gebhart/patrepeval huggingface dataset:
Deletions in the tRNA(Lys) primer-binding site of human immunodeficiency virus type 1 identify essential regions for reverse transcription (1991)

The initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs by the extension of a tRNA primer bound near the 5' end of the genomic RNA at a position termed the primer-binding site (PBS). The PBS is an 18-nucleotide region of the HIV-1 genome complementary to cellular tRNA(Lys). To further investigate the sequence requirements for the PBS in reverse transcription, deletions in the PBS were created and subcloned into a plasmid containing the infectious HIV-1 proviral genome. The mutations deleted the entire PBS (delta PBS) or the first 9 (delta 1-9), the second 9 (delta 10-18), or 12 (delta 7-18) nucleotides of the PBS. An additional mutation in the PBS was created in which the second nine nucleotides were deleted and nine additional nucleotides were substituted [Lys(1-9)]. The transfection of plasmids containing the wild-type or mutant proviral genomes into tissue culture cells resulted in expression of the HIV-1 gag and env gene products, as determined by immunoprecipitation using sera from AIDS patients. HIV-1 virus was released from the transfected cells, as determined by analysis of the supernatants for reverse transcriptase activity. The infectivity of the viruses derived from the transfection was examined by coculture experiments with SupT1 cells, which support high-level replication of HIV-1. The transfection of plasmids containing HIV-1 proviral genomes with the delta PBS and PBS (delta 1-9) mutations did not produce infectious virus. In contrast, the HIV-1 proviral genomes with the delta 10-18, delta 7-18, and Lys(1-9) mutations in the PBS produced infectious virus upon transfection, although the kinetics of appearance was significantly delayed for the mutant viruses compared with the wild type. To further explore the nature of this defect, the PBS region from integrated proviral genomes was amplified by polymerase chain reaction and individual DNA products were subcloned into M13mp19, followed by a sequence analysis of the PBS region from individual M13 phage clones. In each of the PBS regions examined, the 18-nucleotide PBS complementary to tRNA(Lys) was present. However, nucleotide deletions and insertions were found 3' to the PBS from the samples derived from the transfection of plasmids containing mutant proviral genomes. Upon reinfection, the revertant viruses maintained the deletions 3' to the PBS and had kinetics of replication similar to that of the wild-type virus.(ABSTRACT TRUNCATED AT 400 WORDS)
Understanding the luminescence properties of Cu(<scp>i</scp>) complexes: a quantum chemical perusal (2020)

Electronic structures and excited-state properties of Cu(i) complexes with varying coordination numbers have been investigated by means of advanced quantum chemical methods. The computational protocol employs density functional-based methods for geometry optimizations and vibrational analyses including solvent effects through continuum models. Excitation energies, spin-orbit couplings and luminescence properties are evaluated using multireference configuration interaction methods. Rate constants of spin-allowed and spin-forbidden transitions have been determined according to the Fermi golden rule. The computational results for the 4-coordinate (DPEPhos)Cu(PyrTet), the 3-coordinate [IPr-Cu-Py<sub>2</sub>]<sup>+</sup>, and the linear CAAC<sup>Me<sub>2</sub></sup>-Cu-Cl complexes agree well with experimental absorption and emission wavelengths, intersystem crossing (ISC) time constants, and radiative lifetimes in liquid solution. Spectral shifts on the ligand-to-ligand charge transfer (LLCT) and metal-to-ligand charge transfer (MLCT) transitions caused by the polarity of the environment are well represented by the continuum models whereas the shifts caused by pseudo-Jahn-Teller distortions in the MLCT states are too pronounced in comparison to solid-state data. Systematic variation of the ligands in linear Cu(i) carbene complexes shows that only those complexes with S<sub>1</sub> and T<sub>1</sub> states of LLCT character possess sufficiently small singlet-triplet energy gaps ΔE<sub>ST</sub> to enable thermally activated delayed fluorescence (TADF). Complexes whose S<sub>1</sub> and T<sub>1</sub> wavefunctions are dominated by MLCT excitations tend to emit phosphorescence instead. Unlike the situation in metal-free TADF emitters, the presence of low-lying locally excited triplet states does not promote ISC. These states rather hold the danger of trapping the excitation with nonradiative deactivation being the major deactivation channel.
<i>Petunia hybrida</i> genes related to the maize regulatory <i>C1</i> gene and to animal <i>myb</i> proto‐oncogenes (1993)

