gebhart/patrepeval huggingface dataset:
Molecular Basis of Gene-for-Gene Specificity in Bacterial Speck Disease of Tomato (1996)

Transient expression of the Pseudomonas syringae avirulence gene avrPto in plant cells resulted in a Pto-dependent necrosis. The AvrPto avirulence protein was observed to interact directly with the Pto resistance protein in the yeast two-hybrid system. Mutations in the Pto and avrPto genes which reduce in vivo activity had parallel effects on association in the two-hybrid assay. These data suggest that during infection the pathogen delivers AvrPto into the plant host cell and that resistance is specified by direct interaction of Pto with AvrPto.
Development of a fast dissolving film of epinephrine hydrochloride as a potential anaphylactic treatment for pediatrics (2016)

This study presents potential proof for using FDFs as a replacement therapy of epinephrine injections for pediatrics.
The Mouse and Human Homologs of DMC1, the Yeast Meiosis-Specific Homologous Recombination Gene, Have a Common Unique form of Exon-Skipped Transcript in Meiosis (1996)

Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast DMC1 gene. The predicted human and mouse DMC1 proteins showed 54.1% sequence identity with yeast Dmc1 protein. The domain II region, highly conserved in the E.coli RecA-like protein family, was also found in the mammalian DMC1 proteins, including the two ATP binding motifs and DNA binding sites with the region. In situ hybridization analysis revealed expression of the mouse Dmc1 gene in testicular germ cells in meiosis; RT-PCR showed expression in embryonal ovaries. These findings suggest that DMC1 plays an important role in meiotic homologous recombination. From both the man and mouse we have isolated an alternative spliced form of Dmc1 cDNA (Dmc1-d), which is deleted for a region between the two motifs involved in nucleotide binding. Since the alternatively spliced Dmc1-d transcript was detected in both male and female germ cells, the encoded protein DMC1-D may have a novel role in mammalian genetic recombination in meiosis.
Pulsed dye laser therapy for sun damaged skin (1999)

At last follow up 90% (9/10) of the mild to moderate wrinkles and 40% (4/10) of the treated patients with moderate to severe wrinkles had clinically observable improvement in their sun induced skin wrinkles. Histologic examinations of the treated areas showed a superficial dermal band of well organized elastin and collagen fibers replacing pre-treatment elastic tissue. Increased cellularity and mucin deposition was consistent with dermal collagen remodeling.
Proteomic Analysis of Urinary Exosomes in Cardiovascular and Associated Kidney Diseases by Two-Dimensional Electrophoresis and LC–MS/MS (2013)

Urinary exosomes are membranous vesicles 40-100 nm in size containing proteins that are characteristic of every renal tubule epithelial cell type. In this chapter, we describe a methodology to isolate and analyze urinary exosomes proteome by 2-DE and LC-MS/MS, in the search for biomarkers of vascular and associated kidney diseases. We describe an isolation methodology by serial (ultra)centrifugation steps compatible with 2-DE and LC-MS/MS analysis. Exosome purity is confirmed by electron microscopy and Western blot.
Rapid mapping of protein functional epitopes by combinatorial alanine scanning (2000)

A combinatorial alanine-scanning strategy was used to determine simultaneously the functional contributions of 19 side chains buried at the interface between human growth hormone and the extracellular domain of its receptor. A phage-displayed protein library was constructed in which the 19 side chains were preferentially allowed to vary only as the wild type or alanine. The library pool was subjected to binding selections to isolate functional clones, and DNA sequencing was used to determine the alanine/wild-type ratio at each varied position. This ratio was used to calculate the effect of each alanine substitution as a change in free energy relative to that of wild type. Only seven side chains contribute significantly to the binding interaction, and these conserved residues form a compact cluster in the human growth hormone tertiary structure. The results were in excellent agreement with free energy data previously determined by conventional alanine-scanning mutagenesis and suggest that this technology should be useful for analyzing functional epitopes in proteins.
Disubstituted Pyridines:  The Double-Coupling Approach (2007)

A one-pot procedure leading to disubstituted pyridines from the starting dibromopyridines is described. Key features include the ability to couple a range of aryl and even alkenylboronic acids at the 2,3 and/or 2,5 positions with excellent regiocontrol under a standard set of conditions. Further, isolated yields are greatly improved by the use of neutral alumina in place of silica for product purification. Finally, the intrinsic electronic bias of the pyridine ring can be overcome by using a bromoiodopyridine.
Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations (2013)

Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.
Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma (2008)

