gebhart/patrepeval huggingface dataset:
Heterotrimeric G Protein Signaling in Filamentous Fungi (2007)

Filamentous fungi are multicellular eukaryotic organisms known for nutrient recycling as well as for antibiotic and food production. This group of organisms also contains the most devastating plant pathogens and several important human pathogens. Since the first report of heterotrimeric G proteins in filamentous fungi in 1993, it has been demonstrated that G proteins are essential for growth, asexual and sexual development, and virulence in both animal and plant pathogenic filamentous species. Numerous G protein subunit and G protein-coupled receptor genes have been identified, many from whole-genome sequences. Several regulatory pathways have now been delineated, including those for nutrient sensing, pheromone response and mating, and pathogenesis. This review provides a comparative analysis of G protein pathways in several filamentous species, with discussion of both unifying themes and important unique signaling paradigms.
Eighteen-month radiographic and histologic evaluation of sinus grafting with anorganic bovine bone in the chimpanzee. (1999)

Maxillary sinus grafting procedures are currently the treatment of choice when the alveolar crest of the posterior maxilla is in close approximation to the maxillary sinus. The short-term histologic and radiographic healing following sinus grafting with natural bone mineral (Bio-Oss) in the chimpanzee has been evaluated. We have previously shown by histomorphometric and radiographic analysis that the percentage of vital bone area, the vertical height, and the density of new bone in the maxillary sinus was significantly greater with anorganic bovine bone compared to bovine Type I collagen matrix. The purpose of this in vivo study was to determine the bone mineral density (BMD) of the sinus grafts, the vertical height stability, the vital bone area, and the extent of anorganic bovine bone replacement 18 months postoperatively in 4 maxillary sinuses from 4 different animals. Radiographic analysis of computed tomographic scans taken at 1.5 years revealed an average BMD of 658 mg/mL, which was not significantly different from the values found at 6.5 months. The radiographic vertical height was maintained between the 6.5- and 18-month time points. On average, the grafts were found to have a height of 14 mm. Lateral wall biopsy specimens at 7.5 months were compared to those at 18 months. With the anorganic bovine bone treatment, the percentage of vital bone area increased from 62 +/- 3% to 70 +/- 7% and the percentage of natural bone mineral area decreased from 19 +/- 14% to 6 +/- 3%. The bovine Type I collagen matrix vital bone percentage at 7.5 months was 34 +/- 21%. These results demonstrate that sinus grafting with anorganic bovine bone maintains radiographic evidence of density and height stability of 1.5 years. In addition, histologic evidence supports the hypothesis that anorganic bovine bone is replaced by vital bone.
High Concentration of Peripheral Blood Mononuclear Cells Harboring Infectious Virus Correlates with Rapid Progression of Human Immunodeficiency Virus Type 1-Related Diseases (1993)

In a cohort of 103 asymptomatic seropositive subjects (Centers for Disease Control and Prevention [CDC] stage II/III) followed for 2 years, the concentration of peripheral blood mononuclear cells harboring infectious human immunodeficiency virus (HIV) type 1 (viral burden) was correlated with the rate of decrease of CD4 cell count (RD-CD4; R = .857). Rapidly progressing patients (RD-CD4 > or = 60%; n = 18) had a high viral burden (mean +/- SE, 572 +/- 202 cells/mL) and an 89% progression to CDC IV-A-C, while stable patients (RD-CD4 < 30%; n = 55) had a low viral burden (mean +/- SE, 28 +/- 4 cells/mL) and remained asymptomatic. Slowly progressing patients (RD-CD4 > or = 30 and < 60%; n = 30) showed an intermediate viral burden (mean +/- SE, 131 +/- 9 cells/mL) and a 10% CDC IV-A-C progression. Quantitative determination of infectious virus in blood cells adds important information on the prognosis of HIV-1 infection.
Activity of dual SRC-ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance (2006)

