gebhart/patrepeval huggingface dataset:
RNA encoded by the IR1-U2 region of Epstein-Barr virus DNA in latently infected, growth-transformed cells (1983)

The IR1-U2 region of Epstein-Barr virus DNA consists of multiple copies of a 3.1-kilobase (kb) repeat sequence, IR1, which maps to the left of a 3.3-kb unique region, U2. Although hybridizations of cytoplasmic polyadenylated RNA from latently infected cells to viral DNA indicate that the IR1-U2 region encodes a substantial fraction of the viral RNA in these cells, only a single low-abundance 3-kb cytoplasmic polyadenylated RNA has been identified on Northern blots. Further analysis of the cytoplasmic polyadenylated RNA encoded by the IR1-U2 region indicates that (i) the RNA is transcribed from left to right; (ii) there are only three copies of the 3-kb RNA per cell; and (iii) the RNA is spliced. The RNA hybridizes to possibly contiguous 0.56- and 1.3-kb U2 domains. These domains and part of IR1 hybridize to the 3-kb cytoplasmic RNA. DNA between IR1 and the 0.56-kb U2 domain does not hybridize to the 3-kb RNA. The CCAAT-34 nucleotide-TATAA sequence in IR1 may be part of the promotor for the 3-kb cytoplasmic polyadenylated RNA since (i) it enables left-to-right transcription of IR1 by a HeLa cell extract, and (ii) latently infected cells contain giant polyadenylated nuclear RNAs which differ in size by 3 kb, as would be expected if transcription initiates in any copy of IR1 and continues through the rightward remaining copies into U2.
A New and Facile Synthesis of Chroman-3-ols, 3,4-Dihydro-2H-[1]-Benzopyran-3-ols (1991)

Abstract o-Allyl phenols react with m-chloroperoxybenzoic acid (m-CPBA) in dry chloroform to give chroman-3-ols in a single step in good yields (93–96%).
ADP/ATP Translocator from Pea Root Plastids (Comparison with Translocators from Spinach Chloroplasts and Pea Leaf Mitochondria) (1993)

The kinetic properties of the adenosine 5[prime]-diphosphate/adenosine 5[prime]-triphosphate (ADP/ATP) translocator from pea (Pisum sativum L.) root plastids were determined by silicone oil filtering centrifugation and compared with those of spinach (Spinacia oleracea L.) chloroplasts and pea leaf mitochondria. In addition, the ADP/ATP transporting activities from the above organelles were reconstituted into liposomes. The Km(ATP) value of the pea root ADP/ATP translocator was 10 [mu]M and that for ADP was 46 [mu]M. Corresponding values of the spinach ADP/ATP translocator were 25 [mu]M and 28 [mu]M, respectively. Comparable results were obtained for the reconstituted ATP transport activities. The transport was highly specific for ATP and ADP. Adenosine 5[prime]-monophosphate (AMP) caused only a slight inhibition and phosphoenolpyruvate and inorganic pyrophosphate caused no inhibition of ATP uptake. With pea root plastids and spinach chloroplasts, Km values >1 mM were obtained for ADP-glucose. Since the concentrations of ATP and ADP-glucose in the cytosolic compartment of spinach leaves have been determined as 2.5 and 0.6 mM, respectively, a transport of ADP-glucose by the ADP/ATP translocator does not appear to have any physiological significance in vivo. Although both the plastidial and the mitochondrial ADP/ATP translocators were inhibited to some extent by carboxyatractyloside, no immunological cross-reactivity was detected between the plastidial and the mitochondrial proteins. It seems probable that these proteins derive from different ancestors.
Repair of apurinic/apyrimidinic sites by UV damage endonuclease; a repair protein for UV and oxidative damage (1999)

