gebhart/patrepeval huggingface dataset:
Amino acid sequence analysis of the annexin super‐gene family of proteins (1991)

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of the predictions and shows the power of techniques for the determination of tertiary structural information from the amino acid sequences of an aligned protein family.
Efficient Multiple Aggregations of Stream Data (2007)

Recently there has been a great deal of interests in analyzing stream data that can be seen in applications such as network monitoring, web click stream analysis, and sensor networks. Multiple aggregations are regarded as one of the important operations for the high level analysis of stream data as well as business data. However, existing multiple aggregation algorithms for business data are not adequate for stream data because aggregation should be done on a rapidly flowing unsorted data stream, which requires tremendous amount of time and space. We propose an algorithm for efficiently generating user selected aggregation tables from unsorted data stream. For fast aggregation, we use a combination of arrays and AVL trees as temporary storage of aggregation tables. The proposed algorithm can also be used for the cases where aggregation tables are too large to be stored in main memory during aggregation. We showed by experiments that our algorithm is practical.
Age‐related changes in the lipid compositions of rat and human tissues (1989)

Abstract The levels of cholesterol, ubiquinone, dolichol, dolichyl‐P, and total phospholipids in human lung, heart, spleen, liver, kidney, pancreas, and adrenal from individuals from one‐day‐old to 81 years of age were investigated and compared with the corresponding organs from 2 to 300 day‐old rats. The amount of cholesterol in human tissues did not change significantly during aging, but the level of this lipid in the rat was moderately elevated in the organs of the oldest animals. In human pancreas and adrenal the ubiquinone content was highest at one year of age, whereas in other organs the corresponding peak value was at 20 years of age, and was followed by a continuous decrease upon further aging. A similar pattern was observed in the rats, with the highest concentration of ubiquinone being observed at 30 days of age. Dolichol levels in human tissues increase with aging, but they increase to very different extents. In the lungs this increase is seven‐fold, and in the pancreas it is 150‐fold. The elevation in the dolichol contents of rat tissues ranges from 20 to 30‐fold in our material. In contrast, the levels of the phosphorylated derivative of dolichol increased to a more limited extent, i.e., 2 to 6‐fold in human tissues and even less in the rat. These results demonstrate that the levels of a number of lipids in human and rat organs are modified in a characteristic manner during the life‐span. This is in contrast to phospholipids, which constitute the bulk of the cellular lipid mass.
Toxicology and Dermatology (1965)

Journal Article Toxicology and Dermatology Get access INDUSTRIAL TOXICOLOGY AND DERMATOLOGY IN THE PRODUCTION AND PROCESSING OF PLASTICS by K.E. Malten and R.L. Zielhuis. Elsevier 1964. pp. 258. H. OWEN H. OWEN Search for other works by this author on: Oxford Academic PubMed Google Scholar Occupational Medicine, Volume 15, Issue 1, January 1965, Page 75, https://doi.org/10.1093/occmed/15.1.75-a Published: 01 January 1965
<p>Azithromycin-liposomes as a novel approach for localized therapy of cervicovaginal bacterial infections</p> (2019)

The performed studies confirm the potentials of AZI-liposomes for localized cervicovaginal therapy.
Immunocytochemical identification of estrogen receptor in ovarian carcinomas. Localization with monoclonal estrophilin antibodies compared with biochemical assays. (1985)

