gebhart/patrepeval huggingface dataset:
Dominant-negative zeta-associated protein 70 inhibits T cell antigen receptor signaling. (1996)

Zeta-associated protein (ZAP)-70 is a cytoplasmic protein tyrosine required for T cell antigen receptor (TCR) signaling and development. Mutations in ZAP-70 result in severe combined immunodeficiency in humans. ZAP-70 interacts with the TCR by binding to tyrosine-phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) present in the invariant subunits of the TCR complex. Here we report that two ZAP-70 mutants devoid of kinase activity, generated either by a point mutation in the kinase domain to create an inactive kinase, or by truncation of the entire kinase domain (SH2[N+C]), functioned as dominant-negative mutants to specifically suppress TCR-mediated activation of NFAT, a nuclear factor essential for inducible interleukin 2 gene expression. Biochemical studies with the SH2(N+C) mutant showed that it also blocked early TCR signaling events, such as p95vav tyrosine phosphorylation, extracellular signal-regulated kinase 2 activation, and the association of a number of tyrosine-phosphorylated proteins with growth factor receptor-binding protein 2 (GRB2). The inhibitory effects of the SH2(N+C) mutant revealed that it requires an intact phosphotyrosine-binding site in its COOH-terminal SH2 domain. Using a CD8-zeta chimeric receptor to analyze the interaction of the SH2(N+C) mutant with ITAMs of TCR-zeta, we found that this mutant was constitutively bound to the hyperphosphorylated CD8-zeta chimera. These results indicate that tyrosine-phosphorylated ITAM is the target for the action of this dominant-negative mutant, suggesting that the assembly of a functional receptor signaling complex on ITAMs is a critical proximal TCR signaling event leading to downstream activation.
Arabidopsis Contains Nine Long-Chain Acyl-Coenzyme A Synthetase Genes That Participate in Fatty Acid and Glycerolipid Metabolism (2002)

Long-chain acyl-coenzyme A (CoA) synthetases (LACSs) activate free fatty acids to acyl-CoA thioesters and as such play critical roles in fatty acid metabolism. This important class of enzymes factors prominently in several fatty acid-derived metabolic pathways, including phospholipid, triacylglycerol, and jasmonate biosynthesis and fatty acid beta-oxidation. In an effort to better understand the factors that control fatty acid metabolism in oilseeds, we have sought to identify and characterize genes that encode LACSs in Arabidopsis. Nine cDNAs were identified, cloned, and tested for their ability to complement a LACS-deficient strain of yeast (Saccharomyces cerevisiae). Seven of the nine successfully restored growth, whereas two cDNAs encoding putative peroxisomal isoforms did not. Lysates from yeast cells overexpressing each of the nine cDNAs were active in LACS enzyme assays using oleic acid as a substrate. The substrate specificities of the enzymes were determined after overexpression in LACS-deficient Escherichia coli. Most of the LACS enzymes displayed highest levels of activity with the fatty acids that make up the common structural and storage lipids in Arabidopsis tissues. Analysis of the tissue-specific expression profiles for these genes revealed one flower-specific isoform, whereas all others were expressed in various tissues throughout the plant. These nine cDNAs are thought to constitute the entire LACS family in Arabidopsis, and as such, will serve as powerful tools in the study of acyl-CoA metabolism in oilseeds.
Myeloperoxidase-Positive Cell Infiltration in Colorectal Carcinogenesis as Indicator of Colorectal Cancer Risk (2008)

Colorectal mucosa is targeted by toxic agents, which can initiate or promote colon cancer. The mechanism of damage might be a focal irritation with loss of normal epithelial cell barrier function. Genetic alterations in tumors may also affect host inflammatory response. The aim of this study was to define the extent of inflammation in colorectal mucosa, along colorectal carcinogenesis, and in microsatellite stable and unstable colorectal carcinomas. We collected 103 samples of normal colorectal mucosa from 65 patients (35 with colorectal cancer or adenoma, 8 with inflammatory bowel diseases, and 22 controls with normal colonoscopy). We also examined 24 aberrant crypt foci, 14 hyperplastic polyps, 16 adenomas, and 67 samples of colorectal carcinoma. Immunohistochemistry was used to count myeloperoxidase (MPO)-positive cells (neutrophils and monocytes) in x100 optical fields under a light microscope. Patients with colorectal tumors had a higher mean number of MPO-positive cells in normal mucosa than controls (mean +/- SD, 2.7 +/- 2.0 versus 1.4 +/- 1.4; P = 0.017). MPO-positive cell number was tightly linked to dysplasia in aberrant crypt foci and adenomas, and it was higher in carcinomas microsatellite unstable than those microsatellite stable (21.6 +/- 15.5 versus 11.9 +/- 8.0; P < 0.01). MPO immunohistochemistry is a simple and reliable technique for the quantification of inflammation in colorectal mucosa., and it may be a potential marker of colorectal cancer risk. Microsatellite instability seems to influence host immune responses to colorectal carcinoma. These observations strongly support a key role of inflammation in colorectal carcinogenesis.
Evidence of Bacterial Biofilms in a Rabbit Model of Sinusitis (2005)

