gebhart/patrepeval huggingface dataset:
Gene Disruption of Plasmodium falciparum p52 Results in Attenuation of Malaria Liver Stage Development in Cultured Primary Human Hepatocytes (2008)

Difficulties with inducing sterile and long lasting protective immunity against malaria with subunit vaccines has renewed interest in vaccinations with attenuated Plasmodium parasites. Immunizations with sporozoites that are attenuated by radiation (RAS) can induce strong protective immunity both in humans and rodent models of malaria. Recently, in rodent parasites it has been shown that through the deletion of a single gene, sporozoites can also become attenuated in liver stage development and, importantly, immunization with these sporozoites results in immune responses identical to RAS. The promise of vaccination using these genetically attenuated sporozoites (GAS) depends on translating the results in rodent malaria models to human malaria. In this study, we perform the first essential step in this transition by disrupting, p52, in P. falciparum an ortholog of the rodent parasite gene, p36p, which we had previously shown can confer long lasting protective immunity in mice. These P. falciparum P52 deficient sporozoites demonstrate gliding motility, cell traversal and an invasion rate into primary human hepatocytes in vitro that is comparable to wild type sporozoites. However, inside the host hepatocyte development is arrested very soon after invasion. This study reveals, for the first time, that disrupting the equivalent gene in both P. falciparum and rodent malaria Plasmodium species generates parasites that become similarly arrested during liver stage development and these results pave the way for further development of GAS for human use.
Mouse model of Sanfilippo syndrome type B: relation of phenotypic features to background strain. (2003)

Sanfilippo syndrome type B or mucopolysaccharidosis type III B (MPS IIIB) is a lysosomal storage disorder that is inherited in autosomal recessive manner. It is characterized by systemic heparan sulfate accumulation in lysosomes due to deficiency of the enzyme alpha-N-acetylglucosaminidase (Naglu). Devastating clinical abnormalities with severe central nervous system involvement and somatic disease lead to premature death. A mouse model of Sanfilippo syndrome type B was created by targeted disruption of the gene encoding Naglu, providing a powerful tool for understanding pathogenesis and developing novel therapeutic strategies. However, the JAX GEMM Strain B6.129S6-Naglutm1Efn mouse, although showing biochemical similarities to humans with Sanfilippo syndrome, exhibits aging and behavioral differences. We observed idiosyncrasies, such as skeletal dysmorphism, hydrocephalus, ocular abnormalities, organomegaly, growth retardation, and anomalies of the integument, in our breeding colony of Naglu mutant mice and determined that several of them were at least partially related to the background strain C57BL/6. These background strain abnormalities, therefore, potentially mimic or overlap signs of the induced syndrome in our mice. Our observations may prove useful in studies of Naglu mutant mice. The necessity for distinguishing background anomalies from signs of the modeled disease is apparent.
Composition and antioxidant activity ofSenecio nudicaulisWall. ex DC. (Asteraceae): a medicinal plant growing wild in Himachal Pradesh, India (2014)

The composition of essential oil isolated from Senecio nudicaulis Wall. ex DC. growing wild in Himachal Pradesh, India, was analysed, for the first time, by capillary gas chromatography (GC) and GC-mass spectrometry. A total of 30 components representing 95.3% of the total oil were identified. The essential oil was characterised by a high content of oxygenated sesquiterpenes (54.97%) with caryophyllene oxide (24.99%) as the major component. Other significant constituents were humulene epoxide-II (21.25%), α-humulene (18.75%), β-caryophyllene (9.67%), epi-α-cadinol (2.90%), epi-α-muurolol (2.03%), β-cedrene (1.76%), longiborneol (1.76%), 1-tridecene (1.16%) and citronellol (1.13%). The oil was screened for antioxidant activity using DPPH, ABTS and nitric oxide-scavenging assay. The oil was found to exhibit significant antioxidant activity by scavenging DPPH, ABTS and nitric oxide radicals with IC50 values of 10.61 ± 0.14 μg mL(- 1), 11.85 ± 0.28 μg mL(- 1) and 11.29 ± 0.42 μg mL(- 1), respectively.
Measurement of Distribution of Acoustic Radiation Force Perpendicular to Sound Beam Axis (1999)

To clarify the range of force acting on a particle in the direction perpendicular to the sound beam axis of an ultrasonic standing wave for particle manipulation, the radiation force on a polystyrene sphere of submillimeter size was measured through observation of its movement in a 1.75 MHz ultrasonic standing wave. The radiation force was estimated at some points by balancing with the force from viscous drag proportional to the measured velocity of a particle and the gravitational force, and its distribution was determined. The measured distribution of the radiation force agreed qualitatively with the theoretical distribution derived from Nyborg's formula. The influence of gravitational force on a stable position was also investigated. It was shown that the shift from the stable position is marked for particles with large radius. This effect should be considered in particle manipulation.
TNF-α and IL-1β Suppress N-Cadherin Expression in MC3T3-E1 Cells (1999)

