gebhart/patrepeval huggingface dataset:
Automatic datapath tile placement and routing (2001)

We report the very first fully automatic datapath tile layout flow. We subdivided the placement process into two steps: a global placement step using simulated annealing, and a new detailed placement step based on extensive modifications we made to the O-tree algorithm. The modifications have enabled the extended O-tree algorithm to handle the rectilinearly shaped transistor chains and gates common in datapath tile layout. We show that datapath tiles can be placed and routed automatically at the transistor level or at the mixed transistor/gate level, achieving results for the very first time that are competitive to those obtained manually by a skilled designer.
A single adiabatic microring-based laser in 220 nm silicon-on-insulator (2014)

We demonstrate a laser for the silicon photonics platform by hybrid integration with a III/V reflective semiconductor optical amplifier coupled to a 220 nm silicon-on-insulator half-cavity. We utilize a novel ultra-thin silicon edge coupler. A single adiabatic microring based inline reflector is used to select a lasing mode, as compared to the multiple rings and Bragg gratings used in many previous results. Despite the simplified design, the laser was measured to have on-chip 9.8 mW power, less than 220 KHz linewidth, over 45 dB side mode suppression ratio, less than -135 dB/Hz relative intensity noise, and 2.7% wall plug efficiency.
A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties (1990)

With the aid of molecular modeling, both adenosine and adenosine A1 receptor antagonists belonging to various chemical classes were compared with respect to their minimum-energy conformations and molecular electrostatic potentials, as computed by the semiempirical molecular orbital program MOPAC. Distinct steric and electrostatic similarities between adenosine and the prototypic adenosine antagonist theophylline are evident when both compounds are superimposed, with theophylline in a so-called flipped orientation. Similar patterns were found for all other A1 antagonists investigated in this study. A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties contributing to potency, is proposed.
Leuconostoc kimchii sp. nov., a new species from kimchi. (2000)

A Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped bacterium, designated IH25T, was isolated from kimchi, a traditional Korean vegetable product. Phylogenetic analysis based on almost complete 16S rDNA sequences placed the isolate in a monophyletic clade corresponding to the genus Leuconostoc. All validly described species in the genus Leuconostoc, with the exception of Leuconostoc fallax, showed high sequence identity of over 97%. The 16S rDNA sequence of strain IH25T showed the highest homology to those of Leuconostoc gelidum DSM 5578T (98.9%) and Leuconostoc citreum KCTC 3526T (98.3 %). However, DNA-DNA hybridization experiments indicated that the organism represents a novel genomic species in the genus, since the previously known leuconostocs share DNA homology with strain IH25T of less than 70%. In this work, it is proposed that isolate IH25T be classified in the genus Leuconostoc as Leuconostoc kimchii sp. nov. The type strain of Leuconostoc kimchii is IH25T (= KCTC 2386T = IMSNU 11154T).
A Novel Transcription Regulatory Complex Containing Death Domain-associated Protein and the ATR-X Syndrome Protein (2004)

Death domain-associated protein (Daxx) is a multi-functional protein that modulates both apoptosis and transcription. Within the nucleus, Daxx is a component of the promyelocytic leukemia protein (PML) nuclear bodies (NBs) and interacts with a number of transcription factors, yet its precise role in transcription remains elusive. To further define the function of Daxx, we have isolated its interacting proteins in the nucleus using epitope-tagged affinity purification and identified X-linked mental retardation and alpha-thalassaemia syndrome protein (ATRX), a putative member of the SNF2 family of ATP-dependent chromatin remodeling proteins that is mutated in several X-linked mental retardation disorders. We show that substantial amounts of endogenous Daxx and ATRX exist in a nuclear complex. Daxx binds to ATRX through its paired amphipathic alpha helices domains. ATRX has ATPase activity that is stimulated by mononucleosomes, and patient mutations in the ATPase domain attenuate this activity. ATRX strongly represses transcription when tethered to a promoter. Daxx does not affect the ATPase activity of ATRX, however, it alleviates its transcription repression activity. In addition, ATRX is found in the PML-NBs, and this localization is mediated by Daxx. These results show that the ATRX.Daxx complex is a novel ATP-dependent chromatin-remodeling complex, with ATRX being the core ATPase subunit and Daxx being the targeting subunit. Moreover, the localization of ATRX to the PML-NBs supports the notion that these structures may play an important role in transcription regulation.
A Dominant-Negative Strategy for Studying Roles of G Proteins in Vivo (1999)