This is evidence of the presence of bacterial biofilms in an animal model of sinusitis. This model may serve as a means to study the efficacy and safety of pharmacologic and surgical treatments on the disruption and elimination of bacterial biofilms. Additional study into the role of bacterial biofilms in perpetuating chronic sinusitis is warranted.
Carbon Nanotube DNA Sensor and Sensing Mechanism (2006)

We report the fabrication of single-walled carbon nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label-free detection of DNA hybridization is demonstrated with random sequence 15mer and 30mer oligonucleotides. DNA hybridization on gold electrodes, instead of on SWNT sidewalls, is mainly responsible for the acute electrical conductance change due to the modulation of energy level alignment between SWNT and gold contact. This work provides concrete experimental evidence on the effect of SWNT-DNA binding on DNA functionality, which will help to pave the way for future designing of SWNT biocomplexes for applications in biotechnology in general and also DNA-assisted nanotube manipulation techniques.
RXR Partial Agonist CBt-PMN Exerts Therapeutic Effects on Type 2 Diabetes without the Side Effects of RXR Full Agonists (2012)

Treating insulin resistance and type 2 diabetes in rodents, currently known retinoid X receptor (RXR) agonists induce significant adverse effects. Here we introduce a novel RXR partial agonist CBt-PMN (11b), which shows a potent glucose-lowering effect and improvements of insulin secretion and glucose tolerance without the serious adverse effects caused by RXR full agonists. We suggest that RXR partial agonists may be a new class of antitype 2 diabetes drug candidates.
Post‐Synthetic Modification of Tagged Metal–Organic Frameworks (2008)

Playing tag with MOFs: Zinc metal–organic frameworks with pendant aldehyde and methoxy groups are prepared. The aldehyde-tagged MOF takes up 2,4-dinitrophenylhydrazine, reacting to form a hydrazone-functionalized MOF which is crystallographically characterized. Use of both aldehyde- and methoxy-functionalized dicarboxylates leads to MOFs containing both ligands, of which the aldehyde groups can be selectively reacted.
Design and Synthesis of a Novel Series ofN-Alkyl Isatin Acylhydrazone Derivatives that Act as Selective Cannabinoid Receptor 2 Agonists for the Treatment of Neuropathic Pain (2008)

There is growing interest in using cannabinoid receptor 2 (CB2) agonists for the treatment of neuropathic pain. We have synthesized a novel series of N-alkyl isatin acylhydrazone derivatives and have identified and characterized several of them as novel analogues with high functional activity and selectivity at human CB2 receptors using [(35)S]GTP-gamma-S assays. Binding affinities at human CB2 and CB1 were determined for compounds 28, 33, 40, 48, and 58. Structure-activity relationship studies of this novel series led to optimization of our lead compound, compound 33 (MDA19). Compound 33 possessed potent antiallodynic effects in a rat model of neuropathic pain but did not affect rat locomotor activity. More potent and more CB2-receptor-selective compounds, including compounds 37, 40, and 48, were also discovered.
Yohimbine treatment of sexual side effects induced by serotonin reuptake blockers. (1992)

The results of this study indicate that yohimbine may be an effective treatment for the sexual side effects caused by serotonin reuptake blockers. Future controlled studies are needed to further investigate the effectiveness and safety of yohimbine for this indication.
Relevance of vancomycin-intermediate susceptibility and heteroresistance in methicillin-resistant Staphylococcus aureus bacteraemia (2011)