Excessive production of tumor necrosis factor (TNF) and interleukin-1 (IL-1) secondary to estrogen deficiency have been implicated as the cause of osteoporosis in postmenopausal woman. These cytokines appear to stimulate osteoclast precursor proliferation and activate mature osteoclast formation directly and possibly indirectly via osteoblasts. To investigate the other possible roles that these cytokines may play in stimulating the bone resorption process, we examined the effect of TNF-alpha and IL-1beta on cell-cell adhesion molecules, cadherins, in osteoblastic MC3T3-E1 cells. In this study, we investigated cadherin expression and the effect of TNF-alpha, IL-1beta, and parathyroid hormone (PTH) on the expression of cadherins in MC3T3-E1 cells. Confluent cultures of MC3T3-E1 cells were challenged with recombinant human TNF-alpha (1-100 U/ml), recombinant human IL-1beta (1-100 ng/ml) and human PTH(1-34) (1-100 ng/ml), respectively. The results show that MC3T3-E1 cells express functional cadherin molecules, N-cadherin and OB-cadherin. TNF-alpha (10-100 U/ml) and IL-1beta (10-100 ng/ml) suppressed N-cadherin without changing OB-cadherin expression, while PTH (1-100 ng/ml) had no effect on cadherin expression. These results raise the possibility that TNF-alpha and IL-1beta may compromise the cell-cell adhesion of osteoblasts which cover the bone surface. The ensuing compromised cell-cell adhesion of osteoblasts may in turn facilitate the direct adhesion of osteoclasts on the calcified bone matrix surface. These results implicate an indirect role for osteoblasts in the promotion of bone resorption by TNF-alpha and IL-1beta.
Direct blind deconvolution of multiuser-multichannel systems (2003)

This paper addresses the blind deconvolution of multiuser-multichannel systems. First, we find a weaker condition on source signals than the so-called i.i.d. condition so that blind deconvolution is possible. The condition states that the source signals are white and spatially fourth-order uncorrelated. Then, under this condition, we provide a necessary and sufficient condition for blind deconvolution of multiuser-multichannel systems. The result states that blind deconvolution is achieved if and only if the composite output signals are white and spatially fourth-order uncorrelated. Finally, based on this result, we propose two maximization criteria for blind deconvolution of multiuser-multichannel systems. These criteria are simple enough to be implemented by adaptive algorithms.
Locally Optimized Product Quantization for Approximate Nearest Neighbor Search (2014)

We present a simple vector quantizer that combines low distortion with fast search and apply it to approximate nearest neighbor (ANN) search in high dimensional spaces. Leveraging the very same data structure that is used to provide non-exhaustive search, i.e., inverted lists or a multi-index, the idea is to locally optimize an individual product quantizer (PQ) per cell and use it to encode residuals. Local optimization is over rotation and space decomposition, interestingly, we apply a parametric solution that assumes a normal distribution and is extremely fast to train. With a reasonable space and time overhead that is constant in the data size, we set a new state-of-the-art on several public datasets, including a billion-scale one.
Hydrated autoclave pretreatment enhances tau immunoreactivity in formalin-fixed normal and Alzheimer's disease brain tissues. (1991)

We developed a new immunohistochemical method by which normal tau antigenicity can be visualized in paraffin sections of formalin-fixed brain tissue. This method consists of autoclave pretreatment of sections immersed into distilled water (hydrated autoclaving) before incubation with anti-tau antibodies. In normal human brain, immunoreactive tau was detected in neuronal cell bodies and dendrites, axon fibers, astroglia, oligodendroglia and gray matter neuropil. In previous studies on normal tau distribution, different optimized fixations that effectively preserve tau antigenicity were used but none of these revealed all of these compartments together. Our method is therefore considered to be more sensitive for detecting normal tau immunoreactivity. In addition, hydrated autoclaving had an enhancing effect on the abnormally phosphorylated (modified) tau immunoreactivity in formalin-fixed brains. In hydrated autoclaving of sections from patients with Alzheimer's disease, neuropil threads, senile plaques, extracellular and intracellular tangles were enhanced in quantity and in staining intensity. Therefore, modified tau appears to accumulate more densely than expected from conventional immunohistochemistry. Immunoblot analysis showed that normal or modified tau immunoreactivity was totally or partially eliminated on formalin treatment and could be revisualized by hydrated autoclaving, an event presumably related to recovering of formalin-masked tau antigens through denaturation by hydrated autoclaving.
<i>C-myc</i> and <i>c-fos</i> in Human Osteosarcoma: Prognostic Value of mRNA and Protein Expression (1998)

