gebhart/patrepeval huggingface dataset:
Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations (2013)

Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1-F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the "plastics" or "lower dose plastics" mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.
Prediction of homologous protein structures based on conformational searches and energetics (1990)

A "knowledge-based" method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchanging the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
CASIA@V2: A MLN-based Question Answering System over Linked Data (2014)

We present a question answering system (CASIA@V2) over Linked Data (DBpedia), which translates natural language questions into structured queries automatically. Existing systems usually adopt a pipeline framework, which con- tains four major steps: 1) Decomposing the question and detecting candidate phrases; 2) mapping the detected phrases into semantic items of Linked Data; 3) grouping the mapped semantic items into semantic triples; and 4) generat- ing the rightful SPARQL query. We present a jointly learning framework using Markov Logic Network(MLN) for phrase detection, phrases mapping to seman- tic items and semantic items grouping. We formulate the knowledge for resolving the ambiguities in three steps of QALD as first-order logic clauses in a MLN. We evaluate our approach on QALD-4 test dataset and achieve an F-measure score of 0.36, an average precision of 0.32 and an average recall of 0.40 over 50 questions.
Autonomous query-driven index tuning (2004)

Index tuning as part of database tuning is the task of selecting and creating indexes with the goal of reducing query processing times. However, in dynamic environments with various ad-hoc queries it is difficult to identify potentially useful indexes in advance. We investigate an approach addressing this problem by deciding about index creation automatically at runtime in order to speed up processing of subsequent queries. We present a cost model taking into account the benefits of indexes for an evolving query workload and discuss strategies for choosing indexes to be created in a space-limited environment.
RF power amplifier modeling using polynomials with IIR bases functions (2009)

This paper presents a novel technique of modeling a radio frequency (RF) power amplifier (PAs) using polynomials with infinite impulse response (IIR) bases functions. Non-linear PA behavior, including both short-term and long-term memory effects, is described with very few parameters compared to existing Volterra series models. Moreover, the use of polynomials with IIR bases is far less computationally intensive thereby providing a significant advantage over competing methods. Power amplifiers designed for second generation (EDGE) wireless system are investigated for model validation. Excellent results are obtained, where the error between model prediction and measurements is better than 50 dBc, with the amplifier being driven with an EDGE signal at several power levels.
The structure of amphotericin A. II. The complete structure of the antibiotic. (1985)

The structure of amphotericin A without the configuration of asymmetric carbon atoms has been elucidated. The stereochemistry of the sugar moiety has been determined. On the basis of homoscalar correlated 2D 1H spectra. of amphotericin A the position of the hemiketal moiety has been located, and the chemical shifts of all the protons in the antibiotic molecule have been determined.
Metal–Organic Framework Containing Planar Metal-Binding Sites: Efficiently and Cost-Effectively Enhancing the Kinetic Separation of C<sub>2</sub>H<sub>2</sub>/C<sub>2</sub>H<sub>4</sub> (2019)

One of the emerging problems plaguing the chemical industry today is the efficient and cost-effective separation of C<sub>2</sub> hydrocarbons. In order to help address this problem, we report a new material, NbU-1, constructed by extremely cheap starting materials. The special structural characteristics of NbU-1 such as the planar, mixed-valence copper clusters and Lewis-basic adsorption channels enforce interactions with acetylene molecules that lead to the highest kinetic separation efficiency for C<sub>2</sub>H<sub>2</sub>/C<sub>2</sub>H<sub>4</sub>. Via DFT-D calculations, it is indicated that C<sub>2</sub>H<sub>2</sub> molecules are adsorbed onto the two adjacent Cu(I) centers, but not the usual single open metal sites of Cu centers. The reported results not only provide information for a deep investigation into the separation mechanism but also offer an alternative strategy for preparing cost-effective materials that can perform highly efficient separations of light hydrocarbons.
We want more (2011)

Recording and publishing mobile video clips from music concerts is popular. There is a high potential to increase the concert's perceived value when producing video remixes from individual video clips and using them socially. A digital production of a video remix is an interactive process between human and computer. However, it is not clear what the collaboration implications between human and computer are.
The crystal structure of a Cys25 → Ala mutant of human procathepsin S elucidates enzyme–prosequence interactions (2006)