UV damage endonuclease (UVDE) initiates a novel form of excision repair by introducing a nick imme-diately 5" to UV-induced cyclobutane pyrimidine dimers or 6-4 photoproducts. Here, we report that apurinic/apyrimidinic (AP) sites are also nicked by Neurospora crassa and Schizosaccharomyces pombe UVDE. UVDE introduces a nick immediately 5" to the AP site leaving a 3"-OH and a 5"-phosphate AP. Apyrimidinic sites are more effectively nicked by UVDE than apurinic sites. UVDE also possesses 3"-repair activities for AP sites nicked by AP lyase and for 3"-phosphoglycolate produced by bleomycin. The Uvde gene introduced into Escherichia coli cells lacking two types of AP endonuclease, Exo III and Endo IV, gave the host cells resistance to methylmethane sulfonate and t-butyl hydroperoxide. We identified two AP endonuclease activities in S.pombe cell extracts. Besides cyclobutane pyrimidine dimers and 6-4 photoproducts, N. crassa UVDE also nicks Dewar photoproducts. Thus, UVDE is able to repair both of the major forms of DNA damage in living organisms: UV-induced DNA lesions and AP sites.
Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster (2008)

Optical projection tomography is a recently developed tomographic technique used to acquire 3D microscopy data from specimens 1-10 mm thick. In previous work, to reduce scattering and attenuation the specimens were fixed and cleared, but clearing makes in-vivo fluorescence OPT of the sample impossible. We present a novel OPT technique for obtaining 3D images of both anatomy and fluorescent-protein expression in vivo, and we apply these techniques to gene expression mapping of Drosophila melanogaster development. We believe this approach will prove useful for in-vivo follow-up measurements of gene expression patterns in mm-sized samples, traditionally unavailable when using imaging techniques such as confocal microscopy.
Evidence for an essential histidine residue in <scp>d</scp>-xylose isomerases (1988)

Diethyl pyrocarbonate inactivated D-xylose isomerases from Streptomyces violaceoruber, Streptomyces sp., Lactobacillus xylosus and Lactobacillus brevis with second-order rate constants of 422, 417, 99 and 92 M-1.min-1 respectively (at pH 6.0 and 25 degrees C). Activity was completely restored by the addition of neutral hydroxylamine, and total protection was afforded by the substrate analogue xylitol in the presence of either Mg2+ or Mn2+ according to the genus studied. The difference spectra of the modified enzymes revealed an absorption maximum at 237-242 nm, characteristic for N-ethoxycarbonylhistidine. In addition, the spectrum of ethoxycarbonylated D-xylose isomerase from L. xylosus showed absorption minima at both 280 and 230 nm, indicative for modification of tyrosine residues. Nitration with tetranitromethane followed by diethyl pyrocarbonate treatment eliminated the possibility that modification of tyrosine residues was responsible for inactivation, and resulted in modification of one non-essential tyrosine residue and six histidine residues. Inactivation of the other D-xylose isomerases with diethyl pyrocarbonate required the modification of one (L. brevis), two (Streptomyces sp.) and four (S. violaceoruber) histidine residues per monomer. Spectral analysis and maintenance of total enzyme activities further indicated that either xylitol Mg2+ (streptomycetes) or xylitol Mn2+ (lactobacilli) prevented the modification of one crucial histidine residue. The overall results thus provide evidence that a single active-site histidine residue is involved in the catalytic reaction mechanism of D-xylose isomerases.
Inhibition of Ethylene Production by Cobaltous Ion (1976)