The c-myc and c-fos proto-oncogenes have several putative functions, including regulation of cell growth. In many neoplasms c-myc overexpression has been linked to poor prognosis. In order to study the role of c-myc and c-fos expression on the tumorigenesis, and the metastatic spread of osteosarcoma, frozen and paraffin-embedded tissue 38 primary osteosarcoma and 10 lung metastases were analyzed. The mRNA analysis was performed by quantitative reverse transcription-polymerase chain reaction and in situ hybridization. The protein expression was studied by Western blot analysis and immunohistochemistry. C-myc and c-fos were found overexpressed in a high percentage of the relapsed tumors and of the metastases, and overexpression of both oncogenes in the same tumor was strongly correlated to the development of metastases (p < 0.05), as 6 of the 7 primary tumors overexpressing both the oncogenes gave metastases. In conclusion, both c-myc and c-fos are involved in the growth and spread of osteosarcoma and a synchronous overexpression of both oncogenes is highly significant for a metastatic potential of a primary tumor.
Understanding and using the Implicit Association Test: III. Meta-analysis of predictive validity. (2009)

This review of 122 research reports (184 independent samples, 14,900 subjects) found average r = .274 for prediction of behavioral, judgment, and physiological measures by Implicit Association Test (IAT) measures. Parallel explicit (i.e., self-report) measures, available in 156 of these samples (13,068 subjects), also predicted effectively (average r = .361), but with much greater variability of effect size. Predictive validity of self-report was impaired for socially sensitive topics, for which impression management may distort self-report responses. For 32 samples with criterion measures involving Black-White interracial behavior, predictive validity of IAT measures significantly exceeded that of self-report measures. Both IAT and self-report measures displayed incremental validity, with each measure predicting criterion variance beyond that predicted by the other. The more highly IAT and self-report measures were intercorrelated, the greater was the predictive validity of each.
BAC Resources for the Rat Genome Project (2004)

Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male Brown Norway (BN/SsNHsd) rat as a DNA source long before plans for rat genome sequencing had been launched. The second library was prepared from a highly inbred female (BN/SsNHsd/MCW) rat in support of the rat genome sequencing project. The use of an inbred rat strain is essential to avoid problems with genome assembly resulting from the difficulty of distinguishing haplotype variation from variation among duplicons. We have demonstrated the suitability of the library by using a detailed quality assessment of large insert sizes, narrow size distribution, consistent redundancy for many markers, and long-range continuity of BAC contig maps. The widespread use of the two libraries as an integral part of the rat genome project has led to the database annotations for many clones, providing rat researchers with a rich resource of BAC clones that can be screened in silico for genes of interest.
Role of antibody in primary and recurrent herpes simplex virus infection (1985)

When herpes simplex virus was inoculated into the flank of a BALB/c mouse by scarification, the local replication of virus was followed by the establishment of an acute ganglionic infection. The subsequent centrifugal spread of this virus along nerves to the skin of the whole dermatome led to the development of a bandlike "zosteriform" rash. This represents a highly reproducible system in which virus travels through the nervous system synchronously in large numbers of animals. The transection of peripheral nerves at various times after infection showed that the virus had completed the round trip 60 h after inoculation into the upper flank and was detectable as infectious virus by 74 h postinfection. After the administration of virus, neutralizing but not nonneutralizing antibodies prevented the development of the zosteriform rash. The target epitopes of the protective antibodies were not confined to a single glycoprotein. Neutralizing antibody was effective even when given up to 60 h postinfection and was protective even when administered after sensory neurotomy at this time. Antibody was therefore able to prevent clinically and virologically detectable infection of the skin, presumably by acting peripherally on virus emerging from nerve endings. A quantitative estimate of the action of one of the neutralizing monoclonal antibody preparations, AP7, showed that high titers (several times higher than those normally found in immune mice) were needed to prevent this type of infection. These results are discussed in relation to antibody prophylaxis.
Single photon interference in 10 km long optical fibre interferometer (1993)

Single-photon interference fringes with greater than 90% visibility were measured using a 10 km long optical fibre interferometer. The experiment employed a pulsed semiconductor laser source operating at a wavelength of 1.3 μm and a novel single-photon counting scheme using high-speed germanium avalanche photodiodes. Interferometers of this type could form the basis of future quantum cryptography systems.
Use of Major Histocompatibility Complex Class I/Peptide/β2M Tetramers To Quantitate CD8+Cytotoxic T Lymphocytes Specific for Dominant and Nondominant Viral Epitopes in Simian-Human Immunodeficiency Virus-Infected Rhesus Monkeys (1999)

