gebhart/patrepeval huggingface dataset:
Herpes simplex virus type 1 ICP27 is an essential regulatory protein (1985)

The five immediate-early genes of herpes simplex virus are expressed during the initial stages of the infectious cycle, and certain immediate-early proteins have been shown to play a regulatory role in subsequent viral gene expression. Until recently, the functional properties of only one immediate-early protein, ICP4, had been examined in any detail, primarily because mutants had been isolated only in the gene for ICP4. We report herein the genetic and phenotypic characterization of four temperature-sensitive mutants of herpes simplex virus type 1 (tsY46, tsE5, tsE6, and tsLG4) that have begun to elucidate the function(s) of a second immediate-early protein, ICP27. The four mutants complemented each other inefficiently or not at all, indicating that they are defective in the same function. Marker rescue tests placed the mutations in tsY46 and tsE5 in sequences that encode the transcript for ICP27; the mutations in tsE6 and tsLG4 lie in or near these sequences. The ability of wild-type ICP27 expressed from a cloned gene to complement tsY46 and tsLG4 constitutes additional evidence that these mutants are defective in an ICP27-associated function. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of mutant-infected cell polypeptides showed that certain immediate-early (alpha) polypeptides were overproduced, whereas significant levels of early (beta) and drastically reduced levels of several late (gamma) proteins were synthesized at the nonpermissive temperature. Interestingly, the mutants were observed to form a spectrum with regard to their relative abilities to induce the expression of a number of polypeptides, especially those of the delayed-early (beta gamma) class. Consistent with their ability to induce expression of early polypeptides, all of the mutants induced the synthesis of substantial levels of viral DNA at the nonpermissive temperature. Taken together, the results of these studies demonstrate that ICP27 plays an essential regulatory function in virus replication, that this function is required after the onset of early gene expression and viral DNA synthesis, and that the inability of the mutants to induce the synthesis of late proteins is independent of viral DNA synthesis.
UV Irradiation Effects on Seed Germination and Growth, Protein Content, Peroxidase and Protease Activity in Red Bean (2012)

Ultraviolet radiation is energetically capable of disrupting proteins. Ultraviolet radiations are divided into three bands included UV-A (320-390 nm), UV-B (280-320 nm) and UV-C(254-280nm). Several studies have indicated that enhanced UV-B radiation can deleteriously affect physiological processes and overall growth in some plants species.Bean Sayad and Bean Derakhshan seeds irradiated with 220 to 400 nm UV rays were grown in incubator for 8 days at 25±°C. Germination, growth (seedling fresh weight, root shoot length and their ratio), lipid peroxidation, protease and peroxidase activity were measured in leaves. Results showed that percent germination of the seeds and the rates of growth of sprouts were inversely related to the irradiation doses. In Derakhshan, peroxidase and protease activities (two folds) and MDA contents were higher as compared to Bean Sayad while vice versa for protein contents, revealing inherent differences between two types. Data for protein contents, peroxidase and protease activities therefore suggested that irradiation dose should not under 300nm UV in Bean Derakhshan and also 300nm UV in Bean Sayad. In Bean Derakhshan 320 to 400 nm UV irradiation dose non-significantly affected the protein contents and peroxidase activity and uppered MDA contents and protease activity. In Bean Sayad 300 nm UV irradiation dose increased the peroxidase activity,uppered the MDA contents and affect the protein content and protease activity. It was concluded that protein contents, protease, peroxidase and lipid peroxidation may be used in early assessment of effectiveness and superiority of radiation dose to induce mutations.
Differential Ligand Recognition by the Src and Phosphatidylinositol 3-Kinase Src Homology 3 Domains:  Circular Dichroism and Ultraviolet Resonance Raman Studies (2002)