The effect of Co(2+) on ethylene production by mung bean (Phaseolus aureus Roxb.) and by apple tissues was studied. Co(2+), depending on concentrations applied, effectively inhibited ethylene production by both tissues. It also strongly inhibited the ethylene production induced by IAA, kinetin, IAA plus kinetin, Ca(2+), kinetin plus Ca(2+), or Cu(2+) treatments in mung bean hypocotyl segments. While Co(2+) greatly inhibited ethylene production, it had little effect on the respiration of apple tissue, indicating that Co(2+) does not exert its inhibitory effect as a general metabolic inhibitor. Ni(2+), which belongs to the same group as Co(2+) in the periodic table, also markedly curtailed both the basal and the induced ethylene production by apple and mung bean hypocotyl tissues.In a system in which kinetin and Ca(2+) were applied together, kinetin greatly enhanced Ca(2+) uptake, thus enhancing ethylene production. Co(2+), however, slightly inhibited the uptake of Ca(2+) but appreciably inhibited ethylene production, either in the presence or in the absence of kinetin. Tracer experiments using apple tissue indicated that Co(2+) strongly inhibited the in vivo conversion of l-[U-(14)C]methionine to (14)C-ethylene. These data suggest that Co(2+) inhibited ethylene production by inhibiting the conversion of methionine to ethylene, a common step which is required for ethylene formation by higher plants.Co(2+) is known to promote elongation, leaf expansion, and hook opening in excised plant parts in response to applied auxins or cytokinins. Since ethylene is known to inhibit these growth phenomena, it is suggested that Co(2+) exerts its promotive effect, at least in part, by inhibiting ethylene formation.
Suicide Associated with Akathisia and Depot Fluphenazine Treatment (1983)

AKATHISIA is a common and distressing side effect of neuroleptic medication that can he difficult to recognize and treat,1 Several previous reports mention maladaptive behavioral consequences, such as poor compliance with prescribed medication2 and aggressive or self-destructive outbursts2–3 We are reporting suicides in two young Hispanic men who had developed severe akathisia after treatment with depot fluphenazine. Depression with suicidal behavior has been observed following fluphenazine injection,4 but suicide associated with akathisia has not been previously noted.
Comparison of inherent saliency tracking methods for zero speed sensorless control of standard induction machines (2009)

Sensorless control of induction machines around zero frequency can only be achieved by evaluating inherent saliencies of the machine. The signals resulting from signal injection based sensorless control methods are composed of components caused by saturation, slotting, or anisotropy saliencies, as well as inter-modulation effects. In addition there is a strong influence of the load level on some components. Depending on how the different disturbing components are treated and modeled the performance of the resulting sensorless control is influenced. A comparison between the two methods for both rotor position estimation (tracking of rotor-position-dependent saliency) and flux position estimation (tracking of flux-dependent saliency) is experimentally verified for both methods at zero mechanical and electrical frequencies with high load level under sensorless control technique.
Industrial and Laboratory Nitrations (1976)

Electrophilic nitration of aromatics is the most studied, and supposedly best understood of organic reactions (1). Culminating their work, Ingold, Hughes, and their associates in 1950 published simultaneously a series of papers (2) which rightfully ever since is considered the most fundamental study in our understanding of electrophilic nitration reactions. Thus, not unexpectedly, for years following these publications the general view prevailed, that all the significant work in nitration was done, and little additional knowledge was to be gained. Chemists' interest consequently rapidly faded in the field, and by the end of the 1950's from a scientific point of view the study of nitration looked like as one of the most unattractive and inactive areas. In a way, no greater compliment of the achievements of Ingold and his group could have been made than the generally accepted view, that their work indeed, completed what there was worthwhile to study in
Clinical and Immunological Benefits from Highly Active Antiretroviral Therapy in Spite of Limited Viral Load Reduction in HIV Type 1 Infection (2001)

Both naive and memory T lymphocyte responses are lost during advanced HIV infection. Treatment with highly active antiretroviral therapy (HAART) is associated with an increase in T lymphocytes and a reduction in viral load. However, the viral response to HAART in patients with low levels of helper T lymphocytes and a high viral load is often not satisfactory. We investigated the capacity of long-term HAART to reconstitute the immune system in severely ill patients. A nonselected longitudinal patient population with high baseline viral levels and CD4(+) cells below 100 x 10(6)/liter were monitored for 2 years during HAART. Markers to estimate the therapeutic effects included viral levels and cell surface markers representing naive and memory T lymphocytes as well as activation markers, B cells, NK cells, and clinical events. After 2 years of treatment, viral load was reduced to undetectable levels in 55% (viral responders, vRs) and less than 1 log (median value) from baseline in 45% (viral low responders, vLRs). Elevated numbers of memory and naive CD4(+) and CD8(+) cells as well as a decrease in activation markers were seen in both vRs and vLRs. However, the magnitude was greater in vRs. No differences in the clinical outcome were observed between vRs and vLRs. We conclude that most patients, even in advanced stages of HIV disease, benefited from HAART. The magnitude of the response was related to good viral reduction, but even patients with poor viral reduction had a recovery of naive and memory CD4(+) and CD8(+) cells. Even a small reduction in viral load is thus of importance for health and potentially also for years of survival.
A Systematic Review of the Harms of Lung Cancer Screening with Low Dose Computed Tomography (2019)

