gebhart/patrepeval huggingface dataset:
Spam filters: bayes vs. chi-squared; letters vs. words (2003)

We compare two statistical methods for identifying spam or junk electronic mail. Spam filters are classifiers which determine whether an email is junk or not. The proliferation of spam email has made electronic filtering vitally important. The magnitude of the problem is discussed. We examine the Naive Bayesian method in relation to the 'Chi by degrees of Freedom' approach, the latter used in the field of authorship identification. Both methods produce very promising results. However, the 'Chi by degrees of Freedom' has the advantage of providing significance measures, which will help to reduce false positives. Statistics based on character-level tokenization proves more effective than word-level.
Molecular Cloning and Structural Analysis of the Gene Encoding PERF 15 Protein Present in the Perinuclear Theca of the Rat Spermatozoa1 (1997)

We have cloned the PERF 15 gene, which encodes the most abundant protein of the perinuclear theca of rat spermatozoa. PERF 15 is related to the superfamily of lipophilic transport proteins. It has a molecular weight of 15,060 and is present exclusively in the subacrosomal region of the sperm head. Northern blot analysis demonstrated that this gene transcribed PERF 15 mRNA in meiotic and postmeiotic cells. The PERF 15 gene contains four exons and three introns. Exon 1 codes for amino acids 1-24, exon 2 for amino acids 25-82, exon 3 for amino acids 83-116, and exon 4 for amino acids 117-132. The three introns are composed of 2241, 547, and 164 base pairs (bp), respectively. The exon/intron boundaries are identical to those found in the mouse myelin P2 gene, but there is no resemblance in size and sequence between the corresponding introns of the PERF 15 and myelin P2 genes. Localization of the initiation transcription site by primer extension showed that the 5'-untranslated region of this gene is 67 bp upstream of the translation initiation site. Primer extension analysis also suggests that there is one transcription start site for this gene. Inverse polymerase chain reaction generated a 204-bp fragment, located upstream of the translation initiation codon, that has some homology with regions of other mammalian genes.
Model checking programs (2000)

The majority of the work carried out in the formal methods community throughout the last three decades has (for good reasons) been devoted to special languages designed to make it easier to experiment with mechanized formal methods such as theorem provers and model checkers. In this paper, we give arguments for why we believe it is time for the formal methods community to shift some of its attention towards the analysis of programs written in modern programming languages. In keeping with this philosophy, we have developed a verification and testing environment for Java, called Java PathFinder (JPF), which integrates model checking, program analysis and testing. Part of this work has consisted of building a new Java Virtual Machine that interprets Java bytecode. JPF uses state compression to handle large states, and partial order reduction, slicing, abstraction and run-time analysis techniques to reduce the state space. JPF has been applied to a real-time avionics operating system developed at Honeywell, illustrating an intricate error, and to a model of a spacecraft controller, illustrating the combination of abstraction, run-time analysis and slicing with model checking.
Functional effects of interleukin 31 in human primary keratinocytes (2011)

Together, our findings show a functional role of IL-31 in HPKs and provide a new link between TLR-2 ligands and IL-31 which might be dysregulated in AD. Altered function of IL-31 may have implications for cutaneous inflammation in eczema where skin colonization with Staphylococcus aureus and dysregulation of TLR-2 have been described.
Stereospecific recognition of tryptophan agarose by in vitro selected RNA (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific recognition of tryptophan agarose by in vitro selected RNAMichael Famulok and Jack W. SzostakCite this: J. Am. Chem. Soc. 1992, 114, 10, 3990–3991Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/ja00036a065https://doi.org/10.1021/ja00036a065research-articleACS PublicationsRequest reuse permissionsArticle Views586Altmetric-Citations126LEARN 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
Spin Immunoassay of Opiate Narcotics in Urine and Saliva (1972)

Free-radical technology can be combined with immunoassay to yield an entirely new system for detection and assay of small molecules in biologic fluids. The method, called "spin immunoassay," has substantial advantages over radioimmunoassay and standard procedures such as thin-layer and gas-liquid chromatography. The assay requires only a very small volume of the unknown solution (eg, urine, saliva), no chemical manipulations are needed, and the result is obtained by an instantaneous readout on the electron spin resonance spectrometer. This technique can be applied to the quantitative determination of opiate narcotics in urine and saliva.
Association of Major Depression and Binge Eating Disorder with Weight Loss in a Clinical Setting (2007)

Both MDD and BED were prevalent among this obese clinical population, and each disorder was independently associated with worse outcomes. Research is needed to investigate how to increase the efficacy of behavioral weight loss programs for individuals with MDD and/or BED.
Conformational Preferences of Proline Analogues with Different Ring Size (2007)

