Phased-arrays antennas are being employed in new generations of radar and communication systems that require the antenna to provide wide field-of-view (FOV), very narrow beamwidths, and wide instantaneous frequency bandwidths. Phased arrays designed to meet these requirements must have their aperture broken into subarrays with time delay units (TDUs) to minimize the dispersive effects of transmitting and receiving wideband waveforms through large arrays that use modulo 360 degree phase shifters to perform electronic beam scanning. The authors describe an integrated optic TDU. The TDU relies on a folded path optical waveguide to achieve time delays ranging from a few picoseconds to several nanoseconds. The folded path configuration utilizes thick phase gratings as reflective elements. These elements provide large angle deflection, high diffraction efficiency or reflectivity, wavelength multiplexing capabilities and form the basis for an electronically addressable switch. As a switching element they also offer high isolation due to their high diffraction efficiency.
Soluble Salts and Cocrystals of Clotrimazole (2015)

Novel crystalline adducts of clotrimazole with pharmaceutically acceptable coformers were prepared. Five salts and two cocrystals of the antimycotic drug clotrimazole (CLT) were crystallized with carboxylic acid coformers adipic acid (ADA), 2,5-dihydroxybenzoic acid (25DHBA), 2,4,6-trihydroxybenzoic acid (246THBA), p-coumaric acid (PCA), caffeic acid (CFA), maleic acid (MA), and suberic acid (SBA). Molecular overlay diagram of clotrimazole in the four salts (CLT–25DHBA, 1:1; CLT–246THBA, 1:1; CLT–PCA, 1:1; CLT–CFA–ANI, 1:1:1) and CLT–ADA (1:0.5) cocrystal showed conformational flexibility of the phenyl rings in the triaryl methane molecule. The X-ray crystal structures are sustained by N+–H···O–/ N–H···O hydrogen bonds. The solid-state forms were well characterized and analyzed by PXRD, FT-IR, and DSC and confirmed by single crystal X-ray diffraction (except for CLT–MA and CLT–SBA adducts). 15N ss-NMR indicated intermolecular proton transfer in CLT–MA, and the chemical shifts are consistent with salt formation. The acidic coformers for CLT base were selected based on the ΔpKa rule of 3. Solubility measurements showed improved solubility by a factor of 2.9 (CLT–25DHBA), 14.0 (CLT–246THBA), 1.3 (CLT–PCA), 2.8 (CLT–CFA), and 22.4 (CLT–MA) for salts and 5.0 in cocrystals (CLT–ADA and CLT–SBA) compared to CLT in 65% EtOH–water.
Human granulocyte-macrophage colony-stimulating factor: the protein and its current & emerging applications (2007)

Blood cells under a variety of conditions produce cytokines which regulate their proliferation, communication and functioning. The granulocyte-macrophage colony-stimulating factor (GM-CSF) is a hematopoietic growth factor mainly responsible for the proliferation of granulocyte-s and macrophages. It is a molecule of immense therapeutic interest due to its wide-ranging actions on immune cells. Recombinant human GM-CSF has been expressed, purified and characterized. It has diverse biological manifestations, which has led to its being explored for use in cancer therapy, AIDS therapy, as a vaccine adjuvant, in certain types of wound healing, promotion of collateral growth of coronary artery, usefulness in treating Crohn’s disease symptoms and in the management of a host of viral, bacterial and fungal infections. Newer therapeutic applications are also being unveiled. The physico-chemical as well as the biological features and the applications (current and emerging) of GM-CSF are discussed.
Protective Immunity Against neu -Positive Carcinomas Elicited by Electroporation of Plasmids Encoding Decreasing Fragments of Rat Neu Extracellular Domain (2008)

