gebhart/patrepeval huggingface dataset:
Papillomavirus Transforming Functions (2007)

The bovine papillomavirus type 1 (BPV-1) has served as a model for unravelling the molecular genetics of the papillomaviruses. BPV-1 transformation of rodent cells in tissue culture has provided a means to study the viral functions involved in latent infection of cells and in the induction of cellular proliferation functions. BPV-1 has been shown to encode two independent transforming genes, each of which can induce cellular transformation in susceptible rodent cells. These two genes apparently act synergistically in transforming mouse C127 cells. Deletion mutagenesis studies have shown that the expression of one of these genes (E6) is required for efficient tumorigenesis and anchorage independence. BPV-1 also encodes functions which may act indirectly to affect transformation. BPV-1 contains transcriptional enhancers which can act in a position-independent and orientation-independent manner to increase the transcriptional activity of a heterologous gene. One of these elements, which is located in a non-coding region of the genome, can be trans-activated by a specific viral gene product encoded by the E2 open reading frame. Mutations which eliminate this trans-activation function also have a dramatic effect on transformation and on stable plasmid maintenance.
Carcinoembryonic Antigen as a Marker for Colorectal Cancer: Is It Clinically Useful? (2001)

Currently, the most useful application of CEA is in the detection of liver metastasis from colorectal cancers. Because of the relative success of surgery in resecting hepatic metastases, serial determinations of the marker are recommended for detecting cancer spread to the liver. In the future, preoperative concentrations of CEA may be included with the standard staging procedures for assessing prognosis.
Picking up the Pieces: Utilizing Disaster Recovery Project Management to Improve Readiness and Response Time (2002)

When Hurricane Georges hit the Florida Keys in 1998, deflecting its course and putting Pascagoula, Mississippi, USA within its potential path, the local refinery implemented standard hurricane readiness plans. A shutdown of the refinery was initiated when the storm's forecasted path changed from landfall at the mouth of the Mississippi River to landfall to the east along the Mississippi Gulf Coast. All processes were brought to a halt, and the entire refinery was brought to a stop. The four primary buildings, including facility maintenance, were flooded in up to 64 in of salt water. The destruction and disruption was almost overwhelming. The next week was spent in an effort to access the scope of the damage and develop a strategy to recover from the disaster. Since nothing of this magnitude had ever been experienced, all existing planning was insufficient to undertake such a task. This paper discusses the development of the recovery plan and the scope of the work. Establishing priorities, equipment reliability, and economic considerations are discussed. Execution of the recovery plan is described including communication . The key points outlined in this article can be of great assistance identifying key areas in planning and executing a successful recovery.
Virtual screen for repurposing approved and experimental drugs for candidate inhibitors of EBOLA virus infection (2015)

The ongoing Ebola virus epidemic has presented numerous challenges with respect to control and treatment because there are no approved drugs or vaccines for the Ebola virus disease (EVD). Herein is proposed simple theoretical criterion for fast virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection. We performed a repurposing screen of 6438 drugs from DrugBank using this criterion and selected 267 approved and 382 experimental drugs as candidates for treatment of EVD including 15 anti-malarial drugs and 32 antibiotics. An open source Web server allowing screening of molecular libraries for candidate drugs for treatment of EVD was also established.
Aggregation of the FcεRI on Mast Cells Stimulates c-Jun Amino-terminal Kinase Activity (1996)