Mutation in the ABL kinase domain is the principal mechanism of imatinib resistance in patients with chronic myelogenous leukemia. Many mutations favor active kinase conformations that preclude imatinib binding. Because the active forms of ABL and SRC resemble one another, we tested two dual SRC-ABL kinase inhibitors, AP23464 and PD166326, against 58 imatinib-resistant (IM(R)) BCR/ABL kinase variants. Both compounds potently inhibit most IM(R) variants, and in vitro drug selection demonstrates that active (AP23464) and open (PD166326) conformation-specific compounds are less susceptible to resistance than imatinib. Combinations of inhibitors suppressed essentially all resistance mutations, with the notable exception of T315I. Guided by mutagenesis studies and molecular modeling, we designed a series of AP23464 analogues to target T315I. The analogue AP23846 inhibited both native and T315I variants of BCR/ABL with submicromolar potency but showed nonspecific cellular toxicity. Our data illustrate how conformational dynamics of the ABL kinase accounts for the activity of dual SRC-ABL inhibitors against IM(R)-mutants and provides a rationale for combining conformation specific inhibitors to suppress resistance.
Benchmarking of III–V n-MOSFET Maturity and Feasibility for Future CMOS (2010)

With the consideration of III-V channels for future CMOS, an urgent need for standard metrics to assess the maturity of III-V MOSFETs and to investigate their suitability for future CMOS has arisen. By proposing such standard metrics (Q ≡g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> /S), we find that present InGaAs n-MOSFETs are trailing Si MOSFETs by over a factor of 30. Still, experimental PHEMT data make a clear case for the utilization of InAs channels in future CMOS from a performance standpoint both for HP (1.4-1.7 times the current drive increase over Si) and LOP (1.7-3 times) applications.
Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis (2005)

Amyotrophic lateral sclerosis (ALS) is characterized by degeneration of motor neurons. We tested the hypothesis that proteomic analysis will identify protein biomarkers that provide insight into disease pathogenesis and are diagnostically useful. To identify ALS specific biomarkers, we compared the proteomic profile of cerebrospinal fluid (CSF) from ALS and control subjects using surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). We identified 30 mass ion peaks with statistically significant (p < 0.01) differences between control and ALS subjects. Initial analysis with a rule-learning algorithm yielded biomarker panels with diagnostic predictive value as subsequently assessed using an independent set of coded test subjects. Three biomarkers were identified that are either decreased (transthyretin, cystatin C) or increased (carboxy-terminal fragment of neuroendocrine protein 7B2) in ALS CSF. We validated the SELDI-TOF-MS results for transthyretin and cystatin C by immunoblot and immunohistochemistry using commercially available antibodies. These findings identify a panel of CSF protein biomarkers for ALS.
Mapping the Protein Universe (1996)

The comparison of the three-dimensional shapes of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations, reaching back billions of years, between protein molecules. Protein shape comparison also improves tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family. Finally, an exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.
De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock (2013)

Field pennycress (Thlaspi arvense L.) has potential as an oilseed crop that may be grown during fall (autumn) and winter months in the Midwestern United States and harvested in the early spring as a biodiesel feedstock. There has been little agronomic improvement in pennycress through traditional breeding. Recent advances in genomic technologies allow for the development of genomic tools to enable rapid improvements to be made through genomic assisted breeding. Here we report an annotated transcriptome assembly for pennycress. RNA was isolated from representative plant tissues, and 203 million unique Illumina RNA-seq reads were produced and used in the transcriptome assembly. The draft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp. A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family. The final assembly was functionally annotated, allowing for the identification of putative genes controlling important agronomic traits such as flowering and glucosinolate metabolism. Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress. Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.
Characterization of a Novel Human Anti-HIV-1 gp41 IgM Monoclonal Antibody Designated Clone 37 (2004)

