gebhart/patrepeval huggingface dataset:
The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics (2013)

Our results represent the first complete, sequence-based comparison between the venoms of closely related snake species and reveal in unprecedented detail the rapid evolution of snake venoms. We found that the difference in venom properties resulted from major changes in expression levels of toxin gene families, differential gene-family expansion and loss, changes in which paralogs within gene families were expressed at high levels, and higher nonsynonymous substitution rates in the toxin genes relative to nontoxins. These massive alterations in the genetics of the venom phenotype emphasize the evolutionary lability and flexibility of this ecologically critical trait.
Metabolic disturbances in diabetic cardiomyopathy. (1998)

It has been established that diabetes results in a cardiomyopathy, and increasing evidence suggests that an altered substrate supply and utilization by cardiac myocytes could be the primary injury in the pathogenesis of this specific heart muscle disease. For example, in diabetes, glucose utilization is insignificant, and energy production is shifted almost exclusively towards beta-oxidation of free fatty acids (FFA). FFA's are supplied to cardiac cells from two sources: lipolysis of endogenous cardiac triglyceride (TG) stores, or from exogenous sources in the blood (as free acid bound to albumin or as TG in lipoproteins). The approximate contribution of FFA from exogenous or endogenous sources towards beta-oxidation in the diabetic heart is unknown. In an insulin-deficient state, adipose tissue lipolysis is enhanced, resulting in an elevated circulating FFA. In addition, hydrolysis of the augmented myocardial TG stores could also lead to high tissue FFA. Whatever the source of FFA, their increased utilization may have deleterious effects on myocardial function and includes the abnormally high oxygen requirement during FFA metabolism, the intracellular accumulation of potentially toxic intermediates of FFA, a FFA-induced inhibition of glucose oxidation, and severe morphological changes. Therapies that target these metabolic aberrations in the heart during the early stages of diabetes could potentially delay or impede the progression of more permanent sequelae that could ensue from otherwise uncontrolled derangements in cardiac metabolism.
Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters (2014)

We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from the GAL1, ADH1 or ACT1 promoters. Transcription from all three promoters was imaged in live cells and transcriptional increases from the GAL1 promoter were observed with time after adding galactose. Expression of the IMAGEtags did not affect cell proliferation or endogenous gene expression. Advantages of this method are that no foreign proteins are produced in the cells that could be toxic or otherwise influence the cellular response as they accumulate, the IMAGEtags are short lived and oxygen is not required to generate their signals. The IMAGEtag RNA reporter system provides a means of tracking changes in transcriptional activity in live cells and in real time.
Ajulemic acid exerts potent anti-fibrotic effect during the fibrogenic phase of bleomycin lung (2016)

AjA treatment, starting either at day 0 or at day 8 after BLM challenge, counteracts the progression of pulmonary fibrosis. The anti-fibrotic effectiveness of AjA is irrespective of timing of compound administration. Further clinical studies are necessary to establish whether AjA may represent a new therapeutic option for treating fibrotic lung diseases.
Dealing with Misfolded Proteins: Examining the Neuroprotective Role of Molecular Chaperones in Neurodegeneration (2010)

Human neurodegenerative diseases arise from a wide array of genetic and environmental factors. Despite the diversity in etiology, many of these diseases are considered "conformational" in nature, characterized by the accumulation of pathological, misfolded proteins. These misfolded proteins can induce cellular stress by overloading the proteolytic machinery, ultimately resulting in the accumulation and deposition of aggregated protein species that are cytotoxic. Misfolded proteins may also form aberrant, non-physiological protein-protein interactions leading to the sequestration of other normal proteins essential for cellular functions. The progression of such disease may therefore be viewed as a failure of normal protein homeostasis, a process that involves a network of molecules regulating the synthesis, folding, translocation and clearance of proteins. Molecular chaperones are highly conserved proteins involved in the folding of nascent proteins, and the repair of proteins that have lost their typical conformations. These functions have therefore made molecular chaperones an active area of investigation within the field of conformational diseases. This review will discuss the role of molecular chaperones in neurodegenerative diseases, highlighting their functional classification, regulation, and therapeutic potential for such diseases.
Synthesis and characterization of a poly(para-phenyleneethynylene)-block-poly(ethylene oxide) rod-coil block copolymer (1998)