This paper presents computational methods to analyze MALDI-TOF mass spectrometry data for quantitative comparison of peptides and glycans in serum. The methods are applied to identify candidate biomarkers in serum samples of 203 participants from Egypt; 73 hepatocellular carcinoma (HCC) cases, 52 patients with chronic liver disease (CLD) consisting of cirrhosis and fibrosis cases, and 78 population controls. Two complementary sample preparation methods were applied prior to generating mass spectra: (1) low molecular weight (LMW) enrichment of each serum sample was carried out for MALDI-TOF quantification of peptides, and (2) glycans were enzymatically released from proteins in each serum sample and permethylated for MALDI-TOF quantification of glycans. A peak selection algorithm was applied to identify the most useful peptide and glycan peaks for accurate detection of HCC cases from high-risk population of patients with CLD. In addition to global peaks selected by the whole population based approach, where identically labeled patients are treated as a single group, subgroup-specific peaks were identified by searching for peaks that are differentially abundant in a subgroup of patients only. The peak selection process was preceded by peak screening, where we eliminated peaks that have significant association with covariates such as age, gender, and viral infection based on the peptide and glycan spectra from population controls. The performance of the selected peptide and glycan peaks was evaluated in terms of their ability in detecting HCC cases from patients with CLD in a blinded validation set and through the cross-validation method. Finally, we investigated the possibility of using both peptides and glycans in a panel to enhance the diagnostic capability of these candidate markers. Further evaluation is needed to examine the potential clinical utility of the candidate peptide and glycan markers identified in this study.
A new synthesis of alkyl and aryl 2‐aminoimidazoles (1966)

Abstract The condensation of cyanamide with α‐aminocarbonyl compounds has been studied as a method of synthesizing alkyl and aryl 2‐aminoimidazoles. Starting from N ‐alkylamino‐aldehydes, 1,5‐dialkyl‐2‐aminoimidazoles have been prepared. Starting from suitable aminoketones a variety of monosubstituted and disubstituted derivatives were obtained.
Impact of average free‐volume element size on transport in stereoisomers of polynorbornene. I. Properties at 35 °C (2003)

Abstract This article demonstrates that transport of gases through glassy polymers is significantly influenced not only by the absolute amount but also by the distribution of free volume. Two stereoisomers of polynorbornene with nearly equivalent total free volume, but markedly different average free‐volume sizes, were evaluated. The free‐volume element size was probed with positron annihilation lifetime spectroscopy, wide‐angle X‐ray scattering, gas sorption, and molecular modeling. The permeation, sorption, and diffusion of light gases were measured in each stereoisomer at 35 °C. All analytical techniques indicated that one isomer (labeled as Architecture II) had a larger average free‐volume element size but fewer elements. This isomer also had a very slightly higher bulk density (1.000 vs 0.992 g/cm 3 for the other stereoisomer). Architecture II also had gas sorption and diffusion coefficients that were two to three times those of the less dense counterpart. These differences have been attributed to differences in the free‐volume element size available within the polymer matrix. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2185–2199, 2003
Increasing Clinical Presence of Mobile Communication Technology: Avoiding the Pitfalls (2011)

Mobile communication technologies are employed in many diverse areas of healthcare delivery to provide improved quality and efficiency of communication and facilitate increased rapidity of data or information transfer. Mobile phones enable healthcare professionals to possess a portable platform from which to provide many healthcare-related applications and are a popular means to directly communicate with colleagues and patients. As involvement of mobile communication technology in healthcare delivery continues to rapidly expand, there are also important considerations of relevance to patient safety and security as a result. Here, we review the previous evidence of reported clinical risks associated with mobile communication technology, such as electromagnetic interference, confidentiality and data security, distraction/noise, infection control, and cross contamination. In conclusion, although mobile phones provide much putative potential improvement to healthcare delivery, further evaluation and research are required to both inform and protect health professionals and users of such technology in the healthcare environment and provide the evidence base to support the provision of clear and comprehensive guidelines.
Characterization of a chitinase gene (chiA) from Serratia marcescens BJL200 and one-step purification of the gene product (1994)

The nucleotide sequence of the chiA gene from Serratia marcescens strain BJL200 was determined.The gene was found to encode a protein of 563 amino acid residues, with a typical N-terminal signal peptide of 23 residues, that is cleaved off during export.The gene exhibited striking differences with two previously characterized chiA genes of S. marcescens in the region corresponding to amino acid residues 410-467 of the gene product.Periplasmic fractions of an Escherichia coli strain harbouring the cloned gene were used as starting material for the development of a fast, one-step purification protocol for the chitinase that is based on hydrophobic interaction chromatography.
A method for enforcing integrability in shape from shading algorithms (1988)

