gebhart/patrepeval huggingface dataset:
Method for segmenting chest CT image data using an anatomical model: preliminary results (1997)

We present an automated, knowledge-based method for segmenting chest computed tomography (CT) datasets. Anatomical knowledge including expected volume, shape, relative position, and X-ray attenuation of organs provides feature constraints that guide the segmentation process. Knowledge is represented at a high level using an explicit anatomical model. The model is stored in a frame-based semantic network and anatomical variability is incorporated using fuzzy sets. A blackboard architecture permits the data representation and processing algorithms in the model domain to be independent of those in the image domain. Knowledge-constrained segmentation routines extract contiguous three-dimensional (3-D) sets of voxels, and their feature-space representations are posted on the blackboard. An inference engine uses fuzzy logic to match image to model objects based on the feature constraints. Strict separation of model and image domains allows for systematic extension of the knowledge base. In preliminary experiments, the method has been applied to a small number of thoracic CT datasets. Based on subjective visual assessment by experienced thoracic radiologists, basic anatomic structures such as the lungs, central tracheobronchial tree, chest wall, and mediastinum were successfully segmented. To demonstrate the extensibility of the system, knowledge was added to represent the more complex anatomy of lung lesions in contact with vessels or the chest wall. Visual inspection of these segmented lesions was also favorable. These preliminary results suggest that use of expert knowledge provides an increased level of automation compared with low-level segmentation techniques. Moreover, the knowledge-based approach may better discriminate between structures of similar attenuation and anatomic contiguity. Further validation is required.
Posttranslational Elevation of Cell Wall Invertase Activity by Silencing Its Inhibitor in Tomato Delays Leaf Senescence and Increases Seed Weight and Fruit Hexose Level (2009)

Invertase plays multiple pivotal roles in plant development. Thus, its activity must be tightly regulated in vivo. Emerging evidence suggests that a group of small proteins that inhibit invertase activity in vitro appears to exist in a wide variety of plants. However, little is known regarding their roles in planta. Here, we examined the function of INVINH1, a putative invertase inhibitor, in tomato (Solanum lycopersicum). Expression of a INVINH1:green fluorescent protein fusion revealed its apoplasmic localization. Ectopic overexpression of INVINH1 in Arabidopsis thaliana specifically reduced cell wall invertase activity. By contrast, silencing its expression in tomato significantly increased the activity of cell wall invertase without altering activities of cytoplasmic and vacuolar invertases. Elevation of cell wall invertase activity in RNA interference transgenic tomato led to (1) a prolonged leaf life span involving in a blockage of abscisic acid-induced senescence and (2) an increase in seed weight and fruit hexose level, which is likely achieved through enhanced sucrose hydrolysis in the apoplasm of the fruit vasculature. This assertion is based on (1) coexpression of INVINH1 and a fruit-specific cell wall invertase Lin5 in phloem parenchyma cells of young fruit, including the placenta regions connecting developing seeds; (2) a physical interaction between INVINH1 and Lin5 in vivo; and (3) a symplasmic discontinuity at the interface between placenta and seeds. Together, the results demonstrate that INVINH1 encodes a protein that specifically inhibits the activity of cell wall invertase and regulates leaf senescence and seed and fruit development in tomato by limiting the invertase activity in planta.
Endofin, a FYVE Domain Protein, Interacts with Smad4 and Facilitates Transforming Growth Factor-β Signaling (2007)

Transforming growth factor-beta (TGF-beta) signaling is facilitated by scaffold proteins such as SARA (Smad anchor for receptor activation). Endofin, a member of the FYVE domain protein family, has been suggested to regulate membrane trafficking. In this study, we report that endofin functions as a scaffold protein to facilitate TGF-beta signaling. Overexpression of endofin FYVE domain-deletion mutants inhibited TGF-beta-induced expression of CAGA-luciferase. Knockdown of endogenous endofin expression by RNA interference specifically led to reduction of the transcriptional responses of TGF-beta, but had no effect on BMP- or Wnt1-induced reporter expression. Furthermore, in endofin small interfering RNA-expressing stable cells, TGF-beta-mediated expression of plasminogen activator inhibitor-1 and p21(Cip1) was significantly reduced, and TGF-beta-promoted apoptosis was also impaired. We further showed that endofin could interact with Smad4 and TGF-beta type I receptors. Reduction of endogenous endofin expression resulted in a decrease of TGF-beta-induced Smad2 phosphorylation and Smad2-Smad4 complex formation. Together, our findings suggest that endofin facilitates TGF-beta signaling as a scaffold protein to promote the R-Smad-Smad4 complex formation by bringing Smad4 to the proximity of the receptor complex.
BIOTECH THRIVES IN HISTORIC UPPSALA (2003)

