gebhart/patrepeval huggingface dataset:
Timing the Ancestor of the HIV-1 Pandemic Strains (2000)

HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.
A fully distributed simultaneous strain and temperature sensor using spontaneous Brillouin backscatter (1997)

We report here the first simultaneous measurement of strain and temperature using Brillouin backscatter in an optical fiber. A new sensor arrangement is presented which allows the distributed measurement of Brillouin spectra. Simultaneous measurement of spontaneous Brillouin power and Brillouin shift distributions are made from these spectra, and from this information, we obtain fully distributed measurements of strain and temperature. Our sensor achieves a 100-μ/spl epsiv/ strain and 4/spl deg/C temperature resolution, with 40-m spatial resolution, over a sensing length of 1200 m.
Stimulation of Nonspecific Resistance to Infection by a Crude Cell Wall Preparation from Mycobacterium phlei (1966)

Fox, Alfred E. (Warner-Lambert Research Institute, Morris Plains, N.J.), George L. Evans, Frank J. Turner, Benjamin S. Schwartz, and Ansel Blaustein. Stimulation of nonspecific resistance to infection by a crude cell wall preparation from Myocobacterium phlei. J. Bacteriol. 92:1-5. 1966.-Exposure of large quantities of viable Mycobacterium phlei to attrition in a colloid mill resulted in 90 to 95% disruption of the organisms. Isolation of the crude cell wall preparation was accomplished by centrifugation of the broken cells at 10,000 x g, resuspension of the sediment, and repeated centrifugation at 1,000 x g to remove intact cells. Single oral or parenteral doses of the cell wall preparation increased the resistance of mice and guinea pigs to experimental infection with Salmonella enteritidis, and of mice to Staphylococcus aureus, for prolonged periods after administration. Histological examination of the organs of mice treated orally or intraperitoneally revealed a lymphoid hyperplasia of the spleen and a Kupffer cell proliferation of the liver. The preparation was nontoxic to mice by the oral route at doses up to 5,000 mg/kg, and the intraperitoneal ld(50) was approximately 680 mg/kg.
Estrogen, androgen, glucocorticoid, and progesterone receptors in progestin-induced regression of human breast cancer. (1980)

A study was made of basic mechanisms involved in regression of breast cancer exposed to high levels of synthetic progestins. The possibility that progestins act on breast cancer by way of the progesterone receptor mechanism and subsequent increase of estradiol 17 beta-dehydrogenase activity could not be confirmed in this investigation. It is demonstrated that the progestins megestrol acetate and medroxyprogesterone acetate are strong competitors for steroids which bind specifically to androgen, glucocorticoid, and progesterone receptors, indicating that the progestins are able to bind to these receptors with high affinity. In contrast, these progestins do not compete with estradiol for estrogen receptor binding. In 34 patients with progressive metastatic breast cancer, results of receptor studies have been correlated with clinical response during treatment with megestrol acetate. Statistically, regressions were significantly associated with tumors containing large amounts of androgen receptors. Clinical correlation with the quantities of glucocorticoid receptor was weak, while such correlations with estrogen and progesterone receptors were absent. However, we did demonstrate relationships between the quantities of the various receptors in breast cancer. Tumors containing a large amount of androgen receptors also generally contain estrogen receptors. It might be that a favorable response to progestins is confined to the group of patients with hormone-responsive breast cancers, as such characterized by the presence of estrogen receptors, and that within this group the actual androgen receptor levels determine response.
Optimizing a Tone Curve for Backward-Compatible High Dynamic Range Image and Video Compression (2010)

For backward compatible high dynamic range (HDR) video compression, the HDR sequence is reconstructed by inverse tone-mapping a compressed low dynamic range (LDR) version of the original HDR content. In this paper, we show that the appropriate choice of a tone-mapping operator (TMO) can significantly improve the reconstructed HDR quality. We develop a statistical model that approximates the distortion resulting from the combined processes of tone-mapping and compression. Using this model, we formulate a numerical optimization problem to find the tone-curve that minimizes the expected mean square error (MSE) in the reconstructed HDR sequence. We also develop a simplified model that reduces the computational complexity of the optimization problem to a closed-form solution. Performance evaluations show that the proposed methods provide superior performance in terms of HDR MSE and SSIM compared to existing tone-mapping schemes. It is also shown that the LDR image quality resulting from the proposed methods matches that produced by perceptually-based TMOs.
The Degradation of Hyaluronan in the Skin (2022)