G proteins play a critical role in transducing a large variety of signals into intracellular responses. Increasingly, there is evidence that G proteins may play other roles as well. Dominant-negative constructs of the alpha subunit of G proteins would be useful in studying the roles of G proteins in a variety of processes, but the currently available dominant-negative constructs, which target Mg2+-binding sites, are rather leaky. A variety of studies have implicated the carboxyl terminus of G protein alpha subunits in both mediating receptor-G protein interaction and in receptor selectivity. Thus we have made minigene plasmid constructs that encode oligonucleotide sequences corresponding to the carboxyl-terminal undecapeptide of Galphai, Galphaq, or Galphas. To determine whether overexpression of the carboxyl-terminal peptide would block cellular responses, we used as a test system the activation of the M2 muscarinic receptor activated K+ channels in HEK 293 cells. The minigenes were transiently transfected along with G protein-regulated inwardly rectifying K+ channels (GIRK) into HEK 293 cells that stably express the M2 muscarinic receptor. The presence of the Galphai carboxyl-terminal peptide results in specific inhibition of GIRK activity in response to agonist stimulation of the M2 muscarinic receptor. The Galphai minigene construct completely blocks agonist-mediated M2 mAChR K+ channel response whereas the control minigene constructs (empty vector, pcDNA3.1, and the Galpha carboxyl peptide in random order, pcDNA-GalphaiR) had no effect on agonist-mediated M2 muscarinic receptor GIRK response. The inhibitory effects of the Galphai minigene construct were specific because overexpression of peptides corresponding to the carboxyl terminus of Galphaq or Galphas had no effect on M2 muscarinic receptor stimulation of the K+ channel.
Neuroendocrine reactivity, internalizing behavior problems, and control-related cognitions in clinic-referred children and adolescents. (1994)

Literature on neuroendocrine-behavior relations suggests that cortisol reactivity to social challenge may be associated with children's internalizing problem behavior. To explore this possibility, and the role of control-related beliefs, we studied 102 7-17-year-old clinic-referred children. Measures of problem behavior, depression and anxiety, and control-related beliefs were collected, and Ss' saliva was sampled before and after a parent-child conflict task. Neuroendocrine activation (i.e., cortisol increase) in response to the interaction task was associated with Ss' (a) social withdrawal, social anxiety, and social problems; (b) socially inhibited behavior during the task; and (c) low levels of perceived social contingency and high levels of external attributions for personal successes and failures. Our findings are among the first to link children's behavioral response to social challenge, neuroendocrine activation, cognitions, and psychopathology.
Pex/PEX tissue distribution and evidence for a deletion in the 3' region of the Pex gene in X-linked hypophosphatemic mice. (1997)