The conformational study on L-azetidine-2-carboxylic acid (Ac-Aze-NHMe, the Aze dipeptide) and (S)-piperidine-2-carboxylic acid (Ac-Pip-NHMe, the Pip dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in conformational preferences and cis-trans isomerization for proline residue and its analogues with different ring size in the gas phase and in solution (chloroform and water). The change of ring size by deleting a CH2 group from or adding a CH2 group to the prolyl ring results the remarkable changes in backbone and ring structures compared with those of the Pro dipeptide, especially in the C'-N imide bond length and the bond angles around the N-C(alpha) bond. The four-membered azetidine ring can have either puckered structure depending on the backbone structure because of the less puckered structure. The six-membered piperidine ring can adopt chair and boat conformations, but the chair conformation is more preferred than the boat conformation. These calculated preferences for puckering are consistent with experimental results from analysis of X-ray structures of Aze- and Pip-containing peptides. On going from Pro to Aze to Pip, the axiality (i.e., a tendency to adopt the axial orientation) of the NHMe group becomes stronger, which can be ascribed to reduce the steric hindrances between 1,2-substituted Ac and NHMe groups. As the solvent polarity increases, the polyproline II-like conformation becomes more populated and the relative stability of conformation tC with a C7 hydrogen bond between C'=O of the amino group and N-H of the carboxyl group decreases for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. The cis population and rotational barriers for the imide bond increase with the increase of solvent polarity for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. In particular, the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about azetyl and piperidyl peptide bonds in the gas phase and in solution, as seen for alanyl and prolyl peptide bonds. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure, but the lower rotational barriers for the Aze and Pip dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized.
The dynamics of ultrasonically levitated drops in an electric field (1996)

Ultrasonic and electrostatic levitation techniques have allowed the experimental investigation of the nonlinear oscillatory dynamics of free droplets with diameter between 0.1 and 0.4 cm. The measurement of the resonance frequencies of the first three normal modes of large amplitude shape oscillations in an electric field of varying magnitude has been carried out with and without surface charges for weakly conducting liquids in air. These oscillations of nonspherical levitated drops have been driven by either modulating the ultrasonic field or by using a time-varying electric field, and the free decay from the oscillatory state has been recorded. A decrease in the resonance frequency of the driven fundamental quadrupole mode has been measured for increasing oblate deformation in the absence of an electric field. Similarly, a decrease in this frequency has also been found for increasing DC electric field magnitude. A soft nonlinearity exists in the amplitude dependence of the resonant mode frequencies for freely decaying as well as ultrasonically and electrically driven uncharged drops. This decrease in resonance frequency is accentuated by the presence of free surface charge on the drop. Subharmonic resonance excitation has been observed for drops in a time-varying electric field, and hysteresis exists for resonant modes driven to large amplitude. Mode coupling from lower-order resonances to higher-order modes has been found to be very weak, even for fairly large amplitude shape oscillations. Most of these results are in general agreement with predictions from recent analytical and numerical investigations.
Diabetic impairments in NO-mediated endothelial progenitor cell mobilization and homing are reversed by hyperoxia and SDF-1α (2007)

Endothelial progenitor cells (EPCs) are essential in vasculogenesis and wound healing, but their circulating and wound level numbers are decreased in diabetes. This study aimed to determine mechanisms responsible for the diabetic defect in circulating and wound EPCs. Since mobilization of BM EPCs occurs via eNOS activation, we hypothesized that eNOS activation is impaired in diabetes, which results in reduced EPC mobilization. Since hyperoxia activates NOS in other tissues, we investigated whether hyperoxia restores EPC mobilization in diabetic mice through BM NOS activation. Additionally, we studied the hypothesis that impaired EPC homing in diabetes is due to decreased wound level stromal cell-derived factor-1alpha (SDF-1alpha), a chemokine that mediates EPC recruitment in ischemia. Diabetic mice showed impaired phosphorylation of BM eNOS, decreased circulating EPCs, and diminished SDF-1alpha expression in cutaneous wounds. Hyperoxia increased BM NO and circulating EPCs, effects inhibited by the NOS inhibitor N-nitro-L-arginine-methyl ester. Administration of SDF-1alpha into wounds reversed the EPC homing impairment and, with hyperoxia, synergistically enhanced EPC mobilization, homing, and wound healing. Thus, hyperoxia reversed the diabetic defect in EPC mobilization, and SDF-1alpha reversed the diabetic defect in EPC homing. The targets identified, which we believe to be novel, can significantly advance the field of diabetic wound healing.
Single-Microphone LP Residual Skewness-Based Inverse Filtering of the Room Impulse Response (2012)

This paper presents a method based on higher order statistics (HOS), namely the normalized third-order moment (skewness), for blind estimation of the inverse filter of the room impulse response (RIR). Skewness is used as a measure of asymmetry, and a comprehensive comparison with the commonly used metric (kurtosis) is presented. It is shown that a sufficiently long linear predictive (LP) residual of the speech signal has an asymmetric pdf with sufficient skewness to be used as a score function for the HOS-based approach. The proposed algorithm is optimized for the inverse filter estimation problem. This optimization includes an efficient initialization for high reverberation intensities, enabling the method to be employed in highly reverberant rooms. The direct-to-reverberation ratio (DRR) as well as the equalized impulse response clearly show that our method can estimate the inverse filter even in highly reverberant environments. In addition, performance results using recorded background noise and in time-varying environments illustrate that our approach is applicable in real world situations. The proposed method is shown to be superior to the method by Wu and Wang, particularly in terms of reducing the coloration effect. Experiments under different acoustic conditions confirm the effectiveness of the proposed method for time delay estimation (TDE). Finally, the proposed algorithm is used as the first-stage of monaural segregation, and it is shown to improve the performance under different conditions.
Tau Phosphorylation and Aggregation as a Therapeutic Target in Tauopathies (2010)

Tauopathies are neurodegenerative diseases characterized by insoluble hyperphosphorylated deposits of the microtubule-associated protein tau in the central nervous system. In these disorders, tau is believed to cause neurodegeneration and neuronal loss due to the loss of function of the normal protein, and/or the gain of toxic properties by generating multimeric species. The obstacles found in amyloid-based therapies in Alzheimer's disease, the most common tauopathy, have stimulated the search for alternative targets, including tau. In this article, we review the strategies aimed at reducing tau phosphorylation and aggregation as a target for drug intervention in tauopathies.
Evolutionary aspects of accuracy of phenylalanyl-tRNA synthetase. A comparative study with enzymes from Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, and turkey liver using phenylalanine analogs (1983)

The phenylalanyl-tRNA synthetases from Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, and turkey liver activate a number of phenylalanine analogues (tyrosine, leucine, methionine, p-fluorophenylalanine, beta-phenylserine, beta-thien-2-ylalanine, 2-amino-4-methylhex-4-enoic acid, mimosine, N-benzyl-L- or N-benzyl-D-phenylalanine, and ochratoxin A), as demonstrated by Km and kcat of the ATP/PPi pyrophosphate exchange. Upon complexation with tRNA, the enzyme-tRNAPhe complexes show a significantly increased initial discrimination of these amino acid analogues expressed in higher Km and lower kcat values, as determined by amino-acylation of tRNAPhe-C-C-A(3'NH2). The overall accuracy is further enhanced by a second discrimination, a proofreading step. The strategies employed by the enzymes with respect to accuracy differ. Better initial discrimination in the aminoacylation and less elaborated proofreading for the E. coli enzyme can be compared to a more efficient proofreading by other synthetases. In this way the comparatively poor initial amino acid recognition in the case of the S. cerevisiae and N. crassa enzymes is balanced. The extent of initial discrimination is therefore inversely coupled to the hydrolytic capacity of the proofreading. A striking difference can be noted for the proofreading mechanisms. Whereas the enzymes from E. coli, S. cerevisiae, and N. crassa follow the pathway of posttransfer proofreading, namely, enzymatic hydrolysis of the misaminoacylated tRNA, the turkey liver enzyme uses tRNA-dependent pretransfer proofreading in the case of natural amino acids. In spite of the same subunit structure and similar molecular weight, the phenylalanyl-tRNA synthetases from a prokaryotic and lower and higher eukaryotic organisms show obvious mechanistic differences in their strategy to achieve the necessary fidelity.
CD40 ligand-CD40 interactions are necessary for the initiation of insulitis and diabetes in nonobese diabetic mice (1997)

The nonobese diabetic (NOD) mouse spontaneously develops T cell-dependent autoimmune diabetes. Here, we investigate the role of CD40 ligand (CD40L)-CD40 costimulation in the initiation and progression of this disease. Anti-CD40L mAb treatment of 3- to 4-wk-old NOD females (the age at which insulitis typically begins) completely prevented the insulitis and diabetes. In contrast, treatment of such mice with anti-CD40L at >9 wk of age did not inhibit the disease process. These results suggest that a costimulatory signal by CD40L is required early but not in the effector phase of disease development. Anti-CD40L treatment affected the priming of islet Ag-specific T cell responses in vivo. Cytokine analysis revealed a dramatic decrease in IFN-gamma and IL-2 release without a concomitant increase in IL-4 production by T cells from anti-CD40L-treated mice. Thus, anti-CD40L impaired the islet Ag-specific Th1 cell response in vivo, and the prevention of diabetes by anti-CD40L was not associated with switching of the response from a Th1 to a Th2 profile. Cotransfer of splenocytes from anti-CD40L-treated mice with splenocytes from diabetic NOD mice into NOD/scid mice did not inhibit the transfer of disease, indicating that anti-CD40L does not prevent the disease by inducing regulatory cells. Since anti-CD40L clearly prevented the insulitis by inhibiting the development and further accumulation of pathogenic Th1 cells to islets of Langerhans, we conclude that CD40L-CD40 costimulation is required for early events in the development of spontaneous autoimmune diabetes.
Cystinosin is a Component of the Vacuolar H+-ATPase-Ragulator-Rag Complex Controlling Mammalian Target of Rapamycin Complex 1 Signaling (2015)