The synthesis of the poly(para-phenyleneethynylene)-block-poly(ethylene oxide) block copolymer (PPE-b-PEO) (1) via condensation of endfunctionalized poly(para-phenyleneethynylene) (PPE) (5) and poly(ethylene oxide) monomethyl ether (PEO) is reported. This is achieved by the initial synthesis of a PPE homopolymer with quantitative terminal functionalization, as proven by 1H NMR and field desorption mass spectrometry (FD-MS). Reaction of the latter with PEO affords the block copolymer 1, which was characterized by 1H NMR spectroscopy, FD-MS and gel permeation chromatography (GPC). Furthermore it is shown that matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) is a suitable method to investigate PPE-b-PEO with respect to molecular weights and copolymer composition.
Synthesis of Several 3-Substituted 2-Trifluoromethylinodoles via Mannich Reaction of 2-Trifluoromethylindoles. (1997)

Several 2-trifluoromethyl derivatives of biologically active indoles, tryptamine, indole-3-acetic acid, oxypertine and tryptophan, were synthesized starting from 2-trifluoromethylindoles by use of the Mannich reaction and subsequent nucleophilic substitution reaction as key steps. In this study, chemoselective hydrolysis and reductions of the nitrile group to the respective carboxylic acid, amine and aldehyde in the presence of the trifluoromethyl group were achieved.
Mechanisms underlying hematopoietic stem cell mobilization induced by the CXC chemokine interleukin-8 (1999)

The CXC chemokine interleukin-8 induces rapid mobilization of hematopoietic progenitor cells in mice and monkeys. Antibodies against the beta 2-integrin leukocyte function-associated antigen-1 completely blocked interleukin-8-induced mobilization. This was not due to a direct effect on the hematopoietic progenitor cells, as leukocyte function-associated antigen-1 was found not to be expressed on hematopoietic progenitor cells. Additional experiments showed that interleukin-8 induces the rapid release of the metalloproteinase gelatinase B, concurrent with the mobilization of hematopoietic progenitor cells. Mobilization could be completely prevented by anti-gelatinase B antibodies. Because neutrophils express leukocyte function-associated antigen-1 and high affinity interleukin-8 receptors, and release gelatinase B upon stimulation with interleukin-8, we hypothesized that neutrophils are key mediators in interleukin-8-induced stem cell mobilization. Further studies showed that mobilization by interleukin-8 was completely absent in mice rendered neutropenic with anti-granulocytic antibodies. Taken together, these data are consistent with an essential role for neutrophils in interleukin-8-induced stem cell mobilization.
Capillary electrophoresis of polymerase chain reaction‐amplified products in polymer networks: The case of Kennedy's disease (1994)

In Kennedy disease (an X-linked motoneuronal disorder associated with an increase in the number of (CAG)n triplet repeats in the first exon of the Androgen receptor gene; about twice as many as in normal conditions), polymerase chain reaction-amplified genic products exhibit two DNA fragments in the heterozygous female carriers, one with a range between 468 and 495 bp in the normal polymorphic population and a fragment corresponding to the pathological state that reaches 573 bp. These fragments are easily separated by gel-slab electrophoresis and detected by intercalating dye staining (ethidium bromide). As an alternative procedure, capillary zone electrophoresis in polymer networks, consisting of 8% polyacryloylaminoethoxyethanol at 0% cross-linker, offers a simple procedure for separation and on-line detection via UV absorbance at 254 nm, thus avoiding additional staining steps. The capillary column can be repeatedly used for up to 80-100 times and the electropherogram is stored on a magnetic support. Easy comparison among different runs is obtained by aligning all tracings to an internal standard of a 650 bp fragment added as a marker.
High-temperature rheological study of foam fracturing fluids (1984)