We have shown that electroporation of plasmid carrying extracellular and transmembrane domains (EC-TM plasmid) encoded by the rat neu oncogene triggers a protective immune response toward rat p185(neu)-positive tumors in both wild-type BALB/c mice and cancer-prone rat neu-transgenic BALB-neuT mice. To identify the critical fragments that confer this protective immunity, mice were electroporated with plasmids encoding the TM domain associated with decreasing fragments of the EC domain and the antitumor protection afforded, the titer of antibody, and cytotoxic T lymphocyte (CTL) activity elicited to Neu protein were evaluated. Plasmids encoding EC fragments shortened by 70 (EC1-TM plasmid), 150 (EC2-TM), 230 (EC3-TM), 310 (EC4-TM), and 390 (EC5-TM) NH(2)-terminal residues afforded effective protection. Plasmids encoding shorter truncated proteins were ineffective. When the immunogenic protein was retained in the cytoplasm (EC1-TM, EC2-TM, and EC5-TM), only a CTL response was elicited, whereas when it was also expressed on the membrane (EC4-TM) both CTLs and antibodies were induced. EC4-TM encoding a truncated protein with an EC portion of only 344 amino acids conferred protection on both BALB/c and BALB-neuT mice comparable to that of EC-TM.
Signal-Tracing Techniques for In-System FPGA Debugging of High-Level Synthesis Circuits (2016)

High-level synthesis (HLS) promises to increase designer productivity in the face of increasing field-programmable gate array sizes, and broaden the market of use, allowing software designers to reap the benefits of hardware implementation. One roadblock to HLS adoption is the lack of an in-system debugging infrastructure. Although designers can run their software code on a workstation, or simulate the register-transfer level, neither can reliably capture the behaviors, and therefore bugs, that may be present in the final system. Debugging hardware circuits in-system requires using signal-tracing to record circuit behavior for later offline analysis. In this paper, we present a debugging architecture, which automatically records key hardware signals, and relates them back to the original software source code. This architecture allows designers to debug HLS circuits in-system, in the context of the original source code. We present several signal-tracing techniques, tailored to HLS circuits, which allow a much longer execution trace to be captured. These techniques include signal compression, dynamically changing which signals are recorded cycle-by-cycle, and offline signal restoration. Compared to using an embedded logic analyzer to perform signal-tracing, our architecture increases the length of execution trace that can be recorded by 127X. For each 100 Kb of trace buffer memory, our architecture can record 15 369 executed lines of C code.
Circuit Theory for Waveguiding Systems (2009)

This chapter contains sections titled: Equivalent Voltages and Currents Impedance Description of Waveguide Elements and Circuits Foster's Reactance Theorem Even and Odd Properties of Z in N-Port Circuits Two-Port Junctions Scattering-Matrix Formulation Scattering Matrix for a Two-Port Junction Transmission-Matrix Representation Signal Flow Graphs Generalized Scattering Matrix for Power Waves Excitation of Waveguides Waveguide Coupling by Apertures This chapter contains sections titled: Problems References
Adult Hippocampal Neurogenesis and mRNA Expression are Altered by Perinatal Arsenic Exposure in Mice and Restored by Brief Exposure to Enrichment (2013)

Arsenic is a common and pervasive environmental contaminant found in drinking water in varying concentrations depending on region. Exposure to arsenic induces behavioral and cognitive deficits in both human populations and in rodent models. The Environmental Protection Agency (EPA) standard for the allotment of arsenic in drinking water is in the parts-per-billion range, yet our lab has shown that 50 ppb arsenic exposure during development can have far-reaching consequences into adulthood, including deficits in learning and memory, which have been linked to altered adult neurogenesis. Given that the morphological impact of developmental arsenic exposure on the hippocampus is unknown, we sought to evaluate proliferation and differentiation of adult neural progenitor cells in the dentate gyrus after 50 ppb arsenic exposure throughout the perinatal period of development in mice (equivalent to all three trimesters in humans) using a BrdU pulse-chase assay. Proliferation of the neural progenitor population was decreased by 13% in arsenic-exposed mice, but was not significant. However, the number of differentiated cells was significantly decreased by 41% in arsenic-exposed mice compared to controls. Brief, daily exposure to environmental enrichment significantly increased proliferation and differentiation in both control and arsenic-exposed animals. Expression levels of 31% of neurogenesis-related genes including those involved in Alzheimer's disease, apoptosis, axonogenesis, growth, Notch signaling, and transcription factors were altered after arsenic exposure and restored after enrichment. Using a concentration previously considered safe by the EPA, perinatal arsenic exposure altered hippocampal morphology and gene expression, but did not inhibit the cellular neurogenic response to enrichment. It is possible that behavioral deficits observed during adulthood in animals exposed to arsenic during development derive from the lack of differentiated neural progenitor cells necessary for hippocampal-dependent learning. This study is the first to determine the impact of arsenic exposure during development on adult hippocampal neurogenesis and related gene expression.
Direct Sequencing for Cowden Syndrome Gene PTEN ( MMAC1) Mutations (2003)