The crystal structure of the active-site mutant Cys25 --> Ala of glycosylated human procathepsin S is reported. It was determined by molecular replacement and refined to 2.1 Angstrom resolution, with an R-factor of 0.198. The overall structure is very similar to other cathepsin L-like zymogens of the C1A clan. The peptidase unit comprises two globular domains, and a small third domain is formed by the N-terminal part of the prosequence. It is anchored to the prosegment binding loop of the enzyme. Prosegment residues beyond the prodomain dock to the substrate binding cleft in a nonproductive orientation. Structural comparison with published data for mature cathepsin S revealed that procathepsin S residues Phe146, Phe70, and Phe211 adopt different orientations. Being part of the S1' and S2 pockets, they may contribute to the selectivity of ligand binding. Regarding the prosequence, length, orientation and anchoring of helix alpha3p differ from related zymogens, thereby possibly contributing to the specificity of propeptide-enzyme interaction in the papain family. The discussion focuses on the functional importance of the most conserved residues in the prosequence for structural integrity, inhibition and folding assistance, considering scanning mutagenesis data published for procathepsin S and for its isolated propeptide.
Run-Length-Limited Low-Density Parity Check Codes Based on Deliberate Error Insertion (2004)

We propose a novel approach to modulation and error control coding. The idea is to completely eliminate a constrained encoder and, instead, impose the constraint by the deliberate introduction of bit errors before transmission. The redundancy that would have been used for imposing the constraint is used in our scheme to strengthen the error control code (ECC), in such a way that the ECC becomes capable of correcting both deliberate errors as well as channel errors that occur during the detection. Our ECC-modulation scheme is based on iterative decoding of low-density parity check codes and a run-length constraint.
F 15845, a new blocker of the persistent sodium current prevents consequences of hypoxia in rat femoral artery (2010)

F 15845, a selective blocker of the persistent sodium current prevented vascular contraction induced by hypoxic conditions.
Role of protein kinase C-ε in hypertrophy of cultured neonatal rat ventricular myocytes (2001)

Using adenovirus (Adv)-mediated overexpression of constitutively active (ca) and dominant-negative (dn) mutants, we examined whether protein kinase C (PKC)-epsilon, the major novel PKC isoenzyme expressed in the adult heart, was necessary and/or sufficient to induce specific aspects of the hypertrophic phenotype in low-density, neonatal rat ventricular myocytes (NRVM) in serum-free culture. Adv-caPKC-epsilon did not increase cell surface area or the total protein-to-DNA ratio. However, cell shape was markedly affected, as evidenced by a 67% increase in the cell length-to-width ratio and a 17% increase in the perimeter-to-area ratio. Adv-caPKC-epsilon also increased atrial natriuretic factor (ANF) and beta-myosin heavy chain (MHC) mRNA levels 2.5 +/- 0.3- and 2.1 +/- 0.2-fold, respectively, compared with NRVM infected with an empty, parent vector (P < 0.05 for both). Conversely, Adv-dnPKC-epsilon did not block endothelin-induced increases in cell surface area, the total protein-to-DNA ratio, or upregulation of beta-MHC and ANF gene expression. However, the dominant-negative inhibitor markedly suppressed endothelin-induced extracellular signal-regulated kinase (ERK) 1/2 activation. Taken together, these results indicate that caPKC-epsilon overexpression alters cell geometry, producing cellular elongation and remodeling without a significant, overall increase in cell surface area or total protein accumulation. Furthermore, PKC-epsilon activation and downstream signaling via the ERK cascade may not be necessary for cell growth, protein accumulation, and gene expression changes induced by endothelin.
Silicon-based nanosheets synthesized by a topochemical reaction for use as anodes for lithium ion batteries (2015)

Silicon is the most promising anode material for the next generation high-performance lithium ion batteries. However, its commercial application is hindered by its poor performance due to the huge volume change during cycling. Although two-dimensional silicon-based materials show significantly improved performance, flexible synthesis of such materials is still a challenge. In this work, silicon-based nanosheets with a multilayer structure are synthesized for the first time by a topochemical reaction. The morphology and oxidation state of these nanosheets can be controlled by appropriate choice of reaction media and oxidants. Benefiting from the hierarchical structure and ultrathin size, when the silicon-based nanosheets are employed as anodes they exhibit a charge (delithiation) capacity of 800 mAh/g after 50 cycles with a maximum coulombic efficiency of 99.4% and good rate performance (647 mAh/g at 1 A/g). This work demonstrates a novel method for preparing nanosheets not only for lithium ion batteries but also having various potential applications in other fields, such as catalysts, electronics and photonics.
Compact 2D Hilbert microstrip resonators (2005)