RETURN TO ISSUEPREVNewsNEXTBIOTECH THRIVES IN HISTORIC UPPSALACollaboration between industry and university has spurred development of biotechnologyPATRICIA L. SHORTView Author Information C&EN LONDONCite this: Chem. Eng. News 2003, 81, 26, 11–14Publication Date (Print):June 30, 2003Publication History Published online13 November 2010Published inissue 30 June 2003https://pubs.acs.org/doi/10.1021/cen-v081n026.p011https://doi.org/10.1021/cen-v081n026.p011newsACS PublicationsCopyright © 2003 American Chemical SocietyArticle Views13Altmetric-Citations-LEARN 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 options SUBJECTS:Biotechnology Get e-Alerts
Impaired TLR‐2 expression and TLR‐2‐mediated cytokine secretion in macrophages from patients with atopic dermatitis (2009)

Our findings clearly show an impaired TLR-2 expression and functional differences of TLR-2-mediated effects on macrophages of AD patients compared to healthy controls which might contribute to the enhanced susceptibility to skin infections with S. aureus in AD.
Improved silver staining procedure for fast staining in PhastSystem Development Unit. I. Staining of sodium dodecyl sulfate gels (1988)

A new modification of silver staining of proteins in sodium dodecyl sulfate polyacrylamide gels is adapted to automated staining in PhastSystem Development Unit. The use of a reduction step, after fixation, with thiosulfate in alcoholic sodium acetate buffer results in a considerable increase in sensitivity without the need for a recycling step. The detection limit is tenfold lower than in the silver staining procedure recommended so far for PhastSystem and corresponds to 0.05-0.1 ng protein per band. Total staining time with the new procedure is 75 min.
Hepatitis B Virus HBx Peptide 116–138 and Proteasome Activator PA28 Compete for Binding to the Proteasome α4/MC6 Subunit (2003)

PA28 is a modulator of the 20S proteasome. The PA28 binding sites on the 20S proteasome are still not well defined. Using yeast two-hybrid interaction assays and proteasome inactivation kinetics we provide evidence that the proteasome alpha4 subunit is one of the PA28 binding sites. This finding is supported by the observation that a hepatitis B virus X protein-derived polypeptide habouring the alpha4 proteasome subunit binding motif impairs the activation of 20S proteasomes by PA28.
Automated SQL query generation for systematic testing of database engines (2010)

We present a novel approach for generating syntactically and semantically correct SQL queries as inputs for testing relational databases. We leverage the SAT-based Alloy tool-set to reduce the problem of generating valid SQL queries into a SAT problem. Our approach translates SQL query constraints into Alloy models, which enable it to generate valid queries that cannot be automatically generated using conventional grammar-based generators.
Diversity for the direct-sequence spread spectrum system using multiple transmit antennas (2002)

Diversity is employed to improve the performance of a communication system in a fading environment. A novel form of diversity which is useful especially in situations where frequency diversity is not available is proposed. This technique uses multiple transmit antennas and the antennas are weighted by suitably determined time-varying phase offsets. It is shown that with this technique, M transmit antennas and an L-branch RAKE receiver gives rise to diversity of order LM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d (2005)

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (approximately 60 degrees) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant-DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (approximately 50 degrees). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (approximately 80 degrees). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower T m values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.
Longitudinal changes in total body creatine pool size and skeletal muscle mass using the D3‐creatine dilution method (2013)

The LC-MS/MS-based D<sub>3</sub>-creatine dilution method can be applied repeatedly to measure total body creatine skeletal muscle mass change in longitudinal study.
Lambda Interferon Inhibits Hepatitis B and C Virus Replication (2005)

Lambda interferon (IFN-lambda) induces an intracellular IFN-alpha/beta-like antiviral response through a receptor complex distinct from the IFN-alpha/beta receptor. We therefore determined the ability of IFN-lambda to inhibit hepatitis B virus (HBV) and hepatitis C virus (HCV) replication. IFN-lambda inhibits HBV replication in a differentiated murine hepatocyte cell line with kinetics and efficiency similar to IFN-alpha/beta and does not require the expression of IFN-alpha/beta or IFN-gamma. Furthermore, IFN-lambda blocked the replication of a subgenomic and a full-length genomic HCV replicon in human hepatocyte Huh7 cells. These results suggest the possibility that IFN-lambda may be therapeutically useful in the treatment of chronic HBV or HCV infection.
Adults with Attention Deficit Hyperactivity Disorder: Assessment and Treatment Considerations (1996)

Attention Deficit Hyperactivity Disorder (ADHD) has, historically, been viewed as a childhood disorder which would be outgrown by adulthood. More recent findings have established that the disorder often persists into adult-hood in a significant number of those diagnosed as children. Due to increased awareness and media attention being focused on ADHD in adults, greater numbers of adults are seeking evaluation and treatment for this disorder. The symptoms of ADHD are common to a variety of other psychiatric disorders including learning disabilities, so clinicians need to update their knowledge of assessment, treatment, and differential diagnosis issues regarding this often misunderstood disorder. This article discusses some current methods used in the assessment and treatment of adults with ADHD.
Epigenetics and cancer (2004)

