gebhart/patrepeval huggingface dataset:
The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease (2015)

Prokaryotes are frequently exposed to potentially harmful invasive nucleic acids from phages, plasmids, and transposons. One method of defense is the CRISPR-Cas adaptive immune system. Diverse CRISPR-Cas systems form distinct ribonucleoprotein effector complexes that target and cleave invasive nucleic acids to provide immunity. The Type III-B Cmr effector complex has been found to target the RNA and DNA of the invader in the various bacterial and archaeal organisms where it has been characterized. Interestingly, the gene encoding the Csx1 protein is frequently located in close proximity to the Cmr1-6 genes in many genomes, implicating a role for Csx1 in Cmr function. However, evidence suggests that Csx1 is not a stably associated component of the Cmr effector complex, but is necessary for DNA silencing by the Cmr system in Sulfolobus islandicus. To investigate the function of the Csx1 protein, we characterized the activity of recombinant Pyrococcus furiosus Csx1 against various nucleic acid substrates. We show that Csx1 is a metal-independent, endoribonuclease that acts selectively on single-stranded RNA and cleaves specifically after adenosines. The RNA cleavage activity of Csx1 is dependent upon a conserved HEPN motif located within the C-terminal domain of the protein. This motif is also key for activity in other known ribonucleases. Collectively, the findings indicate that invader silencing by Type III-B CRISPR-Cas systems relies both on RNA and DNA nuclease activities from the Cmr effector complex as well as on the affiliated, trans-acting Csx1 endoribonuclease.
Retroviral membrane display of apoptotic effector molecules (2000)

Retroviruses have been widely used in gene transmission studies. In this paper, we show that nonviral apoptotic proteins can be displayed on viral membrane surfaces and that the displayed proteins can execute their normal effector functions. We introduced the genes encoding the apoptosis effector proteins, human CD95 ligand (hFasL) or human tumor necrosis factor-related apoptosis-inducing ligand (hTRAIL), into a cell line that packages Moloney murine leukemia virus vectors. Retrovirus preparations from these lines killed target cells efficiently, and target killing was prevented by Fas-Ig fusion protein or soluble TRAIL receptor (sDR5), respectively. We show that the virus preparation exhibiting Fas-specific cytotoxicity has the same density as a retrovirus, contains full-length FasL protein, and can be depleted of infectivity by immunoadsorption with anti-FasL antibody. This novel property of retroviruses-the display of functional effector proteins-may allow the custom design of reagents whose normal function requires their being embedded in a membrane.
Diagnosis and treatment of chronic lower extremity ischemia (1998)

Chronic lower extremity ischemia is due to progressive atherosclerosis of the aorto-iliac and/or infrainguinal arteries. This disease process is of great importance as millions of patients are affected by lower extremity arterial occlusive disease. Most of these patients are asymptomatic but a growing number of them are symptomatic, with complaints ranging from mild claudication to gangrene. The increasing number of patients affected by lower extremity atherosclerosis is, in part, due to the 'graying' of the general population and to the medical improvements of the past three decades that have allowed patients with generalized atherosclerosis to survive longer. Fortunately, the diagnosis and management of peripheral arterial occlusive disease has also significantly progressed leading to improved graft patency, limb salvage rates, and quality of life for patients.
Transposon mutagenesis as a tool to study the role of hemolysin in the virulence of Listeria monocytogenes (1986)

The role of hemolysin in the virulence of Listeria monocytogenes was studied by using transposon mutagenesis. The 26-kilobase conjugative transposon Tn1545, originally found in Streptococcus pneumoniae, was transferred to a hemolytic virulent strain of L. monocytogenes. The frequency of transfer was estimated to be about 10(-8) per recipient. This allowed us to isolate a nonhemolytic mutant which most likely harbors a single copy of Tn1545. Loss of hemolysin production was associated with loss of virulence. The 50% lethal dose of the mutant was assessed to about 10(9.6) bacteria per mouse after intravenous challenge. Nonhemolytic bacteria were unable to grow in host tissues and were rapidly eliminated from the spleen and liver of infected mice. Virulence was restored in hemolysin-producing revertant obtained by spontaneous loss of transposon Tn1545. These results strongly suggest that hemolysin is a major virulence factor implicated in the intracellular growth of L. monocytogenes.
Complex regulation of somatic hypermutation by cis-acting sequences in the endogenous IgH gene in hybridoma cells (2005)