Human monoclonal antibodies (HuMAbs) demonstrate great potential for passive immunotherapy against HIV-1. The gp41 transmembrane envelope glycoprotein of HIV has an important role in the pathogenicity of AIDS and importantly displays considerably less hypervariability than the gp120 surface envelope HIV glycoprotein, which makes it particularly a better candidate for the development of passive and active immunotherapies. The general aim of this study was to develop HuMAbs to HIV surface glycoproteins and particularly gp41. Peripheral blood mononuclear cells (PBMCs) were isolated from an HIV-seropositive long-term nondisease progressing patient. B-cells from this individual were then immortalized by Epstein-Barr virus (EBV) transformation, and antibody production was stabilized by fusion of transformed cells with a heteromyeloma. Subsets of the human heterohybridomas so generated were analyzed by ELISA. The hybridoma with the highest binding by immunoassay against gp160 was further analyzed. This hybridoma, designated as clone 37 (C37), was determined to be an IgM Kappa antibody and overlapping peptides of HIV envelope proteins (derived from the MN tissue culture line adapted HIV isolate) were used to map the specific binding domain of this HuMAb. Overlapping peptides designated 2026 (SWSNKSLDDIWNN, AA614–626), and 2027 (DDIWNNMTWMQWEREIDNYT, AA621–640) within the HIV-1 gp41 transmembrane glycoprotein were demonstrated to bind to C37 indicating that the specific binding domain for the antibody was DDIWNN. High affinity binding of C37 by ELISA to recombinant gp41 was demonstrated as well. Few IgM HuMAbs against HIV have been generated and characterized. Theoretically, because of the pentameric binding nature of IgM antibodies as well as their very efficient ability to activate complement, such reagents could have potential as anti-HIV agents.
Glucocorticoid-Induced TNF Receptor Expression by T Cells Is Reciprocally Regulated by NF-κB and NFAT (2008)

Although the transcription factor Foxp3 is implicated in regulating glucocorticoid-induced TNF receptor (GITR) expression in the T regulatory cell lineage, little is known about how GITR is transcriptionally regulated in conventional T cells. In this study, we provide evidence that TCR-mediated GITR expression depends on the ligand affinity and the maturity of conventional T cells. A genetic dissection of GITR transcriptional control revealed that of the three transcription factors downstream of the classical NF-kappaB pathway (RelA, cRel, and NF-kappaB1), RelA is a critical positive regulator of GITR expression, although cRel and NF-kappaB1 also play a positive regulatory role. Consistent with this finding, inhibiting NF-kappaB using Bay11-7082 reduces GITR up-regulation. In contrast, NFAT acts as a negative regulator of GITR expression. This was evidenced by our findings that agents suppressing NFAT activity (e.g., cyclosporin A and FK506) enhanced TCR-mediated GITR expression, whereas agents enhancing NFAT activity (e.g., lithium chloride) suppressed TCR-mediated GITR up-regulation. Critically, the induction of GITR was found to confer protection to conventional T cells from TCR-mediated apoptosis. We propose therefore that two major transcriptional factors activated downstream of the TCR, namely, NF-kappaB and NFAT, act reciprocally to balance TCR-mediated GITR expression in conventional T cells, an outcome that appears to influence cell survival.
Functional analysis of microRNAs during the retinoic acid-induced neuronal differentiation of human NT2 cells (2003)

MicroRNAs (miRNAs) are phylogenetically widespread small RNAs in animals and plants. These small RNAs can regulate a gene expression at a translational level and play roles during the development of C. elegans, D. melanogaster and plants. Although more than two hundred miRNAs have been found in mammals, the target mRNAs of miRNAs is unknown. Recently, we identified Hes1, bHLH transcriptional repressor, as a target of miR-23 in NT2 cells. In this study, we further investigate that the expression of Hes1 is regulated by miR-23 during the retinoic acid (RA)-induced neural differentiation of NT2 cells. Reduction in the level of miR-23 by siRNAs resulted in the accumulation of Hes1 in differentiated NT2 cells. Moreover, a reduction in the level of miR-23 by siRNA-miR-23 affected the RA-induced neural differentiation of NT2 cells. Thus, our results indicate that miR-23 has a critical role in the RA-induced neuronal differentiation of NT2 cells.
Intrinsic Multistate Switching of Gold Clusters through Electrochemical Gating (2007)