Src homology 3 (SH3) domains recognize Pro-rich motifs using a hydrophobic cleft which contains several conserved aromatic residues. To investigate how aromatic residues contribute to ligand recognition, circular dichroism (CD) and 235 nm excited ultraviolet resonance Raman spectroscopies have been applied to Src and phosphatidylinositol 3-kinase (PI3K) SH3s. The CD analysis shows that Src SH3 binds to RPLPPLP (R-core) using aromatic residues with a dissociation constant (K(d)) of 10 microM. Moreover, intensity increases of the Trp and Tyr Raman bands suggest that the interaction is mediated by hydrophobic contacts and/or hydrogen bond formation with both Trp and Tyr residues. In the interaction of Src SH3 with VSLARRPLPPLP (VSL12) (K(d) 0.8 microM), Trp118 appears to form a strong hydrogen bond with VSL12, judging from significant intensity increases of the Trp Raman bands and the reported complex structure. In contrast, PI3K SH3 binds to R-core and VSL12 with lower affinities (K(d) 34 and 18 microM, respectively), and the interactions are suggested to be mediated mainly by hydrophobic contacts and/or hydrogen bond formation with Tyr residue(s). In the D21N mutant (Asp21 --> Asn) of PI3K SH3, whose hydrophobic cleft is deformed, Trp55 is shown to be responsible for the interaction with VSL12 by intensity increases of the Trp Raman bands. However, the affinity is severely decreased (K(d) 330 microM). These observations imply that SH3 domains associate with their ligands with distinct use of aromatic residues and that hydrogen bond formation with an SH3-conserved Trp residue in the well-ordered hydrophobic cleft is important for stable complex formation.
Perceptrons an introduction to computational geometry (1969)

Cambridge, Mass.: MIT Press, 1972. 2nd. ed. The book's aim is to seek general results from the close study of abstract version of devices known as perceptrons
Sequential changes in the expression of mitochondrial protein mRNA during the development of brown adipose tissue in bovine and ovine species. Sudden occurrence of uncoupling protein mRNA during embryogenesis and its disappearance after birth (1989)

Samples of adipose tissue were obtained from different sites in bovine and ovine foetuses and newborns. RNA was isolated and analysed using bovine cDNA and ovine genomic probe for uncoupling protein (UCP), cDNA for subunits III and IV of cytochrome c oxidase and cDNA for ADP/ATP carrier. UCP mRNA was characterized for the first time in foetal bovine and ovine adipose tissue. It appeared later than mRNA of cytochrome c oxidase subunit III, and increased dramatically at birth (10-fold). ADP/ATP carrier mRNA was expressed at a lower level but also increased 10-fold at birth. It was demonstrated that UCP mRNA reached its highest level at birth in all bovine adipose tissues studied, except subcutaneous tissue. It disappeared quickly afterwards, being no longer detectable two days after birth. Similar variations were observed in newborn lambs. ADP/ATP carrier mRNA showed the same pattern of expression as UCP mRNA; although it was still lightly expressed two days after birth, it disappeared soon afterwards. Only mRNAs for cytochrome c oxidase subunits III and IV remained at the same level during the first postnatal week. On the basis of these data and of observations reported in the literature a sequence of events for the development of brown adipose cells in vivo is proposed. Soon after birth the perirenal adipose tissue of ruminants, which still contains mitochondria of typical brown adipose tissue morphology and high levels of cytochrome c oxidase mRNA, lacks UCP mRNA. Can it still be considered as brown fat? Ruminant species appear to be attractive models to study both the differentiation of brown adipose tissue and its possible conversion to white fat in large animals.
Purification and characterization of a template-associated protein kinase that phosphorylates RNA polymerase II (1993)

We have recently shown that a template-associated protein kinase, which phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II, is a two-component system. We describe here the purification of these two components to apparent homogeneity from human (HeLa) cell nuclear extract. Kinase component A has a 340-kDa native molecular mass, consists of a single large polypeptide, and contains the kinase active site. Kinase component B, which is identical to the Ku autoantigen, has a 180-kDa native molecular mass, and consists of apparently equimolar 67- and 83-kDa polypeptides. Component B stimulates the activity of component A, and under some conditions, confers DNA dependence on the reaction. The purified kinase converts the CTD to the multiply phosphorylated CTD0 form. Conversion occurs processively, and this processivity is an inherent property of component A. The in vitro phosphorylated CTD0 form contains approximately equimolar phosphoserine and phosphothreonine, but no detectable phosphotyrosine.
Expression of CCL18 and interleukin-6 in the plasma of breast cancer patients as compared with benign tumor patients and healthy controls. (2011)