Hyaluronan (HA) comprises a fundamental component of the extracellular matrix and participates in a variety of biological processes. Half of the total amount of HA in the human body is present in the skin. HA exhibits a dynamic turnover; its half-life in the skin is less than one day. Nevertheless, the specific participants in the catabolism of HA in the skin have not yet been described in detail, despite the essential role of HA in cutaneous biology. A deeper knowledge of the processes involved will act to support the development of HA-based topical and implantable materials and enhance the understanding of the various related pathological cutaneous conditions. This study aimed to characterize the distribution and activity of hyaluronidases and the other proteins involved in the degradation of HA in healthy human full-thickness skin, the epidermis and the dermis. Hyaluronidase activity was detected for the first time in healthy human skin. The degradation of HA occurred in lysates at an acidic pH. HA gel zymography revealed a single band corresponding to approximately 50 kDa. This study provided the first comprehensive view of the distribution of canonic HA-degrading proteins (HYAL1 and HYAL2) in human skin employing IHF and IHC. Furthermore, contrary to previous assumptions TMEM2, a novel hyaluronidase, as well as CEMIP, a protein involved in HA degradation, were localized in the human epidermis, as well as in the dermis.
Inhibition of Angiogenesis in Vivo by Plasminogen Activator Inhibitor-1 (2001)

The process of angiogenesis is important in both normal and pathologic physiology. However, the mechanisms whereby factors such as basic fibroblast growth factor promote the formation of new blood vessels are not known. In the present study, we demonstrate that exogenously added plasminogen activator inhibitor-1 (PAI-1) at therapeutic concentrations is a potent inhibitor of basic fibroblast growth factor-induced angiogenesis in the chicken chorioallantoic membrane. By using specific PAI-1 mutants with either their vitronectin binding or proteinase inhibitor activities ablated, we show that the inhibition of angiogenesis appears to occur via two distinct but apparently overlapping pathways. The first is dependent on PAI-1 inhibition of proteinase activity, most likely chicken plasmin, while the second is independent of PAI-1's anti-proteinase activity and instead appears to act through PAI-1 binding to vitronectin. Together, these data suggest that PAI-1 may be an important factor regulating angiogenesis in vivo.
A Novel Family of Small Cysteine-rich Antimicrobial Peptides from Seed of Impatiens balsaminaIs Derived from a Single Precursor Protein (1997)

Four closely related peptides were isolated from seed of Impatiens balsamina and were shown to be inhibitory to the growth of a range of fungi and bacteria, while not being cytotoxic to cultured human cells. The peptides, designated Ib-AMP1, Ib-AMP2, Ib-AMP3, and Ib-AMP4, are 20 amino acids long and are the smallest plant-derived antimicrobial peptides isolated to date. The Ib-AMPs (I. balsamina antimicrobial peptides) are highly basic and contain four cysteine residues which form two intramolecular disulfide bonds. Searches of protein data bases have failed to identify any proteins with significant homology to the peptides described here. Characterization of isolated cDNAs reveals that all four peptides are encoded within a single transcript. The predicted Ib-AMP precursor protein consists of a prepeptide followed by 6 mature peptide domains, each flanked by propeptide domains ranging from 16 to 35 amino acids in length. Such a primary structure with repeated alternating basic mature peptide domains and acidic propeptide domains has, to date, not been reported in plants.
Algorithms on strings, trees, and sequences computer science and computational biology (1997)

Part I. Exact String Matching: The Fundamental String Problem: 1. Exact matching: fundamental preprocessing and first algorithms 2. Exact matching: classical comparison-based methods 3. Exact matching: a deeper look at classical methods 4. Semi-numerical string matching Part II. Suffix Trees and their Uses: 5. Introduction to suffix trees 6. Linear time construction of suffix trees 7. First applications of suffix trees 8. Constant time lowest common ancestor retrieval 9. More applications of suffix trees Part III. Inexact Matching, Sequence Alignment and Dynamic Programming: 10. The importance of (sub)sequence comparison in molecular biology 11. Core string edits, alignments and dynamic programming 12. Refining core string edits and alignments 13. Extending the core problems 14. Multiple string comparison: the Holy Grail 15. Sequence database and their uses: the motherlode Part IV. Currents, Cousins and Cameos: 16. Maps, mapping, sequencing and superstrings 17. Strings and evolutionary trees 18. Three short topics 19. Models of genome-level mutations.
Guidelines for cardiac pacing and cardiac resynchronization therapy: The Task Force for Cardiac Pacing and Cardiac Resynchronization Therapy of the European Society of Cardiology. Developed in Collaboration with the European Heart Rhythm Association (2007)

Guidelines and Expert Consensus Documents summarize and evaluate all currently available evidence on a particular issue with the aim to assist physicians in selecting the best management strategies for a typical patient, suffering from a given condition, taking into account the impact on outcome, as well as the risk–benefit ratio of particular diagnostic or therapeutic means. Guidelines are no substitutes for textbooks. The legal implications of medical guidelines have been discussed previously.