PEX, a phosphate-regulating gene with homology to endopeptidases on the X chromosome, was recently identified as the candidate gene for X-linked hypophosphatemia. In the present study, we cloned mouse and human Pex/PEX cDNAs encoding part of the 5' untranslated region, the protein coding region, and the entire 3' untranslated region, determined the tissue distribution of Pex/PEX mRNA, and characterized the Pex mutation in the murine Hyp homologue of the human disease. Using the reverse transcriptase/polymerase chain reaction (RT/PCR) and ribonuclease protection assays, we found that Pex/PEX mRNA is expressed predominantly in human fetal and adult mouse calvaria and long bone. With RNA from Hyp mouse bone, an RT/PCR product was generated with 5' but not 3' Pex primer pairs and a protected Pex mRNA fragment was detected with 5' but not 3' Pex riboprobes by ribonuclease protection assay. Analysis of the RT/PCR product derived from Hyp bone RNA revealed an aberrant Pex transcript with retention of intron sequence downstream from nucleotide 1302 of the Pex cDNA. Pex mRNA was not detected on Northern blots of poly (A)+ RNA from Hyp bone, while a low-abundance Pex transcript of approximately 7 kb was apparent in normal bone. Southern analysis of genomic DNA from Hyp mice revealed the absence of hybridizing bands with cDNA probes from the 3' region of the Pex cDNA. We conclude that Pex/PEX is a low-abundance transcript that is expressed predominantly in bone of mice and humans and that a large deletion in the 3' region of the Pex gene is present in the murine Hyp homologue of X-linked hypophosphatemia.
Icosahedral DNA Nanocapsules by Modular Assembly (2009)

It's a trap! DNA polyhedra formed through molecular self-assembly may function as nanocapsules for the targeted delivery of encapsulated entities. This functional aspect was demonstrated for the most complex DNA-based platonic solid: During the stepwise amalgamation of discrete polyhedra to form icosahedra, gold nanoparticles (GNPs) were encapsulated from solution (see illustration and TEM image of icosahedral cages containing GNPs).
Improved survival in the Danish center-treated cystic fibrosis patients: Results of aggressive treatment (1996)

We report survival data for Danish center-treated cystic fibrosis (CF) patients, covering the period 1974-1993 and using cross-sectional cumulative survival probability based on annual age-specific mortality rates. Analyses by age and by years after diagnosis were made. No significant differences were noted in the survival probability when patients were grouped according to sex or absence/presence of meconium ileus. The annual mortality rate for 1989-1993 was 0-1.2%. Using the age-specific mortality rate for 1989-1993, we were unable to calculate the median survival probability because the curve did not fall below 50% (age up to 45 years); however, it was possible to show that the survival probability for a newborn CF child to reach his 45th birthday was 80.4%(confidence interval 76.5-84.6%). The median age at diagnosis was 0.63 years with no sex difference. The probability of surviving 40 years after the diagnosis of CF was made was 83.3% (confidence interval 80.1-86.6%). This is considerably higher than any other published survival probability. An early anti-Pseudomonas aeruginosa treatment regimen seemed important in achieving the observed improved survival.
A Proteomic Study of SUMO-2 Target Proteins (2004)

The SUMO family in vertebrates includes at least three distinct proteins (SUMO-1, -2, and -3) that are added as post-translational modifications to target proteins. A considerable number of SUMO-1 target proteins have been identified, but little is known about SUMO-2. A stable HeLa cell line expressing His6-tagged SUMO-2 was established and used to label and purify novel endogenous SUMO-2 target proteins. Tagged forms of SUMO-2 were functional and localized predominantly in the nucleus. His6-tagged SUMO-2 conjugates were affinity-purified from nuclear fractions and identified by mass spectrometry. Eight novel potential SUMO-2 target proteins were identified by at least two peptides. Three of these proteins, SART1, heterogeneous nuclear ribonucleoprotein (RNP) M, and the U5 small nuclear RNP 200-kDa helicase, play a role in RNA metabolism. SART1 and heterogeneous nuclear RNP M were both shown to be genuine SUMO targets, confirming the validity of the approach.
Estimating Continuous Distributions in Bayesian Classifiers (2013)

When modeling a probability distribution with a Bayesian network, we are faced with the problem of how to handle continuous variables. Most previous work has either solved the problem by discretizing, or assumed that the data are generated by a single Gaussian. In this paper we abandon the normality assumption and instead use statistical methods for nonparametric density estimation. For a naive Bayesian classifier, we present experimental results on a variety of natural and artificial domains, comparing two methods of density estimation: assuming normality and modeling each conditional distribution with a single Gaussian; and using nonparametric kernel density estimation. We observe large reductions in error on several natural and artificial data sets, which suggests that kernel estimation is a useful tool for learning Bayesian models.
YouTubeCat: Learning to categorize wild web videos (2010)

