gebhart/patrepeval huggingface dataset:
Actin-based movement of Listeria monocytogenes: actin assembly results from the local maintenance of uncapped filament barbed ends at the bacterium surface. (1995)

The thermodynamic basis for actin-based motility of Listeria monocytogenes has been investigated using cytoplasmic extracts of Xenopus eggs, initially developed by Theriot et al. (Theriot, J. A., J. Rosenblatt, D. A. Portnoy, P. J. Goldschmidt-Clermont, and T. J. Mitchison. 1994. Cell. 76:505-517) as an in vitro cell-free system. A large proportion (75%) of actin was found unpolymerized in the extracts. The amount of unassembled actin (12 microM) is accounted for by the sequestering functions of T beta 4Xen (20 microM) and profilin (5 microM), the barbed ends being capped. Movement of Listeria was not abolished by depletion of over 99% of the endogenous profilin. The proline-rich sequences of ActA are unlikely to be the target of profilin. All data support the view that actin assembly at the rear of Listeria results from a local shift in steady state due to a factor, keeping filaments uncapped, bound to the surface of the bacterium, while barbed ends are capped in the bulk cytoplasm. Movement is controlled by the energetic difference (i.e., the difference in critical concentration) between the two ends of the filaments, hence a constant ATP supply and the presence of barbed end capped F-actin in the medium are required to buffer free G-actin at a high concentration. The role of membrane components is demonstrated by the facts that: (a) Listeria movement can be reconstituted in the resuspended pellets of high speed-centrifuged extracts that are enriched in membranes; (b) Actin-based motility of endogenous vesicles, exhibiting the same rocketing movement as Listeria, can be observed in the extracts.
Genome Evolution in Yeasts (2015)

Abstract Used empirically over millennia for a variety of fermentation processes, the microscopic yeasts representing unicellular forms of modern fungi adapted to a large diversity of habitats have become powerful model organisms to understand eukaryotic genome evolution. Their broad evolutionary range offers unique views on both short‐ and long‐term genomic changes, with the possibility to confront observations with experimental results. Processes of duplications, gene loss and de novo gene creation form the bases of genome evolution, along with horizontal acquisitions and an unexpectedly high frequency of interspecies hybridisations. This short review summarises our present knowledge about genome evolution focussing on the subphylum of budding yeasts or Saccharomycotina , by far the most extensively studied lineage, without ignoring the multiphyletic origin of yeasts. Key Concepts Yeasts represent long‐evolved unicellular forms of modern fungi, adapted to rapid clonal expansions under favourable conditions, not primitive eukaryotes. Over 1600 yeast species are presently described in the different subphyla of Ascomycota and Basidiomycota , within which the budding yeasts ( Saccharomycotina) represent the largest deep‐branching lineage useful for genome evolution studies. The different genome architectures of well‐circumscribed subgroups of Saccharomycotina indicate major evolutionary divides within which ancient events can be inferred. Important modifications of the role of RNA occurred at the origin of Saccharomycotina (massive loss of spliceosomal introns and loss of RNAi control) and continued during their evolution (fixation of 5S RNA gene, change of deciphering mode and significance for synonymous codons). All yeast genomes exhibit significant levels of redundancy, reflecting small‐scale duplications and, in one lineage, a whole‐genome duplication followed by extensive gene loss. The balance between gene gains and losses accelerated yeast genome evolution beyond sequence divergence and chromosomal dynamics. Novel genes regularly appeared during yeast genome evolution, resulting from duplication followed by sequence divergence, horizontal acquisition and de novo gene creation. Interspecies hybridisation is a common phenomenon. Resolution of hybrid genomes suggests an important role for interspecific exchanges in evolution.
Sequence analysis of the respiratory syncytial virus phosphoprotein gene (1984)

A recombinant cDNA plasmid (pRSA3) containing an almost full-length copy of the mRNA encoding respiratory syncytial virus phosphoprotein was identified in a cDNA library prepared with mRNA from respiratory syncytial virus-infected cells. The cDNA insert was sequenced, and a protein of 27,150 daltons was deduced from the DNA sequence. The protein is relatively acidic, containing two clusters of acidic amino acids, one in the middle of the molecule and the other at the C-terminus. It is devoid of both cysteine and tryptophan. There was no other potential reading frame within the phosphoprotein gene of respiratory syncytial virus. This situation is unlike that with Sendai virus, a paramyxovirus, which has a nonstructural C protein encoded by a second overlapping reading frame near the 5' end of the mRNA for phosphoprotein.
Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists (2004)