Estrogen receptor (estrophilin) has been identified in ovarian carcinomas by a variety of physicochemical methods. Since these methods require disruption of the tissue, they do not provide any anatomic information about the cellular distribution and location of receptor. The authors have used monoclonal estrophilin antibodies and an indirect immunoperoxidase technique to study the immunocytochemical localization of estrogen receptor in 43 tissue samples of ovarian carcinoma from 27 patients. The immunocytochemical findings were compared with the results of conventional estrogen receptor assays of cytosolic and nuclear extracts prepared from adjacent pieces of ovarian carcinoma. Exclusively nuclear localization of estrogen receptor was observed with the immunocytochemical technique in all of the 25 tumor samples which had a cytosolic estrogen receptor content, determined by either the dextran-coated charcoal or hydroxylapatite techniques, greater than 700 fmoles/gm wet weight of tissue. Only 3 of 16 tumor samples with cytosolic estrophilin concentrations of less than 700 fmoles/gm wet weight displayed nuclear staining for estrogen receptor; two of these three were metastases from receptor-rich primaries. Specific cytoplasmic staining for estrogen receptor was not observed. These results indicate that many ovarian carcinomas have estrogen receptor, predominantly localized in the nucleus, which is similar to tissues of the female genital tract (vagina, cervix, endometrium, fallopian tube) and breast carcinoma.
A biophysical protein folding model accounts for most mutational fitness effects in viruses (2011)

Fitness effects of mutations fall on a continuum ranging from lethal to deleterious to beneficial. The distribution of fitness effects (DFE) among random mutations is an essential component of every evolutionary model and a mathematical portrait of robustness. Recent experiments on five viral species all revealed a characteristic bimodal-shaped DFE featuring peaks at neutrality and lethality. However, the phenotypic causes underlying observed fitness effects are still unknown and presumably, are thought to vary unpredictably from one mutation to another. By combining population genetics simulations with a simple biophysical protein folding model, we show that protein thermodynamic stability accounts for a large fraction of observed mutational effects. We assume that moderately destabilizing mutations inflict a fitness penalty proportional to the reduction in folded protein, which depends continuously on folding free energy (ΔG). Most mutations in our model affect fitness by altering ΔG, whereas based on simple estimates, ~10% abolish activity and are unconditionally lethal. Mutations pushing ΔG > 0 are also considered lethal. Contrary to neutral network theory, we find that, in mutation/selection/drift steady state, high mutation rates (m) lead to less stable proteins and a more dispersed DFE (i.e., less mutational robustness). Small population size (N) also decreases stability and robustness. In our model, a continuum of nonlethal mutations reduces fitness by ~2% on average, whereas ~10-35% of mutations are lethal depending on N and m. Compensatory mutations are common in small populations with high mutation rates. More broadly, we conclude that interplay between biophysical and population genetic forces shapes the DFE.
Polar Codes (2020)

Abstract Polar codes have been recently adopted as control channel coding scheme for upcoming 5G NR framework. Their mathematical foundations lay on the polarization effect, whose discovery in late 2000s represented a real breakthrough for the information theory community. In order to be included in an industrial standard, polar codes went through a refinement process that permitted 3GPP to improve their error correcting performance while keeping a limited decoding latency. The results of these efforts is a synthesis of all known advancements in the field and truly represents the state‐of‐the‐art of polar coding knowledge today.
Collective Segmentation and Labeling of Distant Entities in Information Extraction (2004)

In information extraction, we often wish to identify all mentions of an entity such as a person or organization. Traditionally a group of words is labeled as an entity based only on local information. But information from throughout a document can be useful; for example if the same word is used multiple times it is likely to have the same label each time. We present a CRF that explicitly represents dependencies between the labels of pairs of similar words in a document. On a standard information extraction data set we show that learning these dependencies leads to a 13.7% reduction in error on the field that had caused the most repetition errors.
Plasma Vascular Endothelial Growth Factor-A (VEGF-A) and VEGF-A Gene Polymorphism are Associated with Hydrocele Development in Lymphatic Filariasis (2007)