Nitrogen foam properties were measured up to 300/sup 0/F in a high temperature and pressure recirculating loop viscometer. Foam fluids did not thin as rapidly as gel fluids under similar conditions. Therefore, foams offer inherent advantages for high temperature stimulation work. Higher gelling agent concentrations do not improve dynamic foam stability. Rather, high temperature dynamic stability is dependent upon surfactant type and concentration. Mathematical equations have been developed to describe foam rheological behavior from 75 to 300/sup 0/F, 0 to 80 quality, containing 0 to 80 lb HPG/Mgal in the aqueous phase. Basic physical properties were previously outlined which determined foam rheological behavior at 75/sup 0/F. Foams were classified as yield pseudoplastic type fluids. This paper extends the previous work from 75 to 300/sup 0/F, and covers a broader range of external liquid phase compositions applicable to foam stimulation work.
Role of MEKK1 in Cell Survival and Activation of JNK and ERK Pathways Defined by Targeted Gene Disruption (1998)

Targeted disruption of the gene encoding MEK kinase 1 (MEKK1), a mitogen-activated protein kinase (MAPK) kinase kinase, defined its function in the regulation of MAPK pathways and cell survival. MEKK1(-/-) embryonic stem cells from mice had lost or altered responses of the c-Jun amino-terminal kinase (JNK) to microtubule disruption and cold stress but activated JNK normally in response to heat shock, anisomycin, and ultraviolet irradiation. Activation of JNK was lost and that of extracellular signal-regulated protein kinase (ERK) was diminished in response to hyperosmolarity and serum factors in MEKK1(-/-) cells. Loss of MEKK1 expression resulted in a greater apoptotic response of cells to hyperosmolarity and microtubule disruption. When activated by specific stresses that alter cell shape and the cytoskeleton, MEKK1 signals to protect cells from apoptosis.
The Biological and Therapeutic Importance of Gastrin Gene Expression in Pancreatic Adenocarcinomas (2004)

The gastrin gene is expressed widely in pancreatic adenocarcinomas and the study aimed to assess its role in both the resistance of cancer cells to apoptosis and the sensitivity of cells to chemotherapeutic agents. Two human pancreatic cell lines, PAN1 and BXPC3, expressed gastrin at both the RNA and protein levels and are shown to be representative of human pancreatic adenocarcinomas in terms of gastrin expression. Inhibition of endogenous gastrin production by tumor cells was achieved with neutralizing gastrin antiserum and transfection with a gastrin antisense plasmid. Gastrin antiserum synergized with both taxotere and gemcitabine in inhibiting the in vitro growth of the PAN1 cell line with the inhibitory effect of the antiserum increasing from 12.7% to 70.2% with taxotere (P < 0.05) and 28.6% with gemcitabine (P < 0.01) after controlling for the effects of the cytotoxics. Synergy was only achieved with taxotere in BXPC3 cells with the inhibitory effect of gastrin antiserum increasing from 22.9% to 50.0% (P < 0.005). Cells transfected with gastrin antisense had reduced in vitro growth in low serum conditions and were poorly tumorigenic in nude mice at an orthotopic site. Gastrin antisense-transfected PAN1 cells had increased sensitivity to the antiproliferative effects of both gemcitabine (IC50 of > 100 microg/ml reduced to 0.1 microg/ml) and taxotere (IC50 of 20 microg/ml reduced to < 0.01 microg/ml) when compared with vector controls. The increased sensitivity of PAN1 antisense coincided with increased caspase-3 activity and reduced protein kinase B/Akt phosphorylation in response to both gemcitabine and taxotere. Gastrin gene circumvention may be an optimal adjunct to chemotherapeutic agents, such as taxotere and gemcitabine, in pancreatic adenocarcinoma.
Targeted In Vivo Imaging of Angiogenesis: Present Status and Perspectives (2006)