Background: Lung cancer causes the majority of cancer-related deaths in the United States. Screening for lung cancer with low dose CT (LDCT) has become a prominent topic. This modality has the potential to contribute to a decrease in lung cancer associated mortality. Preliminary data from a large randomized controlled trial have shown a 20% decrease in mortality. Currently, no guidelines endorse LDCT screening for lung cancer. The harms of screening for lung cancer have not been fully characterized in a focused systematic review. Purpose: To explore and characterize the harms associated with low dose CT screening for lung cancer in high risk populations by evaluating the current evidence. This information will assist policy makers and clinicians as they weigh the risks and benefits of screening high risk populations for lung cancer. Data Sources: MEDLINE, EMBASE, Cochrane Library, reviews, reference lists, experts Study Selection: Studies were included that evaluated low dose screening for lung cancer. Those that characterized harms were central to this review. Data Extraction: Data were abstracted to abstraction forms. Studies were graded according to methods used by the United States Preventive Services Task Force (USPSTF). Data Synthesis: Studies reported variable rates of abnormal results with positivity of 8 to 45%. A range of 4 to 55% of total invasive procedures and none to 40% of surgeries were performed for benign indications. Incidental findings were reported in 0.77 to 62% of participants. Of the included studies, 30% discussed anxiety, 55% discussed overdiagnosis, 50% reported morbidity and mortality of workup, and 35% reported false negative cases. False positives at baseline ranged from 86 to 98%. Limitations: This review included observational studies, randomized trials, and systematic reviews of observational studies and short randomized trials. Data from completed large scale randomized trials is currently unavailable. No data from unpublished literature or studies unavailable in English were included so this review has a potential for publication and language bias. Conclusions: The harms of low dose CT screening for lung cancer are poorly reported in screening trials. Even though harms are incompletely characterized in the included studies, these harms are likely clinically significant. Clinicians must weigh the risks and benefits of the screening procedure if they are to implement mass screening for lung cancer with LDCT.
Using plant tannin as natural amphiphilic stabilizer to construct an aqueous–organic biphasic system for highly active and selective hydrogenation of quinoline (2013)

Black wattle tannin (BWT), a typical natural plant polyphenol, was used as natural amphiphilic stabilizer to prepare BWT-stabilized Pd nanoparticles (BWT-Pd) catalyst. The as-prepared catalyst was found to be highly active in aqueous–organic biphasic hydrogenation of quinoline, which exhibited 100% selectivity to 1,2,3,4-tetrahydroquinoline (py-THQ). Furthermore, the BWT-Pd catalyst can be reused 3 times without significant loss of catalytic activity, thus providing an effective and environmentally benign strategy for the production of py-THQ.
Standardized One-Step Real-Time Reverse Transcription-PCR Assay for Universal Detection and Quantification of Hepatitis Delta Virus from Clinical Samples in the Presence of a Heterologous Internal-Control RNA (2012)

As for other chronic viral diseases, quantification of hepatitis delta virus (HDV) loads may be useful for patient management. We describe a one-step quantitative reverse transcription-PCR assay that is reliable and automatable and meets the regulatory authorities' standards for accurate quantification of the major HDV genotypes. It includes an internal control and uses in vitro-transcribed RNAs as standards. Its linearity range is 500 to 1.7 × 10(11) copies/ml, its sensitivity is around 150 copies/ml, its repeatability is around 15%, and its reproducibility is below 0.25 log(10) copies/ml.
Molecular characterization of limulin, a sialic acid binding lectin from the hemolymph of the horseshoe crab, Limulus polyphemus (1977)