Cowden syndrome is a rare dominantly inherited condition with predisposition to benign hamartomatous polyposis of the intestine, as well as malignant tumors of the breast and thyroid, and possibly some other cancer types. Other features include macrocephaly and dysplastic cerebellar gangliocytomatosis with ataxia, as well as predisposition to formation of trichilemmomas of the skin (1). The latter are tumors of the hair root sheath.
A novel approach to knee kinematics. (2001)

We describe our experience with in vivo dynamic fluoroscopy that uses simple 2-plane video fluoroscopy of subjects performing maneuvers such as deep knee-bends, gait, and stair climbing after total knee arthroplasty (TKA). Kinematic analysis has evolved from 2-dimensional vector calculations to automated 3-dimensional computer-assisted design matching techniques that are accurate to 0.75-mm translation and 0.75 degrees rotation and that allow simultaneous determination of medial and lateral condyle contact positions. TKAs that retain the posterior cruciate ligament (PCL) have consistently shown posterior contact in extension and anterior translation with flexion with a large variability among subjects. PCL-stabilized implants and mobile bearings with high conformity have posterior femoral rollback more consistent with normal knees--which is a function of prosthetic geometry. Condylar liftoff and screw-home rotation are typical kinematic features of all TKAs.
Continuous anti-solvent method for the production of liposomes (2010)

International audience
Aerosol Exposure to the Angola Strain of Marburg Virus Causes Lethal Viral Hemorrhagic Fever in Cynomolgus Macaques (2010)

Cynomolgus macaques were exposed to the Angola strain of Lake Victoria Marburg virus (MARV) by aerosol to examine disease course and lethality. Macaques became febrile 4 to 7 days postexposure; the peak febrile response was delayed 1 to 2 days in animals that received a lower dose; viremia coincided with the onset of fever. All 6 macaques succumbed to the infection, with the 3 macaques in the low-dose group becoming moribund on day 9, a day later than the macaques in the high-dose group. Gross pathologic lesions included maculopapular cutaneous rash; pulmonary congestion and edema; pericardial effusion; enlarged, congested, and/or hemorrhagic lymphoid tissues; enlarged friable fatty liver; and pyloric and duodenal congestion and/or hemorrhage. Fibrinous interstitial pneumonia was the most consistent pulmonary change. Lymphocytolysis and lymphoid depletion, as confirmed by TUNEL (terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling), were observed in the mediastinal lymph nodes and spleen. MARV antigen was detected in the lungs, mediastinal lymph nodes, spleen, and liver of all animals examined. In infected macaques, nuclear expression of interleukin-33 was lost in pulmonary arteriolar and mediastinal lymph node high endothelial venule endothelial cells; interleukin-33-positive fibroblastic reticular cells in the mediastinal lymph node were consistently negative for MARV antigen. These macaques exhibited a number of features similar to those of human filovirus infections; as such, this model of aerosolized MARV-Angola might be useful in developing medical countermeasures under the Animal Rule.
Data for: Optimization of the ITER Vertical Neutron Camera Detectors and Collimators (2021)

Calculation results for fission chambers and diamond detectors for different geometries. FC_LOW - fission chambers with low sensitivity FC_HIGH - fission chambers iwth high sensitivity DD_1 and DD_2 - neutron spectra in diamond detectors.
Electropulsation as an alternative method for protein extraction from yeast (1999)

The application of series of high intensity electric pulses to a yeast suspension provoked a considerable release of some cytoplasmic proteins, glutathione reductase, 3-phosphoglycerate kinase and alcohol dehydrogenase. A maximal yield was achieved 3–8 h after pulsation. The electro-induced protein efflux was accelerated by pretreatment with the reducing agent dithiothreitol and showed a strong dependence on the growth phase and the presence of monovalent ions in the post-pulse incubation medium. The results obtained for two strains of Saccharomyces cerevisiae, PV3 (diploid) and Y47 (wild haploid), showed that electropulsation can be used for the effective extraction of cytoplasmic proteins with a preserved functional activity.