No adverse outcome was documented with hVISA phenotype, whereas VISA contributed to vancomycin treatment failure. VISA and hVISA appear to emerge in SCCmec II isolates among vancomycin-exposed patients and are better detected by Etest.
Type-specific neutralization of the human immunodeficiency virus with antibodies to env-encoded synthetic peptides. (1988)

A synthetic peptide (SP-10-IIIB) with an amino acid sequence [Cys-Thr-Arg-Pro-Asn-Asn-Asn-Thr-Arg-Lys-Ser-Ile-Arg-Ile-Gln-Arg-Gly-Pro -Pro-Gly-(Tyr); amino acids 303-321] from the human immunodeficiency virus (HIV) isolate human T-cell lymphotropic virus type III (HTLV-III) HTLV-IIIB envelope glycoprotein gp120 was coupled to tetanus toxoid and used to raise goat antibodies to HIV gp120. Goat anti-SP-10-IIIB serum bound to the surface of HTLV-IIIB-infected CEM T cells but not to the surface of HTLV-IIIRF-infected or uninfected CEM T cells. Anti-SP-10-IIIB antibodies also selectively bound to gp120 from lysates of HTLV-IIIB cells in immunoblot assays. Twenty-one percent of sera (28 of 175) from patients seropositive for HIV contained antibodies that reacted with SP-10-IIIB in RIA. Human anti-SP-10-IIIB antibodies affinity purified from acquired immunodeficiency syndrome (AIDS) patient serum bound to HTLV-IIIB-infected cells and immunoprecipitated gp120. Goat antibodies to SP-10-IIIB neutralized HTLV-IIIB (80% neutralization titer of 1/600), inhibited HTLV-IIIB-induced syncytium formation, but did not neutralize HIV isolates HTLV-IIIRF or HTLV-IIIMN or inhibit syncytium formation with these isolates. Also, goat antiserum to an homologous synthetic peptide [SP-10-IIIRF(A), (Cys)-Arg-Lys-Ser-Ile-Thr-Lys-Gly-Pro-Gly-Arg-Val-Ile-Tyr] from gp120 of HIV isolate HTLV-IIIRF inhibited syncytium formation by HTLV-IIIRF, but did not inhibit syncytium formation by HTLV-IIIB or by HTLV-IIIMN. Thus, the amino acid sequences of SP-10-IIIB and SP-10-IIIRF(A) define homologous regions of gp120 that are important in type-specific virus neutralization. The identification of these type-specific neutralizing epitopes should facilitate the design of a polyvalent, synthetic vaccine for AIDS.
Notch signaling in hematopoiesis and early lymphocyte development (2002)

Notch signals regulate multiple cell fate decisions during metazoan development. During hematopoiesis, Notch affects both hematopoietic stem cells and committed progenitors. In hematopoietic stem cells, Notch signaling has the propensity to expand the stem cells, promote their self-renewal, and influence their survival. In committed progenitors, Notch signaling plays a key role in determining lymphoid cell fates. This review focuses on recent developments to understand the role of Notch signaling in early events in hematopoiesis.
Linkage Disequilibrium Inflates Type I Error Rates in Multipoint Linkage Analysis when Parental Genotypes Are Missing (2005)

This observation strongly supports the evaluation of LD in multipoint linkage analyses, and further suggests that unaccounted for LD may be suspected when two-point and multipoint linkage analyses show a marked disparity in regions with elevated r2 measures of LD. Given the increasing popularity of high-density genome-wide SNP screens, inter-marker LD should be a concern in future linkage studies.
Hyaluronan‐based polymers in the treatment of osteochondral defects (2000)