Aggregation of the high-affinity Fc receptors for immunoglobulin E (IgE) (FcepsilonRI) on the surface of mast cells initiates intracellular signal transduction pathways including the tyrosine phosphorylation of cellular proteins, phosphoinositide hydrolysis, an increase in intracellular calcium, and protein kinase C activation. These signals are believed to be involved in the exocytic release of inflammatory mediators such as vasoactive amines, cytokines, and lipid metabolites. However, the downstream consequences of these early activation events are not well defined. One exception is the activation of the extracellular signal-regulated kinases/mitogen-activated protein kinases. One member of the mitogen-activated protein kinase superfamily, designated c-Jun amino-terminal kinase (JNK), has been recently identified. JNK is activated following dual phosphorylation at a Thr-Pro-Tyr motif in response to diverse stimuli including tumor necrosis factor-alpha, heat shock, or ultraviolet irradiation. We found that JNK was strongly activated by antigen cross-linking in a mouse mast cell line passively sensitized with ovalbumin-specific IgE. Anti-mouse IgE antibody also activated JNK. MEK kinase 1 (MEKK1) which activates the JNK activator, JNK kinase (JNKK), was similarly activated by antigen stimulation. JNK but not p42(erk2) activation induced by antigen was significantly inhibited in the presence of wortmannin, a known inhibitor of phosphatidylinositol 3-kinase. These results indicate that in response to the aggregation of FcepsilonRI on mast cells, phosphatidylinositol 3-kinase activation is involved in the stimulation of the MEKK1, JNKK, JNK pathway.
Principles of tissue engineering applied to programmable osteogenesis (1998)

This article presents a strategy for design, engineering, and fabrication of a bioresorbable, manufactured bone graft substitute (BGS) device. The approach is based on established precepts of osteogenesis, molecular biology of hyaluronic acid and osteoinductive proteins, and theoretical preformance criteria for such a device collated from the literature of 1991 to 1996. Application of this design and engineering strategy results in a composite device consisting of a D,D-L,L-polylactic acid macrostructure optimized to the architecture of cancellous bone, a microstructure composed of a filamentous velour of hyaluronan and a recombinant human bone morphogenetic protein 2 (rhBMP-2). The performance of this construct was tested in vivo in the dog, intertransverse process, spinal fusion model and in a critical sized defect of the rabbit radius. Data from these studies are used to illustrate principle points of the design and engineering concept.
Two Isoforms of the MouseEther-a-go-go–Related Gene Coassemble to Form Channels With Properties Similar to the Rapidly Activating Component of the Cardiac Delayed Rectifier K+Current (1997)

HERG, the human ether-a-go-go-related gene, encodes a K(+)-selective channel with properties similar to the rapidly activating component of the delayed rectifier K+ current (IKr). Mutations of HERG cause the autosomal-dominant long-QT syndrome (LQTS), presumably by disrupting the normal function of IKr. The current produced by HERG is not identical to IKr, however, and the mechanism by which HERG mutations cause LQTS remains uncertain. To better define the role of Erg in the heart, we cloned Merg1 from mouse genomic and cardiac cDNA libraries. Merg1 has 16 exons and maps to mouse chromosome 5 in an area syntenic to human chromosome 7q, the map locus of HERG. We isolated three cardiac isoforms of Merg1: Merg1a is homologous to HERG and is expressed in heart, brain, and testes, Merg1a' lacks the first 59 amino acids of Merg1a and is not expressed abundantly, and Merg1b has a markedly shorter divergent N-terminal cytoplasmic domain and is expressed specifically in the heart. The Merg1 isoforms, like HERG, produce inwardly rectifying E-4031-sensitive currents when heterologously expressed in Xenopus oocytes. Merg1a and HERG produce currents with slow deactivation kinetics, whereas Merg1a' and Merg1b currents deactivate more rapidly. Merg1b coassembles with Merg1a to form channels with deactivation kinetics that are more rapid than those of Merg1a or HERG and nearly identical to IKr. In addition, a homologue of Merg1b is present in human cardiac and smooth muscle. Thus, we have identified a novel N-terminal Erg isoform that is expressed specifically in the heart, has rapid deactivation kinetics, and coassembles with the longer isoform in Xenopus oocytes. This N-terminal Erg isoform may determine the properties of IKr and contribute to the pathogenesis of LQTS.
Homocoupling of Arylboronic Acids Catalyzed by 1,10‐Phenanthroline‐Ligated Copper Complexes in Air (2009)