The electrochemical behavior of small metal nanoparticles is governed by Coulomb-like charging and equally spaced charge-transfer transitions. Using electrochemical gating at constant bias voltage, we show, for the first time, that individual nanoparticles can be operated as multistate switches in condensed media at room temperature, displaying distinct peak features in the tunneling current. The tunneling conductance increases with particle charge, suggesting that solvent reorganization and dielectric saturation become increasingly important.
Purification and Characterization of a Human Factor That Assembles and Remodels Chromatin (2000)

We have previously reported the isolation and characterization of a nucleosome remodeling and spacing factor, RSF. One of the RSF subunits is hSNF2h, a SNF2 homologue. Here we set out to isolate and characterize other hSNF2h-containing complexes. We have identified a novel hSNF2h complex that facilitates ATP-dependent chromatin assembly with the histone chaperone NAP-1. The complex possesses ATPase activity that is DNA-dependent and nucleosome-stimulated. This complex is capable of facilitating ATP-dependent nucleosome remodeling and transcription initiation from chromatin templates. In addition to hSNF2h, this complex also contains a 190-kDa protein encoded by the BAZ1A gene. Since both subunits are homologues of the Drosophila ACF complex (ATP-utilizing chromatin assembly and remodeling factor), we have named this factor human ACF or hACF.
Synthesis of Quantum Dot-Tagged Submicrometer Polystyrene Particles by Miniemulsion Polymerization (2006)

Submicrometer fluorescent polystyrene (PS) particles have been synthesized via miniemulsion polymerization using CdSe/ZnS core-shell quantum dots (QDs). The influence of QD concentration, QD coating (either trioctylphosphine oxide (TOPO)-coated or vinyl-functionalized), and surfactant concentration on the polymerization kinetics and the photoluminescence properties of the prepared particles has been analyzed. Polymerization kinetics were not altered by the presence of QDs, whatever their surface coating. Latexes exhibited particle sizes ranging from 100 to 350 nm, depending on surfactant concentration, and a narrow particle size distribution was obtained in all cases. The fluorescence signal of the particles increased with the number of incorporated TOPO-coated QDs. The slight red shift of the emission maximum was correlated with phase separation between PS and QDs, which occurred during the polymerization, locating the QDs in the vicinity of the particle/water interface. QD-tagged particles displayed higher fluorescence intensity with TOPO-coated QDs compared to those with the vinyl moiety. The obtained fluorescent particles open up new opportunities for a variety of applications in biotechnology.
4 Biogenesis and Function of the Yeast Vacuole (1997)

I. INTRODUCTION A defining characteristic of all eukaryotic cells is the presence of distinct endomembrane organelles. These compartments allow a cell to carry out competing processes in separate environments suited to the particular requirements of each process (e.g., biosynthesis vs. degradation). The presence of endomembrane organelles requires not only the formation and maintenance of the lipid components that delineate the different compartments, but also the synthesis and targeting of proteins that serve either structural or enzymatic functions in the organelles. The vacuole of Saccharomyces cerevisiae is a large organelle, comprising as much as 25% of the cellular volume (Wiemken and Durr 1974). There are some indications that vacuolar morphology is correlated with the cell’s position in the cell cycle (Hartwell 1970; Wiemken et al. 1970; Jones et al. 1993); logarithmically growing cells often have a multilobed vacuole, with interconnections between lobes indicative of a reticulum, whereas stationary-phase cells and cells in G 1 typically have a single large vacuole that is relatively less dense (Hartwell 1970; Wiemken et al. 1970; Preston et al. 1989; Pringle et al. 1989; Jones et al. 1993). The vacuole is a very dynamic organelle. When cells are starved of a carbon source, the vacuolar lobes rapidly fuse to give a single large vacuole that is less dense than prior to fusion; it will be phase bright, whereas the reticular vacuole is not. Refeeding results in a rapid return to the denser reticular form (Pringle et al. 1989). The yeast vacuole shares features with lysosomes. It contains...
Independent component approach to the analysis of EEG and MEG recordings (2000)