Hydrocele is a build-up of fluid in the scrotal regions of a proportion of men infected with the filarial nematode Wuchereria bancrofti. Vascular endothelial growth factors (VEGF) are major mediators of vascular permeability and angiogenesis in the development and progression of many diseases, making them candidates in hydrocele development. We assessed the role of VEGF-A genetic polymorphisms in hydrocele development in a cohort of lymphatic filariasis patients from Ghana. Three VEGF-A promoter polymorphisms were examined. The C/C genotype at -460 was significantly higher in hydrocele patients ([P = 0.0007], OR = 3.8 [95% CI = 1.9-8.2]) than in non-hydrocele patients. Furthermore, plasma levels of VEGF-A were significantly higher in subjects with the C/C genotype than in those with other genotypes. Also, a positive correlation (R(2) = 0.412, P = 0.026) was observed between plasma VEGF-A and stage of hydrocele. The data suggest that the C polymorphism at -460 is a genetic risk factor for hydrocele development in lymphatic filariasis.
Immunogenicity of a ‘pre‐S2 plus S’ hepatitis B vaccine in healthy adults (1994)

The product of the pre-S plus S gene of hepatitis B virus appears to be more immunogenic in mice than the S-gene product (HBsAg) alone. Therefore, we tested the immunogenicity in healthy adults of a hepatitis B vaccine containing the 'middle protein' gene product of pre-S2 plus S (pre-S vaccine). We compared the immunogenicity of three doses of the pre-S vaccine with that of a commercially available recombinant hepatitis B vaccine (Recombivax-HB); 87 seronegative adults were randomized to receive 12 micrograms (group 1), 24 micrograms (group 2), or 48 micrograms (group 3) of the pre-S vaccine or 10 micrograms of Recombivax-HB (group 4) by deltoid injection at 0, 1 and 6 months. Antibody to HBsAg (anti-HBs) appeared after booster vaccination in > or = 94% of vaccinees. Immunogenicity was best in recipients of 48 micrograms of the pre-S vaccine and Recombivax-HB, and geometric mean titres (GMT) for the pre-S vaccine were higher than those for Recombivax-HB only at the pre-S vaccine dose of 48 micrograms (group 3). Antibody to pre-S2 developed in 75% of the pre-S2 vaccine recipients (not in Recombivax-HB recipients) within 7 months. These findings indicate that the pre-S vaccine is immunogenic in healthy adults but that a dose of 48 micrograms of the current formulation is required to equal or exceed the immunogenicity of currently available, recombinant S-only vaccine. Studies in non-responders to S-only vaccines will be necessary to define an immunological advantage of the pre-S vaccines, and additional assessments will be necessary to determine whether anti-pre-S2 enhances protective efficacy.
Adenovirus Knob Trimers as Tailorable Scaffolds for Nanoscale Assembly (2008)

The biomimetic assembly of nanoparticles into controllable nanostructures hinges on the ability to regulate system reactivity. The introduction of structural elements with predesigned symmetries and quantized number of binding sites may aid in this effort. Symmetric adenovirus knob proteins are used as scaffolds for nano-assembly (see image). By way of genetic mutation, solvent-accessible Cys residues are incorporated onto a knob's trimeric surface, and the resulting symmetric tridentate crosslinker is shown to possess tunable assembly characteristics with gold nanoparticles.
Regulating Gene Expression With Light-Activated Oligonucleotides (2014)

The work in this thesis identifies new photochemical approaches to gain high spatiotemporal control over molecular structure and function, for broad applications in materials and biological science. "Caged" compounds provide a method for temporarily blocking function until acted upon by an external trigger, typically near-UV light. To enable multiplexing studies, three new biomolecular caging strategies were developed that can be activated with various wavelengths of near-UV or visible light. The first method, an oligonucleotide hairpin structure incorporating one or two nitrobenzyl photolinkers, was applied to a miRNA antagomir and used to "turn off" let-7 miRNA in zebrafish embryos with 365 nm light. To achieve bidirectional control over miRNA, a circular construct was designed for the ability to "turn on" the release of exogenous miRNA into zebrafish embryos with 365 nm light. A second oligonucleotide caging method, using a ruthenium-based photolinker (RuBEP), was designed to extend photoactivation to the visible spectrum, with additional potential for two-photon activation. RuBEP was used to cage antisense morpholinos through circularization via a Cu(I)-mediated [3+2] Huisgen cycloaddition reaction. RuBEP-caged morpholinos were photoactivated to "turn on" antisense activity and successfully knocked down zebrafish chd and ntl genes with 450 nm light, with limited background activity prior to irradiation. A third method of caging was based on encapsulation within photoresponsive nano-polymersomes. Self-assembly of nano-polymersomes was optimized to generate visible-light-responsive vesicles that incorporate a porphyrin dimer in the hydrophobic membrane. These nanovesicles were shown to encapsulate a variety of cargo, including 25mer oligonucleotides, a small molecule fluorescent dye, and two biologically relevant metal ions, Zn2+ and Ca2+. The photoresponsiveness of the system was modulated with light wavelength, irradiation time, and the presence of dextran in the aqueous core.
Transition Metal-Doped Sb2Te3 and Bi2Te3 Diluted Magnetic Semiconductors (2007)