The maize C1 gene is a regulatory gene of the anthocyanin pathway. It is a part of a multigene family whose predicted protein products contain a region with homology to the DNA-binding domain of myb proto-oncogene products. Using as a probe an oligonucleotide mixture encoding a highly conserved region in plant MYB proteins, cDNAs encoding three related polypeptides expressed in the flower of Petunia hybrida have been isolated. Predicted proteins are 280-517 amino acids long and show sequence similarities among themselves as well as with other MYB proteins (45-80% amino acid identity) in the MYB DNA-binding domain. Outside this domain no significant sequence similarity was found. However, in all cases regions with structural characteristics of activator domains were found. Analysis with Southern blots allowed an estimation of at least 20-30 myb genes in P. hybrida. Expression patterns were specific for each gene as shown by Northern blotting analysis. Subcellular location studies of the largest MYB product, by both immunoblotting of the protein in subcellular fractions and by 'in situ' immunolocation experiments, showed that it is a nuclear protein. The role of MYB proteins as transcriptional activators regulating the synthesis of different anthocyanin(flavonoid)-related compounds is discussed.
DIRECTED RING CLOSURE IN THE SYNTHESIS OF CHROMANS AND COUMARANS FROM o-ALLYLPHENOLS (1940)

ADVERTISEMENT RETURN TO ISSUEPREVArticleDIRECTED RING CLOSURE IN THE SYNTHESIS OF CHROMANS AND COUMARANS FROM o-ALLYLPHENOLSCHARLES D. HURD and WILLIAM A. HOFFMANCite this: J. Org. Chem. 1940, 05, 2, 212–222Publication Date (Print):March 1, 1940Publication History Published online1 May 2002Published inissue 1 March 1940https://pubs.acs.org/doi/10.1021/jo01208a018https://doi.org/10.1021/jo01208a018research-articleACS PublicationsRequest reuse permissionsArticle Views321Altmetric-Citations45LEARN 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
El análisis factorial exploratorio de los ítems: análisis guiado según los datos empíricos y el software. (2017)

<span style="font-family: 'Garamond',serif; font-size: 8pt; mso-bidi-font-size: 10.0pt; mso-fareast-font-family: 'Times New Roman'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA;" lang="EN-US">The aim of the present study is to illustrate how the appropriate or inappropriate application of exploratory factor analysis (EFA) can lead to quite different conclusions. To reach this goal, we evaluated the degree to which four different programs used to perform an EFA, specifically SPSS, FACTOR, PRELIS and MPlus, allow or limit the application of the currently recommended standards. In addition, we analyze and compare the results offered by the four programs when factor analyzing empirical data from scales that fit the assumptions of the classic linear EFA modeling adequately, ambiguously, or optimally, depending on the case, through the possibilities the different programs offer. The results of the comparison show the consequences of choosing one program or another; and the consequences of selecting some options or others within the same program, depending on the nature of the data. Finally, the study offers practical recommendations for applied researchers with a methodological orientation.</span>
Recent Advances in Hydrogen Production from Biomass (2017)

Hydrogen is an energy carrier, analogous in many ways to electricity, but with the potential for more advantageous applications in some situations, especially in industry and transportation. Hydrog...
‘User pays’ and other approaches to the funding of long-term care for older people in Australia (2000)

It has been argued that without some system in which future generations of users are able to pay for their care the cost of services for an increasingly large group of older people will be borne by a declining base of economically active younger people. Is the answer a user pays approach to the financing of aged care, as promoted by recent changes to aged care financing? This paper reviews this concept and its recent history in Australia. On the basis of a brief review of alternative funding systems, it also considers the potential of public and private insurance schemes to increase funding by potential service users and underwrite the long-term viability of funding for aged care services.
Lineage Diversion of T Cell Receptor Transgenic Thymocytes Revealed by Lineage Fate Mapping (2008)