Multichannel recordings of the electromagnetic fields emerging from neural currents in the brain generate large amounts of data. Suitable feature extraction methods are, therefore, useful to facilitate the representation and interpretation of the data. Recently developed independent component analysis (ICA) has been shown to be an efficient tool for artifact identification and extraction from electroencephalographic (EEG) and magnetoencephalographic (MEG) recordings. In addition, ICA has been applied to the analysis of brain signals evoked by sensory stimuli. This paper reviews our recent results in this field.
Impact of Plasma Oxidized Low-Density Lipoprotein Removal on Atherosclerosis (2008)

OxLDL has a major atherogenic impact, and oxLDL removal is a promising therapeutic strategy against atherosclerosis.
A transient increase in c-myc precedes the transdifferentiation of hepatic stellate cells to myofibroblast-like cells (1999)

This study shows a high initial level of c-fos expression and a transient increase in c-myc expression followed by a decrease to lower levels prior to transdifferentiation and collagen production by stellate cells. A total loss of retinoid autofluorescence or a decrease in RAR-alpha or RAR-beta are not required for initial transdifferentiation of stellate cells or collagen production.
Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation (1999)

Array technologies have made it straightforward to monitor simultaneously the expression pattern of thousands of genes. The challenge now is to interpret such massive data sets. The first step is to extract the fundamental patterns of gene expression inherent in the data. This paper describes the application of self-organizing maps, a type of mathematical cluster analysis that is particularly well suited for recognizing and classifying features in complex, multidimensional data. The method has been implemented in a publicly available computer package, GENECLUSTER, that performs the analytical calculations and provides easy data visualization. To illustrate the value of such analysis, the approach is applied to hematopoietic differentiation in four well studied models (HL-60, U937, Jurkat, and NB4 cells). Expression patterns of some 6,000 human genes were assayed, and an online database was created. GENECLUSTER was used to organize the genes into biologically relevant clusters that suggest novel hypotheses about hematopoietic differentiation-for example, highlighting certain genes and pathways involved in "differentiation therapy" used in the treatment of acute promyelocytic leukemia.
Revisiting the mouse mitochondrial DNA sequence (2003)

The existence of reliable mtDNA reference sequences for each species is of great relevance in a variety of fields, from phylogenetic and population genetics studies to pathogenetic determination of mtDNA variants in humans or in animal models of mtDNA-linked diseases. We present compelling evidence for the existence of sequencing errors on the current mouse mtDNA reference sequence. This includes the deletion of a full codon in two genes, the substitution of one amino acid on five occasions and also the involvement of tRNA and rRNA genes. The conclusions are supported by: (i) the re-sequencing of the original cell line used by Bibb and Clayton, the LA9 cell line, (ii) the sequencing of a second L-derivative clone (L929), and (iii) the comparison with 12 other mtDNA sequences from live mice, 10 of them maternally related with the mouse from which the L cells were generated. Two of the latest sequences are reported for the first time in this study (Balb/cJ and C57BL/6J). In addition, we found that both the LA9 and L929 mtDNAs also contain private clone polymorphic variants that, at least in the case of L929, promote functional impairment of the oxidative phosphorylation system. Consequently, the mtDNA of the strain used for the mouse genome project (C57BL/6J) is proposed as the new standard for the mouse mtDNA sequence.
Cross-reacting serum opsonins in patients with meningococcal disease (1992)

We have examined the opsonic activity of sera from patients with Neisseria meningitidis (B:15:P1.16) infections against different meningococcal strains, using flow cytometry and luminol-enhanced chemiluminescence. A marked increase in the phagocytosis of ethanol-fixed meningococcal strains of different serogroups, serotypes, and serosubtypes was demonstrated in the presence of convalescence sera compared with acute sera. Convalescence sera also caused a significant increase of leukocyte oxidative metabolism during phagocytosis, as measured by luminol-enhanced chemiluminescence. The sera contained a broad range of opsonins cross-reacting with serogroup A, B, C, W-135, and Y meningococci of different serotypes and serosubtypes, indicating that the cross-reacting opsonins recognized surface epitopes other than those determined by current serotyping schemes.