gebhart/patrepeval huggingface dataset:
Efficient Editing of Malaria Parasite Genome Using the CRISPR/Cas9 System (2014)

Malaria parasites are unicellular organisms residing inside the red blood cells, and current methods for editing the parasite genes have been inefficient. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and Cas9 endonuclease-mediated genome editing) system is a new powerful technique for genome editing and has been widely employed to study gene function in various organisms. However, whether this technique can be applied to modify the genomes of malaria parasites has not been determined. In this paper, we demonstrated that Cas9 is able to introduce site-specific DNA double-strand breaks in the Plasmodium yoelii genome that can be repaired through homologous recombination. By supplying engineered homologous repair templates, we generated targeted deletion, reporter knock-in, and nucleotide replacement in multiple parasite genes, achieving up to 100% efficiency in gene deletion and 22 to 45% efficiencies in knock-in and allelic replacement. Our results establish methodologies for introducing desired modifications in the P. yoelii genome with high efficiency and accuracy, which will greatly improve our ability to study gene function of malaria parasites. Importance: Malaria, caused by infection of Plasmodium parasites, remains a world-wide public health burden. Although the genomes of many malaria parasites have been sequenced, we still do not know the functions of approximately half of the genes in the genomes. Studying gene function has become the focus of many studies; however, editing genes in malaria parasite genomes is still inefficient. Here we designed several efficient approaches, based on the CRISPR/Cas9 system, to introduce site-specific DNA double-strand breaks in the Plasmodium yoelii genome that can be repaired through homologous recombination. Using this system, we achieved high efficiencies in gene deletion, reporter tagging, and allelic replacement in multiple parasite genes. This technique for editing the malaria parasite genome will greatly facilitate our ability to elucidate gene function.
Enterovirus 68 3C Protease Cleaves TRIF To Attenuate Antiviral Responses Mediated by Toll-Like Receptor 3 (2014)

EV68 is a globally emerging pathogen, but the molecular basis of EV68 pathogenesis is unclear. Here we report that EV68 inhibits TLR3-mediated innate immune responses by targeting TRIF. Further investigations revealed that TRIF is cleaved by 3C(pro). These results suggest that control of TRIF by 3C(pro) may be a mechanism by which EV68 impairs type I IFN production in response to TLR3 activation.
O corpo na educação física escolar (2002)

O presente artigo vem abordar a questão do corpo nas aulas de Educação Física. O trabalho parte de uma revisão histórica da Educação Física, e apresenta a situação atual, aonde o esporte estudantil de rendimento vem tomando conta da Educação Física Escolar. Os conceitos de trabalho de Marcel Mauss entram na discussão no que se refere à forma de trabalho, onde essas formas analisam, primeiro o passado do aluno, para depois aplicar uma metodologia na aula que tem por base as experiências vividas pelo aluno. Muito diferente da que temos hoje, que é à busca do rendimento no esporte estudantil, inclusive nas aulas de Educação Física.
Role of Hedgehog Signaling Pathway in NASH (2016)

Non-alcoholic fatty liver disease (NAFLD) is the number one cause of chronic liver disease in the Western world. Although only a minority of patients will ultimately develop end-stage liver disease, it is not yet possible to efficiently predict who will progress and, most importantly, effective treatments are still unavailable. Better understanding of the pathophysiology of this disease is necessary to improve the clinical management of NAFLD patients. Epidemiological data indicate that NAFLD prognosis is determined by an individual's response to lipotoxic injury, rather than either the severity of exposure to lipotoxins, or the intensity of liver injury. The liver responds to injury with a synchronized wound-healing response. When this response is abnormal, it leads to pathological scarring, resulting in progressive fibrosis and cirrhosis, rather than repair. The hedgehog pathway is a crucial player in the wound-healing response. In this review, we summarize the pre-clinical and clinical evidence, which demonstrate the role of hedgehog pathway dysregulation in NAFLD pathogenesis, and the preliminary data that place the hedgehog pathway as a potential target for the treatment of this disease.
Cutting Edge: Activation of Toll-Like Receptor 2 Induces a Th2 Immune Response and Promotes Experimental Asthma (2004)