Articular cartilage in adults has limited ability for self-repair. Some methods devised to augment the natural healing response stimulate some regeneration, but the repair is often incomplete and lacks durability. Hyaluronan-based polymers were tested for their ability to enhance the natural healing response. It is hypothesized that hyaluronan-based polymers recreate an embryonic-like milieu where host progenitor cells can regenerate the damaged articular surface and underlying bone. Osteochondral defects were made on the femoral condyles of 4-month-old rabbits and were left empty or filled with hyaluronan-based polymers. The polymers tested were ACP sponge, made of crosslinked hyaluronan, and HYAFF-11 sponge, made of benzylated hyaluronan. The rabbits were killed 4 and 12 weeks after surgery, and the condyles were processed for histology. All 12-week defects were scored with a 29-point scale, and the scores were compared with a Kruskall-Wallis analysis of variance on ranks. Untreated defects filled with bone tissue up to or beyond the tidemark, and the noncalcified surface layer varied from fibrous to hyaline-like tissue. Four weeks after surgery, defects treated with ACP exhibited bone filling to the level of the tidemark and the surface layer was composed of hyaline-like cartilage well integrated with the adjacent cartilage. At 12 weeks, the specimens had bone beyond the tidemark that was covered with a thin layer of hyaline cartilage. Four weeks after surgery, defects treated with HYAFF-11 contained a rim of chondrogenic cells at the interface of the implant and the host tissue. In general, the 12-week defects exhibited good bone fill and the surface was mainly hyaline cartilage. Treated defects received significantly higher scores than untreated defects (p < 0.05), and ACP-treated defects scored significantly higher than HYAFF-11-treated defects (p < 0.05). The introduction of these hyaluronan-based polymers into defects provides an appropriate scaffolding and favorable microenvironment for the reparative process. Further work is required to fully assess the long-term outcome of defects treated with these polymers.
Seven Aneurysms: Tenets and Techniques for Clipping (2011)

Chapter 1: Middle Cerebral Artery Surgical Anatomy Pterional approach Sylvian fissure Microsurgery The Sylvian fissure split Endovascular Perspective Case Examples Chapter 2: Posterior Communicating Artery Surgical Anatomy Supraclinoid ICA Anterior clinoid process, CN3, tentorium Microsurgery Carotid dissection Neighboring aneurysms (AChA, posterior wall, ICAB) Endovascular Perspective Case Examples Chapter 3: Anterior Communicating Artery Surgical Anatomy ACoA Complex Microsurgery Endovascular Perspective Case Examples Chapter 4: Ophthalmic Artery Surgical Anatomy Dural rings Aneurysm variants: clinoidal segment, carotid cave, posterior wall, SHA Microsurgery Endovascular Perspective Case Examples Chapter 5: Basilar bifurcation Surgical Anatomy Orbitozygomatic approach Interpeduncular fossa Cavernous sinus anatomy Microsurgery Endovascular Perspective Case Examples Chapter 6: Posterior Inferior Cerebellar Artery Surgical Anatomy Far Lateral approach Lower cranial nerves Occipital condyle Microsurgery Endovascular Perspective Case Examples Chapter 7: Pericallosal Artery Aneurysm Surgical Anatomy Bifrontal Craniotomy Anterior interhemispheric fissure Microsurgery Endovascular Perspective Case Examples
Modeling ontologies as executable domain specific languages (2010)

Ontologies, one of the cornerstone technologies of the Semantic Web are a very expressive and powerful means for domain modeling. To become really usable and ubiquitous, the implementations of ontology languages yet have to deliver satisfactory performance and before anything else have to be developer-friendly. We present an example of using Magic Potion, a description logics-based domain specific meta-language for building executable domain models. We are using LOCO ontology framework developed to support personalised learning contexts in learning applications to illustrate how ontologies in the form of executable domain-specific languages can blend the Semantic Web ideas into classical software engineering to improve expressiveness of domain models.
Hydrophile scanning as a complement to alanine scanning for exploring and manipulating protein–protein recognition: Application to the Bim BH3 domain (2008)

Alanine scanning has been widely employed as a method of identifying side chains that play important roles in protein-protein and protein-peptide interactions. Here we show how an analogous and complementary technique, hydrophile scanning, can provide additional insight on such interactions. Mutation of a wild-type residue to alanine removes most of the side-chain atoms, and the effect of this removal is typically interpreted to indicate contribution of the deleted side chain to the stability of the complex. Hydrophile scanning involves systematic mutation of wild-type residues to a cationic or anionic residue (lysine or glutamic acid, in this case). We find that the results of these mutations provide insights on interactions between polypeptide surfaces that are complementary to the information obtained via alanine scanning. We have applied this technique to a peptide that corresponds to the BH3 domain of the pro-apoptotic protein Bim. The wild-type Bim BH3 domain binds strongly to the anti-apoptotic proteins Bcl-x(L) and Mcl-1. Combining information from the alanine, lysine, and glutamic acid scans has enabled us to identify Bim BH3 domain mutants containing only two or three sequence changes that bind very selectively either to Bcl-x(L) or Mcl-1. Our findings suggest that hydrophile scanning may prove to be a broadly useful tool for revealing sources of protein-protein recognition and for engineering selectivity into natural sequences.
Source and fate of circulating citrulline (1981)

Previous work has demonstrated a continuous release of citrulline from the small intestine into the circulation. To evaluate the physiologic significance of this process, we have now measured citrulline uptake and release by isolated, perfused livers and, through surgical means and arteriovenous difference measurements, by various organs of the rat in vivo. Intestinally derived citrulline, an end product of glutamine nitrogen metabolism, passes through the liver without appreciable uptake. No significant extraintestinal source of circulating citrulline was found. Contrary to earlier suggestions, the liver releases no citrulline normally, but only when supplied with unphysiological high levels of ornithine and ammonia. Renal citrulline uptake was equivalent to approximately 83% the rate of intestinal release; kidneys, in turn, released arginine equivalent to approximately 75% of the citrulline taken up. Acute experiments in which the intestine, intestine plus liver, or kidneys were excluded from the circulation indicate that additional organs may also participate in citrulline exchange, at least when the circulating citrulline level is abnormal. The intestinal-renal pathway seems to account for a large though still unmeasured portion of the citrulline turnover in the circulation.
Measurement of gastrin and transforming growth factor alpha messenger RNA levels in colonic carcinoma cell lines by quantitative polymerase chain reaction. (1992)

A synthetic DNA template has been constructed that is suitable for the quantitation of mRNAs encoding gastrin, transforming growth factor alpha (TGF alpha), cholecystokinin, and the 78-kDa gastrin-binding protein. The template was used to measure levels of gastrin and TGF alpha mRNA in 7 colonic and 2 gastric carcinoma cell lines by the polymerase chain reaction. All lines produced detectable gastrin and TGF alpha mRNA with amounts varying between 2.1 and 540 molecules of gastrin mRNA/10(3) cells and 1.1 and 28 molecules of TGF alpha mRNA/10(3) cells. These results are consistent with the hypothesis that both gastrin and TGF alpha act as autocrine growth factors in colon carcinoma cell lines.
Apoptosis in the developing cerebellum of the thyroid hormone deficient rat (1998)

The mechanism underlying transient reduction of cell number in the developing cerebellum have been studied for several decades. In this study we analyzed cell death by apoptosis in the developing cerebellum of euthyroid and hypothyroid rats. Results showed that in both groups the apoptotic activity is limited to the internal granular layer from postnatal (p) day 2 to day 12 in euthyroid animals, with the peak at 8 days. No apoptotic cells were detected in the cerebellum of 22 days old euthyroid rats. The level of apoptosis in the cerebellum of hypothyroid rats also reached a peak at 8 days but was four times higher than in control animals. Apoptosis in hypothyroid animals was also observed at p22 and corresponds to the value found in the time of the apoptotic peak in euthyroid cerebellum. At the age of 42 days, no apoptotic cells were found in the cerebellum of either group. Furthermore, it appears that the hormone also plays a role in the disappearance of the external germinal layer, since its presence is still apparent in 42 day old hypothyroid cerebellum. Hence, our results suggest that the deficiency of thyroid hormone (TH) not only increases, but also extends apoptosis during rat cerebellum development and affects the disappearance of the external germinal layer.
Synthesis and silencing properties of siRNAs possessing lipophilic groups at their 3'-termini (2008)

Short interfering RNAs (siRNAs) conjugated with lipophilic groups at their 3'-termini were synthesized. The silencing activities of these siRNAs were examined by a dual-luciferase assay. It was found that the '-end of the passenger strand (sense strand) was better than the guide strand (antisense strand) for connecting bulky lipophilic molecules, particularly a rigid molecule such as cholesterol.
HIV-1 Ribonuclease H Inhibitory Phenolic Glycosides from Eugenia hyemalis (2008)

Three new galloyl arbutins, hyemalosides A-C (1-3), along with nine known compounds were isolated from the evergreen tree Eugenia hyemalis. The structures of compounds 1-3 were determined by analysis of NMR and MS data. Compounds 1-3 inhibited HIV-1 RNase H in vitro with IC50 values of 1.46, >18, and 1.19 microM, respectively. However, in a XTT-based cell viability assay using the human T-cell line CEM-SS infected with HIV-1 RT, none of the compounds inhibited the cytopathic effect of HIV-1 infection at the highest dose tested (20 microg/mL).