gebhart/patrepeval huggingface dataset:
Oral adeno‐associated virus‐sTRAIL gene therapy suppresses human hepatocellular carcinoma growth in mice† (2005)

The extracellular domain of the tumor necrosis factor-related apoptosis-inducing ligand (sTRAIL) may function as a soluble cytokine to selectively kill various cancer cells without toxicity to most normal cells. We constructed a series of recombinant adeno-associated virus (AAV) vectors expressing the extracellular domain of human TRAIL fused with signal peptides of human insulin, interferon, human growth hormone, and serum albumin and designated them as AAV-ISN-T, AAV-IFN-T, AAV-HGH-T, and AAV-Alb-T, respectively. Transduction of human SMMC-7721 liver cancer cells with AAV-ISN-T led to higher levels of TRAIL(95-281) protein expression in the cell culture media and produced more apoptosis of the cells in vitro than those with AAV-IFN-T, AAV-HGH-T, and AAV-Alb-T. The therapeutic potential of AAV-ISN-T was then evaluated in a transplanted mouse model established by injection of human liver cancer SMMC-7721 cells subcutaneously. Subsequent oral or intraperitoneal administration of AAV-ISN-T resulted in a rapid, high level and long time expression of soluble TRAIL in the sera and livers of the animals, as well as effective suppression of tumor growth, with no toxicity to normal hepatocytes. These data strongly suggest that it is possible to increase soluble TRAIL expression to make full use of tumoricidal activity of TRAIL as a therapeutic strategy. In conclusion, we provide evidence that oral administration of AAV-TRAIL might be an important alternative route with practical significance for cancer gene therapy.
Development of Virus-Specific CD4 + and CD8 + Regulatory T Cells Induced by Human Herpesvirus 6 Infection (2013)

Human herpesvirus 6 (HHV-6) is an important immunosuppressive and immunomodulatory virus. The mechanisms by which HHV-6 establishes latency and immunosuppression in its host are not well understood. Here we characterized HHV-6-specific T cells in peripheral blood mononuclear cells (PBMCs) from HHV-6-infected donors. Our results showed that HHV-6 infection could induce both CD4(+) and CD8(+) HHV-6-specific regulatory T (Treg) cells. These HHV-6-specific Treg cells had potent suppressive activity and expressed high levels of Treg-associated molecules CD25, FoxP3, and GITR. Both CD4(+) and CD8(+) Treg cells secreted gamma interferon (IFN-γ) and interleukin-10 (IL-10) but little or no IL-2, IL-4, or transforming growth factor β (TGF-β). Furthermore, HHV-6-specifc Treg cells not only could suppress naive and HHV-6-specific CD4(+) effector T cell immune responses but also could impair dendritic cell (DC) maturation and functions. In addition, the suppressive effects mediated by HHV-6-specific Treg cells were mainly through a cell-to-cell contact-dependent mechanism but not through the identified cytokines. These results suggest that HHV-6 may utilize the induction of Treg cells as a strategy to escape antivirus immune responses and maintain the latency and immunosuppression in infected hosts.
Preferential recognition of a microbial metabolite by human V 2V 2 T cells (2007)

Human Vgamma2Vdelta2 T cells are stimulated by prenyl pyrophosphates, such as isopentenyl pyrophosphate (IPP), and play important roles in mediating immunity against microbial pathogens and have potent anti-tumor activity. (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) has been identified as a metabolite in the 2-C-methyl-D-erythritol-4 phosphate (MEP) pathway for isoprenoid biosynthesis that is used by many bacteria and protozoan parasites. We find that HMBPP is the major Vgamma2Vdelta2 T-cell antigen for many bacteria, including Mycobacterium tuberculosis, Yersinia enterocolitica and Escherichia coli. HMBPP was a 30 000-fold more potent antigen than IPP. Using mutant bacteria, we show that bacterial antigen levels for Vgamma2Vdelta2 T cells are controlled by MEP pathway enzymes and find no evidence for the production of 3-formyl-1-butyl pyrophosphate. Moreover, HMBPP reactivity required only germ line-encoded Vgamma2Vdelta2 TCR elements and is present at birth. Importantly, we show that bacterial HMBPP levels correlated with their ability to expand Vgamma2Vdelta2 T cells in vivo upon engraftment into severe combined immunodeficiency-beige mice. Thus, the production of HMBPP by a microbial-specific isoprenoid pathway plays a major role in determining whether bacteria will stimulate Vgamma2Vdelta2 T cells in vivo. This preferential stimulation by a common microbial isoprenoid metabolite allows Vgamma2Vdelta2 T cells to respond to a broad array of pathogens using this pathway.
Critical role of zinc in hardening of Nereis jaws (2006)

Hardening of invertebrate jaws and mandibles has been previously correlated to diverse, potentially complex modifications. Here we demonstrate directly, for the first time, that Zn plays a critical role in the mechanical properties of histidine-rich Nereis jaws. Using nanoindentation, we show that removal of Zn by chelation decreases both hardness and modulus by over 65%. Moreover, reconstitution of Zn yields a substantial recovery of initial properties. Modulus and hardness of Zn-replete jaws exceed those attainable by current engineering polymers by a factor of >3. Zn-mediated histidine cross-links are proposed to account for this enhancement in mechanical properties.
Targeted deletion of MMP-2 attenuates early LV rupture and late remodeling after experimental myocardial infarction (2003)

Matrix metalloproteinase-2 (MMP-2) is prominently overexpressed both after myocardial infarction (MI) and in heart failure. However, its pathophysiological significance in these conditions is still unclear. We thus examined the effects of targeted deletion of MMP-2 on post-MI left ventricular (LV) remodeling and failure. Anterior MI was produced in 10- to 12-wk-old male MMP-2 knockout (KO) and sibling wild-type (WT) mice by ligating the left coronary artery. By day 28, MI resulted in a significant increase in mortality in association with LV cavity dilatation and dysfunction. The MMP-2 KO mice had a significantly better survival rate than WT mice (56% vs. 85%, P < 0.05), despite a comparable infarct size (50 +/- 3% vs. 51 +/- 3%, P = not significant), heart rate, and arterial blood pressure. The KO mice had a significantly lower incidence of LV rupture (10% vs. 39%, P < 0.05), which occurred within 7 days of MI. The KO mice exerted less LV cavity dilatation and improved fractional shortening after MI by echocardiography. The LV zymographic MMP-2 level significantly increased in WT mice after coronary artery ligation; however, this was completely prevented in KO mice. In contrast, the increase in the LV zymographic MMP-9 level after MI was similar between KO and WT mice. MMP-2 activation is therefore considered to contribute to an early cardiac rupture as well as late LV remodeling after MI. The inhibition of MMP-2 activation may therefore be a potentially useful therapeutic strategy to manage post-MI hearts.
Comparative Evaluation of Spin-Transfer-Torque and Magnetoelectric Random Access Memory (2016)

Spin-transfer torque random access memory (STT-RAM), as a promising nonvolatile memory technology, faces challenges of high write energy and low density. The recently developed magnetoelectric random access memory (MeRAM) enables the possibility of overcoming these challenges by the use of voltage-controlled magnetic anisotropy (VCMA) effect and achieves high density, fast speed, and low energy simultaneously. As both STT-RAM and MeRAM suffer from the reliability problem of write errors, we implement a fast Landau–Lifshitz–Gilbert equation-based simulator to capture their write error rate (WER) under process and temperature variation. We utilize a multi-write peripheral circuit to minimize WER and design reliable STT-RAM and MeRAM. With the same acceptable WER, MeRAM shows advantages of 83% faster write speed, 67.4% less write energy, 138% faster read speed, and 28.2% less read energy compared with STT-RAM. Benefiting from the VCMA effect, MeRAM also achieves twice the density of STT-RAM with a 32 nm technology node, and this density difference is expected to increase with technology scaling down.
Relationship between Neural, Vascular, and BOLD Signals in Isoflurane-Anesthetized Rat Somatosensory Cortex (2006)

Functional magnetic resonance imaging (fMRI) in anesthetized rodents has been commonly performed with alpha-chloralose, which can be used only for terminal experiments. To develop a survival fMRI protocol, an isoflurane (ISO) -anesthetized rat model was systematically evaluated by simultaneous measurements of field potential (FP) and cerebral blood flow (CBF) in the somatosensory cortex. A conventional forepaw stimulation paradigm with 0.3 ms pulse width, 1.2 mA current, and 3 Hz frequency induced 54% less evoked FP and 84% less CBF response under ISO than alpha-chloralose. To improve stimulation-induced responses under ISO, 10-pulse stimulations were performed with variations of width, current, and frequency. For widths of 0.1-5.0 ms and currents of 0.4-2.0 mA, evoked FP and CBF increased similarly and reached a plateau. The evoked FP increased monotonically for intervals from 50 to 500 ms, but the CBF peaked at an interval of 83 ms (approximately 12 Hz frequency). These data suggest that different anesthetics profoundly affect FP and CBF responses in different ways, which requires optimizing stimulation parameters for each anesthetic. With the refined stimulation parameters, fMRI consistently detected a well-localized activation focus at the primary somatosensory cortex in ISO-anesthetized rats. Thus, the ISO-anesthetized rat model can be used for cerebrovascular activation studies, allowing repeated noninvasive survival experiments.
Statistics, axes and cats: Three studies of Paranoia (1989)

So you agree with the Judge. I know. You agree with the Judge and Mr Clerk. You also think the filling in of stat forms is a cinch. That I'm complaining about nothing. You too, think there's nothing unreasonable, doesn't sound as though there could be anything unreasonable in being expected to fill in a few stat forms. That a mere five or six stat forms should pose no problems, should easily be dealt with during a day...
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge (2008)

Abstract Background: Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a range of text-mining and information-extraction tools have recently been developed specifically for the biological domain. Such tools are only useful if they are designed to meet real-life tasks and if their performance can be estimated and compared. The BioCreative challenge (Critical Assessment of Information Extraction in Biology) consists of a collaborative initiative to provide a common evaluation framework for monitoring and assessing the state-of-the-art of text-mining systems applied to biologically relevant problems. Results: The Second BioCreative assessment (2006 to 2007) attracted 44 teams from 13 countries worldwide, with the aim of evaluating current information-extraction/text-mining technologies developed for one or more of the three tasks defined for this challenge evaluation. These tasks included the recognition of gene mentions in abstracts (gene mention task); the extraction of a list of unique identifiers for human genes mentioned in abstracts (gene normalization task); and finally the extraction of physical protein-protein interaction annotation-relevant information (protein-protein interaction task). The 'gold standard' data used for evaluating submissions for the third task was provided by the interaction databases MINT (Molecular Interaction Database) and IntAct. Conclusion: The Second BioCreative assessment almost doubled the number of participants for each individual task when compared with the first BioCreative assessment. An overall improvement in terms of balanced precision and recall was observed for the best submissions for the gene mention (F score 0.87); for the gene normalization task, the best results were comparable (F score 0.81) compared with results obtained for similar tasks posed at the first BioCreative challenge. In case of the protein-protein interaction task, the importance and difficulties of experimentally confirmed annotation extraction from full-text articles were explored, yielding different results depending on the step of the annotation extraction workflow. A common characteristic observed in all three tasks was that the combination of system outputs could yield better results than any single system. Finally, the development of the first text-mining meta-server was promoted within the context of this community challenge.
Controlled access and dissemination of XML documents (1999)

XML (eXtensible Markup Language) is becoming the most relevant standardization effort in the area of document representation through markup languages. Through XML, it is possible to define complex documents, containing information at different degrees of sensitivity. Moreover, the processes of document exchange and acquisition, which can be very frequent in Web-based information systems, are simplified and standardized. In this scenario, there is a strong need for policies to control and regulate the access and dissemination of XML documents. In the paper, we discuss main protection requirements posed by XML documents and we present a set of authorization and dissemination policies that enable both a controlled access to XML documents in a given source and the exchange of XML documents across different sources.
First report of Aspergillus flavus causing fruit rots of peaches in Greece (2007)

In July 2005, rotted peaches (about 1% of the total) of cvs Sun Crest, Andross and Sun Cloud were observed in commercial orchards in Imathia County (northern Greece). Infected tissues were pale and water soaked, and the spores were green and powdery and easily liberated when matured. Aspergillus flavus was isolated and identified based on morphological characteristics. Isolation of the pathogen was made on acidified potato dextrose agar (2·5 mL 85% lactic acid per L nutrient medium) incubated at 23°C for 5 to 7 days. Koch's postulates were completed in the laboratory by inoculating mature peach fruits (cv. Andross) previously surface sterilized by dipping in a 0·1% chlorine solution and allowed to dry in a laminar flow hood, wounded with a sharp glass rod of 2 mm in diameter, and applying a 40 µL drop of a 5 × 105 conidia per mL suspension of fungus over each wound. There were 30 inoculated and 30 control fruits (similarly wounded and inoculated with a 40 µL drop of sterile-distilled water) in a randomized design and incubated at 24–26°C for 7 days. Koch's postulates were satisfied after re-isolating the fungus from inoculated fruit that developed symptoms similar to those observed on fruit collected from orchards. This is the first report of Aspergillus flavus causing a rot of peaches in Greece. Fruit rots caused by A. flavus have been reported previously in peach orchards (Jamaluddin, 1980; Singh & Prashar, 1989). Measures should be taken to limit any possible spread of this pathogen in future, since toxigenic strains of Aspergillus produce aflatoxins that are known carcinogens and toxic to the liver (Marasas & Nelson, 1987; Molina & Giannuzzi, 2002).
Liquid micromotor driven by continuous electrowetting (2002)

This paper aims to acclaim surface tension as a practical microactuation force for MEMS, by developing the ground micromachining technologies and demonstrating a few prototypes including a liquid micromotor. A mechanism called continuous electrowetting is used to drive liquid-metal droplets along microchannels by controlling surface tension with electric potential. The paper first identifies and addresses key issues in employing this powerful surface-tension drive for MEMS throughout the design, fabrication, and testing of a simple test device. The development eventually leads us to a device called liquid micromotor, which demonstrates continuous travel of a mercury drop along a loop of microchannel. Wear-free and smooth rotation is achieved with a speed of 9.4 cm/s at a driving voltage of 10 V.
Follow-up of Children Exposed In Utero to 17 α-Hydroxyprogesterone Caproate Compared With Placebo (2007)

17 alpha-hydroxyprogesterone caproate seems to be safe for the fetus when administered in the second and third trimesters.
Expression of Human Factor IX by Microencapsulated Recombinant Fibroblasts (1993)

Deficiency of clotting factor IX (FIX) causes hemophilia B in humans. We propose a novel approach to its treatment by engineering FIX-secreting cell lines suitable for implantation in different allogeneic hosts. To prevent graft rejection following implantation, the recombinant cells can be protected with biocompatible membranes that permit exit of FIX but not entry of cellular immune mediators. To explore the feasibility of this approach, we now report on the creation of mouse Ltk- fibroblast cell lines that can deliver FIX through such immune-protective membranes. Mouse fibroblasts (Ltk-) were transfected with the cDNA for human FIX and clones secreting high levels of FIX were isolated. About 70% of the secreted FIX was biologically active. Over 98% of the recovered biological activity was precipitable by barium citrate, indicating appropriate. gamma-carboxylation of the secreted FIX. The secreted FIX was similar in molecular weight and immunoreactivity to plasma-derived human FIX. Upon enclosure in microcapsules fabricated from the biocompatible polymers, alginate-polylysine-alginate, the cells survived the encapsulation procedure with about 70-90% viability, proliferated within the microcapsules to twice their original number within 2 weeks, and continued to secrete FIX into the culture medium at similar rates as the unencapsulated cells. The biological activity, degree of post-translational gamma-carboxylation, and immunoreactivity of the FIX recovered from the culture media of the encapsulated cells were identical to those of the FIX secreted by the unencapsulated cells. In conclusion, fibroblasts engineered to secrete recombinant human FIX can proliferate and continue to secrete biologically active FIX through the alginate microcapsules. This demonstrates the feasibility of using microencapsulated recombinant cells to deliver human FIX and the potential for allogeneic somatic gene therapy for hemophilia B.
Computerized analysis of mammographic parenchymal patterns for breast cancer risk assessment: Feature selection (2000)

Our purpose in this study was to identify computer-extracted, mammographic parenchymal patterns that are associated with breast cancer risk. We extracted 14 features from the central breast region on digitized mammograms to characterize the mammographic parenchymal patterns of women at different risk levels. Two different approaches were employed to relate these mammographic features to breast cancer risk. In one approach, the features were used to distinguish mammographic patterns seen in low-risk women from those who inherited a mutated form of the BRCA1/BRCA2 gene, which confers a very high risk of developing breast cancer. In another approach, the features were related to risk as determined from existing clinical models (Gail and Claus models), which use well-known epidemiological factors such as a woman's age, her family history of breast cancer, reproductive history, etc. Stepwise linear discriminant analysis was employed to identify features that were useful in differentiating between "low-risk" women and BRCA1/BRCA2-mutation carriers. Stepwise linear regression analysis was employed to identify useful features in predicting the risk, as estimated from the Gail and Claus models. Similar computer-extracted mammographic features were identified in the two approaches. Results show that women at high risk tend to have dense breasts and their mammographic patterns tend to be coarse and low in contrast.
Comparison of inorganic elements from autopsy tissue of young and elderly subjects. (1991)

Concentrations of nine inorganic elements in autopsy samples of kidney, liver, heart and skeletal muscle from 33 aged subjects, mean age 80 years, were compared with concentrations in similar samples from 12 young healthy accident victims, mean age 29 years. Tissue samples were removed within 48 hours of death and dry weight was used as a frame of reference. Potassium and magnesium were significantly lower in muscle (P less than 0.001) and heart tissue (P less than 0.001) of elderly subjects. There was evidence of accumulation of zinc in liver tissue of the elderly (P less than 0.01). Copper was significantly lower in the heart tissue of elderly subjects (P less than 0.001) whereas manganese was lower in both the heart (P less than 0.01) and the kidney tissue (P less than 0.001) of the elderly. Selenium concentrations were lower in the kidney (P less than 0.001) of the elderly. Elderly heart tissue appeared to accumulate chromium (P = 0.007) and aluminium (P less than 0.001). No significant differences were found for iron concentrations between these two populations. These major differences in tissue element concentrations between young and aged subjects merit further attention.
Morphological Effects on the Electrical and Electrochemical Properties of Carbon Aerogels (2001)

Carbon aerogels are prepared by a sol-gel process. By controlling the mass ratio of reactants and the molar ratio of resorcinol to catalyst (R/C), carbon aerogels with different microstructures can be developed. The electrical conductivity is measured by the van der Pauw method. The results show that the electrical conductivity increases with increase of both temperature and density of carbon aerogel. Cyclic voltammetry is a useful technique to investigate the electrochemical properties of carbon aerogel electrodes. The maximum specific capacitance of carbon aerogel electrode in electrolyte is ∼86 F/g. © 2001 The Electrochemical Society. All rights reserved.
Protein glycosylation in yeast: transcript heterogeneity of the ALG7 gene. (1987)

The first enzyme in the lipid-linked oligosaccharide biosynthetic pathway, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (UDP-N-acetyl-D-glucosamine:dolichyl-phosphate-N-acetyl- D-glucosaminephosphotransferase, EC 2.7.8.15), is encoded by the ALG7 gene. We show that this gene is essential for cell growth, since a null mutation constructed with standard gene disruption techniques results in cell lethality. The ALG7 gene is transcribed into two major messages, approximately 1.38 and 1.56 kilobase pairs (kbp) in size, and this heterogeneity has been mapped to the 3' untranslated region. Two sets of tripartite sequences implicated in transcription termination begin 15 bp and 256 bp past the translation stop codon, TGA. The ratios of the two major transcripts change with gene dosage, with the longer mRNA becoming more abundant in cells containing higher levels of the ALG7 gene. Changes in transcript ratios are also observed in mutants defective in lipid-linked sugar-donor biosynthesis. In addition, there is 5' heterogeneity in the ALG7 mRNAs. The transcripts start at four initiation sites located within a 20-bp region. Two potentially functional TATA elements have been identified at positions -157 and -139, which may be involved in initiation from multiple sites. These features point to numerous factors that may be involved in the regulation of the expression of the ALG7 gene.