Abstract Novel compact microstrip resonators consisting of multiple 2D Hilbert prefractal curves are presented. Proposed resonators use fractal curves of the 3 rd and 4 th orders to achieve length reduction of over 64% and 81%, respectively, when compared to the conventional capacitively coupled resonators tuned to the same frequency. A configuration with fractal curves of the 3 rd order, fabricated in standard PCB technology, exhibits improvement of unloaded Q ‐factor within range from 15% to 90%, depending on the resonant frequency. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 48: 270–273, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.21324
Cell adhesion to streptavidin via RGD-dependent integrins. (1993)

Biotin-blocked streptavidin binds specifically (Kd approximately 3 x 10(-8) M) to cell surfaces, presumably via an RYD-containing sequence. This site is distinct from the biotin-binding cleft of the protein and bears high homology to the RGD-containing cell-binding domain of fibronectin. We show here that various cell types adhere to immobilized streptavidin and that the soluble protein interferes specifically with cell adhesion to fibronectin substrata (with an IC50 of about 1 x 10(-7) M) but less so to other adhesive glycoproteins (e.g., collagen type I, vitronectin). Immunochemical evidence combined with peptide competition studies demonstrated that cells bind to streptavidin primarily via the major fibronectin receptor (the alpha 5 beta 1 integrin). The results suggest that streptavidin acts as a relatively strict fibronectin mimetic, thus reflecting the great similarity in their respective RYD/RGD sequence and the immediate flanking regions. The bacterial protein emulates and competes with fibronectin and other extracellular matrix adhesive proteins in the initial recognition and binding to cell surfaces, but appears not to induce subsequent processes (e.g., anchorage and spreading). Streptavidin may thus represent a novel example of bacterial protein mimicry of a key adhesion motif.
Adhesins and ligands involved in the interaction of Candida spp. with epithelial and endothelial surfaces. (1994)

Adhesion of candidal species to the epithelium of the gastrointestinal or genitourinary tract stands as a critical first step in the pathogenesis of candidal infection. After colonization and replication at mucosal surfaces, Candida albicans and other pathogenic species may penetrate the mucosal barrier, enter the vascular tree, and disseminate hematogenously. The consequences of this pathogenic cascade evoke considerable morbidity and mortality, especially among immunocompromised patients. Thus, interactions of C. albicans and other candidal species with epithelium and endothelium may lead to serious consequences for the human host. This review evaluates candidate candidal adhesions for epithelial and endothelial surfaces, with emphasis on the specificity of the interaction, the inhibitors that have been employed, and the ligands that have been identified on mammalian cells or matrices. Three types of interactions are described: protein-protein interactions, lectin-like interactions, and incompletely defined interactions in which the adhesive ligand is as yet unidentified. Special attention is given to the roles of integrin-like proteins. Differences in the mechanisms of candidal attachment to epithelium and endothelium are delineated. Last, on the basis of the available literature, avenues of potentially fruitful investigation are proposed.
The Anorectic Effect of CNTF Does Not Require Action in Leptin-Responsive Neurons (2012)

Leptin resistance is a feature of obesity that poses a significant therapeutic challenge. Any treatment that is effective to reduce body weight in obese patients must overcome or circumvent leptin resistance, which promotes the maintenance of excess body fat in obese individuals. Ciliary neurotrophic factor (CNTF) is unique in its ability to reduce food intake and body weight in obese, leptin-resistant humans and rodents. Although attempts to use CNTF as an obesity therapy failed due to the development of neutralizing antibodies to the drug, efforts to understand mechanisms for CNTF's anorectic effects provide an opportunity to develop new drugs for leptin-resistant individuals. CNTF and leptin share several structural, anatomic, and signaling properties, but it is not understood whether or how the two cytokines might interact to affect energy balance. Here, we conditionally deleted the CNTF receptor (CNTFR) subunit, CNTFRα, in cells expressing leptin receptors. We found that CNTFR signaling in leptin-responsive neurons is not required for endogenous maintenance of energy balance and is not required for the anorectic response to exogenous administration of a CNTF agonist. These results indicate that despite anatomical overlap for CNTF and leptin action, CNTF appears to act within a distinct neuronal population to elicit its potent anorectic effect.
Analysis of GSM calls data for understanding user mobility behavior (2013)