Abstract The efficient homocoupling of arylboronic acids was achieved by using the catalytic combination of inexpensive copper salts and 1,10‐phenanthroline as a ligand. The homocoupling reaction proceeds at ambient temperature in air without any additives such as base or oxidant. This method tolerates various substituents on the arylboronic acids such as halogens, carbonyls, and a nitro group. As a result, 25 symmetrical biaryls were obtained from readily availablearylboronic acids in 19–92 % isolated yields. A binuclear (μ‐hydroxido)copper complex is assumed as the catalytically active species, which undergoes efficient transmetalation with arylboronic acids to produce dinuclear arylcopper complexes. The binuclear structure is assumed to be essential for the bimetallic reductive elimination of biaryls as well as the oxidative restoration of the catalyst.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Platelet-derived growth factor (PDGF)-dependent association of phospholipase C-gamma with the PDGF receptor signaling complex. (1990)

We investigated the interaction of phospholipase C-gamma (PLC-gamma) with wild-type and mutant forms of the platelet-derived growth factor (PDGF) beta-receptor both in vivo and in vitro. After PDGF treatment of CHO cell lines expressing wild-type or either of two mutant (delta Ki and Y825F) PDGF receptors, PLC-gamma became tyrosine phosphorylated and associated with the receptor proteins. The receptor association and tyrosine phosphorylation of PLC-gamma correlated with the ability of these receptors to mediate ligand-induced phosphatidylinositol turnover. However, both the delta Ki and Y825F mutant receptors were deficient in transmitting mitogenic signals, suggesting that the PDGF-induced tyrosine phosphorylation and receptor association of PLC-gamma are not sufficient to account for the growth-stimulatory activity of PDGF. Wild-type and delta Ki mutant PDGF receptor proteins expressed with recombinant baculovirus vectors also associated in vitro with mammalian PLC-gamma. However, baculovirus-expressed c-fms, v-fms, c-src, and Raf-1 proteins failed to associate with PLC-gamma under similar conditions. Phosphatase treatment of the baculovirus-expressed PDGF receptor greatly decreased its association with PLC-gamma. This requirement for receptor phosphorylation was also observed in vivo, where PLC-gamma could not associate with a mutant PDGF receptor (K602A) defective in autophosphorylation. PLC-gamma also coimmunoprecipitated with two other putative receptor substrates, the serine-threonine kinase Raf-1 and the 85-kilodalton phosphatidylinositol-3' kinase, presumably through its association with the ligand-activated receptor. Furthermore, baculovirus-expressed Raf-1 phosphorylated purified PLC-gamma in vitro at sites which showed increased serine phosphorylation in vivo in response to PDGF. These results suggest that PDGF directly influences PLC activity by inducing the association of PLC-gamma with a receptor signaling complex, resulting in increased tyrosine and serine phosphorylation of PLC-gamma.
Nucleotide sequence of the gene coding for the 85-B antigen ofMycobacterium leprae (1991)

Nucleotide sequence of the gene coding for the 85-B antigen of Mycobacterium leprae Get access Leila de Mendonça Lima, Leila de Mendonça Lima Search for other works by this author on: Oxford Academic PubMed Google Scholar Jean Content, Jean Content 1lnstitut Pasteur du Brabant, Department of VirologyB-1180 Brussels Search for other works by this author on: Oxford Academic PubMed Google Scholar Hugo van Heuverswyn, Hugo van Heuverswyn 2lnnogeneticsIndustriepark Zwijnaarde 7, box 4, B-9052 Gent, Belgium Search for other works by this author on: Oxford Academic PubMed Google Scholar Wim Degrave Wim Degrave * * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 20, 25 October 1991, Page 5789, https://doi.org/10.1093/nar/19.20.5789 Published: 25 October 1991 Article history Received: 20 August 1991 Published: 25 October 1991
How Iris Recognition Works (2004)

Algorithms developed by the author for recognizing persons by their iris patterns have now been tested in many field and laboratory trials, producing no false matches in several million comparison tests. The recognition principle is the failure of a test of statistical independence on iris phase structure encoded by multi-scale quadrature wavelets. The combinatorial complexity of this phase information across different persons spans about 249 degrees of freedom and generates a discrimination entropy of about 3.2 b/mm/sup 2/ over the iris, enabling real-time decisions about personal identity with extremely high confidence. The high confidence levels are important because they allow very large databases to be searched exhaustively (one-to-many "identification mode") without making false matches, despite so many chances. Biometrics that lack this property can only survive one-to-one ("verification") or few comparisons. The paper explains the iris recognition algorithms and presents results of 9.1 million comparisons among eye images from trials in Britain, the USA, Japan, and Korea.
Bendamustine Versus Chlorambucil in Treatment-Naive Patients with B-Cell Chronic Lymphocytic Leukemia (B-CLL): Results of an International Phase III Study. (2007)