Vitamin-K epoxide reductase is encoded by the VKORC1 gene in mammals and other vertebrates, which also have a paralog, VKORC1L1. Single homologs are present in basal deuterostome and insect genomes, including Drosophila, and three trypanosomatid protists. VKOR is therefore an ancient gene/protein that can be studied in the Drosophila model system.
The Employment of an Iterative Design Process to Develop a Pulmonary Graphical Display (2003)

With this rapid iterative development process, an intuitive graphical display can be developed inexpensively prior to formal testing in an experimental setting.
Thymocyte Expression of RAG-1 and RAG-2: Termination by T Cell Receptor Cross-Linking (1991)

The expression of the V(D)J [variable (diversity) joining elements] recombination activating genes, RAG-1 and RAG-2, has been examined during T cell development in the thymus. In situ hybridization to intact thymus and RNA blot analysis of isolated thymic subpopulations separated on the basis of T cell receptor (TCR) expression demonstrated that both TCR- and TCR+ cortical thymocytes express RAG-1 and RAG-2 messenger RNA's. Within the TCR+ population, RAG expression was observed in immature CD4+CD8+ (double positive) cells, but not in the more mature CD4+CD8- or CD4-CD8+ (single positive) subpopulations. Thus, although cortical thymocytes that bear TCR on their surface continue to express RAG-1 and RAG-2, it appears that the expression of both genes is normally terminated during subsequent thymic maturation. Since thymocyte maturation in vivo is thought to be regulated through the interaction of the TCR complex with self major histocompatibility complex (MHC) antigens, these data suggest that signals transduced by the TCR complex might result in the termination of RAG expression. Consistent with this hypothesis, thymocyte TCR cross-linking in vitro led to rapid termination of RAG-1 and RAG-2 expression, whereas cross-linking of other T cell surface antigens such as CD4, CD8, or HLA class I had no effect.
EX VIVO T-LYMPHOCYTE DERIVED CYTOKINE PRODUCTION IN SIRS PATIENTS IS INFLUENCED BY EXPERIMENTAL PROCEDURES (2000)

Ex vivo production of interleukin-2 (IL-2), IL-4, IL-5, and IL-10 by peripheral blood mononuclear cells (PBMC) was studied in 13 septic patients with infectious systemic inflammatory response syndrome (SIRS) and 13 patients undergoing cardiac surgery with cardiopulmonary bypass (CPB) (noninfectious SIRS). We have investigated the levels of cytokines after activation by either concanavalin A (ConA), phytohemagglutinin (PHA), or anti-CD3 antibodies. In whole blood assays, ConA-induced IL-10 was significantly reduced in both groups of patients compared with healthy controls. In sepsis patients, IL-2, IL-5, and IL-10 productions by isolated PBMC were diminished on ConA-induced activation but not in response to PHA and anti-CD3; in CPB patients, only anti-CD3-induced IL-10 production was significantly reduced. Our data indicate that subtle modifications of the reactivity of circulating cells occur during infectious and noninfectious SIRS. Production of both Th1 and Th2 cytokines can be down-regulated; however, the nature of the SIRS, of the cell population, and of the activator may influence the observation.
Nitrogen-Doped Carbon Nanotube Arrays with High Electrocatalytic Activity for Oxygen Reduction (2009)

The large-scale practical application of fuel cells will be difficult to realize if the expensive platinum-based electrocatalysts for oxygen reduction reactions (ORRs) cannot be replaced by other efficient, low-cost, and stable electrodes. Here, we report that vertically aligned nitrogen-containing carbon nanotubes (VA-NCNTs) can act as a metal-free electrode with a much better electrocatalytic activity, long-term operation stability, and tolerance to crossover effect than platinum for oxygen reduction in alkaline fuel cells. In air-saturated 0.1 molar potassium hydroxide, we observed a steady-state output potential of -80 millivolts and a current density of 4.1 milliamps per square centimeter at -0.22 volts, compared with -85 millivolts and 1.1 milliamps per square centimeter at -0.20 volts for a platinum-carbon electrode. The incorporation of electron-accepting nitrogen atoms in the conjugated nanotube carbon plane appears to impart a relatively high positive charge density on adjacent carbon atoms. This effect, coupled with aligning the NCNTs, provides a four-electron pathway for the ORR on VA-NCNTs with a superb performance.
A Study on the Association of the Chromosome 12p13 Locus with Sporadic Late-Onset Alzheimer’s Disease in Chinese (2009)