To create high-affinity antibodies, B cells target a high rate of somatic hypermutation (SHM) to the Ig variable-region genes that encode the antigen-binding site. This mutational process requires transcription and is triggered by activation-induced cytidine deaminase (AID), which converts deoxycytidine to deoxyuridine. Mistargeting of AID to non-Ig genes is thought to result in the malignant transformation of B cells, but the mechanism responsible for targeting SHM to certain DNA regions and not to others is largely unknown. Cis-acting elements have been proposed to play a role in directing the hypermutation machinery, but the motifs required for targeting SHM have been difficult to identify because many of the candidate elements, such as promoters or enhancers, are also required for transcription of Ig genes. Here we describe a system in cultured hybridoma cells in which transcription of the endogenous heavy-chain Ig gene continues in the absence of the core intronic enhancer (Emu) and its flanking matrix attachment regions (MARs). When AID is expressed in these cells, SHM occurred at the WT frequency even when Emu and the MARs were absent together. Interestingly, SHM occurred at less than the WT frequency when Emu or the MARs were individually absent. Our results suggest that these intronic regulatory elements can exert a complex influence on SHM that is separable from their role in regulating transcription.
Ubiquitous and Endoplasmic Reticulum–Located Lysophosphatidyl Acyltransferase, LPAT2, Is Essential for Female but Not Male Gametophyte Development in Arabidopsis (2005)

Lysophosphatidyl acyltransferase (LPAT) is a pivotal enzyme controlling the metabolic flow of lysophosphatidic acid into different phosphatidic acids in diverse tissues. We examined putative LPAT genes in Arabidopsis thaliana and characterized two related genes that encode the cytoplasmic LPAT. LPAT2 is the lone gene that encodes the ubiquitous and endoplasmic reticulum (ER)-located LPAT. It could functionally complement a bacterial mutant with defective LPAT. LPAT2 and 3 synthesized in recombinant bacteria and yeast possessed in vitro enzyme activity higher on 18:1-CoA than on 16:0-CoA. LPAT2 was expressed ubiquitously in diverse tissues as revealed by RT-PCR, profiling with massively parallel signature sequencing, and promoter-driven beta-glucuronidase gene expression. LPAT2 was colocalized with calreticulin in the ER by immunofluorescence microscopy and subcellular fractionation. LPAT3 was expressed predominately but more actively than LPAT2 in pollen. A null allele (lpat2) having a T-DNA inserted into LPAT2 was identified. The heterozygous mutant (LPAT2/lpat2) had minimal altered vegetative phenotype but produced shorter siliques that contained normal seeds and remnants of aborted ovules in a 1:1 ratio. Results from selfing and crossing it with the wild type revealed that lpat2 caused lethality in the female gametophyte but not the male gametophyte, which had the redundant LPAT3. LPAT2-cDNA driven by an LPAT2 promoter functionally complemented lpat2 in transformed heterozygous mutants to produce the lpat2/lpat2 genotype. LPAT3-cDNA driven by the LPAT2 promoter could rescue the lpat2 female gametophytes to allow fertilization to occur but not to full embryo maturation. Two other related genes, putative LPAT4 and 5, were expressed ubiquitously albeit at low levels in diverse organs. When they were expressed in bacteria or yeast, the microbial extract did not contain LPAT activity higher than the endogenous LPAT activity. Whether LPAT4 and 5 encode LPATs remains to be elucidated.
Nuclear localization of the p120 ctn Armadillo-like catenin is counteracted by a nuclear export signal and by E-cadherin expression (1999)