An approach for enforcing integrability, a particular implementation of the approach, an example of its application to extending an existing shape-from-shading algorithm, and experimental results showing the improvement that results from enforcing integrability are presented. A possibly nonintegrable estimate of surface slopes is represented by a finite set of basis functions, and integrability is enforced by calculating the orthogonal projection onto a vector subspace spanning the set of integrable slopes. The integrability projection constraint was applied to extending an iterative shape-from-shading algorithm of M.J. Brooks and B.K.P. Horn (1985). Experimental results show that the extended algorithm converges faster and with less error than the original version. Good surface reconstructions were obtained with and without known boundary conditions and for fairly complicated surfaces.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells (2013)

Transfusion of red blood cells (RBCs) is a standard and indispensable therapy in current clinical practice. In vitro production of RBCs offers a potential means to overcome a shortage of transfusable RBCs in some clinical situations and also to provide a source of cells free from possible infection or contamination by microorganisms. Thus, in vitro production of RBCs may become a standard procedure in the future. We previously reported the successful establishment of immortalized mouse erythroid progenitor cell lines that were able to produce mature RBCs very efficiently. Here, we have developed a reliable protocol for establishing immortalized human erythroid progenitor cell lines that are able to produce enucleated RBCs. These immortalized cell lines produce functional hemoglobin and express erythroid-specific markers, and these markers are upregulated following induction of differentiation in vitro. Most importantly, these immortalized cell lines all produce enucleated RBCs after induction of differentiation in vitro, although the efficiency of producing enucleated RBCs remains to be improved further. To the best of our knowledge, this is the first demonstration of the feasibility of using immortalized human erythroid progenitor cell lines as an ex vivo source for production of enucleated RBCs.
Adhesion molecules, mycophenolate mofetil and systemic lupus erythematosus (2005)

Mycophenolate mofetil (MMF) has been reproducibly shown to inhibit lymphocyte adhesion and penetration of endothelial cell surfaces. The mechanism is not yet elucidated. In vitro studies on the effects of MMF on cell adhesion molecules (CAM) using human umbilical vein endothelial cells (HUVEC) have shown conflicting results. Different studies have independently shown that MMF increased, decreased or had no effect on intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule (VCAM-1). Several studies suggest MMF may reduce the endothelial expression of E-selectin. Recent studies have been unable to replicate initial work, which suggested that MMF impaired glycosylation of lymphocyte CAM. The same studies concluded that MMF had no effect on the surface expression of lymphocyte CAM, but altered the binding ability of these molecules. ICAM-1/LFA-1 (lymphocyte function-associated antigen-1), VCAM-1/VLA-4 (very late antigen-4) and P-selectin/PSGL-1 (P-selectin glycoprotein ligand-1) ligand pairs are most likely to be involved. Few in vivo and no conclusive human studies have been carried out. The literature relevant to cell adhesion molecules in systemic lupus erythematosus (SLE) is reviewed in detail.
Hepatic Stem Cells: In Search of (2006)

The field of stem cell biology has exploded with the study of a wide range of cellular populations involving endodermal, mesenchymal, and ectodermal organs. One area of extensive study has included the identification of hepatic stem and progenitor cell subpopulations. Liver stem cells provide insights into the potential pathways involving liver regeneration that are independent of mature hepatocytes. Hepatic progenitor cells are either bipotent or multipotent and capable of multiple rounds of replication. They have been identified in fetal as well as adult liver. Various injury models have been used to expand this cellular compartment. The nomenclature, origin, and function of the hepatic progenitor cell populations are areas of ongoing debate. In this review, we will discuss the different definitions and functions of hepatic progenitor cells as well as the current research efforts examining their therapeutic potential.
Isolation and characterization of a gene specifically expressed in different metastatic cells and whose deduced gene product has a high degree of homology to a Ca2+-binding protein family. (1989)

The gene mts1, which is expressed specifically in metastatic cells, was isolated by molecular cloning coupled with differential DNA reassociation. Transcription of mts1 was found not only in tumor cells, but also in normal cells; homologous RNA was detected only in spleen, thymus, bone marrow, and blood lymphocytes. DNA sequencing of mts1 revealed an open reading frame containing information for a peptide of 101 amino acids, and the amino acid sequence suggested that the mts1 protein was identical to the previously isolated Ca2+-binding mouse protein (Jackson-Grusby et al. 1987; Goto et al. 1988). Thus, the mts1 protein is a member of the calcium-modulated protein family, and our data indicate that mts1 is involved in regulating the metastatic behavior of tumor cells.
Calcium localization in walls of Tuber melanosporum associated with Corylus avellana: advantages and limits of different techniques (1994)