A great number of Guidelines and Expert Consensus Documents have been issued in recent years by the European Society of Cardiology (ESC) as well as by other societies and organizations. Because of the impact on clinical practice, quality criteria for development of guidelines have been established in order to make all decisions transparent to the user. The recommendations for formulating and issuing ESC Guidelines and Expert Consensus Documents can be found on the ESC website (http://www.escardio.org/knowledge/guidelines/rules).

In brief, experts in the field are selected and undertake a comprehensive review of the published evidence for management and/or prevention of a given condition. A critical evaluation of diagnostic and therapeutic procedures is performed including the assessment of the risk/benefit ratio. Estimates of expected health outcomes for larger societies are included, where data exist. The level of evidence and the strength of recommendation of particular treatment options are weighed and graded according to pre-defined scales, as outlined in Tables 1 and  2 .

View this table:

 Table 1 
Classes of recommendations



View this table:

 Table 2 
Levels of evidence



The experts of the writing panels have provided disclosure statements of all relationships they may have which might be perceived as real or potential sources of conflicts of interest. These disclosure forms are kept on file at the European Heart House, headquarters of the ESC. Any changes in conflict of interest that arise during the writing period must be notified …
Multiple-Component Condensation Strategies for Combinatorial Library Synthesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiple-Component Condensation Strategies for Combinatorial Library SynthesisRobert W. Armstrong*Robert W. ArmstrongDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.More by Robert W. Armstrong, Andrew P. CombsAndrew P. CombsDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095More by Andrew P. Combs, Paul A. TempestPaul A. TempestDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095More by Paul A. Tempest, S. David BrownS. David BrownDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095More by S. David Brown, and Thomas A. KeatingThomas A. KeatingDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095More by Thomas A. KeatingCite this: Acc. Chem. Res. 1996, 29, 3, 123–131Publication Date (Web):March 13, 1996Publication History Received16 October 1995Published online13 March 1996Published inissue 13 March 1996https://pubs.acs.org/doi/10.1021/ar9502083https://doi.org/10.1021/ar9502083research-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views3950Altmetric-Citations1009LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aldehydes,Chemical reactions,Chemical structure,Condensation,Inorganic carbon compounds Get e-Alerts
The Level of CD81 Cell Surface Expression Is a Key Determinant for Productive Entry of Hepatitis C Virus into Host Cells (2006)

Recently a cell culture model supporting the complete life cycle of the hepatitis C virus (HCV) was developed. Searching for host cell determinants involved in the HCV replication cycle, we evaluated the efficiency of virus propagation in different Huh-7-derived cell clones. We found that Huh-7.5 cells and Huh7-Lunet cells, two former replicon cell clones that had been generated by removal of an HCV replicon by inhibitor treatment, supported comparable levels of RNA replication and particle production, whereas virus spread was severely impaired in the latter cells. Analysis of cell surface expression of CD81 and scavenger receptor class B type I (SR-BI), two molecules previously implicated in HCV entry, revealed similar expression levels for SR-BI, while CD81 surface expression was much higher on Huh-7.5 cells than on Huh7-Lunet cells. Ectopic expression of CD81 in Huh7-Lunet cells conferred permissiveness for HCV infection to a level comparable to that for Huh-7.5 cells. Modulation of CD81 cell surface density in Huh-7.5 cells by RNA interference indicated that a certain amount of this molecule (approximately 7 x 10(4) molecules per cell) is required for productive infection with a low dose of HCV. Consistent with this, we show that susceptibility to HCV infection depends on a critical quantity of CD81 molecules. While infection is restricted in cells expressing very small amounts of CD81, susceptibility rapidly rises within a narrow range of CD81 levels, reaching a plateau where higher expression does not further increase the efficiency of infection. Together these data indicate that a high density of cell surface-exposed CD81 is a key determinant for productive HCV entry into host cells.
Professor Arthur L. Corbin: Creator of the Present-Day Yale Law School (1964)

After obtaining the B.A. degree at the University of Kansas in 1894, he came East three years later to study law at Yale.The regular course of study for the LL.B. degree was three years but the catalogue provided that Bachelors of Arts "of approved colleges will be permitted to complete the three years' course in two years, if they are able to do so."Arthur Corbin had no difficulty in doing so, and obtained his law degree in
Learning Noise-Invariant Representations for Robust Speech Recognition (2018)