Recognition of microbial components by APCs and their activation through Toll-like receptors (TLR) leads to the induction of adaptive immune responses. In this study, we show that activation of TLR2 by its synthetic ligand Pam3Cys, in contrast to activation of TLR9 by immunostimulatory DNA (ISS-ODN), induces a prominent Th2-biased immune response. Activation of APCs by Pam3Cys resulted in the induction of Th2-associated effector molecules like IL-13, and IL-1beta, GM-CSF and up-regulation of B7RP-1, but low levels of Th1-associated cytokines (IL-12, IFNalpha, IL-18, IL-27). Accordingly, TLR2 ligands aggravated experimental asthma. These data indicate that the type of TLR stimulation during the initial phase of immune activation determines the polarization of the adaptive immune response and may play a role in the initiation of Th2-mediated immune disorders, such as asthma.
Endometrial regeneration using autologous adult stem cells followed by conception by in vitro fertilization in a patient of severe Asherman's syndrome (2011)

In a woman with severe Asherman's syndrome, curettage followed by placement of intrauterine contraceptive device (IUCD) (IUCD with cyclical hormonal therapy) was tried for 6 months, for development of the endometrium. When this failed, autologous stem cells were tried as an alternative therapy. From adult autologous stem cells isolated from patient's own bone marrow, endometrial angiogenic stem cells were separated using immunomagnetic isolation. These cells were placed in the endometrial cavity under ultrasound guidance after curettage. Patient was then given cyclical hormonal therapy. Endometrium was assessed intermittently on ultrasound. On development of endometrium with a thickness of 8 mm and good vascularity, in vitro fertilization and embryo transfer was done. This resulted in positive biochemical pregnancy followed by confirmation of gestational sac, yolk sac, and embryonic pole with cardiac activity on ultrasound. Endometrial angiogenic stem cells isolated from autologous adult stem cells could regenerate injured endometrium not responding to conventional treatment for Asherman's syndrome.
Effective dielectric function of ferroelectric LC suspensions (2004)

We study dielectric properties of a dilute suspension of ferroelectric particles in a nematic liquid crystal(LC)host. It is supposed that submicron particles do not disturb the LC alignment and the suspension macroscopically appears similar to a pure LC. We propose theoretical model for effective dielectric function of ferroelectric LC suspension. It is found that particles permanent polarisation may significantly increase the effective value of suspension dielectric function in comparison with pure LC. For more elongated particles depolarisation factor is smaller and respectively the contribution of induced polarisation of particles to the effective dielectric function is higher.
Toward Spinal Cord Injury Repair Strategies: Peptide Surface Modification of Expanded Poly(Tetrafluoroethylene) Fibers for Guided Neurite Outgrowth In Vitro (2003)

Expanded poly(tetrafluoroethylene) fibers were surface modified using an ultraviolet-activated mercury/ammonia reaction to yield amine-functional groups for the coupling of laminin-derived cell adhesive peptides CYIGSR, CDPGYIGSR, CIKVAV, and CQAASIKVAV. Surface elemental composition, determined by X-ray photoelectron spectroscopy, and radiolabeling data indicated that the amount of peptide introduced was approximately equivalent regardless of peptide type, yet mixed peptide surfaces had approximately 60% YIGSR and 40% IKVAV. The peptide-modified surfaces were compared in terms of the response of dorsal root ganglia with neurite length and number of cells attached to each fiber measured. All peptide-functionalized surfaces had a greater cellular response than the aminated ePTFE and ePTFE controls. Surfaces modified with extended peptide sequences CDPGYIGSR and CQAASIKVAV demonstrated a greater cellular response than those modified with the shorter peptide sequences CYIGSR and CIKVAV, respectively, likely because the extended peptides more closely mimic the three-dimensional conformation that the peptides maintain in laminin. Differences in neurite extension were evident among the peptide-functionalized surfaces, with the longest neurites observed on surfaces modified with both CQAASIKVAV and CDPGYIGSR. The "guidance capacity" of the fibers as a function of fiber diameter was investigated in terms of length and directionality of neurite outgrowth. As fiber diameter decreased (from 100+ to 10 microm), the neurites tended to grow to a greater degree down the length of the fiber. The thinnest fibers (with diameters <20 microm) extended shorter neurites than the fibers with a wider diameter. Combining neurite length with guidance indicated that of the fiber diameters investigated, the optimal fiber diameter for neurite guidance was between 30 and 50 microm.
Selective BRAFV600E Inhibition Enhances T-Cell Recognition of Melanoma without Affecting Lymphocyte Function (2010)

Targeted therapy against the BRAF/mitogen-activated protein kinase (MAPK) pathway is a promising new therapeutic approach for the treatment of melanoma. Treatment with selective BRAF inhibitors results in a high initial response rate but limited duration of response. To counter this, investigators propose combining this therapy with other targeted agents, addressing the issue of redundancy and signaling through different oncogenic pathways. An alternative approach is combining BRAF/MAPK-targeted agents with immunotherapy. Preliminary evidence suggests that oncogenic BRAF (BRAF(V600E)) contributes to immune escape and that blocking its activity via MAPK pathway inhibition leads to increased expression of melanocyte differentiation antigens (MDA). Recognition of MDAs is a critical component of the immunologic response to melanoma, and several forms of immunotherapy capitalize on this recognition. Among the various approaches to inhibiting BRAF/MAPK, broad MAPK pathway inhibition may have deleterious effects on T lymphocyte function. Here, we corroborate the role of oncogenic BRAF in immune evasion by melanoma cells through suppression of MDAs. We show that inhibition of the MAPK pathway with MAPK/extracellular signal-regulated kinase kinase (MEK) inhibitors or a specific inhibitor of BRAF(V600E) in melanoma cell lines and tumor digests results in increased levels of MDAs, which is associated with improved recognition by antigen-specific T lymphocytes. However, treatment with MEK inhibitors impairs T lymphocyte function, whereas T-cell function is preserved after treatment with a specific inhibitor of BRAF(V600E). These findings suggest that immune evasion of melanomas mediated by oncogenic BRAF may be reversed by targeted BRAF inhibition without compromising T-cell function. These findings have important implications for combined kinase-targeted therapy plus immunotherapy for melanoma.
Molecular cloning and nucleotide sequence of the DNA polymerase gene fromThermus flavus (1992)

Journal Article Molecular cloning and nucleotide sequence of the DNA polymerase gene from Thermus flavus Get access A.A. Akhmetzjanov, A.A. Akhmetzjanov Department of Biochemistry and Cytochemistry, Bashkirian Scientific Centre, Russian Academy of Sciencespr. Oktyabrya, 69, Ufa, 450054, Russia Search for other works by this author on: Oxford Academic PubMed Google Scholar V.A. Vakhitov V.A. Vakhitov Department of Biochemistry and Cytochemistry, Bashkirian Scientific Centre, Russian Academy of Sciencespr. Oktyabrya, 69, Ufa, 450054, Russia Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 21, 11 November 1992, Page 5839, https://doi.org/10.1093/nar/20.21.5839 Published: 11 November 1992 Article history Received: 29 September 1992 Accepted: 06 October 1992 Published: 11 November 1992
A Pilot Study of the Effect of Gentamicin on Nasal Potential Difference Measurements in Cystic Fibrosis Patients Carrying Stop Mutations (2000)

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene containing a premature termination signal are expected to produce little or no CFTR chloride channels. It has been shown in vitro, that aminoglycoside antibiotics can increase the frequency of erroneous insertion of nonsense codons hence permitting the translation of CFTR alleles carrying missense mutations to continue reading to the end of the gene. This led to the appearance of functional CFTR channels at the apical plasma membrane. The aim of this research was to determine if topical application of gentamicin to the nasal epithelium of patients with cystic fibrosis (CF) carrying stop mutations can express, in vivo, functional CFTR channels. Nine CF patients carrying stop mutations (mean age 23 +/- 11 yr, range 12 to 46 yr) received gentamicin drops (0.3%, 3 mg/ml) three times daily intranasally for a total of 14 d. Nasal potential difference (PD) was measured before and after the treatment. Before gentamicin application all the patients had abnormal nasal PD typical of CF. After gentamicin treatment, significant repolarization of the nasal epithelium representing chloride transport was increased from -1 +/- 1 mV to -10 +/- 11 mV (p < 0. 001). In conclusion, gentamicin may influence the underlying chloride transport abnormality in patients with CF carrying stop mutations.
Eudragit® E as Coating Material for the pH-Controlled Drug Release in the Topical Treatment of Inflammatory Bowel Disease (IBD) (1998)

During an attack of ulcerative colitis the colonic pH of normally 6.4-7.0 drops to values of 2.3-4.7. The objective of this study was to investigate an acid-soluble polymer (Eudragit E) as coating material for multiple units (mini tablets) with regard to its ability to allow drug release only under the acidic conditions of the inflamed colon. Mini tablets (diameter 3 mm) containing 20% (w/w) of the model drug dexamethasone with or without the mucoadhesive swelling agent carbomer 934 (neutralized) were coated in a small coating pan with different amounts of an organic solution of Eudragit E leading to coating thicknesses of 150-400 microm. Drug release from the Eudragit E-coated cores at pH 2.0-5.0 starts after 10-50 min due to the rapid dissolution of the Eudragit E film. At pH 6.8 lag times of drug release depend on the composition of the cores and the thickness of the coating film: In the case of the carbomer-containing cores drug release is induced by disruption of the coating film due to swelling of the cores and lag times (up to 20 h) increase overproportionately with increasing coating thickness. With no swelling agent in the cores drug release at pH 6.8 is delayed due to the low erosion/dissolution rate of Eudragit E. Lag times of drug release (up to 33 h) increase in a linear manner with increasing coating thickness. Thus, Eudragit E, protected against dissolution in the stomach by an enteric coating, is a suitable coating polymer for drug release in acidic regions such as the inflamed colon.
On-chip sample preparation by controlled release of antibodies for simple CD4 counting (2011)

We present a simple system for CD4 and CD8 counting for point-of-care HIV staging in low-resource settings. Automatic sample preparation is achieved through a dried reagent coating inside a thin (26 μm) counting chamber, allowing the delayed release of fluorochrome conjugated monoclonal antibodies after the filling of the chamber with whole blood by capillary flow. A custom-built image cytometer is used to capture fluorescence images representing more than 1 μl of blood. The thin layer of blood in combination with the large image area allows the use of whole blood from a finger prick without the need for dilution, lysis or cell enrichment. Automatic cell counting of CD4(+) and CD8(+) T-lymphocytes correlates well with results obtained by flow cytometry.
A steerable leaky-wave antenna using a tunable impedance ground plane (2002)

A steerable leaky-wave antenna is built using a mechanically tunable impedance surface. A horizontally polarized antenna couples energy into leaky transverse electric waves on a tunable textured ground plane. By tuning the resonance frequency of the surface, the band structure is shifted in frequency, which changes the tangential wave vector of the leaky waves for a fixed frequency. This steers the elevation angle of the resulting radiated beam. This steerable leaky-wave antenna can scan over a range of 45/spl deg/ using a mechanical movement of about 1/500 wavelength.
Visualizing implicit queries for information management and retrieval (1999)

In this paper, we describe the use of similarity metrics in a novel visual environment for storing and retrieving favorite web pages. The similarity metrics, called Implicit Queries, are used to automatically highlight stored web pages that are related to the currently selected web page. Two experiments explored how users manage their personal web information space with and without the Implicit Query highlighting and later retrieve their stored web pages. When storing and organizing web pages, users with Implicit Query highlighting generated slightly more categories. Implicit Queries also led to faster web page retrieval time, although the results were not statistically significant.
Advances in gastro retentive drug-delivery systems (2011)

In conclusion, numerous mechanisms like floating, sinking, effervescence, swelling, bioadhesion, magnetic, etc. have been proposed over the years. While most of the proposed systems show promising dissolution profiles and in-vitro retention, only few of them have also shown success in-vivo. Currently, the polymeric swelling monolithic systems are the most prominent marketed forms. The possibility to combine different mechanisms in order to ensure true gastric retention even in the fasted state should be further investigated.
Dendrimer-Based Targeted Delivery of an Apoptotic Sensor in Cancer Cells (2006)

Our previous studies have demonstrated the applicability of poly(amidoamine) (PAMAM) dendrimers as a platform for the targeted delivery of chemotherapeutic drugs both in vitro and in vivo. To monitor the rate and extent of cell-killing caused by the delivered chemotherapeutic drug, we wished to analyze the degree of apoptosis in targeted cells on a real-time basis. As the apoptosis-regulating caspases are activated during the apoptotic process, several caspase-hydrolyzable, fluorescence resonance energy transfer (FRET)-based substrates have been marketed for the detection of apoptosis. However, the applicability of these agents is limited because of their nonspecificity and the consequent high background fluorescence in tissues. Here we show the synthesis, characterization, and in vitro targeting of an engineered PAMAM nanodevice in which folic acid (FA) is conjugated as the targeting molecule and a caspase-specific FRET-based agent (PhiPhiLux G1D2) is conjugated as the apoptosis-detecting agent. This conjugate specifically targets FA-receptor-positive, KB cells. In these cells, the apoptosis-inducing agent staurosporine caused a 5-fold increase in the cellular fluorescence. These results show, for the first time, the potential applicability of a targeted apoptosis-measuring nanodevice, which could be used for simultaneously monitoring the apoptotic potential of a delivered drug.
Distinct Pathways of Gi- and Gq-mediated Mitogen-activated Protein Kinase Activation (1995)