Angiogenesis, the process whereby new capillaries are formed by outgrowth from existing microvessels, is required for tumor growth and metastasis, and is also necessary for natural healing after ischemic injury. Because angiogenesis, excessive or deficient, underlies many pathological situations, there is a need for the development of noninvasive imaging to allow monitoring of angiogenesis related molecular events. Furthermore, specific imaging of angiogenesis would help define the pathophysiology of angiogenesis in living subjects, identify those patients likely to respond to anti-angiogenic or angiogenic therapies, and enable the efficacies of these molecular therapies to be assessed. Herein, we review the targeted imaging of angiogenesis using nuclear medicine modalities (positron emission tomography; PET and single photon emission computed tomography; SPECT) and suitable radiotracers based on potential targets including integrin, extracellular matrix, VEGF and its receptors, activated endothelial cells, and matrix metalloproteinases.
Spin optodynamics analog of cavity optomechanics (2010)

The dynamics of a large quantum spin coupled parametrically to an optical resonator is treated in analogy with the motion of a cantilever in cavity optomechanics. Distinct spin optodynamic phenomena are predicted, such as cavity-spin bistability, optodynamic spin-precession frequency shifts, coherent amplification and damping of spin, and the spin optodynamic squeezing of light.
CD4+ T cells that express high levels of CD45RB induce wasting disease when transferred into congenic severe combined immunodeficient mice. Disease development is prevented by cotransfer of purified CD4+ T cells. (1993)

Purified CD4+ lymph node T cells were sorted into two populations on the basis of their expression of CD45RB (CD45RBhi and CD45RBlo) and injected into congenic severe combined immunodeficient (SCID) mice. After a period of time that was dependent on the number of cells injected, the SCID mice that received CD45RBhi/CD4+ T cells developed a wasting disease that was not seen in SCID mice that received the CD4+/CD45RBlo cells or whole lymph node cells. At death, SCID mice that received the CD4+/CD45RBhi cells had increased spleen and lymph node cellularity compared with normal SCID mice and SCID mice that received the CD4+/CD45RBlo T cells. The spleen and lymph node contained CD4+ cells and neither CD8+ nor surface immunoglobulin M-positive cells, plus a population of cells that did not express any of those markers. At necropsy, the SCID mice that received the CD4+/CD45RBhi cells had significant hyperplasia of the intestinal mucosa with significant lymphoid cell accumulation in the lamina propria. Interestingly, mice that received mixtures of whole lymph node or purified CD4+ cells with CD4+/CD45RBhi cells did not develop weight loss, indicating that the unseparated CD4+ population contained cells that were capable of regulating the reactivity of the CD4+/CD45RBhi cells.
TGF-beta (transforming growth factor-beta) in chronic inflammatory conditions - a new diagnostic and prognostic marker? (2002)

TGF-beta is a cytokine with varied properties and pleiotropic activity. It is released in an inactive form. To exhibit its biological activity, it requires binding to extracellular matrix proteins and, after that, proteolytic elimination of LAP (Latent Associated Protein) and LTBP (Latent TGF-beta Binding Protein). The process involves, among others, tissue transglutaminase, thrombin and plasmin. By stimulation of specific receptors, it influences transcription of some genes and translation of formed mRNA. Locally, it demonstrates proinflammatory properties whereas systemically, it has primarily a potent immunosuppressive effect. TGF-beta, by affecting proliferation, differentiation and migration of cells, as well as stimulation of extracellular matrix protein production, plays an important role in tissue regeneration and remodeling, but also in fibrosis. TGF-beta is also indispensable to maintain immune homeostasis of the organism. Reduced TGF-beta activity is considered to be responsible for development of autoimmune disorders in the course of several pathologic conditions. This cytokine plays an important role in the pathogenesis of chronic inflammatory processes taking place, among others, in inflammatory bowel diseases (IBD) and chronic hepatitis B and C. The paper presents a review of literature concerning diagnostic and prognostic value of TGF-beta level determinations in blood and tissue bioptates of patients with chronic non-specific enteritis and chronic hepatitis B and C.
Gain and differential gain of single layer InAs/GaAs quantum dot injection lasers (1996)