Despite rapid advances in speech recognition, current models remain brittle to superficial perturbations to their inputs. Small amounts of noise can destroy the performance of an otherwise state-of-the-art model. To harden models against background noise, practitioners often perform data augmentation, adding artificially-noised examples to the training set, carrying over the original label. In this paper, we hypothesize that a clean example and its superficially perturbed counterparts shouldn't merely map to the same class - they should map to the same representation. We propose invariant-representation-learning (IRL): At each training iteration, for each training example, we sample a noisy counterpart. We then apply a penalty term to coerce matched representations at each layer (above some chosen layer). Our key results, demonstrated on the LibriSpeech dataset are the following: (i) IRL significantly reduces character error rates (CER) on both `clean' (3.3% vs 6.5%) and `other' (11.0% vs 18.1%) test sets; (ii) on several-of-domain noise settings (different from those seen during training) IRL's benefits are even more pronounced. Careful ablations confirm that our results are not simply due to shrinking activations at the chosen layers.
Dual-mode operation of flexible piezoelectric polymer diaphragm for intracranial pressure measurement (2010)

The dual-mode operation of a polyvinylidene fluoride trifluoroethylene (PVDF-TrFE) piezoelectric polymer diaphragm, in a capacitive or resonant mode, is reported as a flexible intracranial pressure (ICP) sensor. The pressure sensor using a capacitive mode exhibits a higher linearity and less power consumption than resonant mode operated pressure sensor. In contrast, the latter provides better sensitivity and easier adaption for wireless application. The metrological properties of the dual-mode ICP sensor being described are satisfactory in vitro. We propose that the piezoelectric polymer diaphragm has a promising future in intracranial pressure monitoring.
Th17 cells generated in the absence of TGF-β induce experimental allergic encephalitis upon adoptive transfer (2011)

The discovery of IL-17-producing helper T cells (Th17) has led to new concepts of T-cell differentiation and immunity. Importantly, Th17 cells are thought to be important drivers of autoimmunity. TGF-β and IL-6 in combination were shown to induce differentiation of murine naive CD4 T cells into IL-17-producing cells in vitro. By contrast, human Th17 differentiation was shown to be independent of TGF-β and could be induced by IL-6 in conjunction with IL-21 or with IL-1. Ghoreschi et al. have elegantly demonstrated that mouse Th17 cell differentiation can also occur in the absence of TGF-β. A combination of IL-23, IL-1 and IL-6 can give rise to IL-17-producing cells, which are characterized by the expression of T-bet. Intriguingly, the adoptive transfer of such in vitro differentiated Th17 cells into lymphocyte-deficient mice resulted in the induction of experimental allergic encephalitis, which was more severe than in mice receiving Th17 cells differentiated in the presence of TGF-β. Collectively, the results suggest that a subpopulation of Th17 cells differentiated in the absence of TGF-β, expressing T-bet and RORγt, occur in vivo and may be responsible for autoimmunity.
Photogenerated Polyelectrolyte Bilayers from an Aqueous-Processible Photoresist for Multicomponent Protein Patterning (2004)

A novel photoresist (PR) that can be processed under mild aqueous conditions was synthesized and used to create photogenerated polyelectrolyte bilayers. Thin films of the PR cast on polycation-coated substrates were exposed to UV irradiation to generate carboxylate groups in the photoresist. The bulk of the UV-exposed PR film was dissolved by rinsing with pH 7.4 phosphate-buffered saline, but a polyelectrolyte bilayer formed in situ at the PR/polycation interface on exposure remained bound to the substrate. The UV-exposed photoresist also exhibited pH-dependent solubility; it was soluble in water above pH 6.6, but insoluble at lower pHs. Using these unique properties, two-component protein patterning was achieved using biotinylated PR films under conditions that avoid exposing the proteins to conditions outside the narrow range of physiological pH, ionic strength, and temperature where their stability is greatest.
On the Improvement of Fiber Reinforced Concrete through Surface Modification of Polypropylene by Grafting Method (2011)

Polypropylene (PP) fiber reinforced concrete is an important composite. In order to improve the mechanical properties of PP fiber reinforced concrete, polyacrylamide (PAM) was grafted onto the PP surface by the UV irradiation to enhance the hydrophilic property of PP in this study. IR spectra showed the existence of carboxylic acid functional groups on the treated PP surface. AFM images depicted that the treated PP surface had the lower height fluctuation, roughness, and had the acicular appearance. Contact angles of the treated PP were reduced in comparison with that of the original PP. All of these experimental results gave the evidences that PAM had been successfully grafted onto the treated PP surface. Furthermore, OM images depicted that the treated PP adhered to cement hydrate products (C-S-H) more tightly than that of the original PP did. We therefore expect that PP grafted with PAM can enhance mechanical properties of PP fiber reinforced concrete.