Receptors that couple to the heterotrimeric G proteins, Gi or Gq, can stimulate phosphoinositide (PI) hydrolysis and mitogen-activated protein kinase (MAPK) activation. PI hydrolysis produces inositol 1,4,5-trisphosphate and diacylglycerol, leading to activation of protein kinase C (PKC), which can stimulate increased MAPK activity. However, the relationship between PI hydrolysis and MAPK activation in Gi and Gq signaling has not been clearly defined and is the subject of this study. The effects of several signaling inhibitors are assessed including expression of a peptide derived from the carboxyl terminus of the beta adrenergic receptor kinase 1 (beta ARKct), which specifically blocks signaling mediated by the beta gamma subunits of G proteins (G beta gamma), expression of dominant negative mutants of p21ras (RasN17) and p74raf-1 (N delta Raf), protein-tyrosine kinase (PTK) inhibitors and cellular depletion of PKC. The Gi-coupled alpha 2A adrenergic receptor (AR) stimulates MAPK activation which is blocked by expression of beta ARKct, RasN17, or N delta Raf, or by PTK inhibitors, but unaffected by cellular depletion of PKC. In contrast, MAPK activation stimulated by the Gq-coupled alpha 1B AR or M1 muscarinic cholinergic receptor is unaffected by expression of beta ARKct or RasN17 expression or by PTK inhibitors, but is blocked by expression of N delta Raf or by PKC depletion. These data demonstrate that Gi- and Gq-coupled receptors stimulate MAPK activation via distinct signaling pathways. G beta gamma is responsible for mediating Gi-coupled receptor-stimulated MAPK activation through a mechanism utilizing p21ras and p74raf independent of PKC. In contrast, G alpha mediates Gq-coupled receptor-stimulated MAPK activation using a p21ras-independent mechanism employing PKC and p74raf. To define the role of G beta gamma in Gi-coupled receptor-mediated PI hydrolysis and MAPK activation, direct stimulation with G beta gamma was used. Expression of G beta gamma resulted in MAPK activation that was sensitive to inhibition by expression of beta ARKct, RasN17, or N delta Raf or by PTK inhibitors, but insensitive to PKC depletion. By comparison, G beta gamma-mediated PI hydrolysis was not affected by beta ARKct, RasN17, or N delta Raf expression or by PTK inhibitors. Together, these results demonstrate that G beta gamma mediates MAPK activation and PI hydrolysis via independent signaling pathways.
Neuroinflammation of the nigrostriatal pathway during progressive 6‐OHDA dopamine degeneration in rats monitored by immunohistochemistry and PET imaging (2002)

We investigated the microglial response to progressive dopamine neuron degeneration using in vivo positron emission tomography (PET) imaging and postmortem analyses in a Parkinson's disease (PD) rat model induced by unilateral (right side) intrastriatal administration of 6-hydroxydopamine (6-OHDA). Degeneration of the dopamine system was monitored by PET imaging of presynaptic dopamine transporters using a specific ligand (11)C-CFT (2beta-carbomethoxy-3beta-(4-fluorophenyl) tropane). Binding of (11)C-CFT was markedly reduced in the striatum indicating dopaminergic degeneration. Parallel PET studies of (11)C-PK11195 (1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3 isoquinoline carboxamide) (specific ligand for activated microglia) showed increased binding in the striatum and substantia nigra indicative of a microglial response. Postmortem immunohistochemical analyses were performed with antibodies against CR3 for microglia/macrophage activation. Using a qualitative postmortem index for microglial activation we found an initially focal, then widespread microglial response at striatal and nigral levels at 4 weeks postlesion. These data support the hypothesis that inflammation is a significant component of progressive dopaminergic degeneration that can be monitored by PET imaging.