International audience
Nucleotide sequence of the thrB gene of E. coli, and its two adjacent regions; the thrAB and thrBC junctions (1981)

We have sequenced a DNA fragment containing the Escherichia coli thrA-thrB junction, the complete thrB gene and the thrB-thrC junction. The intergenic sequence thrA and thrB is only one base pair. The coding region for homoserine kinase is 927 base pairs long. It is followed by 114 base pair segment in an open reading frame predicting that thrC begins just after non-sense codon of thrB. The presence at the end of thrA and of thrB of sequences that can pair with the 3' end of the 16 S ribosomal RNA suggests that reinitiation of translation occurs at the end of the two genes. The deduced aminoacid sequence for homoserine kinase shows no striking homology with aspartokinase I homoserine dehydrogenase I.
Variation in Word Frequency Distributions: Definitions, Measures and Implications for a Corpus-Based Language Typology (2017)

Word frequencies are central to linguistic studies investigating processing difficulty, learnability, age of acquisition, diachronic transmission and the relative weight given to a concept in society. However, there are few cross-linguistic studies on entire distributions of word frequencies, and even less on systematic changes within them. Here, we first define and test an exact measure for the relative difference between distributions – the Normalised Frequency Difference (NFD). We then apply this measure to parallel corpora in overall 19 languages, explaining systematic variation in the frequency distributions within the same language and across different languages. We further establish the NFD between lemmatised and un-lemmatised corpora as a frequency-based measure of inflectional productivity of a language. Finally, we argue that quantitative measures like the NFD can advance language typology beyond abstract, theory-driven expert judgments, towards more corpus-based, empirical and reproducible analyses.
Complementary carbon nanotube-gated carbon nanotube thin-film transistor (2006)

We introduce, a complementary carbon nanotube (CNT)-gated CNT thin-film field effect transistor (FET). By using two perpendicularly crossed single-wall CNT (SWNT) bundles as the gate and the channel interchangeably, a sub-50nm complementary CNT-FET is demonstrated. It is found that the new CNT-FET shows acceptable FET characteristics by interchanging the roles of the gate and the channel. The unique dual functionality of the device will open up a new possibility and flexibility in the design of future complementary CNT electronic circuits.
Intradermal recombinant human nerve growth factor induces pressure allodynia and lowered heat-pain threshold in humans (1997)

Nerve growth factor (NGF) plays a biologic role in the development and maintenance of sympathetic and small sensory neurons. Because it facilitates nerve fiber regeneration, lowers heat-pain threshold (hyperalgesia), and prevents or improves nerve dysfunction in experimental neuropathy, it is being considered as a putative treatment for certain human polyneuropathies. In 16 healthy subjects, we tested whether intradermal injection of minute doses of recombinant human NGF (1 or 3 micrograms) compared with saline induces hyperalgesia or alters cutaneous sensation (at the site of injection) as measured by symptom scores, clinical examination, or quantitative sensory testing with Computer Assisted Sensory Examination (CASE IV). Most subjects had, as their only symptom, localized tenderness of the NGF-injected site and only when the site was bumped or compressed. Slight discomfort developed in volar wrist structures (with flexion of fingers) or tenderness of deep structures to palpation over the bicipital groove or supraclavicular region. The Neuropathy Symptoms and Change questionnaire indicated that pressure allodynia was significantly localized to the NGF-injected side from 3 hours to 21 days after injections. Light stroking of the skin did not induce tactile allodynia. Compression of injected sites induced pressure allodynia that occurred more frequently and significantly on the NGF-injected side after 3 hours and was maintained for several weeks. No abnormality of vibratory or cooling detection threshold developed from NGF injection. By contrast, heat-pain threshold (HP 0.5, p = 0.003) and an intermediate level of heat-pain (HP 5.0, p < 0.001) were significantly lowered 1, 3, and 7 days (and in some cases at 3 hours and 14 and 21 days) after NGF injection. The time course of pressure allodynia and heat-pain hyperalgesia is too rapid to be explained by uptake of NGF by nociception terminals, retrograde transport, and upregulation of pain modulators. Local tissue mechanisms appear to be implicated. It remains to be tested whether recombinant human NGF prevents, stabilizes, or ameliorates small fiber human neuropathies.