The Armadillo protein p120(ctn) associates with the cytoplasmic domain of cadherins and accumulates at cell-cell junctions. Particular Armadillo proteins such as beta-catenin and plakophilins show a partly nuclear location, suggesting gene-regulatory activities. For different human E-cadherin-negative carcinoma cancer cell lines we found expression of endogenous p120(ctn) in the nucleus. Expression of E-cadherin directed p120(ctn) out of the nucleus. Previously, we reported that the human p120(ctn) gene might encode up to 32 protein isoforms as products of alternative splicing. Overexpression of p120(ctn) isoforms B in various cell lines resulted in cytoplasmic immunopositivity but never in nuclear staining. In contrast, upon expression of p120(ctn) cDNAs lacking exon B, the isoforms were detectable within both nuclei and cytoplasm. A putative nuclear export signal (NES) with a characteristic leucine-rich motif is encoded by exon B. This sequence element was shown to be required for nuclear export and to function autonomously when fused to a carrier protein and microinjected into cell nuclei. Moreover, the NES function of endogenously or exogenously expressed p120(ctn) isoforms B was sensitive to the nuclear export inhibitor leptomycin B. Expression of exogenous E-cadherin down-regulated nuclear p120(ctn) whereas activation of protein kinase C increased the level of nuclear p120(ctn). These results reveal molecular mechanisms controlling the subcellular distribution of p120(ctn).
THE SCHMIDT REACTION WITH 2,2,6-TRIMETHYL- AND 1,3-DIMETHYL-4-PIPERIDONES1 (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE SCHMIDT REACTION WITH 2,2,6-TRIMETHYL- AND 1,3-DIMETHYL-4-PIPERIDONES1S. C. DICKERMAN and E. J. MORICONICite this: J. Org. Chem. 1955, 20, 2, 206–209Publication Date (Print):February 1, 1955Publication History Published online1 May 2002Published inissue 1 February 1955https://pubs.acs.org/doi/10.1021/jo01120a008https://doi.org/10.1021/jo01120a008research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations6LEARN 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
Brightly Luminescent and Color-Tunable Colloidal CH3NH3PbX3 (X = Br, I, Cl) Quantum Dots: Potential Alternatives for Display Technology (2015)

Organometal halide perovskites are inexpensive materials with desirable characteristics of color-tunable and narrow-band emissions for lighting and display technology, but they suffer from low photoluminescence quantum yields at low excitation fluencies. Here we developed a ligand-assisted reprecipitation strategy to fabricate brightly luminescent and color-tunable colloidal CH3NH3PbX3 (X = Br, I, Cl) quantum dots with absolute quantum yield up to 70% at room temperature and low excitation fluencies. To illustrate the photoluminescence enhancements in these quantum dots, we conducted comprehensive composition and surface characterizations and determined the time- and temperature-dependent photoluminescence spectra. Comparisons between small-sized CH3NH3PbBr3 quantum dots (average diameter 3.3 nm) and corresponding micrometer-sized bulk particles (2-8 μm) suggest that the intense increased photoluminescence quantum yield originates from the increase of exciton binding energy due to size reduction as well as proper chemical passivations of the Br-rich surface. We further demonstrated wide-color gamut white-light-emitting diodes using green emissive CH3NH3PbBr3 quantum dots and red emissive K2SiF6:Mn(4+) as color converters, providing enhanced color quality for display technology. Moreover, colloidal CH3NH3PbX3 quantum dots are expected to exhibit interesting nanoscale excitonic properties and also have other potential applications in lasers, electroluminescence devices, and optical sensors.
Tyrosine and its catabolites: from disease to cancer. (1996)

Hereditary tyrosinemia type I (HT I, McKusick 276,700) is a metabolic disease with a pattern of autosomal recessive inheritance. The disease is caused by a deficiency of the enzyme involved in the last step in the degradation of the amino acid tyrosine, fumarylacetoacetate hydrolase (FAH). The result of this block is the accumulation of catabolites some of which have been proposed to be highly toxic due to their alkylating potential. In humans, hereditary tyrosinemia is often associated with the development of hepatocellular carcinoma in young patients. The reasons for the high incidence of hepatocellular carcinoma are unknown but it has been suggested that it may be caused by accumulated metabolites such as fumarylacetoacetate (FAA) and maleylacetoacetate (MAA). The various mutational defects in the FAH gene are reviewed. The use of two mouse models of this disease to study the molecular basis of the pathologies associated with HT I are discussed. Finally, some preliminary data on the mutagenic potential of FAA and MAA in a gene reversal assay are presented.
Enhanced Triboelectric Nanogenerators and Triboelectric Nanosensor Using Chemically Modified TiO2 Nanomaterials (2013)