Recent linkage and association studies have implicated the chromosome 12p13 locus as possibly harboring genetic variants predisposed to Alzheimer's disease (AD). We attempted to replicate this association in a Chinese data set comprised of 256 AD cases and 264 age-matched normal controls. A total of 14 single nucleotide polymorphisms (SNPs) were examined. Single marker association revealed the two SNPs in NCAPD2 (rs7311174 and rs2072374) as showing nominal significant p values (p = 0.0491 and 0.0116, respectively). Haplotype analysis found LD block one to be significantly associated with AD (global p = 0.0250). Haplotypes CGGATG and CAGTCG were also significantly associated with AD (p = 0.0498 and p = 0.0482, respectively). These genetic analyses provide evidence that the chromosome 12p13 locus is associated with AD in Chinese.
NUBPL mutations in patients with complex I deficiency and a distinct MRI pattern (2013)

Our data show that NUBPL mutations are associated with a unique, consistent, and recognizable MRI pattern, which facilitates fast diagnosis and obviates the need for other tests, including assessment of mitochondrial complex activities in muscle or fibroblasts.
Imaging Cleared Intact Biological Systems at a Cellular Level by 3DISCO (2014)

Tissue clearing and subsequent imaging of transparent organs is a powerful method to analyze fluorescently labeled cells and molecules in 3D, in intact organs. Unlike traditional histological methods, where the tissue of interest is sectioned for fluorescent imaging, 3D imaging of cleared tissue allows examination of labeled cells and molecules in the entire specimen. To this end, optically opaque tissues should be rendered transparent by matching the refractory indices throughout the tissue. Subsequently, the tissue can be imaged at once using laser-scanning microscopes to obtain a complete high-resolution 3D image of the specimen. A growing list of tissue clearing protocols including 3DISCO, CLARITY, Sca/e, ClearT2, and SeeDB provide new ways for researchers to image their tissue of interest as a whole. Among them, 3DISCO is a highly reproducible and straightforward method, which can clear different types of tissues and can be utilized with various microscopy techniques. This protocol describes this straightforward procedure and presents its various applications. It also discusses the limitations and possible difficulties and how to overcome them.
Study of the in vitro cytotoxicity testing of medical devices (2015)

The cytotoxicity test is one of the biological evaluation and screening tests that use tissue cells <i>in vitro</i> to observe the cell growth, reproduction and morphological effects by medical devices. Cytotoxicity is preferred as a pilot project test and an important indicator for toxicity evaluation of medical devices as it is simple, fast, has a high sensitivity and can save animals from toxicity. Three types of cytotoxicity test are stated in the International Organization for Standardization 109993-5: Extract, direct contact and indirect contact tests. The xCELLigence real-time cell analysis system shows a significant potential in regards to cytotoxicity in recent years. The present review provides a brief insight into the <i>in vitro</i> cytotoxicity testing of medical devices.
HIGS: Host-Induced Gene Silencing in the Obligate Biotrophic Fungal Pathogen Blumeria graminis (2010)

Powdery mildew fungi are obligate biotrophic pathogens that only grow on living hosts and cause damage in thousands of plant species. Despite their agronomical importance, little direct functional evidence for genes of pathogenicity and virulence is currently available because mutagenesis and transformation protocols are lacking. Here, we show that the accumulation in barley (Hordeum vulgare) and wheat (Triticum aestivum) of double-stranded or antisense RNA targeting fungal transcripts affects the development of the powdery mildew fungus Blumeria graminis. Proof of concept for host-induced gene silencing was obtained by silencing the effector gene Avra10, which resulted in reduced fungal development in the absence, but not in the presence, of the matching resistance gene Mla10. The fungus could be rescued from the silencing of Avra10 by the transient expression of a synthetic gene that was resistant to RNA interference (RNAi) due to silent point mutations. The results suggest traffic of RNA molecules from host plants into B. graminis and may lead to an RNAi-based crop protection strategy against fungal pathogens.
Right ventricular free wall circumferential strain reflects graded elevation in acute right ventricular afterload (2008)