Automatic categorization of videos in a Web-scale unconstrained collection such as YouTube is a challenging task. A key issue is how to build an effective training set in the presence of missing, sparse or noisy labels. We propose to achieve this by first manually creating a small labeled set and then extending it using additional sources such as related videos, searched videos, and text-based webpages. The data from such disparate sources has different properties and labeling quality, and thus fusing them in a coherent fashion is another practical challenge. We propose a fusion framework in which each data source is first combined with the manually-labeled set independently. Then, using the hierarchical taxonomy of the categories, a Conditional Random Field (CRF) based fusion strategy is designed. Based on the final fused classifier, category labels are predicted for the new videos. Extensive experiments on about 80K videos from 29 most frequent categories in YouTube show the effectiveness of the proposed method for categorizing large-scale wild Web videos.
Antibody Recognition and Conformational Flexibility of a Plaque-Specific β-Amyloid Epitope Modulated by Non-native Peptide Flanking Regions (2008)

Here we report on the synthesis, antibody binding, and QSAR studies of a series of linear and cyclic peptides containing a beta-amyloid plaque-specific epitope (Abeta(4-10); FRHDSGY). In these constructs, two or three alpha- l-Ala, alpha- d-Ala, or beta-Ala residues were introduced at both N- and C-termini of the epitope as non-native flanking sequences. Cyclization of the linear Abeta(4-10) epitope peptide resulted in reduced antibody binding. However, the antibody binding could be fully compensated by insertion of alanine flanks into the corresponding cyclic peptides. These results indicate that the modification of a beta-amyloid plaque-specific epitope by combination of cyclization and flanking sequences could generate highly antigenic peptides compared to the native sequence. A novel 3D QSAR method, which explicitly handles conformational flexibility, was developed for the case of such molecular libraries. This method led to the prediction of the binding conformation for the common FRHDSGY sequence.
Clinical use of lenvatinib in combination with everolimus for the treatment of advanced renal cell carcinoma (2017)

The combination therapy with lenvatinib plus everolimus might be a promising choice for second-line treatment of mRCC patients. Based on the results of the Phase II trial, it is possible to speculate that the combination therapy could be appropriate for patients with high disease burden or strongly symptomatic patients.
Quantitative Detection of Hepatitis C Virus (HCV) RNA in Saliva and Gingival Crevicular Fluid of HCV-Infected Patients (2005)

The search for hepatitis C virus (HCV) in body fluids other than blood is important when assessing possible nonparenteral routes of viral transmission. However, the role of oral fluids in HCV transmission remains controversial. Here we quantitatively determined HCV RNA in saliva and gingival crevicular fluid (GCF) of anti-HCV-positive patients. Most patients (14 of 18; 78%) whose saliva specimens were negative had HCV RNA in their GCF. Most patients (20 of 26; 77%) had higher HCV RNA levels in their GCF than in their saliva. Although there was not a statistically significant correlation between the serum viral load and HCV level in saliva or GCF, patients with low serum HCV loads were less likely to have detectable HCV in their saliva. These findings have important implications for medical personnel and suggest that epidemiological studies designed to understand the significance of the oral route of transmission of HCV are warranted.
NKT cells are necessary for maximal expression of allergic conjunctivitis1 (2010)