Mechanical energy harvesting based on triboelectric effect has been proven to be a simple, cost-effective, and robust method for electricity generation. In this study, we developed a rationally designed triboelectric nanogenerator (TENG) by utilizing the contact electrification between a polytetrafluoroethylene (PTFE) thin film and a layer of TiO2 nanomaterial (nanowire and nanosheet) array. The as-developed TENG was systematically studied and demonstrated as a self-powered nanosensor toward catechin detection. The high sensitivity (detection limit of 5 μM) and selectivity are achieved through a strong interaction between Ti atoms of TiO2 nanomaterial and enediol group of catechin. The output voltage and current density were increased by a factor of 5.0 and 2.9, respectively, when adsorbed with catechin of a saturated concentration, because of the charge transfer from catechin to TiO2. This study demonstrates the possibility of improving the electrical output of TENG through chemical modification.
Tetramine cupruretic agents: a comparison in dogs. (1987)

The cupruretic effects of 2 tetramine (N,N'-bis (2-aminoethyl) alkane diamine) chelators were examined in healthy dogs fed a commercial dog food containing 12.2 micrograms of copper/g of dry diet. Two groups of 3 dogs each were given either 300 mg of 2,2,2-tetramine tetrahydrochloride or 2,3,2-tetramine tetrahydrochloride for 23 consecutive days. Serum and 24-hour urine samples obtained before drug administration and during therapy were analyzed for copper, zinc, and iron concentrations. Both tetramines produced a significant cupruresis without significant changes in serum copper or in serum or urine zinc and iron concentrations. The 2,3,2-tetramine tetrahydrochloride produced a 4- to 9-fold greater cupruresis than did 2,2,2-tetramine tetrahydrochloride and resulted in a daily loss of more than 2 mg of copper in the urine. The dogs had no laboratory or clinical evidence of toxic side effects to either cupruretic agent during the treatment period. The results of the present study indicate that 2,3,2-tetramine should be an effective decoppering drug for use in dogs.
Hydrocarbon Control for Los Angeles by Reducing Gasoline Volatility (1969)

&lt;div class="htmlview paragraph"&gt;Evaporative emissions from automobiles can be reduced by lowering gasoline volatility. A 3 psi reduction in Reid vapor pressure will reduce evaporative losses by about 50%. A test program was conducted to determine if new and used cars presently on the road in the Los Angeles basin could operate satisfactorily on lower volatility gasoline. The results of this program indicated that gasoline with reduced volatility gave acceptable driveability and could be used to provide a significant reduction in hydrocarbon emission.&lt;/div&gt;
Diagnostic Exercise: Myocarditis Due to Histophilus somni in Feedlot and Backgrounded Cattle (2009)

A backgrounding operation for calves in Wyoming identified a disease syndrome presenting as lethargy, fever, and death between November and January each year. An unfixed heart was submitted for examination, along with samples of lung. There was focal red discoloration in papillary muscle of the left ventricular myocardium. Histologically, the lesion corresponded to acute necrotizing myocarditis with myriad intravascular and intralesional gram-negative coccobacilli. Histophilus somni was detected by bacterial culture and immunohistochemistry. Focal myocarditis due to H. somni occurs in fall-placed cattle in western provinces and states of North America, and it can be an appreciable source of death loss. Gross lesions are readily detected in affected hearts. The presence of such changes in papillary muscles of left ventricular myocardium in feedlot or backgrounded cattle should prompt a differential diagnosis of H. somni myocarditis.
Cloning of Mycobacterium bovis BCG DNA and expression of antigens in Escherichia coli (1985)

A gene bank of Mycobacterium bovis BCG DNA in Escherichia coli was constructed by cloning Sau3A-cleaved mycobacterium DNA fragments into the lambda vector EMBL3. The expression of mycobacterial antigens was analyzed by Western blotting with hyperimmune rabbit sera. Among 770 clones tested, several were found that produced various mycobacterial antigens in low amounts, with concentrations generally close to the detection limit. One particular clone was chosen for further investigation. This clone produced a 64-kilodalton (kDa) antigen. By placing the lambda promoter PL in front of the structural gene of this antigen, an overproducing E. coli strain was obtained. Rocket-line immunoelectrophoresis experiments showed that antigens cross-reacting with the 64-kDa protein are present in a wide variety of mycobacteria and also in so-called purified protein derivatives which are routinely used for skin tests. Preliminary experiments indicate the presence of antibodies against the 64-kDa antigen in sera from tuberculosis patients.
Soccer Jersey Number Recognition Using Convolutional Neural Networks (2015)