Abstract Introduction: Bendamustine (BEN) is a purine analog / alkylator hybrid agent with a particular mechanisms of action that provides effective treatment for a number of hematologic and non-hematologic malignancies. It is used primarily for chemo-naïve, relapsed or refractory B-CLL as well as for other types of non-Hodgkin’s lymphomas. The aim of this randomized phase III, open-label, multicenter study was to compare the efficacy and safety of BEN versus chlorambucil (CLB) in treatment-naïve patients (pts) with B-CLL Binet stage B/C. Patients and Methods: Pts with untreated B-CLL were randomized to receive BEN (100 mg/m2 on days 1+2) or CLB (0.8 mg/kg on days 1+15) for up to 6 treatment cycles. Primary endpoints were overall remission rate (ORR), defined as complete response (CR), nodular partial response (nPR) and partial response (PR), confirmed after 8 weeks, and progression-free survival (PFS). Secondary endpoints were duration of remission, overall survival (OS), safety, and quality of life (QoL). Follow-up was for ≥12 months after completion of treatment of the last patient, or until progression for pts with CR, nPR or PR and stable disease, or until death or lost to follow-up. A 5-stage, adaptive-group, sequential procedure was used with planned interim analyses to adjust the number of pts. Safety and efficacy were assessed by an Independent Data Monitoring Committee. Results: 305 pts were randomized to receive BEN (n=156) or CLB (n=149). As 7 pts did not receive study medication, 298 pts were included in the safety analysis. At the time of this analysis, 264 pts (139 BEN; 125 CLB) were available for the efficacy analysis. For both treatment groups: median age was 64 years; 70% had Binet stage B and 30% Binet stage C disease; median number of cycles/patient was 6; median follow-up was 18.5 months. ORR was significantly higher with BEN than with CLB (68% vs 39%; p&amp;lt;0.0001), with a CR of 30% vs 2%, respectively. Among the subgroups with Binet stage B and C disease, ORR was 70% and 61%, respectively, with BEN, vs 47% and 22%, respectively, with CLB. Median PFS (Kaplan-Meier estimate) was 21.7 months with BEN and 9.3 months with CLB (p&amp;lt;0.0001), and median duration of remission was 18.9 months with BEN and 6.1 months with CLB (p&amp;lt;0.0001). No difference in OS was seen between groups. Toxicity of BEN was manageable and did not impair QoL when compared with CLB. Infection rates (common toxicity criteria grades III+IV) were low in both groups (5.8% BEN; 3.5% CLB). Conclusions: BEN was significantly more effective than CLB in achieving remissions in treatment-naïve pts with B-CLL Binet stage B/C; median PFS and duration of remission were also significantly longer. Furthermore, safety data indicate that BEN toxicities are manageable and the drug is well tolerated. On the basis of these results, BEN should be considered as first-line chemotherapy for patients with B-CLL Binet stage B or C.
Suppression of Glycogen Synthase Kinase Activity Is Not Sufficient for Leukemia Enhancer Factor-1 Activation (1999)

Glycogen synthase kinase-3 (GSK) can be regulated by different signaling pathways including those mediated by protein kinase Akt and Wnt proteins. Wnt proteins are believed to activate a transcription factor leukemia enhancer factor-1 (LEF-1) by inhibiting GSK, and Akt was shown to phosphorylate GSK and inhibit its kinase activity. We investigated the effect of an activated Akt on the accumulation of cytosolic beta-catenin and LEF-1-dependent transcription. Although the activated Akt, mAkt, clearly inhibited the kinase activity of GSK, mAkt alone did not induce accumulation of cytosolic beta-catenin or activate LEF-1-dependent transcription. On the contrary, coexpressed Wnt-1 and Frat activated LEF-1 but did not show significant inhibition of GSK-mediated phosphorylation of a peptide substrate. However, mAkt could act synergistically with Wnt-1 or Frat to activate LEF-1. In addition, the interaction of GSK for Axin appeared to decrease in the presence of mAkt, whereas the interaction for Frat remained unchanged. Consistently, a GSK mutant with substitution of a Phe residue for residue Tyr-216, which showed one-fifth of kinase activity of the wild-type GSK, exhibited a reduced association for Axin than the wild-type GSK. These results suggest that inhibition of GSK kinase activity is not sufficient for activation of LEF-1 but may facilitate the activation by reducing the interaction of GSK for Axin. The additional mechanism for LEF-1 activation may require dissociation of GSK from Axin as Frat facilitates the dissociation of GSK from Axin.
Alicyclobacillus acidiphilus sp. nov., a novel thermo-acidophilic, omega-alicyclic fatty acid-containing bacterium isolated from acidic beverages (2002)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Logistic Regression: A Primer (2021)