Allergic conjunctivitis (AC) is elicited by immediate hypersensitivity responses to environmental agents. It is initiated by a T(h)2-dominated immune response that is characterized by production of IgE antibodies and eosinophilic infiltration. By using an experimental mouse model of AC induced by short ragweed (SRW) pollen, we show that sensitized Jalpha18(-/-) mice, which lack type I NKT cells, and CD1d(-/-) mice, which lack type I and type II NKT cells, exhibited a decrease in tearing, lid edema, conjunctival edema and vasodilatation and eosinophil infiltration into the conjunctiva when compared with wild-type (WT) mice in both T(h)1- and T(h)2-prone hosts (C57BL/6 and BALB/c mice, respectively). This demonstrates that NKT cells are needed for both the early and late phases of AC. Adoptive transfer of SRW-primed CD4(+) T cells from Jalpha18(-/-) mice into naive WT BALB/c mice revealed that NKT cells were needed for the maximal induction of allergen-specific T(h)2 cells. Results from adoptive transfer of SRW-primed CD4(+) T cells from WT BALB/c mice to naive Jalpha18(-/-) mice indicated that NKT cells were also needed for the expression of AC produced by allergen-primed CD4(+) T cells. The decreased expression of AC in NKT cell-deficient mice was correlated with significant reduction in the production of T(h)2 cytokines in SRW pollen-sensitized mice compared with WT mice and in the capacity of SRW pollen-sensitized CD4(+) T cells to mediate ocular inflammation when the hosts were confronted with SRW pollen at the ocular surface.
The Sexual Acceptability of Contraception: Reviewing the Literature and Building a New Concept (2016)

How contraceptives affect women's sexual well-being is critically understudied. Fortunately, a growing literature focuses on sexual aspects of contraception, especially hormonal contraception's associations with libido. However, a more holistic approach to contraceptive sexual acceptability is needed to capture the full range of women's sexual experiences. We conducted a narrative literature review of this topic, working with an original sample of 3,001 citations published from 2005 to 2015. In Part 1, we draw from a subset of this literature (264 citations) to build a new conceptual model of sexual acceptability. Aspects include macro factors (gender, social inequality, culture, and structure), relationship factors (dyadic influences and partner preferences), and individual factors (sexual functioning, sexual preferences, such as dis/inhibition, spontaneity, pleasure, the sexual aspects of side effects, such as bleeding, mood changes, sexual identity and sexual minority status, and pregnancy intentions). In Part 2, we review the empirical literature on the sexual acceptability of individual methods (103 citations), applying the model as much as possible. Results suggest contraceptives can affect women's sexuality in a wide variety of positive and negative ways that extend beyond sexual functioning alone. More attention to sexual acceptability could promote both women's sexual well-being and more widespread, user-friendly contraceptive practices.
Hydrophobic "Collapse" in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in Water (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrophobic "Collapse" in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in WaterCarlos Simmerling and Ron ElberCite this: J. Am. Chem. Soc. 1994, 116, 6, 2534–2547Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ja00085a038https://doi.org/10.1021/ja00085a038research-articleACS PublicationsRequest reuse permissionsArticle Views121Altmetric-Citations43LEARN 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 Get e-Alerts
Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus (2009)

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has recently emerged worldwide. The United States, in particular, is experiencing a serious epidemic of CA-MRSA that is almost entirely caused by an extraordinarily infectious strain named USA300. However, the molecular determinants underlying the pathogenic success of CA-MRSA are mostly unknown. To gain insight into the evolution of the exceptional potential of USA300 to cause disease, we compared the phylogeny and virulence of USA300 with that of closely related MRSA clones. We discovered that the sublineage from which USA300 evolved is characterized by a phenotype of high virulence that is clearly distinct from other MRSA strains. Namely, USA300 and its progenitor, USA500, had high virulence in animal infection models and the capacity to evade innate host defense mechanisms. Furthermore, our results indicate that increased virulence in the USA300/USA500 sublineage is attributable to differential expression of core genome-encoded virulence determinants, such as phenol-soluble modulins and alpha-toxin. Notably, the fact that the virulence phenotype of USA300 was already established in its progenitor indicates that acquisition of mobile genetic elements has played a limited role in the evolution of USA300 virulence and points to a possibly different role of those elements. Thus, our results highlight the importance of differential gene expression in the evolution of USA300 virulence. This finding calls for a profound revision of our notion about CA-MRSA pathogenesis at the molecular level and has important implications for design of therapeutics directed against CA-MRSA.