In this paper, a deep convolutional neural network based approach to the problem of automatically recognizing jersey numbers from soccer videos is presented. Two different jersey number vector encoding schemes are presented and compared to each other. The first treats every number as a separate class, while the second one treats each digit as a class. Additionally, the semi-automatic process for the annotation of a jersey number dataset consisting of 8281 jersey numbers is described. The best recognition rate of 0.83 was achieved by the proposed approach with data augmentation and without using dropout, compared to 0.4 for a more traditional histogram of oriented gradients (HOG) and support vector machine (SVM) based approach.
Comparison of a Two-Stage and Three-Stage Interim-Analysis Procedure (1992)

A statistical model for combining p values from multiple tests of significance is used to define rejection and acceptance regions for two-stage and three-stage sampling plans. Type I error rates, power, frequencies of early termination decisions, and expected sample sizes are compared. Both the two-stage and three-stage procedures provide appropriate protection against Type I errors. The two-stage sampling plan with its single interim analysis entails minimal loss in power and provides substantial reduction in expected sample size as compared with a conventional single end-of-study test of significance for which power is in the adequate range. The three-stage sampling plan with its two interim analyses introduces somewhat greater reduction in power, but it compensates with greater reduction in expected sample size. Either interim-analysis strategy is more efficient than a single end-of-study analysis in terms of power per unit of sample size.
SPARKy 3: Design of an active robotic ankle prosthesis with two actuated degrees of freedom using regenerative kinetics (2008)

The goal of modern prosthetics is to replicate the function of the replaced limb or organ in the most capable and discreet fashion possible. However, even the most advanced, commercial, transtibial prostheses available today only passively adjust the position of the ankle during the swing phase of gait and return a portion of the userpsilas own gravitational input. To greatly improve the quality of life of a transtibial amputee, new technologies and approaches must be used to create a cutting-edge robotic ankle prosthesis which can perform on par with, if not outperform, the equivalent able-bodied human ankle. Initial attempts by us and others have had great success in providing the natural gait power and motion through all ranges of walking speeds. A new design is presented which governs both the coronal and sagittal angles and moments of the ankle joint to potentially provide unprecedented levels of athleticism and agility among transtibial amputees.
Clonal analysis of hematopoietic stem-cell differentiation in vivo. (1991)

Previous work has shown that the 0.02-0.05% of adult mouse bone marrow cells that bear the cell surface phenotype Thy-1loLin-Sca-1+ are enriched 1000- to 2000-fold for hematopoietic stem-cell activity in a variety of assays. When 50-100 cells of this phenotype are injected into an irradiated animal, they can permanently repopulate the entire hematopoietic system. In the present study, limiting-dilution and single-cell experiments were used to address the question of how individual Thy-1loLin-Sca-1+ stem cells contribute to repopulation of the hematopoietic system following irradiation. We calculated that 1 of 13 Thy-1loLin-Sca-1+ cells formed a clone comprising greater than 1% of peripheral white blood cells 3-7 weeks after injection. The majority of these clones included both lymphoid and myeloid lineages. Approximately one-third of the clones continued to produce new blood cells for 9 weeks or more, but the remainder disappeared earlier, including many that were multilineage. Thus, while the majority of Thy-1loLin-Sca-1+ bone marrow cells whose progeny are detected in the in vivo repopulation assay are pluripotential, only a subset undergo long-term self-renewal in vivo. Repopulation appears to be oligoclonal when limiting numbers of Thy-1loLin-Sca-1+ cells are injected. However, the number of clones contributing to hematopoiesis increases in proportion to the number of Thy-1loLin-Sca-1+ cells injected, bringing into question the notion that steady-state hematopoiesis in normal individuals is oligoclonal.