To evaluate the impact of the diversity of antigen recognition by T lymphocytes on disease pathogenesis, we must be able to identify and analyze simultaneously cytotoxic T-lymphocyte (CTL) responses specific for multiple viral epitopes. Many of the studies of the role of CD8(+) CTLs in AIDS pathogenesis have been done with simian immunodeficiency virus (SIV)- and simian-human immunodeficiency virus (SHIV)-infected rhesus monkeys. These studies have frequently made use of the well-defined SIV Gag CTL epitope p11C,C-M presented to CTL by the HLA-A homologue molecule Mamu-A*01. In the present study we identified and fine mapped two novel Mamu-A*01-restricted CTL epitopes: the SIVmac Pol-derived epitope p68A (STPPLVRLV) and the human immunodeficiency virus type 1 (HIV-1) Env-derived p41A epitope (YAPPISGQI). The frequency of CD8(+) CTLs specific for the p11C,C-M, p68A, and p41A epitopes was quantitated in the same animals with a panel of tetrameric Mamu-A*01/peptide/beta2m complexes. All SHIV-infected Mamu-A*01(+) rhesus monkeys tested had a high frequency of SIVmac Gag-specific CTLs to the p11C,C-M epitope. In contrast, only a fraction of the monkeys tested had detectable CTLs specific for the SIVmac Pol p68A and HIV-1 Env p41A epitopes, and these responses were detected at very low frequencies. Thus, the p11C,C-M-specific CD8(+) CTL response is dominant and the p41A- and p68A-specific CD8(+) CTL responses are nondominant. These results indicate that CD8(+) CTL responses to dominant CTL epitopes can be readily quantitated with the tetramer technology; however, CD8(+) CTL responses to nondominant epitopes, due to the low frequency of these epitope-specific cells, may be difficult to detect and quantitate by this approach.
Multidimensional quantum well laser and temperature dependence of its threshold current (1982)

A new type of semiconductor laser is studied, in which injected carriers in the active region are quantum mechanically confined in two or three dimensions (2D or 3D). Effects of such confinements on the lasing characteristics are analyzed. Most important, the threshold current of such laser is predicted to be far less temperature sensitive than that of conventional lasers, reflecting the reduced dimensionality of electronic state. In the case of 3D-QW laser, the temperature dependence is virtually eliminated. An experiment on 2D quantum well lasers is performed by placing a conventional laser in a strong magnetic field (30 T) and has demonstrated the predicted increase of T0 value from 144 to 313 °C.
A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing (2012)

Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC.
Proangiogenic Factor PlGF Programs CD11b+ Myelomonocytes in Breast Cancer during Differentiation of Their Hematopoietic Progenitors (2011)

Tumor-mobilized bone marrow-derived CD11b(+) myeloid cells promote tumor angiogenesis, but how and when these cells acquire proangiogenic properties is not fully elucidated. Here, we show that CD11b(+) myelomonocytic cells develop proangiogenic properties during their differentiation from CD34(+) hematopoietic progenitors and that placenta growth factor (PlGF) is critical in promoting this education. Cultures of human CD34(+) progenitors supplemented with conditioned medium from breast cancer cell lines or PlGF, but not from nontumorigenic breast epithelial lines, generate CD11b(+) cells capable of inducing endothelial cell sprouting in vitro and angiogenesis in vivo. An anti-Flt-1 mAb or soluble Flt-1 abolished the generation of proangiogenic activity during differentiation from progenitor cells. Moreover, inhibition of metalloproteinase activity, but not VEGF, during the endothelial sprouting assay blocked sprouting induced by these proangiogenic CD11b(+) myelomonocytes. In a mouse model of breast cancer, circulating CD11b(+) cells were proangiogenic in the sprouting assays. Silencing of PlGF in tumor cells prevented the generation of proangiogenic activity in circulating CD11b(+) cells, inhibited tumor blood flow, and slowed tumor growth. Peripheral blood of breast cancer patients at diagnosis, but not of healthy individuals, contained elevated levels of PlGF and circulating proangiogenic CD11b(+) myelomonocytes. Taken together, our results show that cancer cells can program proangiogenic activity in CD11b(+) myelomonocytes during differentiation of their progenitor cells in a PlGF-dependent manner. These findings impact breast cancer biology, detection, and treatment.
The structure of aridicin A. An integrated approach employing 2D NMR, energy minimization and distance constraints (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe structure of aridicin A. An integrated approach employing 2D NMR, energy minimization and distance constraintsPeter W. Jeffs, Luciano. Muller, Charles. DeBrosse, Sarah L. Heald, and Richard. FisherCite this: J. Am. Chem. Soc. 1986, 108, 11, 3063–3075Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/ja00271a042https://doi.org/10.1021/ja00271a042research-articleACS PublicationsRequest reuse permissionsArticle Views155Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts