gebhart/patrepeval huggingface dataset:
A Single BIR Domain of XIAP Sufficient for Inhibiting Caspases (1998)

The inhibitor of apoptosis proteins (IAPs) constitute an evolutionarily conserved family of homologous proteins that suppress apoptosis induced by multiple stimuli. Some IAP family proteins, including XIAP, cIAP-1, and cIAP-2, can bind and directly inhibit selected caspases, a group of intracellular cell death proteases. These caspase-inhibiting IAP family proteins all contain three tandem BIR domains followed by a RING zinc finger domain. To determine the structural basis for caspase inhibition by XIAP, we analyzed the effects of various fragments of this IAP family protein on caspase activity in vitro and on apoptosis suppression in intact cells. The RING domain of XIAP failed to inhibit the activity of recombinant caspases-3 or -7, whereas a fragment of XIAP encompassing the three tandem BIR domains potently inhibited these caspases in vitro and blocked Fas (CD95)-induced apoptosis when expressed in cells. Further dissection of the XIAP protein demonstrated that only the second of the three BIR domains (BIR2) was capable of binding and inhibiting these caspases. The apparent inhibition constants (Ki) for BIR2-mediated inhibition of caspases-3 and -7 were 2-5 nM, indicating that this single BIR domain possesses potent anti-caspase activity. Expression of the BIR2 domain in cells also partially suppressed Fas-induced apoptosis and blocked cytochrome c-induced processing of caspase-9 in cytosolic extracts, whereas BIR1 and BIR3 did not. These findings identify BIR2 as the minimal caspase-inhibitory domain of XIAP and indicate that a single BIR domain can be sufficient for binding and inhibiting caspases.
cDNA cloning of a novel cdc2+/CDC28‐related protein kinase from rice (1991)

A cDNA clone, named R2, has been isolated by screening a rice cell cDNA library with a redundant oligonucleotide probe derived from the conserved ATP binding site of cdc2+/CDC28 protein kinases. The cDNA contained the entire coding sequence for a 424 amino acid polypeptide with a molecular mass of 47.6 kDa. The R2 mRNA, 2.1 kb in size, was expressed in both cultured rice cells and rice seedlings at similar levels. The predicted R2 protein has canonical motifs for ATP binding and catalysis, and is significantly homologous (up to 47%) to members of the cdc2+/CDC28 subfamily of serine/threonine protein kinase. The R2 protein is a novel member of the subfamily.
The Politics of Same-Sex Marriage in Canada and the United States (2005)

“Nobody listens to us. There is not a single person in Washington who will get us…anything but shit and more shit. I'm sorry. This is where we are now. Nowhere.”
Visual cluster exploration of web clickstream data (2012)

Web clickstream data are routinely collected to study how users browse the web or use a service. It is clear that the ability to recognize and summarize user behavior patterns from such data is valuable to e-commerce companies. In this paper, we introduce a visual analytics system to explore the various user behavior patterns reflected by distinct clickstream clusters. In a practical analysis scenario, the system first presents an overview of clickstream clusters using a Self-Organizing Map with Markov chain models. Then the analyst can interactively explore the clusters through an intuitive user interface. He can either obtain summarization of a selected group of data or further refine the clustering result. We evaluated our system using two different datasets from eBay. Analysts who were working on the same data have confirmed the system's effectiveness in extracting user behavior patterns from complex datasets and enhancing their ability to reason.
Dynamic Collision-Induced Dissociation of Peptides in a Quadrupole Ion Trap Mass Spectrometer (2007)

The fragmentation of natural peptides using dynamic collision-induced dissociation (DCID), a novel fragmentation method for quadrupole ion traps, is demonstrated. Using leucine enkephalin as a diagnostic molecule, the fragmentation efficiencies and energetics of DCID are compared with other methods of collisional activation in ion traps such as conventional on-resonance excitation and high-amplitude short-time excitation (HASTE). A typical fragmentation efficiency of approximately 20% is achieved for DCID, which is significantly lower than conventional CID (maximum near 80%). Tandem mass spectra of two other peptides, substance P and oxidized insulin alpha-chain, demonstrate that product ion spectra for DCID are comparable to conventional or HASTE CID. Because DCID achieves fragmentation during the standard mass acquisition scan, no extra time is necessary for on-resonance excitation or product ion collection, so analysis times are reduced by a minimum of 10-15% depending on the scanning conditions. DCID therefore offers more tandem mass spectra per second than conventional methods of collisional activation, which could be highly advantageous for bottom-up proteomics separations.
Protein kinase C expression and activity in the human brain after ischaemic stroke (1998)

We examined the expression of protein kinase C isoforms in infarcted tissue, penumbra and contralateral brain tissue from 10 patients who died between 1-52 days after ischaemic stroke. Ten patients aged 61-89 years were used in the study. Tissue samples were assayed for protein kinase C activity using a non-radioactive method, and specific isoforms expression determined by Western blotting and staining with anti-PKC polyclonal antibodies. There was a 2-24 fold increase in PKC gamma in the ischaemic penumbra of nine out of 10 patients compared to contralateral tissue. In infarcted tissue expression of PKC gamma was not significantly changed in any of 10 samples but the beta I isoform increased in eight and the beta II in nine patients. There was no significant change in expression in PKC alpha or in infarct or penumbra. Differences in total PKC activity were not specific in seven out of eight patients and it is difficult to estimate their significance. In conclusion after ischaemia there was an altered expression of PKC isoforms with an increase of PKC gamma in the surviving penumbra and beta I and beta II in the infarcted core.
A SARCOMA OF THE FOWL TRANSMISSIBLE BY AN AGENT SEPARABLE FROM THE TUMOR CELLS (1911)

A transmissible sarcoma of the chicken has been under observation in this laboratory for the past fourteen months, 1 and it has assumed of late a special interest because of its extreme malignancy and a tendency to wide-spread metastasis3 In a careful study of the growth, tests have been made to determine whether it can be transmitted by a filtrate free of the tumor cells.Attempts to so transmit rat, mouse, and dog tumors have never succeeded; and it was supposed that the sarcoma of the fowl would not differ from them in this regard, since it is a typical neoplasm.On the contrary, small quantities of a cell-free filtrate have sufficed to transmit the growth to susceptible fowls.EXPERIMENTS.
Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences (1987)

A partial nucleotide sequence that included 1,693 base pairs of the M12 (emm12) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P1 and P3) separated by 30 bases. The transcription start sites of the emm12 gene were located more than 400 bases downstream of a deletion that causes decreased M-protein gene transcription in strain CS64. Deletion analysis of M protein-expressing plasmids indicated that an upstream region greater than 1 kilobase is required for M-protein gene expression. The M-protein gene transcriptional unit appears to be monocistronic. Analysis of the emm12 DNA sequence revealed three major repeat regions. Two copies of each repeat, A and B, existed within the variable 5' end of the gene; repeat C demarcated the 5' end of the constant region shared by emm12 and emm6.
TARGETED PHOTOCHEMICAL MODIFICATION OF HIV‐DERIVED OLIGORIBONUCLEOTIDES BY ANTISENSE OLIGODEOXYNUCLEOTIDES LINKED TO PORPHYRINS (1994)

Antisense oligodeoxynucleotides directed against a 24-mer RNA derived from the long terminal repeat (LTR) region of HIV were linked to proto- and methylpyrroporphyrin and their zinc derivatives. The oligonucleotide-porphyrin conjugates were tested for their ability to induce photodamage on the target RNA. Upon hybridization followed by irradiation at 405 nm, the photochemical reaction led to photocross-linking of the antisense derivative to the RNA substrate. The protoporphyrin exhibited a much higher cross-linking yield than the methylpyrroporphyrin while the Zn-porphyrin derivatives were found to be less efficient than their corresponding nonmetallated congeners. The specificity of the photocross-linking reaction between the porphyrin-oligomer and its target RNA was demonstrated by the following evidence: (1) hybrid formation was required for photocross-linking to occur, (2) the sites of cross-linking on the target RNA were identified at G residues located in close proximity to the porphyrin photoactive center in the hybrid and (3) addition of bulk calf liver RNA did not affect the photocross-linking efficiency.
Serum Interleukin-6 and interleukin-8 are early biomarkers of acute kidney injury and predict prolonged mechanical ventilation in children undergoing cardiac surgery: a case-control study (2009)

Serum IL-6 and IL-8 values identify AKI early in patients undergoing CPB surgery. Furthermore, among patients with AKI, high IL-6 levels are associated with prolonged mechanical ventilation, suggesting that circulating cytokines in patients with AKI may have deleterious effects on other organs, including the lungs.
Asymmetric septal hypertrophy in heterozygous cMyBP-C null mice (2004)

These data provide evidence that heterozygous cMyBP-C null mice represent the first model with a key feature of human FHC that is asymmetric septal hypertrophy.
Infrared Photodetectors: A Review of Operational Detectors (1962)

A comparison is given, in terms of D*, of the characteristics of most of the photodetectors of both quantum and thermal types, which are available for operational use at the near and intermediate infrared. A discussion of detectors for use at longer wavelengths (up to the mm range) includes two quantum types as well as the cooled bolometers and the pneumatic cell. The review of thermal detectors emphasizes noise limitations as well as spectral characteristics. The need for gray body detectors for use in spectral response measurements is discussed. It is pointed out that a complete noise power spectrum is essential in order to evaluate effectively a detector and determine the operational limitations.
Lymphadenopathy Associated Virus Infection of a Blood Donor—Recipient Pair with Acquired Immunodeficiency Syndrome (1984)

A retrovirus isolated from three patients with the acquired immunodeficiency syndrome (AIDS) in the United States was morphologically and antigenically identical to lymphadenopathy associated virus isolated in France. Two of these isolates were from a blood donor-recipient pair, each of whom developed AIDS. Lymphadenopathy associated virus was isolated from the blood donor's lymphocytes 12 months after his onset of AIDS symptoms and from the blood recipient's lymphocytes 1 month after her onset of AIDS symptoms. Two isolates from the blood donor-recipient pair and an isolate from an epidemiologically unrelated homosexual man were examined by competitive radioimmunoassay to determine their antigenic relatedness to each other and to other human retroviruses. The major core proteins (p25) of the isolates were antigenically identical and all three isolates were identical to prototype lymphadenopathy associated virus isolated in France.
The cell surface proteoglycan of mouse mammary epithelial cells. The extracellular domain contains N terminus and a peptide sequence present in a conditioned medium proteoglycan. (1988)

The cell surface proteoglycan of mouse mammary epithelial (NMuMG) cells behaves as a receptor for interstitial matrix materials and consists of a membrane-associated domain and an extracellular domain (ectodomain). The ectodomain can be released intact from the cell surface by mild trypsin treatment and appears to be shed from the cells into the culture medium by cleavage from the membrane-associated domain. We have examined the chemical relationship between the trypsin-released proteoglycan and shed proteoglycan to assess their relationship to each other and to the cell surface. Purification and amino acid sequencing of the ectodomain released by mild trypsin treatment resulted in no clear signal until the protein was cleaved by CNBr treatment, suggesting that its N terminus is blocked and oriented extracellularly. The amino acid sequence identified in the trypsin-released ectodomain is present near the N terminus of the shed proteoglycan purified from conditioned medium, indicating that both forms possess closely related (if not identical) core proteins. The sequence reveals a pentapeptide identical to one near the C terminus of the rat hepatic lectin (RHL-1, rat asialoglycoprotein receptor). The medium proteoglycan, which migrates as a smear on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (between 93 and 200 kDa), is heterogeneous due to varying amounts of glycosaminoglycan and substituted O-linked oligosaccharide present on an approximately 46-kDa polypeptide.
Gene expression profiling provides insights into the pathways involved in solid pseudopapillary neoplasm of the pancreas (2009)

Solid-pseudopapillary neoplasms (SPNs) are rare human pancreatic neoplasms usually associated with a good prognosis. In contrast to other pancreatic tumours, aberrant activation of the Wnt-beta-catenin pathway appears to be a constant feature in SPN. Aside from activation of the Wnt-beta-catenin pathway, little is known about biological pathways deregulated in SPN. We carried out transcriptome profiling of SPN to gain insights into the pathogenesis of these tumours. As expected, the over-expression of AXIN2, TBX3, SP5 and NOTUM demonstrated activation of the beta-catenin pathway. Members of the Notch pathway (HEY1, HEY2, NOTCH2) were also up-regulated, relative to their expression in ductal adenocarcinomas (DAC) or pancreatic endocrine tumours (PET). Other genes, such as EDN3, HAND2, netrin-G2 and the receptor netrin-G1 ligand, involved in neural crest differentiation, were also identified as altered. Increased levels of SOX10 and TuJ-1 proteins were also indicative of neural-like differentiation. In conclusion, SPN display a complex expression profile, distinct from that observed in PET and DAC and involving both the beta-catenin and Notch pathways, together with expression of neural differentiation markers.
Back Cover: Aerogel Architectures Boost Oxygen‐Evolution Performance of NiFe2Ox Spinels to Activity Levels Commensurate with Nickel‐Rich Oxides (ChemElectroChem 9/2016) (2016)

The Back Cover picture shows that activity for NiFe2Ox–catalyzed O2 evolution linearly tracks the surface area of the nanostructured oxide: aerogel > xerogel > precipitated nanopowder. More information can be found in the Full Paper by C. N. Chervin et al. on page 1369 in Issue 9, 2016 (DOI: 10.1002/celc.201600206).
Identification of the UDP-glucosyltransferase gene UGTA1, responsible for the first glucosylation step in the sophorolipid biosynthetic pathway of Candida bombicola ATCC 22214 (2010)

Candida bombicola ATCC 22214 is applied commercially for the production of sophorolipids from renewable resources such as vegetable oils or waste streams. Although much research has been performed on optimization of fermentation conditions and on the influence of feed source and process parameters on sophorolipid structures and yields, the metabolic pathway of these important bioproducts remains unclear. Here, we identify a glucosyltransferase gene UGTA1 and show that the gene product is responsible for the first glucosylation step in the biosynthetic pathway of sophorolipids. Moreover, we provide evidence that the second glucosylation step is catalysed by a different glucosyltransferase that acts independently from the first. Therefore, the biosynthesis of sophorolipids by C. bombicola involves two glucosyltransferases that act in a stepwise manner. The UGTA1 gene described here is the first identified gene with a clear function in sophorolipid production by this economically important yeast.
Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes (2004)

Measurement of the expression of six genes is sufficient to predict overall survival in diffuse large-B-cell lymphoma.
Effects of Multisite Ventricular Pacing on Cardiac Function in Normal Dogs and Dogs with Heart Failure (1999)

We conclude that pacing simultaneously at two right and two left ventricular sites significantly improves cardiac function compared with single RVA pacing, with or without sequential AV synchrony, in dogs with rapid ventricular pacing-induced heart failure and no BBB.
Diabetes mellitus: The epidemic of the century (2015)

The epidemic nature of diabetes mellitus in different regions is reviewed. The Middle East and North Africa region has the highest prevalence of diabetes in adults (10.9%) whereas, the Western Pacific region has the highest number of adults diagnosed with diabetes and has countries with the highest prevalence of diabetes (37.5%). Different classes of diabetes mellitus, type 1, type 2, gestational diabetes and other types of diabetes mellitus are compared in terms of diagnostic criteria, etiology and genetics. The molecular genetics of diabetes received extensive attention in recent years by many prominent investigators and research groups in the biomedical field. A large array of mutations and single nucleotide polymorphisms in genes that play a role in the various steps and pathways involved in glucose metabolism and the development, control and function of pancreatic cells at various levels are reviewed. The major advances in the molecular understanding of diabetes in relation to the different types of diabetes in comparison to the previous understanding in this field are briefly reviewed here. Despite the accumulation of extensive data at the molecular and cellular levels, the mechanism of diabetes development and complications are still not fully understood. Definitely, more extensive research is needed in this field that will eventually reflect on the ultimate objective to improve diagnoses, therapy and minimize the chance of chronic complications development.
Involvement of Stat3 in interleukin‐6‐induced IgM production in a human B‐cell line (1997)

Interleukin-6 (IL-6) is an important B-cell growth and differentiation factor. IL-6 treatment of the human lymphoblastoid cell line, SKW6.4, leads to increased IgM production. We have previously shown that IL-6 induces activation of JAK1 and JAK2 in human B cell lines. A chimeric IL-6 receptor, comprised of the intracellular tail of the IL-6 receptor subunit gp130 fused to the extracellular domain of the epidermal growth factor (EGF) receptor, was stably transfected into SKW6.4 cells. EGF treatment induced IgM production in cells transfected with an intact gp130 cytoplasmic tail, but not in untransfected cells or cells transfected with a cytoplasmic tail lacking all four signal transducers and activators of transcription (Stat) binding sites. Moreover, EGF treatment induced Stat3 phosphorylation in cells transfected with the intact chimeric EGF-gp130 receptor along with induction of DNA-mobility shift of a classical interferon-gamma-activated site. To define further the relation between Stat3 activation and enhanced IgM production, we determined the effect of chimeric gp130 on the transcriptional activation of a genetic element linked to immunoglobulin production, namely the immunoglobulin heavy chain enhancer (IgH-enhancer). Parental as well as transfected SKW6.4 cells were transiently transfected with an IgH-enhancer-luciferase construct. The transcriptional activity of the IgH-luciferase construct was induced upon ligation of the full-length chimeric receptor but not by truncated gp130 receptors. Moreover, the gp130-induced activity of this reporter gene was abrogated by Stat3EE, a mutant Stat3 incapable of binding DNA. These results indicate that IL-6-induced B-cell differentiation, as measured by IgM production, may be controlled by Stat3 proteins.
Identification of a Novel Splice Variant Isoform of TREM-1 in Human Neutrophil Granules (2015)

Triggering receptor expressed on myeloid cells-1 (TREM-1) is critical for inflammatory signal amplification. Humans have two forms of TREM-1: a membrane receptor, associated with the adaptor DAP12, and a soluble receptor detected at times of infection. The membrane receptor isoform acts synergistically with the TLR pathway to promote cytokine secretion and neutrophil migration, whereas the soluble receptor functions as a counterregulatory molecule. In multiple models of sepsis, exogenous administration of soluble forms of TREM-1 attenuates inflammation and markedly improves survival. Despite intense interest in soluble TREM-1, both as a clinical predictor of survival and as a therapeutic tool, the origin of native soluble TREM-1 remains controversial. Using human neutrophils, we identified a 15-kDa TREM-1 isoform in primary (azurophilic) and secondary (specific) granules. Mass spectrometric analysis, ELISA, and immunoblot confirm that the 15-kDa protein is a novel splice variant form of TREM-1 (TREM-1sv). Neutrophil stimulation with Pseudomonas aeruginosa, LPS, or PAM(3)Cys4 resulted in degranulation and release of TREM-1sv. The addition of exogenous TREM-1sv inhibited TREM-1 receptor-mediated proinflammatory cytokine production. Thus, these data reveal that TREM-1 isoforms simultaneously activate and inhibit inflammation via the canonical membrane TREM-1 molecule and this newly discovered granular isoform, TREM-1sv.
Development and characterization of a Yucatan miniature biomedical pig permanent middle cerebral artery occlusion stroke model (2014)

Efforts to develop stroke treatments have met with limited success despite an intense need to produce novel treatments. The failed translation of many of these therapies in clinical trials has lead to a close examination of the therapeutic development process. One of the major factors believed to be limiting effective screening of these treatments is the absence of an animal model more predictive of human responses to treatments. The pig may potentially fill this gap with a gyrencephalic brain that is larger in size with a more similar gray-white matter composition to humans than traditional stroke animal models. In this study we develop and characterize a novel pig middle cerebral artery occlusion (MCAO) ischemic stroke model. Eleven male pigs underwent MCAO surgery with the first 4 landrace pigs utilized to optimize stroke procedure and 7 additional Yucatan stroked pigs studied over a 90 day period. MRI analysis was done at 24 hrs and 90 days and included T2w, T2w FLAIR, T1w FLAIR and DWI sequences and associated ADC maps. Pigs were sacrificed at 90 days and underwent gross and microscopic histological evaluation. Significance in quantitative changes was determined by two-way analysis of variance and post-hoc Tukey’s Pair-Wise comparisons. MRI analysis of animals that underwent MCAO surgery at 24 hrs had hyperintense regions in T2w and DWI images with corresponding ADC maps having hypointense regions indicating cytotoxic edema consistent with an ischemic stroke. At 90 days, region of interest analysis of T1 FLAIR and ADC maps had an average lesion size of 59.17 cc, a loss of 8% brain matter. Histological examination of pig brains showed atrophy and loss of tissue, consistent with MRI, as well as glial scar formation and macrophage infiltration. The MCAO procedure led to significant and consistent strokes with high survivability. These results suggest that the pig model is potentially a robust system for the study of stroke pathophysiology and potential diagnostics and therapeutics.