gebhart/patrepeval huggingface dataset:
Programmed ribosomal frameshifting generates theEscherichia coliDNA polymerase III γ subunit from within the τ subunit reading frame (1990)

The Escherichia coli dnaX gene encodes both the tau and gamma subunits of DNA polymerase III holoenzyme in one reading frame. The 71.1 kDa tau and the shorter gamma share N-terminal sequences. Mutagenesis of a potential ribosomal frameshift signal located at codons 428-430 without changing the amino acid sequence of the tau product, eliminated detectable synthesis of the gamma subunit, suggesting that the reading frame is shifted at that sequence and gamma is terminated by a nonsense codon located in the -1 frame 3 nucleotides downstream of the signal. This seems to be the first known case of a frameshift which is used, along with the termination codon in the -1 frame, to terminate a peptide within a reading frame. [Mutagenesis of a dibasic peptide (lys-lys) at codons 498-499, the site at which a tau'-'LacZ fusion protein was cleaved in vitro (1) had no effect on gamma formation in vivo, suggesting that cleavage observed in vitro is not the mechanism of gamma formation in vivo.
Changes in activation gating of IsK potassium currents brought about by mutations in the transmembrane sequence (1994)

Expression of the rat kidney IsK protein in Xenopus oocytes produces slowly-activating potassium channel currents. We have investigated the relationship between structure and function of the single putative membrane-spanning domain using site-directed mutagenesis. Six mutants were constructed in which consecutive individual amino acids (53 to 58) of the transmembrane region were substituted by cysteine. Expression of four of these mutants in Xenopus oocytes resulted in currents which were similar to wild-type. However, for one mutant (position 55) activation curves were shifted in a hyperpolarising direction and for another mutant (position 58) activation curve were shifted in a depolarising direction. This suggests that the hydrophobic phenylalanine residues at positions 55 and 58 may play a critical role in IsK activation gating. This spacing of functional amino acids at every third residue may indicate an alpha-helical conformation for the membrane-spanning domain of IsK. Furthermore, these results also indicate that one face of the helix may represent a region of subunit association.
Convection-Enhanced Delivery of Adeno-Associated Virus Type 2 (AAV2) into the Striatum and Transport of AAV2 Within Monkey Brain (2006)

Adeno-associated virus type 2 (AAV2)-based vectors are promising transgene carriers for experimental gene therapy treatments of brain diseases. However, detailed evaluation of transgene distribution, trafficking, and transport within the brain is of the utmost importance before applying any type of gene therapy in humans. We examined the distribution of AAV2-thymidine kinase (AAV2-TK) and AAV2-aromatic L-amino acid decarboxylase (AAV2-AADC) in monkey brain after convection-enhanced delivery (CED). The AADC group consisted of two 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned monkeys that received unilateral infusions of AAV2-AADC into six sites in the right hemisphere. The TK group consisted of three monkeys that received bilateral CED infusion of AAV2-TK into the putamen; one side in all three monkeys was coinfused with heparin. Six weeks after AAV delivery, the brains were collected and processed for immunohistochemical staining. Volumetric measurement of TK distribution showed that at least 75% of the putamen could be covered by a single infusion of the vector; however, no effects of heparin coadministration were found, most likely because of the already robust gene transfer achieved by CED. Interestingly, TK- and AADCimmunoreactive cells were also present outside the striatum, in the globus pallidus, subthalamic nucleus, thalamus, and substantia nigra. CED proved to be an efficient method for delivery of the AAV2 vector. Detection of the transgenes in brain structures distant from the site of injection emphasizes the potential for gene transport, and the advantages and disadvantages of CED for gene therapy deserve further study.
Lentivirus Vector Gene Expression during ES Cell-Derived Hematopoietic Development In Vitro (2000)

The murine embryonal stem (ES) cell virus (MESV) can express transgenes from the long terminal repeat (LTR) promoter/enhancer in undifferentiated ES cells, but expression is turned off upon differentiation to embryoid bodies (EBs) and hematopoietic cells in vitro. We examined whether a human immunodeficiency virus type 1-based lentivirus vector pseudotyped with the vesicular stomatitis virus G protein (VSV-G) could transduce ES cells efficiently and express the green fluorescent protein (GFP) transgene from an internal phosphoglycerate kinase (PGK) promoter throughout development to hematopoietic cells in vitro. An oncoretrovirus vector containing the MESV LTR and the GFP gene was used for comparison. Fluorescence-activated cell sorting analysis of transduced CCE ES cells showed 99.8 and 86.7% GPF-expressing ES cells in the VSV-G-pseudotyped lentivirus (multiplicity of infection [MOI] = 59)- and oncoretrovirus (MOI = 590)-transduced cells, respectively. Therefore, VSV-G pseudotyping of lentiviral and oncoretrovirus vectors leads to efficient transduction of ES cells. Lentivirus vector integration was verified in the ES cell colonies by Southern blot analysis. When the transduced ES cells were differentiated in vitro, expression from the oncoretrovirus LTR was severely reduced or extinct in day 6 EBs and ES cell-derived hematopoietic colonies. In contrast, many lentivirus-transduced colonies, expressing the GFP gene in the undifferentiated state, continued to express the transgene throughout in vitro development to EBs at day 6, and many continued to express in cells derived from hematopoietic colonies. This experimental system can be used to analyze lentivirus vector design for optimal expression in hematopoietic cells and for gain-of-function experiments during ES cell development in vitro.
A MEMS-based multi-sensor system for attitude determination (2009)

This paper presents an original multi-sensor system for 3D orientation determination based on only 4 MEMS sensors. MEMS sensors are manufactured on a cheap standard technology from NXP Semiconductors using TMAH front side wet etching with no additional masking step. This very low cost manufacturing process makes the system suitable for various consumer applications. Electronic architecture for signal conditioning is detailed covering issues regarding the design of piezoresistor based systems (offsets, flicker noise…). Finally, the complete system has been prototyped proving the interest and the feasibility of such devices.
[Identification of the TRIM5/TRIMCyp heterozygous genotype in Macaca assamensis]. (2011)

The lack of appropriate animal models that utilizes HIV-1 as the challenge virus is a major impediment to HIV/AIDS research. A major reason underlying the inability of HIV-1 to replicate in nonhuman primate cells is the existence of host antiviral restriction factors. The intrinsic antiviral proteins in host cells are described as restriction factors. The understanding of restriction factors and their mechanism in different primates would undoubtedly facilitate the development of HIV/AIDS animal models. TRIM5alpha is an important restriction factor and can restrict the infection of several retroviruses including HIV-1 in a species-specific fashion. TRIM5-cyclophilin A (TRIMCyp) gene is an unusual TRIM5 locus found in New World and Old World monkeys. The different TRIMCyp genotypes of four primates (110 samples) including assam macaque (Macaca assamensis), tibetan macaque (M. thibetana), stump-tailed macaque (M. arctoides) and Chinese rhesus macaques (M. mulatta) were studied in this paper. We firstly found that TRIM5-CypA fusion gene exist in M. assamensis. The TRIMCyp of M. assamensis also results from the retrotransposition of CypA pseudogene cDNA into 3'-UTR of TRIM5 gene like TRIMCyp of M. leonina. Moreover, there is an extremely high sequence homology between TRIMCyp genes from M. assamensis and M. leonina. Besides, we also found the G-to-T mutation (G/T) in the 3'splicing site of TRIM5 intron 6, which was identical to M. leonina. These results indicate M. assamensis may also encode TRIMCyp protein like M. leonine, which imply M. assamensis might be infected by HIV-1. Therefore, it is very possible that M. assamensis will be used as a new HIV/AIDS animal model.
Bitonic sorting on Benesˇ networks (2002)

An algorithm to sort via a Benes/spl caron/ network is derived from the logic of the fired data routings found in bitonic sorting networks. The appropriate routings are developed and presented using an expanded version of Knuth diagrams for sorting networks. These diagrams illustrate the address line logic within the network.
Validity and reliability of the twenty-eight-joint count for the assessment of rheumatoid arthritis activity (1995)

The 28-joint count is a reliable and valid measure for joint assessment. It is easier to perform than the 66/68-joint count, and it addresses the joints that are critically involved.
Selective ortho and meta Migration of an Acyl Group in the Fries Rearrangement of Creosol Esters (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective ortho and meta Migration of an Acyl Group in the Fries Rearrangement of Creosol EstersPAOLO Da RE and LUIGI CIMATORIBUSCite this: J. Org. Chem. 1961, 26, 10, 3650–3653Publication Date (Print):October 1, 1961Publication History Published online1 May 2002Published inissue 1 October 1961https://pubs.acs.org/doi/10.1021/jo01068a007https://doi.org/10.1021/jo01068a007research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations16LEARN 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
Inhibition of Autotaxin by Lysophosphatidic Acid and Sphingosine 1-Phosphate (2005)

Autotaxin (ATX) or nucleotide pyrophosphatase/phosphodiesterase 2 (NPP2) is an NPP family member that promotes tumor cell motility, experimental metastasis, and angiogenesis. ATX primarily functions as a lysophospholipase D, generating the lipid mediator lysophosphatidic acid (LPA) from lysophosphatidylcholine. ATX uses a single catalytic site for the hydrolysis of both lipid and non-lipid phosphodiesters, but its regulation is not well understood. Using a new fluorescence resonance energy transfer-based phosphodiesterase sensor that reports ATX activity with high sensitivity, we show here that ATX is potently and specifically inhibited by LPA and sphingosine 1-phosphate (S1P) in a mixed-type manner (Ki approximately 10(-7) M). The homologous ecto-phosphodiesterase NPP1, which lacks lysophospholipase D activity, is insensitive to LPA and S1P. Our results suggest that, by repressing ATX activity, LPA can regulate its own biosynthesis in the extracellular environment, and they reveal a novel role for S1P as an inhibitor of ATX, in addition to its well established role as a receptor ligand.
Recessively inherited L-DOPA-responsive parkinsonism in infancy caused by a point mutation (L205P) in the tyrosine hydroxylase gene (1996)

Tyrosine hydroxylase (TH) catalyzes the conversion of L-tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of dopamine. This report describes a missense point mutation in the human TH (hTH) gene in a girl presenting parkinsonian symptoms in early infancy and a very low level of the dopamine metabolite homovanillic acid in the CSF. DNA sequencing revealed a T614-to-C transition in exon 5 (L205P). Both parents and the patient's brother are heterozygous for the mutation. Site-directed mutagenesis and expression in different systems revealed that the recombinant mutant enzyme had a low homospecific activity, i.e. approximately 1.5% of wt-hTH in E. coli and approximately 16% in a cell-free in vitro transcription-translation system. When transiently expressed in human embryonic kidney (A293) cells a very low specific activity (approximately 0.3% of wt-hTH) and immunoreactive hTH (< 2%) was obtained. The expression studies are compatible with the severe clinical phenotype of the L205P homozygous patient carrying this recessively inherited mutation. Treatment with L-DOPA resulted in normalisation of the CSF homovanillic acid concentration and a sustained improvement in parkinsonian symptoms.
MRI-based prediction of adverse cardiac remodeling after murine myocardial infarction (2012)

Myocardial infarction (MI) results in adverse cardiac remodeling leading to heart failure and increased mortality. Experimental mouse models of MI are extensively used to identify mechanisms underlying adverse remodeling, but the extent of remodeling that occurs may be highly variable and can limit the utility to discover new disease pathways. The ability to predict the development of significant late post-MI remodeling would be invaluable in conducting such studies by increasing throughput and efficiency. This study aimed to identify potential thresholds of cardiac magnetic resonance imaging (MRI) parameters measured early after murine MI that would predict the development of significant adverse remodeling at 4 wk. MI was achieved by permanent coronary ligation and animals (n = 84) were followed up for 4 wk subsequently. MRI was used to assess left ventricular (LV) volumes, mass and ejection fraction, as well as infarct size (IS). Late gadolinium enhancement cine-MRI was performed at 2 days with standard cine-MRI at 30 days post-MI. Utilizing multiple logistic regression, we found that IS >36%, at 2 days post-MI, was the overall best single predictor of adverse remodeling at 30 days (sensitivity 80.7%, specificity 88.9%; C-statistic of 0.939 from receiver-operating curve analysis). LV end-systolic volume (LVESV) >32 μl was also an excellent predictor comparable to IS. The combination of IS >36% and/or LVESV >32 μl provided the highest predictive values for late adverse remodeling among multiple predictors. This study demonstrates that MRI-based estimation of IS and ESV during the acute phase of murine MI are good predictors of subsequent adverse remodeling that may aid experimental design.
Mitochondrial Integrity and Function in Atherogenesis (2002)

Mitochondrial DNA damage may result from RS production in vascular tissues and may in turn be an early event in the initiation of atherosclerotic lesions.
Very low frequency oscillations in arterial blood pressure after autonomic blockade in conscious dogs (1997)

The aim of this study was to investigate spontaneous variability of arterial blood pressure in conscious foxhounds in the absence of direct sympathetic and parasympathetic influences. Autonomic blockade was achieved by administration of the ganglionic blocking agent hexamethonium (n = 7). In contrast to the control group (n = 7), marked oscillations with a cycle length of 100 s (0.01 Hz) were observed. The relationship of the power densities of the oscillation band (0.01 +/- 0.005 Hz) to the total power increased threefold (0.213 +/- 0.007 vs. 0.057 +/- 0.005; P < 0.01). The 0.01-Hz oscillations typically commenced after some delay. To test whether the absence of the mechanoreceptor afferents was responsible for these fluctuations, we investigated an additional group of foxhounds that were subjected to total baroreceptor and cardiopulmonary receptor denervation (n = 7). Neither in this protocol, nor in a group subjected to denervation and ganglionic blockade (n = 6), did we observe sustained oscillations in this frequency range. Since the oscillations were not seen after combined afferent (mechanoreceptor denervation) and efferent (ganglionic) blockade, central oscillators as a source of the oscillations can be ruled out. A simple model of a circulating pressoric factor may explain the fluctuations, provided that there is a time delay between the stimulus and the release or action of the factor. The findings suggest that a circulating factor accounts for the 0.01-Hz oscillations, which is dependent on intact pathways from the cardiac receptors or baroreceptors to the central nervous system. This hypothesis is put forward since cardiopulmonary and baroreceptor denervation blocked the oscillations seen after ganglionic blockade.
Electronic transport properties of a tilted graphenep−njunction (2009)

Spatial manipulation of current flow in graphene could be achieved through the use of a tilted $p\text{\ensuremath{-}}n$ junction. We show through numerical simulation that a pseudo-Hall effect (i.e., nonequilibrium charge and current density accumulating along one of the sides of a graphene ribbon) can be observed under these conditions. The tilt angle and the $p\text{\ensuremath{-}}n$ transition length are two key parameters in tuning the strength of this effect. This phenomenon can be explained using classical trajectory via ray analysis, and is therefore relatively robust against disorder. Lastly, we propose and simulate a three terminal device that allows direct experimental access to the proposed effect.
The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment (1993)

The facile detection and purification of a recombinant protein without detailed knowledge about its individual biochemical properties constitutes a problem of general interest in protein engineering. The use of a novel kind of random peptide library for the stepwise engineering of a C-terminal fusion peptide which confers binding activity towards streptavidin is described in this study. Because of its widespread use as part of a variety of conjugates and other affinity reagents, streptavidin constitutes the binding partner of choice both for detection and purification purposes. The streptavidin-affinity tag was engineered at the C-terminus of the VH domain as part of the D1.3 Fv fragment which was functionally expressed in Escherichia coli. Irrespective of whether it was displayed by the VH or the VL domain, the optimized version of the affinity peptide termed 'Strep-tag' allowed the detection of the Fv fragment both on Western blots and in ELISAs by a streptavidin-alkaline phosphatase conjugate. In addition, the one-step purification of the intact Fv fragment carrying a single Strep-tag at the C-terminus of only one of its domains was achieved by affinity chromatography with streptavidin-agarose using very mild elution conditions.
Adaptation and Constraint at Toll-Like Receptors in Primates (2010)

Frequent positive selection is a hallmark of genes involved in the adaptive immune system of vertebrates, but the incidence of positive selection for genes underlying innate immunity in vertebrates has not been well studied. The toll-like receptors (TLRs) of the innate immune system represent the first line of defense against pathogens. TLRs lie directly at the host-environment interface, and they target microbial molecules. Because of this, they might be subject to frequent positive selection due to coevolutionary dynamics with their microbial counterparts. However, they also recognize conserved molecular motifs, and this might constrain their evolution. Here, we investigate the evolution of the ten human TLRs in the framework of these competing ideas. We studied rates of protein evolution among primate species and we analyzed patterns of polymorphism in humans and chimpanzees. This provides a window into TLR evolution at both long and short timescales. We found a clear signature of positive selection in the rates of substitution across primates in most TLRs. Some of the implicated sites fall in structurally important protein domains, involve radical amino acid changes, or overlap with polymorphisms with known clinical associations in humans. However, within species, patterns of nucleotide variation were generally compatible with purifying selection, and these patterns differed between humans and chimpanzees and between viral and nonviral TLRs. Thus, adaptive evolution at TLRs does not appear to reflect a constant turnover of alleles and instead might be more episodic in nature. This pattern is consistent with more ephemeral pathogen-host associations rather than with long-term coevolution.
Transfer of structured and patterned thin siliconfilms using the Smart-Cut® process (1996)

The feasibility of transferring patterned and multilayered thin films, simulating part of the stacked structure of a CMOS integrated circuit, from their original bulk silicon substrate to a final substrate, was demonstrated using the Smart-Cut process .
The Lymphatic Anatomy of the Breast and its Implications for Sentinel Lymph Node Biopsy: A Human Cadaver Study (2007)

These anatomical findings are discordant with our current knowledge based on previous studies and demand closer examination by clinicians. These anatomical studies may help explain the percentage of false-negative sentinel node biopsy studies and suggest the peritumoral injection site for accurate sentinel lymph node detection.
Type 1 diabetes mellitus and the use of flexible insulin regimens. (1999)

The management of type 1 diabetes mellitus (formerly known as insulin-dependent diabetes) has changed dramatically over the past 30 years. In particular, new insulin strategies have improved the ability to maintain near-normal glycemia. Factors such as onset, peak and duration of action can influence the ability of a particular insulin regimen to help control glucose levels. Patient factors, including individual variations in insulin absorption, levels of exercise and types of meals consumed, also influence the effectiveness of an insulin regimen. Rapid-acting insulin lispro is an ideal mealtime insulin. The premeal dose of insulin lispro can be adjusted based on the content of the meal and the patient's blood glucose level. Intermediate-acting and long-acting insulins should not be given to account for the content of a specific meal. Long-acting insulin can be administered once daily at bedtime or, ideally, twice daily in addition to another type of insulin. Patients with type 1 diabetes typically require an insulin dosage of 0.5 to 1.0 unit per kg per day. Newly diagnosed patients may have lower initial requirements because of continued endogenous insulin production. Flexible insulin regimens are based on predetermined actions in response to self-monitoring of blood glucose levels and carbohydrate intake.
The Internet Assigned Number Authority (IANA) Header Field Parameter Registry for the Session Initiation Protocol (SIP) (2004)

This document creates an Internet Assigned Number Authority (IANA)
registry for the Session Initiation Protocol (SIP) header field
parameters and parameter values. It also lists the already existing
parameters and parameter values to be used as the initial entries for
this registry. This document specifies an Internet Best Current
Practices for the Internet Community, and requests discussion and
suggestions for improvements.