The results further support the hypothesis that the premature expression of the TCRalphabeta can divert DN thymocytes into gamma delta lineage cells.
Modeling and feedback (2015)

Meanwhile, a small group of young children on the other side of the pool – who were 
supposed to be watching one of their peers 
conquer his fear of doing a back dive from the 
one-meter springboard – were drawn like 
magnets to the Olympian’s dive. Despite the 
repeated exhortations from their teacher to 
watch their hapless classmate perform his 
dive and to listen to her feedback about what 
he did correctly and incorrectly, the children 
were mesmerized and awed by the Olympi-an’s ability to do what they had considered to 
be impossible.
The Hydrophilic Domain of Small Ankyrin-1 Interacts with the Two N-terminal Immunoglobulin Domains of Titin (2003)

Little is known about the mechanisms that organize the internal membrane systems in eukaryotic cells. We are addressing this question in striated muscle, which contains two novel systems of internal membranes, the transverse tubules and the sarcoplasmic reticulum (SR). Small ankyrin-1 (sAnk1) is an approximately 17-kDa transmembrane protein of the SR that concentrates around the Z-disks and M-lines of each sarcomere. We used the yeast two-hybrid assay to determine whether sAnk1 interacts with titin, a giant myofibrillar protein that organizes the sarcomere. We found that the hydrophilic cytoplasmic domain of sAnk1 interacted with the two most N-terminal Ig domains of titin, ZIg1 and ZIg2, which are present at the Z-line in situ. Both ZIg1 and ZIg2 were required for binding activity. sAnk1 did not interact with other sequences of titin that span the Z-disk or with Ig domains of titin near the M-line. Titin ZIg1/2 also bound T-cap/telethonin, a 19-kDa protein of the Z-line. We show that titin ZIg1/2 could form a three-way complex with sAnk1 and T-cap. Our results indicate that titin ZIg1/2 can bind sAnk1 in muscle homogenates and suggest a role for these proteins in organizing the SR around the contractile apparatus at the Z-line.
Blood transcriptomic diagnosis of pulmonary and extrapulmonary tuberculosis (2016)

<b>BACKGROUND.</b> Novel rapid diagnostics for active tuberculosis (TB) are required to overcome the time delays and inadequate sensitivity of current microbiological tests that are critically dependent on sampling the site of disease. Multiparametric blood transcriptomic signatures of TB have been described as potential diagnostic tests. We sought to identify the best transcript candidates as host biomarkers for active TB, extend the evaluation of their specificity by comparison with other infectious diseases, and to test their performance in both pulmonary and extrapulmonary TB. <b>METHODS.</b> Support vector machine learning, combined with feature selection, was applied to new and previously published blood transcriptional profiles in order to identify the minimal TB‑specific transcriptional signature shared by multiple patient cohorts including pulmonary and extrapulmonary TB, and individuals with and without HIV-1 coinfection. <b>RESULTS.</b> We identified and validated elevated blood basic leucine zipper transcription factor 2 (<i>BATF2</i>) transcript levels as a single sensitive biomarker that discriminated active pulmonary and extrapulmonary TB from healthy individuals, with receiver operating characteristic (ROC) area under the curve (AUC) scores of 0.93 to 0.99 in multiple cohorts of HIV-1-negative individuals, and 0.85 in HIV-1-infected individuals. In addition, we identified and validated a potentially novel 4-gene signature comprising CD177, haptoglobin, immunoglobin J chain, and galectin 10 that discriminated active pulmonary and extrapulmonary TB from other febrile infections, giving ROC AUCs of 0.94 to 1. <b>CONCLUSIONS.</b> Elevated blood <i>BATF2</i> transcript levels provide a sensitive biomarker that discriminates active TB from healthy individuals, and a potentially novel 4-gene transcriptional signature differentiates between active TB and other infectious diseases in individuals presenting with fever. <b>FUNDING.</b> MRC, Wellcome Trust, Rosetrees Trust, British Lung Foundation, NIHR.
The effect of PHEV and HEV duty cycles on battery and battery pack performance (2007)

The lithium ion battery has excellent energy density and its columbic efficiency is nearly 100 per cent. As such, the Li-ion battery will play a significant role in the development of hybrid electric vehicles (HEVs) and plug-in hybrid electric vehicles (PHEVs). E-One Moli Energy Canada Ltd., recently announced the launch of batteries for the world's first complete line of cylindrical Li-ion rechargeable cell powered, cordless professional power tools. The production facility in Maple Ridge, British Columbia produces 2 million cells per month. Energy efficiency is commonly regarded as the most important characteristic for the successful implementation of a battery. It was emphasized that this is not the same as charge efficiency and the amount of energy loss will depend on the severity of the application duty cycle. This paper discussed the process of determining duty cycles for HEV driving profiles and how they deviate from the constant current state. The duty cycle, together with cell impedance, is often used to predict how a cell will respond. It was shown that pulsed current profiles can be characterized by quantifying the average current and the ratio of the standard deviation of the current to the mean current. Average current was found to be insufficient for characterizing real life duty cycles. It was concluded that the performance of any battery depends on the duty cycle. As such, knowledge of the power profile is essential. The authors recommended that in order to design optimal batteries and battery packs, standard tools must be developed for characterizing and grouping duty cycles. 1 ref., 6 figs.
Synthesis of a hapten to be used in development of immunoassays for trans-3'-hydroxycotinine, a major metabolite of cotinine (1991)

4-Carboxyl-substituted analogues of trans-3'-hydroxycotinine were synthesized to be covalently linked to macromolecules for antibody production. 3-Pyridyl-N-methylnitrone was condensed with dimethyl fumarate to give two isomeric isoxazolidines. Hydrogenolysis of the major product [2RS-(2 alpha,3 alpha,3 beta)]-3-carbomethoxy-3- [[(benzyloxy)carbonyl]oxy]-1-methyl-5-oxo-2-(3-pyridinyl)pyrrolidine with Pd/C followed by hydrolysis gave [2RS-(2 alpha,3 beta,4 beta)]-4-hydroxy-1-methyl-5-oxo-2-(3-pyridinyl)-3- pyrrolidinecarboxylic acid. The same compound was also prepared in two steps in high yield starting with dibenzyl fumarate and 3-pyridyl-N-methylnitrone.
The Long Non-Coding RNA PCAT-1 Promotes Prostate Cancer Cell Proliferation through cMyc (2014)

Long non-coding RNAs (lncRNAs) represent an emerging layer of cancer biology, contributing to tumor proliferation, invasion, and metastasis. Here, we describe a role for the oncogenic lncRNA PCAT-1 in prostate cancer proliferation through cMyc. We find that PCAT-1-mediated proliferation is dependent on cMyc protein stabilization, and using expression profiling, we observed that cMyc is required for a subset of PCAT-1-induced expression changes. The PCAT-1-cMyc relationship is mediated through the post-transcriptional activity of the MYC 3' untranslated region, and we characterize a role for PCAT-1 in the disruption of MYC-targeting microRNAs. To further elucidate a role for post-transcriptional regulation, we demonstrate that targeting PCAT-1 with miR-3667-3p, which does not target MYC, is able to reverse the stabilization of cMyc by PCAT-1. This work establishes a basis for the oncogenic role of PCAT-1 in cancer cell proliferation and is the first study to implicate lncRNAs in the regulation of cMyc in prostate cancer.
Diastasis Recti Abdominis (2012)

Objective: The purpose of this study was to determine and describe intervention techniques used by physical therapists to address diastasis recti abdominis (DRA) in postpartum women. Study Design: Descriptive survey. Background: Diastasis recti abdominis is defined as a separation of the rectus abdominis muscle as a result of partitioning at the linea alba, and it occurs in 60% of postpartum women. Despite this high prevalence, information regarding therapeutic approaches for DRA is scarce. Methods and Measures: The survey was distributed to 2200 members of the Women's Health Section of the American Physical Therapy Association. The survey contained 18 multiple-choice questions on clinician experience, patient presentation, evaluation, interventions, and estimated success. The survey was distributed via Survey Monkey. Descriptive statistics were collected. Results: The response rate was 16.4% with 13.45% used in the final data analysis. All of the 296 respondents incorporated therapeutic exercise into their plan of care, such as general transverse abdominis (TA) training (89.2%), TA training with functional activities (82.8%), and the Noble technique (62.5%). Fifty-nine percent of the physical therapists use manual therapy techniques, and 81.2% use therapeutic modalities. The average number of visits per week was 1.56. The most common length of treatment was 4 to 6 weeks. Sixty-nine percent of the respondents reported a success rate of 41% to 100%. Conclusion: The focus of conservative treatment for postpartum women with DRA is therapeutic exercise, specifically TA training. Current practice for postpartum DRA includes multiple intervention techniques. Future studies should assess the effectiveness of individual interventions to refine and advance treatment on the basis of evidence.
Computer image analysis of pigmented skin lesions (1991)

To assist in the distinction of melanoma from benign pigmented lesions, an imaging system was developed, comprising a frame grabber, a microcomputer, a colour video camera and flash lighting with red, green and infrared filters. Over an 18-month period, video images of 70 unselected pigmented lesions for which complete diagnostic data were available, were successfully captured using the camera. Analysis software extracted features relevant to the size, colour, shape and boundary of each lesion, and these features were correlated with clinical and histological characteristics on which standard diagnoses of skin tumours are based. For discriminant analysis based on image analysis measurements, equal probabilities were assigned to three specified diagnostic groups, namely melanoma, naevi and 'other', and four of five melanomas were correctly classified when infrared data were included. However when infrared measurements were omitted, all five melanomas were correctly classified, and the overall accuracy of classification of pigmented lesions was 71%. This system holds promise as an aid in the clinical distinction of melanoma from benign pigmented skin lesions.
The Application of Nanoparticle-Stabilized CO Foam for Oil Recovery (2013)

Abstract This paper presents a process for CO2 foam generation in the presence of nanosilica particles as supercritical CO2 and nanosilica dispersion flow through a sandstone core at reservoir conditions of 20°C and 1,200 psig. The generation of CO2 foam was observed in an online sapphire tube. Pressure drop across the core was measured to estimate the fluid mobility and foam resistance factor. Foam mobility and particle retention were investigated and core permeability after the CO2/nanosilica dispersion flooding was also measured to determine the particle plugging in the core. The application of the nanoparticle-stabilized CO2 foam for waterfloods residual oil recovery from sandstone cores was investigated. The results indicated that nanoparticle-stabilized CO2 foam could improve oil recovery after waterfloods in both low and high permeability cores. The total oil recovery by CO2 and nanosilica flood was 48.7% from the core with permeability of 33 md and 35.8% from the core with permeability of 270 md under the pressure of 1,200 psig.
An artificial enzymatic reaction cascade for a cell-free bio-system based on glycerol (2014)

(3<italic>R</italic>)-Acetoin was produced from glycerol by a cell-free bio-system comprised of Aldo, catalase, DHAD, ALS and ALDC.
A Fast and Efficient Method to Compensate for Brain Shift for Tumor Resection Therapies Measured Between Preoperative and Postoperative Tomograms (2010)

In this paper, an efficient paradigm is presented to correct for brain shift during tumor resection therapies. For this study, high resolution preoperative (pre-op) and postoperative (post-op) MR images were acquired for eight in vivo patients, and surface/subsurface shift was identified by manual identification of homologous points between the pre-op and immediate post-op tomograms. Cortical surface deformation data were then used to drive an inverse problem framework. The manually identified subsurface deformations served as a comparison toward validation. The proposed framework recaptured 85% of the mean subsurface shift. This translated to a subsurface shift error of 0.4 +/- 0.4 mm for a measured shift of 3.1 +/- 0.6 mm. The patient's pre-op tomograms were also deformed volumetrically using displacements predicted by the model. Results presented allow a preliminary evaluation of correction both quantitatively and visually. While intraoperative (intra-op) MR imaging data would be optimal, the extent of shift measured from pre- to post-op MR was comparable to clinical conditions. This study demonstrates the accuracy of the proposed framework in predicting full-volume displacements from sparse shift measurements. It also shows that the proposed framework can be extended and used to update pre-op images on a time scale that is compatible with surgery.