The Logic of Logistic Regression Interpreting Logistic Regression Coefficients Estimation and Model Fit Probit Analysis Conclusion
Prebiotics and gut microbiota in chickens (2015)

Prebiotics are non-digestible feed ingredients that are metabolized by specific members of intestinal microbiota and provide health benefits for the host. Fermentable oligosaccharides are best known prebiotics that have received increasing attention in poultry production. They act through diverse mechanisms, such as providing nutrients, preventing pathogen adhesion to host cells, interacting with host immune systems and affecting gut morphological structure, all presumably through modulation of intestinal microbiota. Currently, fructooligosaccharides, inulin and mannanoligosaccharides have shown promising results while other prebiotic candidates such as xylooligosaccharides are still at an early development stage. Despite a growing body of evidence reporting health benefits of prebiotics in chickens, very limited studies have been conducted to directly link health improvements to prebiotic-dependent changes in the gut microbiota. This article visits the current knowledge of the chicken gastrointestinal microbiota and reviews most recent publications related to the roles played by prebiotics in modulation of the gut microbiota and immune functions. Progress in this field will help us better understand how the gut microbiota contributes to poultry health and productivity, and support the development of new prebiotic products as an alternative to in-feed antibiotics.
Supercooled and glassy water (2003)

The anomalous properties of cold and supercooled water, such as the fact that at sufficiently low temperatures it becomes more compressible and less dense when cooled, and more fluid when compressed, have attracted the attention of physical scientists for a long time. The discovery in the 1970s that several thermodynamic and transport properties of supercooled water exhibit a pronounced temperature dependence and appear to diverge slightly below the homogeneous nucleation temperature inspired a large number of experimental and theoretical studies. Likewise, an important body of work on glassy water has been stimulated by experiments, starting in the mid-1980s and continuing to this date, which suggest that vitreous water can exist in at least two apparently distinct forms. A coherent theory of the thermodynamic and transport properties of supercooled and glassy water does not yet exist. Nevertheless, significant progress towards this goal has been made during the past 20 years. This article summarizes the known experimental facts and reviews critically theoretical and computational work aimed at interpreting the observations and providing a unified viewpoint on cold, non-crystalline, metastable states of water.
Lactobacillus gasseri CRISPR-Cas9 characterization In Vitro reveals a flexible mode of protospacer-adjacent motif recognition (2018)

While the CRISPR-Cas9 system from S. pyogenes is a powerful genome engineering tool, additional programmed nucleases would enable added flexibility in targeting space and multiplexing. Here, we characterized a CRISPR-Cas9 system from L. gasseri and found that it has modest activity in a cell-free lysate assay but no activity in mammalian cells even when altering promoter, position of tag sequences and NLS, and length of crRNA:tracrRNA. In the lysate assay we tested over 400 sequential crRNA target sequences and found that the Lga Cas9 PAM is NNGA/NDRA, different than NTAA predicted from the native bacterial host. In addition, we found multiple instances of consecutive crRNA target sites, indicating flexibility in either PAM sequence or distance from the crRNA target site. This work highlights the need for characterization of new CRISPR systems and highlights the non-triviality of porting them into eukaryotes as gene editing tools.
Melanoma (2006)

This review summarizes the molecular and genetic lesions underlying the progression from benign nevus to malignant melanoma.