Epigenetic mechanisms act to change the accessibility of chromatin to transcriptional regulation locally and globally via modifications of the DNA and by modification or rearrangement of nucleosomes. Epigenetic gene regulation collaborates with genetic alterations in cancer development. This is evident from every aspect of tumor biology including cell growth and differentiation, cell cycle control, DNA repair, angiogenesis, migration, and evasion of host immunosurveillance. In contrast to genetic cancer causes, the possibility of reversing epigenetic codes may provide new targets for therapeutic intervention.
Multiple mechanisms participate in the generation of diversity of human H chain CDR3 regions (1991)

The area of highest variability in the antibody-combining site is the third complementarity determining region or CDR3. Based on our preliminary observation of the tremendous variability of this region in the human system we have studied the potential of CDR3 regions for generating diversity in the human B cell repertoire. To this end we generated CDR3-specific cDNA libraries from tissues collected at several stages of human development. Detailed computer analysis of more than 500 sequences reveals that human CDR3 region have the potential to generate more than 10(14) different peptides. The mechanisms responsible for this diversity include rearrangement by inversion, D-D fusion, gene conversion and the frequent utilization of the recently described DIR genes. The specific recombination mechanisms which may explain aberrant rearrangements as well as differences between fetal and adult repertoires are discussed in detail.
Multichannel Signal Processing Based on Logic Averaging (1982)

The multichannel signal processor described provides an excellent capability for the detection of any kind of signal, on-line, with a SNR of 0.1 dB at a wide frequency range. This very efficient and inexpensive approach to improving the SNR by the processor wiUl reduce the need for other signal processing techniques. The processor's reaction on an input signal and noise has been analyzed by a mathematical model. This effect is IMustrated by an in vivo noninvasive detection on a beat-by-beat basis of electrical activity of the His-Purkinje system of the heart, and the detection of a pulse-like signal from a generator.
Phenotypic characteristics of cell lines requiring interleukin 3 for growth. (1982)

A number of cell lines have been derived from bone marrow cultures in the presence of WEHI-3 conditioned media (CM) that continue to require WEHI-3 CM for growth in vitro. Because the WEHI-3 cell line has been shown to constitutively produce a lymphokine (IL 3) that induces the expression of 20 alpha-hydroxysteroid dehydrogenase (20 alpha SDH) in cultures of splenic lymphocytes from athymic mice, we examined whether these cell lines were dependent upon IL 3 for growth. The results demonstrate that the factor required for growth of these cell lines copurifies with IL 3 activity on G-100, DEAE cellulose, and CM cellulose column chromatography as well as in preparative isoelectric focusing and on hydrophobic supports in reverse phase high pressure liquid chromatography. The biologic activity of peak fractions in each case was similar in both types of assays. These results strongly suggest that the WEHI-3 CM-dependent cell lines are dependent on IL 3 for growth in vitro. All the cell lines have readily detectable levels of 20 alpha SDH but have differing cell surface phenotypes. The C3HSFFV line is devoid of conventional lymphoid cell surface markers with the exception of Lyt-1, whereas the FDC-P1 expresses Thy-1, Ly-5, and H-11. Other cell lines have intermediate phenotypes.
Protein Kinase C-ε Primes the Cardiac Sarcolemmal Adenosine Triphosphate–sensitive Potassium Channel to Modulation by Isoflurane (2004)

The PKC-epsilon isozyme primed the sarcKATP channel to open in the presence of isoflurane. The PKC-delta isozyme was significantly less effective in modulating the isoflurane effect on this channel.
Antibacterial Agents That Target Lipid A Biosynthesis in Gram-negative Bacteria (2000)

UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) catalyzes the second step in the biosynthesis of lipid A, a unique amphiphilic molecule found in the outer membranes of virtually all Gram-negative bacteria. Since lipid A biosynthesis is required for bacterial growth, inhibitors of LpxC have potential utility as antibiotics. The enzymes of lipid A biosynthesis, including LpxC, are encoded by single copy genes in all sequenced Gram-negative genomes. We have now cloned, overexpressed, and purified LpxC from the hyperthermophile Aquifex aeolicus. This heat-stable LpxC variant (the most divergent of all known LpxCs) displays 32% identity and 51% similarity over 277 amino acid residues out of the 305 in Escherichia coli LpxC. Although A. aeolicus LpxC deacetylates the substrate UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine at a rate comparable with E. coli LpxC, a phenyloxazoline-based hydroxamate that inhibits E. coli LpxC with K(i) of approximately 50 nM (Onishi, H. R., Pelak, B. A., Gerckens, L. S., Silver, L. L., Kahan, F. M., Chen, M. H., Patchett, A. A., Galloway, S. M., Hyland, S. A., Anderson, M. S., and Raetz, C. R. H. (1996) Science 274, 980-982) does not inhibit A. aeolicus LpxC. To determine whether or not broad-spectrum deacetylase inhibitors can be found, we have designed a new class of hydroxamate-containing inhibitors of LpxC, starting with the structure of the physiological substrate. Several of these compounds inhibit both E. coli and A. aeolicus LpxC at similar concentrations. We have also identified a phosphinate-containing substrate analog that inhibits both E. coli and A. aeolicus LpxC, suggesting that the LpxC reaction proceeds by a mechanism similar to that described for other zinc metalloamidases, like carboxypeptidase A and thermolysin. The differences between the phenyloxazoline and the substrate-based LpxC inhibitors might be exploited for developing novel antibiotics targeted either against some or all Gram-negative strains. We suggest that LpxC inhibitors with antibacterial activity be termed "deacetylins."
Differentiation of mouth versus gut as site of origin of odoriferous breath gases after garlic ingestion (1999)

Utilizing the sulfur-containing gases of garlic as probes, we investigated the gut versus mouth origin of odoriferous breath gases. Five individuals ingested 6 g of garlic, and sulfur gases in mouth, alveolar air, and urine samples were measured. The mouth normally contained low concentrations of hydrogen sulfide, methanethiol, and dimethyl sulfide. Immediately after garlic ingestion, transient high concentrations of methanethiol and allyl mercaptan and lesser concentrations of allyl methyl sulfide (AMS), allyl methyl disulfide, and allyl disulfide were observed. With the exception of AMS, all gases were present in far greater concentrations in mouth than alveolar air, indicating an oral origin. Only AMS was of gut origin as evidenced by similar partial pressures in mouth, alveolar air, and urine. After 3 h, AMS was the predominant breath sulfur gas. The unique derivation of AMS from the gut is attributable to the lack of gut and liver metabolism of this gas versus the rapid metabolism of the other gases. Breath odor after garlic ingestion initially originates from the mouth and subsequently from the gut.
Parasite-Derived Neurotrophic Factor/trans-Sialidase of Trypanosoma cruzi Links Neurotrophic Signaling to Cardiac Innate Immune Response (2014)

The Chagas' disease parasite Trypanosoma cruzi elicits a potent inflammatory response in acutely infected hearts that keeps parasitism in check and triggers cardiac abnormalities. A most-studied mechanism underlying innate immunity in T. cruzi infection is Toll-like receptor (TLR) activation by lipids and other parasite molecules. However, yet-to-be-identified pathways should exist. Here, we show that T. cruzi strongly upregulates monocyte chemoattractant protein 1 (MCP-1)/CCL2 and fractalkine (FKN)/CX3CL1 in cellular and mouse models of heart infection. Mechanistically, upregulation of MCP-1 and FKN stems from the interaction of parasite-derived neurotrophic factor (PDNF)/trans-sialidase with neurotrophic receptors TrkA and TrkC, as assessed by pharmacological inhibition, neutralizing antibodies, and gene silencing studies. Administration of a single dose of intravenous PDNF to naive mice results in a dose-dependent increase in MCP-1 and FKN in the heart and liver with pulse-like kinetics that peak at 3 h postinjection. Intravenous PDNF also augments MCP-1 and FKN in TLR signaling-deficient MyD88-knockout mice, underscoring the MyD88-independent action of PDNF. Although single PDNF injections do not increase MCP-1 and FKN receptors, multiple PDNF injections at short intervals up the levels of receptor transcripts in the heart and liver, suggesting that sustained PDNF triggers cell recruitment at infection sites. Thus, given that MCP-1 and FKN are chemokines essential to the recruitment of immune cells to combat inflammation triggers and to enhance tissue repair, our findings uncover a new mechanism in innate immunity against T. cruzi infection mediated by Trk signaling akin to an endogenous inflammatory and fibrotic pathway resulting from cardiomyocyte-TrkA recognition by matricellular connective tissue growth factor (CTGF/CCN2).
Dispersion Interactions Enable the Self-Directed Growth of Linear Alkane Nanostructures Covalently Bound to Silicon (2004)

Current interest in methods for controllably adding organic molecules to silicon surfaces relates to proposed hybrid silicon-organic devices. It was recently shown that a "self-directed" growth process, requiring only limited scanned probe intervention, has the potential to permit rapid, parallel production of ordered molecular nanostructures on silicon with predefined absolute position, structure, composition, and extent of growth. The hybrid organic-silicon structures formed are bound by strong covalent interactions. In this work, we use scanning tunneling microscopy and density functional theory techniques to show that molecule-surface dispersion interactions enable the growth process and play a crucial role in the final configurations of the nanostructures.