This study was designed to evaluate the concurrent changes in the right ventricular free wall (RVFW) movement in experimentally induced, acute mild, moderate, and severe right ventricle (RV) afterload conditions. In 14 open-chest pigs (weight 43 +/- 4 kg) with preserved pericardia, acute mild (>35 and <50 mmHg), moderate (> or =50 and < or =60 mmHg), and severe (>60 mmHg) increases in RV systolic pressure (RVSP) were induced by constriction of the pulmonary artery. At each step, longitudinal, radial, and circumferential strains and strain rates were measured in both the RVFW and the interventricular septum. The mean RVSPs were 31.0 +/- 4.3 mmHg at baseline and 41.1 +/- 2.7 mmHg during mild, 52.7 +/- 3.4 mmHg during moderate, and 61.7 +/- 1.6 mmHg during severe afterload conditions. The RVFW circumferential strains showed significant differences among baseline, mild, moderate, and severe afterload conditions (-10.5 +/- 3.9, -8.3 +/- 3.3, -5.4 +/- 2.7, and -7.5 +/- 5.3%, respectively, P = 0.008) and had significant linear correlation with RVSP (r = 0.636, P < 0.001) if the severe condition was excluded. Decrease of the RVFW circumferential strain magnitude is the most distinct response in acute mild and moderate RV afterload that could aid in detection of clinical conditions associated with acutely increasing RV afterload.
[The effect of sedation on pulmonary function]. (1995)

Opioids, benzodiazepines and hypnotics all affect central respiratory drive, muscular activity of the oropharynx, thoracic wall and diaphragm, bronchomotor tone and pulmonary vascular resistance (PVR), and may thus influence respiratory function during sedation and weaning. Opioids and benzodiazepines will attenuate hypercapnic and hypoxic stimulation of the respiratory centres. Compromise of respiratory drive must also be anticipated with ketamine, in view of recent evidence contradicting earlier findings of central respiratory stimulation. Coordinated muscular activity of the oropharynx is important for airway patency. Since this mechanism is impaired more by benzodiazepines than by ketamine the latter may be advantageous during weaning. Respiratory frequency and tidal volume are both diminished by opioids, benzodiazepines and propofol. The differential impact on intercostal and diaphragmatic muscle activity may prove important in COPD and emphysema. With ketamine spontaneous respiration is increased. Gas distribution and airway pressures are influenced by bronchomotor tone. Bronchodilator effects are well known to arise with ketamine, but have also been demonstrated with benzodiazepines, propofol and some opioids. PVR is a critical factor in respiratory insufficiency. An increase in PVR with ketamine has been found during spontaneous respiration. Since evidence for pulmonary vasodilation during controlled ventilation has been recorded in humans and in vitro experiments, sedation regimens applied in respiratory insufficiency can also include ketamine.
FRL, a Novel Formin-Related Protein, Binds to Rac and Regulates Cell Motility and Survival of Macrophages (2000)

We have isolated a cDNA, frl (formin-related gene in leukocytes), a novel mammalian member of the formin gene family. The frl cDNA encodes a 160-kDa protein, FRL, that possesses FH1, FH2, and FH3 domains that are well conserved among other Formin-related proteins. An FRL protein is mainly localized in the cytosol and is highly expressed in spleen, lymph node, and bone marrow cells. Formin-related genes and proteins have been reported to play crucial roles in morphogenesis, cell polarity, and cytokinesis through interaction with Rho family small GTPases. FRL binds to Rac at its N-terminal region including the FH3 domain and associates with profilin at the FH1 domain. In a macrophage cell line, P388D1, overexpression of a truncated form of FRL containing only the FH3 domain (FH3-FRL) strongly inhibited cell adhesion to fibronectin and migration upon stimulation with a chemokine. Moreover, expression of the truncated FH3-FRL protein resulted in apoptotic cell death of P388D1 cells, suggesting that the truncated FH3-FRL protein may interfere with signals of FRL. Overexpression in the P388D1 cells of full-length FRL or of the truncated protein containing the FH3 and FH1 domains, with simultaneous expression of the truncated FH3-FRL protein, blocked apoptotic cell death and inhibition of cell adhesion and migration. These results suggest that FRL may play a role in the control of reorganization of the actin cytoskeleton in association with Rac and also in the regulation of the signal for cell survival.
Estradiol Enhances Recovery After Myocardial Infarction by Augmenting Incorporation of Bone Marrow–Derived Endothelial Progenitor Cells Into Sites of Ischemia-Induced Neovascularization via Endothelial Nitric Oxide Synthase–Mediated Activation of Matrix Metalloproteinase-9 (2006)

Estradiol preserves the integrity of ischemic tissue by augmenting the mobilization and incorporation of BM-derived EPCs into sites of neovascularization by eNOS-mediated augmentation of MMP-9 expression in the BM. Moreover, these data have broader implications with regard to our understanding of the role of EPCs in post-MI recovery and on the sex discrepancy in cardiac events.
A Free‐Running DNA Motor Powered by a Nicking Enzyme (2005)

DNA burns its bridges: A unidirectional molecular motor that moves an oligonucleotide cargo along a self-assembled track is powered by restriction endonuclease hydrolysis of the phosphodiester backbone (see scheme). Damage caused to the track by the restriction enzyme prevents the cargo from stepping backwards and therefore imposes directionality. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501262_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Conformity in condylar replacement knee prosthesis (1977)

Experiments were carried out to determine the optimum conformity between the femoral and tibial condyles in condylar replacement knee prostheses. Wear tests and observations from removed prostheses indicated that both high and low conformity produced characteristic abrasion and fatigue. Partly conforming condyles provided stability under load-bearing but allowed laxity to occur. Fixation to resist the various forces on the tibial components was enhanced by a short central intramedullary peg. Partial conformity is proposed as the optimum configuration between femoral and tibial components.
Delivery Vehicles for Small Interfering RNA In Vivo (2008)

RNA interference (RNAi) as a mechanism to selectively silence messenger mRNA (mRNA) expression has revolutionized the biological sciences. With the identification and sequencing of the entire human genome complete, RNAi can be harnessed to rapidly develop novel drugs against any disease target. The ability of synthetic small interfering RNA (siRNA) to potently, but reversibly, silence genes in vivo, has made them particularly well suited as a drug therapeutic. Development of therapeutics using siRNA has advanced rapidly, with five different clinical trials ongoing and several more poised to enter the clinic in the coming years. Although challenges remain, delivery represents the main hurdle for faster and broader development of siRNA therapeutics. In this review, a summary of the advances in in vivo siRNA delivery is presented and discussed. Multiple different delivery approaches have demonstrated success ranging from the relative simplicity of direct local administration of saline-formulated siRNA, to liposome- and polymer-based nanoparticle approaches, to conjugation and complexation approaches. For siRNA therapeutics to achieve their full potential as a revolutionary class of drug molecules, multiple distinct delivery technologies will likely be needed, with selection of delivery approach being dependent on the nature of the clinical indication, the route of administration to be used, and the cell types to be targeted. Lastly, a status report on current clinical trials using siRNA is given.
Sequence-dependent enhancement of cytotoxicity produced by ecteinascidin 743 (ET-743) with doxorubicin or paclitaxel in soft tissue sarcoma cells. (2001)

Ecteinascidin 743 (ET-743) is a potent antitumor agent from the Caribbean tunicate Ecteinascidin turbinata and is presently in clinical trials for human cancers. To better understand how ET-743 might be used clinically, the present study used SRB assays to examine the cytotoxicity resulting from combining ET-743 with three other antineoplastic agents: doxorubicin (DXR), trimetrexate, and paclitaxel in different administration schedules in two soft tissue sarcoma cell lines, HT-1080 and HS-18, in vitro. Concurrent exposure of ET-743 with DXR resulted in synergistic interactions in both cell lines. Addition of ET-743 for 24 h before DXR was the most effective cytotoxic regimen against both cell lines. Morphological study by fluorescence microscopy revealed that combination treatment of both cells with ET-743 and DXR induced apoptosis. Exposure to paclitaxel before ET-743 was also an effective regimen. These results encourage studies of the combination of ET-743 and DXR in the treatment of soft tissue sarcoma, because each of these agents have activity in this disease.