We present gain measurements and calculations for InAs/GaAs quantum dot injection lasers. Measurements of the modal gain and estimation of the confinement factor by transmission electron microscopy yield an exceptionally large material gain of 6.8(±1)×104 cm−1 at 80 A cm−2. Calculations including realistic quantum dot energy levels, dot size fluctuation, nonthermal coupling of carriers in different dots, and band filling effects corroborate this result. A large maximum differential gain of 2×10−12 cm2 at 20 A cm−2 is found. The width of the gain spectrum is determined by participation of excited quantum dot states. We record a low transparency current density of 20 A cm−2. All experiments are carried out at liquid nitrogen temperature.
Control of Transcription Initiation In Vitro Requires Binding of a Transcription Factor to the Distal Promoter of the Ovalbumin Gene (1986)

We used a cell-free HeLa cell transcription system to identify and characterize transcription factors and the promoter elements that they recognize in RNA polymerase II-transcribed genes. Deletion of the region (-71 to -83) containing the GTCAAA direct repeat resulted in a marked decrease of specific transcription of the ovalbumin gene; transcription could be competed with DNA fragments containing this sequence. Furthermore, DNase I footprinting identified a protein-binding site including this direct repeat with crude extracts and one of the partially purified protein fractions required for transcription. We propose that a soluble factor activates transcription through binding to the direct repeat of GTCAAA sequence upstream from the ovalbumin gene.
The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation (2014)

Highly diverse bacterial populations inhabit the gastrointestinal tract and modulate host inflammation and promote immune tolerance. In allogeneic hematopoietic stem cell transplantation (allo-HSCT), the gastrointestinal mucosa is damaged, and colonizing bacteria are impacted, leading to an impaired intestinal microbiota with reduced diversity. We examined the impact of intestinal diversity on subsequent mortality outcomes following transplantation. Fecal specimens were collected from 80 recipients of allo-HSCT at the time of stem cell engraftment. Bacterial 16S rRNA gene sequences were characterized, and microbial diversity was estimated using the inverse Simpson index. Subjects were classified into high, intermediate, and low diversity groups and assessed for differences in outcomes. Mortality outcomes were significantly worse in patients with lower intestinal diversity; overall survival at 3 years was 36%, 60%, and 67% for low, intermediate, and high diversity groups, respectively (P = .019, log-rank test). Low diversity showed a strong effect on mortality after multivariate adjustment for other clinical predictors (transplant related mortality: adjusted hazard ratio, 5.25; P = .014). In conclusion, the diversity of the intestinal microbiota at engraftment is an independent predictor of mortality in allo-HSCT recipients. These results indicate that the intestinal microbiota may be an important factor in the success or failure in allo-HSCT.
Discovering event correlation rules for semi-structured business processes (2011)

In this paper we describe an algorithm to discover event correlation rules from arbitrary data sources. Correlation rules can be useful for determining relationships between events in order to isolate instances of a running business process for the purposes of monitoring, discovery and other applications. We have implemented our algorithm and validate our approach on events generated by a simulator that implements a real-world inspired export compliance regulations scenario consisting of 24 activities and corresponding event types. This simulated scenario involves a wide range of heterogeneous systems (e.g. Order Management, Document Management, E-Mail, and Export Violation Detection Services) as well as workflow-supported human-driven interactions (Process Management System). Experimental results demonstrate that our algorithm achieves a high level of accuracy in the detection of correlation rules. This paper confirms that our algorithm is a step towards semi-automating the task of detecting correlations. We also demonstrate how correlation rules discovered by our algorithm can be used to create aggregation nodes that allow more efficient querying, filtering and analytics. The results in this paper encourage future directions such as distributed statistics calculation, and scalability in terms of handling massive data sets.
Performance measurement in a fuzzy retrieval environment (1981)

We shall consider retrieval performance measures for generalized (non-Boolean) queries and indexing functions. The meanings of recall and precision in such a generalized system will be discussed. Finally, we shall explore the meaning and difficulty of using such measures to compare Boolean and non-Boolean retrieval systems.