This information about our GSM calls is stored by the TelCo operator in large volumes and with strict privacy constraints making it challenging the analysis of these fingerprints for inferring mobility behavior. This paper proposes a strategy for mobility behavior identification based on aggregated calling profiles of mobile phone users. This compact representation of the user call profiles is the input of the mining algorithm for automatically classifying various kinds of mobility behavior. A further advantage of having defined the call profiles is that the analysis phase is based on summarized privacy-preserving representation of the original data. We show how these call profiles permit to design a two step process - implemented into a system - based on a bootstrap phase and a running phase for classifying users into behavior categories. We evaluated the system in two case studies where individuals are classified into residents, commuters and visitors. We conclude the paper with a discussion which emphasizes the role of the call profiles for the design of a new collaboration model between data provider and data analyst.
A comparative simulation study of four multilevel DRAMs (2003)

Multilevel DRAM (MLDRAM) attempts to increase storage density by recording more than one bit per cell. Several different two-bit-per-cell schemes have been described in the literature; however it is difficult to compare them directly because the original papers use different technologies and operating conditions. This paper presents a detailed simulation study that compares three published MLDRAM schemes, along with a new MLDRAM scheme that combines the speed of a MLDRAM proposed by Furuyama et al. (1989) and the noise cancellation techniques of a MLDRAM proposed by Gillingham (1996). Our SPICE simulation models use the same array size and process models for each to allow us to make direct comparisons.
The <i>cidA</i> murein hydrolase regulator contributes to DNA release and biofilm development in <i>Staphylococcus aureus</i> (2007)

The Staphylococcus aureus cidA and lrgA genes have been shown to affect cell lysis under a variety of conditions during planktonic growth. It is hypothesized that these genes encode holins and antiholins, respectively, and may serve as molecular control elements of bacterial cell lysis. To examine the biological role of cell death and lysis, we studied the impact of the cidA mutation on biofilm development. Interestingly, this mutation had a dramatic impact on biofilm morphology and adherence. The cidA mutant (KB1050) biofilm exhibited a rougher appearance compared with the parental strain (UAMS-1) and was less adherent. Propidium iodide staining revealed that KB1050 accumulated more dead cells within the biofilm population relative to UAMS-1, indicative of reduced cell lysis. In agreement with this finding, quantitative real-time PCR experiments demonstrated the presence of 5-fold less genomic DNA in the KB1050 biofilm relative to UAMS-1. Furthermore, treatment of the UAMS-1 biofilm with DNase I caused extensive cell detachment, whereas similar treatment of the KB1050 biofilm had only a modest effect. These results demonstrate that cidA-controlled cell lysis plays a significant role during biofilm development and that released genomic DNA is an important structural component of S. aureus biofilm.
Salivary Proteome and Peptidome Profiling in Type 1 Diabetes Mellitus Using a Quantitative Approach (2013)

In the present study, we applied iTRAQ-based quantitative approach to explore the salivary proteome and peptidome profile in selected subjects with type 1 diabetes, with and without microvascular complications, aiming to identify disease-related markers. From a total of 434 distinct proteins, bactericidal/permeability-increasing protein-like 1 and pancreatic adenocarcinoma up-regulated factor were found in higher levels in the saliva of all patients while increased content of other proteins like alpha-2-macroglobulin, defensin alpha 3 neutrophil-specific, leukocyte elastase inhibitor, matrix metalloproteinase-9, neutrophil elastase, plastin-2, protein S100-A8 and protein S100-A9 were related with microvascular complications as retinopathy and nephropathy. Protein-protein interaction network analysis suggests the functional clusters defense, inflammation and response to wounding as the most significantly associated with type 1 diabetes pathogenesis. Peptidome data not only support a diabetes-related higher susceptibility of salivary proteins to proteolysis (mainly of aPRP, bPRP1 and bPRP2), but also evidenced an increased content of some specific protein fragments known to be related with bacterial attachment and the accumulation of phosphopeptides involved in tooth protection. Overall, the salivary protein and peptide profile highlights the importance of the innate immune system in the pathogenesis of type 1 diabetes mellitus and related complications. This study provides an integrated perspective of salivary proteome and peptidome that should be further explored in future studies targeting specific disease markers.