Motivated by the discovery of the ferromagnetic order in V-doped Sb2Te3 and Fe-doped Bi2Te3 bulk crystals, the study of the transition metal (TM) doped tetradymite-type semiconductors was extended to their thin film forms with the hope of significantly increasing the content of TM and thus enhancing the Curie temperature. High quality Sb2-xVxTe3 (x up to 0.35) and Sb2-xCrxTe3 (x up to 0.59) epitaxial films have been successfully prepared on sapphire (0001) substrates by non-equilibrium MBE growth technique, and their structural, transport and magnetic properties have been determined. Magnetization studies, Arrott plot analyses, and anomalous Hall effect measurements indicate that long range magnetic order persists to temperatures of at least 177K (in the case of Sb2-xVxTe3) and 190K (for Sb2-xCrxTe3). The observed carrier mediated, p-type favored ferromagnetic behavior supports a scenario of RKKY interaction with mean-field approximation. Bi2-xFexTe3 samples have also been prepared (for x up to 0.46), and they displayed n-type behavior and no signature of spontaneous magnetic ordering down to 2K. Trilayer structures with a normal Sb2Te3 layer sandwiched between two ferromagnetic Sb2-xCrxTe3 layers were fabricated in order to explore the influence of the interlayer exchange coupling mechanism (IEC). Such coupling was found to be present for small thickness of the spacer layer at low temperatures. Transition metal-doped tetradymite-type semiconductors represent a new class of diluted magnetic semiconductors that are octahedrally coordinated and that possess highly anisotropic structural and magnetic properties.
Loss of αT-catenin alters the hybrid adhering junctions in the heart and leads to dilated cardiomyopathy and ventricular arrhythmia following acute ischemia (2012)

It is generally accepted that the intercalated disc (ICD) required for mechano-electrical coupling in the heart consists of three distinct junctional complexes: adherens junctions, desmosomes and gap junctions. However, recent morphological and molecular data indicate a mixing of adherens junctional and desmosomal components, resulting in a 'hybrid adhering junction' or 'area composita'. The α-catenin family member αT-catenin, part of the N-cadherin-catenin adhesion complex in the heart, is the only α-catenin that interacts with the desmosomal protein plakophilin-2 (PKP2). Thus, it has been postulated that αT-catenin might serve as a molecular integrator of the two adhesion complexes in the area composita. To investigate the role of αT-catenin in the heart, gene targeting technology was used to delete the Ctnna3 gene, encoding αT-catenin, in the mouse. The αT-catenin-null mice are viable and fertile; however, the animals exhibit progressive cardiomyopathy. Adherens junctional and desmosomal proteins were unaffected by loss of αT-catenin, with the exception of the desmosomal protein PKP2. Immunogold labeling at the ICD demonstrated in the αT-catenin-null heart a preferential reduction of PKP2 at the area composita compared with the desmosome. Furthermore, gap junction protein Cx43 was reduced at the ICD, including its colocalization with N-cadherin. Gap junction remodeling in αT-catenin-knockout hearts was associated with an increased incidence of ventricular arrhythmias after acute ischemia. This novel animal model demonstrates for the first time how perturbation in αT-catenin can affect both PKP2 and Cx43 and thereby highlights the importance of understanding the crosstalk between the junctional proteins of the ICD and its implications for arrhythmogenic cardiomyopathy.
Colorectal cancer: risk factors and recommendations for early detection. (1999)