A growing body of laboratory research has shown that pro-inflammatory cytokines can facilitate tumor growth and metastasis. Our goal was to quantify the expression of CCL18 and IL-6 in patients with breast cancer compared with benign breast tumors patients and healthy women, in order to evaluate if these cytokines could serve for breast cancer diagnosis and evaluation. We also correlated the cytokines level of expression with some clinical and pathological characteristics known as prognostic markers for breast cancer. Plasma samples were obtained before treatment from 58 breast cancers, 41 benign breast tumors and 30 healthy women. The quantitative dosage was performed using ELISA. Wilcoxon test was used to compare groups. IL-6 and CCL18 were dramatically upregulated in breast cancers in comparison with healthy controls, but in comparison with benign tumors only CCL18÷PARC was overexpressed at borderline significance in cancers (p=0.05). The plasma from benign breast tumor patients exhibited also significant higher levels of the two cytokines than normal controls. The cytokines profile was not linked to patient age, tumor size, histopathological type, lymph node status or histological grade. IL-6 was significantly upregulated in ER-positive and metastasized cancers. CCL18÷PARC presented a significantly higher expression in advanced stage and highly proliferative carcinomas. In summary, IL-6 and CCL18 could clearly distinguish between women with breast cancers and healthy controls. High expression of IL-6 seems to confer a poor prognosis for ER-positive cancers. CCL18 was associated with worse prognosis parameters like high Ki67.
Glial Neuronal Ratio: A Novel Index for Differentiating Injury Type in Patients with Severe Traumatic Brain Injury (2011)

Neurobiochemical marker levels in blood after traumatic brain injury (TBI) may reflect structural changes detected by neuroimaging. This study evaluates whether correlations between neuronal (ubiquitin carboxy-terminal hydrolase-L1 [UCH-L1]) and glial (glial fibrillary acidic protein [GFAP]) biomarkers may be used as an indicator for differing intracranial pathologies after brain trauma. In 59 patients with severe TBI (Glasgow Coma Scale [GCS] score≤8) serum samples were obtained at the time of hospital admission and analyzed for UCH-L1 and GFAP. Glial neuronal ratio (GNR) was evaluated as the ratio between GFAP and UCH-L1 concentrations. A logistic regression analysis was used to identify variables associated with type of injury. GNR had a median of 0.85 and was positively correlated with age (R=0.45, p=0.003). Twenty-nine patients presented with diffuse injury and 30 with focal mass lesions as assessed by CT scan at admission and classified according to the Marshall Classification. GNR was significantly higher in the focal mass lesion group compared with the diffuse injury group (1.77 versus 0.48, respectively; p=0.003). Receiver operating characteristic curve analysis showed that GNR discriminated between types of injury (area under the curve [AUC]=0.72; p=0.003). GNR was more accurate earlier (≤12 h after injury) than later (AUC=0.80; p=0.002). Increased GNR was independently associated with type of injury, but not age, gender, GCS score, or mechanism of injury. GNR was significantly higher in patients who died, but was not an independent predictor of death. The data from the present study indicate that GNR provides valuable information about different injury pathways, which may be of diagnostic significance. In addition, GNR may help to identify different pathophysiological mechanisms following different types of brain trauma, with implications for therapeutic interventions.
Surface morphology and stress analysis of piezoelectric strontium-doped lead zirconate titanate thin films (2006)

Strontium-doped lead zirconate titanate (PSZT) is a piezoelectric ceramic with relatively high values of piezoelectric coefficients. Perovskite oriented PSZT thin films are also reported to exhibit a variety of other properties including ferroelectricity and pyroelectricity. This paper reports on a study of the surface morphology and resulting stress of PSZT thin films, deposited under a variety of RF magnetron sputtering conditions. The study compares PSZT thin films deposited on metal (gold and platinum) coated silicon wafers. The surface morphology of the deposited PSZT thin films was studied using Atomic Force Microscopy (AFM). Grain size and average surface roughness measurements were used to study the quality of the films. The thin film stress was determined using the changes in the radius of curvature of the sample due to an added layer of thin film, and by applying Stoney's equation to relate the stress to the radius of curvature. The variations in the level of stress for different thermodynamic conditions during RF magnetron sputter deposition are also reported.
Mix-and-Match Riboswitches (2006)