Cystinosis is a rare autosomal recessive storage disorder characterized by defective lysosomal efflux of cystine due to mutations in the CTNS gene encoding the lysosomal cystine transporter, cystinosin. Lysosomal cystine accumulation leads to crystal formation and functional impairment of multiple organs. Moreover, cystinosis is the most common inherited cause of renal Fanconi syndrome in children. Oral cysteamine therapy delays disease progression by reducing intracellular cystine levels. However, because cysteamine does not correct all complications of cystinosis, including Fanconi syndrome, we hypothesized that cystinosin could have novel roles in addition to transporting cystine out of the lysosome. By coimmunoprecipitation experiments and mass spectrometry, we found cystinosin interacts with almost all components of vacuolar H + -ATPase and the Ragulator complex and with the small GTPases Ras-related GTP-binding protein A (RagA) and RagC. Furthermore, the mammalian target of rapamycin complex 1 (mTORC1) pathway was downregulated in proximal tubular cell lines derived from Ctns−/− mice. Decrease of lysosomal cystine levels by cysteamine did not rescue mTORC1 activation in these cells, suggesting that the downregulation of mTORC1 is due to the absence of cystinosin rather than to the accumulation of cystine. Our results show a dual role for cystinosin as a cystine transporter and as a component of the mTORC1 pathway, and provide an explanation for the appearance of Fanconi syndrome in cystinosis. Furthermore, this study highlights the need to develop new treatments not dependent on lysosomal cystine depletion alone for this devastating disease.
Adenoviral vectors persist in vivo and maintain activated CD8+ T cells: implications for their use as vaccines (2007)

CD8(+) T cell-numbers rapidly expand and then contract after exposure to their cognate antigen. Here we show that the sustained frequencies of transgene product-specific CD8(+) T cells elicited by replication-defective adenovirus vectors are linked to persistence of low levels of transcriptionally active adenovirus vector genomes at the site of inoculation, in liver, and lymphatic tissues. Continuously produced small amounts of antigen maintain fully active effector CD8(+) T cells, while also allowing for their differentiation into central memory cells. The long-term persistence of adenoviral vectors may be highly advantageous for their use as vaccines against pathogens for which T-cell-mediated protection requires both fully activated T cells for immediate control of virus-infected cells and central memory CD8(+) T cells that, because of their higher proliferative capacity, may be suited best to eliminate cells infected by pathogens that escaped the initial wave of effector T cells.
Isolation and partial characterization of Borrelia burgdorferi inner and outer membranes by using isopycnic centrifugation (1994)

In order to characterize the protein composition of the outer membrane of Borrelia burgdorferi, we have isolated inner and outer membranes by using discontinuous sucrose density step gradients. Outer and inner membrane fractions isolated by this method contained less than 1 and 2%, respectively, of the total lactate dehydrogenase activity (soluble marker) in cell lysate. More importantly, the purified outer membranes contained less than 4% contamination by the C subunit of F1/F0 ATPase (inner membrane marker). Very little flagellin protein was present in the outer membrane sample. This indicated that the outer membranes were relatively free of contamination by cytoplasmic, inner membrane or flagellar components. The outer membrane fractions (rho = 1.19 g/cm3) contained 0.15 mg (dry weight) of protein per mg. Inner membrane samples (rho = 1.12 g/cm3) contained 0.60 mg (dry weight) of protein per mg. Freeze-fracture electron microscopy revealed that the outer membrane vesicles contained about 1,700 intramembranous particles per micron 2 while inner membrane densities for inner and outer membranes. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and nonequilibrium pH gel electrophoresis-SDS-PAGE analyses of inner and outer membrane samples revealed several proteins unique to the inner membrane and 20 proteins that localized specifically to the outer membrane. This analysis clearly shows that the inner and outer membranes isolated by this technique are unique structures.
Decreased expression of catenins (? and ?), p120 CTN, and E-cadherin cell adhesion proteins and E-cadherin gene promoter methylation in prostatic adenocarcinomas (2001)

Decreased expression of catenin/E-cadherin complex cell adhesion proteins is associated with aggressive phenotype in prostatic adenocarcinoma. E-cadherin gene promote methylation is a common event in prostate carcinoma but does not appear to bear prognostic significance in the subset of cases analyzed.