Spurred by mounting evidence that the detection and treatment of early-stage colorectal cancers and adenomatous polyps can reduce mortality, Medicare and some other payors recently authorized reimbursement for colorectal cancer screening in persons at average risk for this malignancy. A collaborative group of experts convened by the U.S. Agency for Health Care Policy and Research has recommended screening for average-risk persons over the age of 50 years using one of the following techniques: fecal occult blood testing each year, flexible sigmoidoscopy every five years, fecal occult blood testing every year combined with flexible sigmoidoscopy every five years, double-contrast barium enema every five to 10 years or colonoscopy every 10 years. Screening of persons with risk factors should begin at an earlier age, depending on the family history of colorectal cancer or polyps. These recommendations augment the colorectal cancer screening guidelines of the American Academy of Family physicians. Recent advances in genetic research have made it possible to identify persons at high risk for colorectal cancer because of an inherited predisposition to develop this malignancy. These patients require aggressive screening, usually by lower endoscopy performed at an early age. In some patients, genetic testing can guide screening and may be cost-effective.
Mountain meteorology: fundamentals and applications (2000)

Preface About the author Acknowledgments PART 1. MOUNTAIN CLIMATES 1. Four factors that determine climate PART 2. AN INTRODUCTION TO THE ATMOSPHERE 2. Mountain climates of North America 3. Atmospheric scales of motion and atmospheric composition 4. Vertical structure, temperature, stability and the atmospheric boundary layer 5. Pressure and winds 6. Air masses and fronts 7. Clouds and fogs 8. Precipitation 9. Weather maps, forecasts and data PART 3. MOUNTAIN WINDS 10. Terrain-forced flows 11. Diurnal mountain winds PART 4. SELECTED APPLICATIONS OF MOUNTAIN METEOROLOGY 12. Air pollution dispersion 13. Fire weather and smoke management 14. Aerial spraying References Appendices Glossary Acronyms Abbreviations Index
Tunneling spectroscopy and spectroscopic imaging of granular metallicity of polyaniline (1999)

The band-gap electronic structures of two forms of the conducting polymer polyaniline, emeraldine base (EB) and emeraldine salt (ES), have been studied. Tunneling spectroscopy measurements show that ES is metallic in nature with a finite electron density of state at the Fermi energy (EF), while EB behaves as an insulator with a gap at EF in agreement with theoretical calculations. These results allowed us to obtain direct evidence of the granular metallicity of ES by spectroscopic imaging. The spectroscopic images show different spatial distributions of nanometer-sized metallic particles in ES and EB samples, providing important information needed in studying electrical conductivities of conducting polymers.
Whiskers of poly(3‐alkylthiophene)s (1993)

Abstract It is shown that poly(3‐alkylthiophene)s may readily crystallize from poor solvents in the form of whiskers. The experimental conditions required for the formation of whiskers were found to depend upon the alkyl side‐chain length, solvent quality, and temperature. In all cases studied for alkyl side‐chain lengths of 3‐12 carbon atoms, the widths of the whiskers were of the order of 15nm, while their lengths often exceeded tens of microns. The thickness of the whiskers formed under the experimental conditions employed was found to scale with side‐chain length, and was approximately 2 or 3 times the a/2 lattice dimension of the polymer unit cell. Packing of the macromolecules within the whiskers was such that the polymer backbones were normal to the whisker length; that is, the b‐axis was oriented parallel to the long axis of the whiskers. These results are thought to be relevant to known thermochromism phenomena associated with poly(3‐alkylthiophene)s. © 1993 John Wiley & Sons, Inc.