Riboswitches are noncoding RNA elements found in the 5'-untranslated region of messenger RNA (mRNA) that mediate gene expression in a cis fashion in the absence of protein. This common regulatory strategy in bacteria is achieved through the interplay of two distinct domains: an aptamer domain responsible for sensing intracellular concentrations of a specific metabolite and a domain containing a secondary structural switch directly controlling expression. In a recent study, riboswitches have been discovered that are capable of regulating transcription by using an RNA architecture mimicking a Boolean NOR logic gate. Tandem arrangement of elements that recognize S-adenosylmethionine and coenzyme B12 yields an mRNA that is only expressed when both metabolites are in low concentration in the cell.
Mechanistic biomarkers for cytotoxic acute kidney injury (2006)

Acute kidney injury is a common condition and is associated with a high mortality rate. It has been recognised that routinely used measures of renal function, such as levels of blood urea nitrogen and serum creatinine, increase significantly only after substantial kidney injury occurs and then with a time delay. Insensitivity of such tests delays the diagnosis in humans, making it particularly challenging to administer putative therapeutic agents in a timely fashion. Furthermore, this insensitivity affects the evaluation of toxicity in preclinical studies by allowing drug candidates, which have low, but nevertheless important, nephrotoxic side effects in animals, to pass the preclinical safety criteria only to be found to be clinically nephrotoxic with great human costs. This review presents the current status of sensitive and specific biomarkers to detect preclinical and clinical renal injury and summarises the techniques used to quantitate these biomarkers in biological fluids.
Iron–ligand bonding properties of synthetic iron–porphyrin complexes with oxygen transporting ability in aqueous media (1987)

Mössbauer spectra, i.r. spectra (Fe–CO stretching), and photodissociation quantum yields of the oxygen and CO adducts were measured for synthetic iron–porphyrin complexes with oxygen transporting ability in aqueous media: the 5,10,15,20-tetra{α-o-[2′,2′-dimethyl-20′-(2″-trimethyl-ammonioethylphosphonatoxy)eicosanamido]phenyl}porphyrinatoiron(II)(lipid-heme) complex of 1-laurylimidazole (lauryl = dodecyl) or 1-lauryl-2-methylimidazole embedded in the bilayer of phospholipid liposome (abbreviated as liposome–lipid-heme) and the tetradecyl-substituted copper–iron(II)–diporphyrin (diheme) complex of 1-laurylimidazole solubilized in a surfactant micelle (micelle–diheme). The quadrupole splitting (ΔEQ) for the CO adduct of the diheme indicated a large electric-field gradient at the iron nucleus, probably due to steric hindrance of the diheme structure. Its CO-stretching vibration (νCO) and photodissociation quantum yield (Φ), obtained by flash photolysis, were similar to those of carboxy hemoproteins and suggested the distorted ligation of CO to Fe. Mössbauer parameters for the oxygen adducts of liposome–lipid-heme and micelle–diheme in aqueous media agreed with those for the oxy hemoproteins.
Recombinant retroviruses encoding human papillomavirus type 18 E6 and E7 genes stimulate proliferation and delay differentiation of human keratinocytes early after infection. (1992)

Human papillomavirus (HPV) DNAs are detected in most genital dysplasias and cancers, suggesting that these viruses perturb epithelial growth and differentiation. The E6 and E7 genes of HPV type 18 induce immortality in keratinocytes cultured from genital tract epithelia, and the immortal cell lines display aberrant squamous differentiation. To examine whether the E6 and E7 proteins directly alter keratinocyte growth and differentiation, high-titer recombinant retroviruses were constructed for efficient transfer and expression of HPV-18 genes E6, E6* and E7 in cultures of normal human keratinocytes. Infection with retroviruses encoding E6 and E7 stimulated cell proliferation, reduced the requirement for bovine pituitary extract and induced immortality. E6 and E7 also delayed but did not prevent the onset of terminal squamous differentiation. The magnitude of effects on growth and differentiation of cultured cells was directly related to levels of E7 protein expression. Thus, expression of the HPV-18 E6 and E7 genes stimulates cell proliferation and delays differentiation of keratinocytes in vitro.
The alpha and beta chains of human platelet glycoprotein Ib are both transmembrane proteins containing a leucine-rich amino acid sequence. (1988)

The primary structure of the beta chain of human glycoprotein Ib (GPIb), the platelet receptor for von Willebrand factor, has been established by a combination of cDNA cloning and amino acid sequence analysis. A lambda phage cDNA expression library prepared from human erythroleukemia cells (HEL cells) was screened with a radiolabeled affinity-purified rabbit polyclonal antibody to the beta chain of GPIb. Eighteen positive clones were isolated and plaque-purified and the nucleotide sequences of three were determined. The composite sequence spanned 968 nucleotides and included a 5' untranslated region of 22 nucleotides, an open reading frame of 618 nucleotides encoding a signal peptide of 28 amino acids and a mature protein of 181 amino acids, a stop codon, and a 3' noncoding region of 307 nucleotides. The 3' noncoding sequence also contained a polyadenylylation signal (AATAAA) 14 nucleotides upstream from the poly(A) tail of 18 nucleotides. Edman degradation of the intact beta chain and of peptides produced by chemical cleavage yielded amino acid sequences spanning 76 residues that were identical to those predicted from the cDNA. The amino-terminal region of the beta chain contains a leucine-rich sequence of 24 amino acids that is similar to a sequence that occurs as seven tandem repeats in the alpha chain of GPIb and nine tandem repeats in leucine-rich alpha 2-glycoprotein. The leucine-rich sequence in the beta chain of GPIb is flanked on both sides by amino acid sequences that are similar to those flanking the leucine-rich tandem repeats of the alpha chain of GPIb and leucine-rich alpha 2-glycoprotein. The amino-terminal region of the beta chain of GPIb is followed by a transmembrane segment of 25 amino acids and an intracellular segment of 34 amino acids at the carboxyl terminus of the protein. The intracellular segment contains an unpaired cysteine and two potential sites for phosphorylation by cAMP-dependent protein kinase.
Pedestrian Detection with Unsupervised Multi-stage Feature Learning (2013)

Pedestrian detection is a problem of considerable practical interest. Adding to the list of successful applications of deep learning methods to vision, we report state-of-the-art and competitive results on all major pedestrian datasets with a convolutional network model. The model uses a few new twists, such as multi-stage features, connections that skip layers to integrate global shape information with local distinctive motif information, and an unsupervised method based on convolutional sparse coding to pre-train the filters at each stage.
Membrane protein structure: experimental approaches (1994)

Part I: The Nature of the Membrane Protein Structure Problem. 1.: D.C. Rees, A.J. Chirino, K.-H. Kim, and H. Komiya: Membrane Protein Structure and Stability: Implications of the First Crystallographic Analyses. 2.: Gunnar von Heijne: Decoding the Signals of Membrane Protein Sequences. 3.: Jean-Luc Popot, Catherine de Vitry, and Ariane Atteia: Folding and Assembly of Integral Membrane Proteins: An Introduction. 4.: Stephen White: Hydropathy Plots and the Prediction of Membrane Protein Topology. Part II: Biochemical and Molecular Biological Approaches: Protein Topology. 5.: David S. Cafiso: Experimental Determination of the Topography of Membrane Proteins: Lessons from the Nicotinic Acetycholine Receptor, a Multisubunit Polytopic Protein. 6.: Dana Boyd: The Use of Gene Fusions to Determine Membrane Protein Topology. 7.: L. Mario Amzel, Mario A. Bianchet, and Peter L. Pederson: The Structure of F1F0ATPases Determined by Indirect and Direct Methods. Part III: Direct Structural Methods. 8.: Robert W. Williams: Experimental Determination of Membrane Protein Secondary Structure using Vibrational and CD Spectroscopies. 9.: Werner Kuhlbrandt: High-Resolution Electron Crystallography of Membrane Proteins. 10.: Wayne L. Hubbell and Christian Altenbach: Site-Directed Spin Labeling of Membrane Proteins. 11.: Stanley J. Opella: NMR Approaches to Membrane Protein Structure. 12.: J. Kent Blasie: Structure of Integral Membrane Proteins within Membranes via X-Ray and neutron Diffraction: From Oriented Multilayers to a Single Monolayer. Part IV: Model and Physiocochemical Approaches. 13.: Lukas K. Tamm: Physical Studies of Peptide-Bilayer Interactions. 14.: G. Andrew Woolley and B.A. Wallace: Membrane Protein Structure: Lessons from Gramicidin. 15.: J.D. Lear, Z.R. Wasserman, and W.F. DeGrado: The Use of Synthetic Peptides for the Study of Membrane Protein Structure. 16.: Isabella L. Karle: Diffraction Studies of Model and Natural Helical Peptides