The sialic acid binding lectin, limulin, was isolated by gel filtration and ion-exchange chromatography from the hemolymph of Limulus polyphemus. When the purified protein was characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the presence of beta-mercaptoethanol, two major protein bands were observed. These two bands, subsequently found to contain carbohydrate as well, corresponded to molecular weights of 25 000 and 27 000. Amino acid sequence analyses were performed on both the intact protein and isolated cyanogen bromide fragments. The following primary structural features were noted in the amino-terminal region of limulin: (1) the absence of histidine and alanine from the NH2-terminal 50 residues; (2) the presence of five of the total eight prolines of the molecule between positions 13 and 30; and (3) a possible carbohydrate attachment site consisting of only the amino acids proline and serine between residues 13 and 19. The resultsof cyanogen bromide cleavage studies confirmed the presence of 2 methionine residues per subunit, at positions 25 and 58 respectively. No sequence heterogeneity was observed in this study. While it is quite possible that limulin plays some role in the defense mechanisms of the horseshoe crab, there is no obvious sequence homology between this invertebrate lectin and vertebrate immunoglobulins.
Interpreting the layout of web pages (2009)

Web pages such as news and shopping sites often use modular layouts. When used effectively this practice allows authors to present clearly large amounts of information in a single page. However, while sighted people can visually parse and understand these complex layouts in seconds, current assistive technologies such as screen readers cannot. This puts visually impaired users at a great disadvantage. In order to design better assistive technologies, we conducted a study of how people interpret modular layouts of news and shopping Web pages. The study revealed that when the layout complexity increases, the interpretation process gets longer and the reading gets more varied. Also, before looking at the main content, users first frame the Web page by looking for familiar structural elements that can be used as references and entry points. These elements include navigational bars, search boxes, and ads. This implies that assistive technologies can reduce the time required to frame the pages if they help users identify reference points and entry points.
Differential Effect of E-Selectin Antibodies on Neutrophil Rolling and Recruitment to Inflammatory Sites (1997)

The selectins are inducible adhesion molecules critically important for the inflammatory response. We investigate here the functional effects of three monoclonal antibodies (MoAbs) raised against murine E-selectin (9A9, 10E6, and 10E9.6) on neutrophil recruitment in vivo, leukocyte rolling and circulating leukocyte concentrations in vivo, and adhesion of myeloid cells to E-selectin transfectants and recombinant E-selectin-IgG fusion protein in vitro. MoAbs 9A9 and 10E6 map to the lectin and epidermal growth factor (EGF)-like domains of murine E-selectin, whereas 10E9.6 binds to the consensus repeat region. 10E9.6 blocked neutrophil recruitment in a model of thioglycollate-induced peritonitis in Balb/c mice by more than 90% but had no effect in C57BL/6 mice. 9A9 and 10E6 blocked neutrophil recruitment in this assay only when combined with a P-selectin antibody, 5H1. Neither 9A9 nor 10E9.6 alone blocked leukocyte rolling in tumor necrosis factor-alpha-treated venules of Balb/c mice, but 9A9 almost completely inhibited leukocyte rolling when combined with the function-blocking murine P-selectin MoAb, RB40.34. In contrast, 10E9.6 had no effect on leukocyte rolling in RB40.34-treated Balb/c or C57BL/6 mice. 10E9.6 did not affect adhesion of myeloid cells to E-selectin transfectants or attachment, rolling, and detachment of myeloid cells to murine E-selectin-IgG fusion protein. However, adhesion was completely blocked in the same assays by 9A9. Taken together, these results indicate that E-selectin serves a function, other than rolling, that appears to be critically important for neutrophil recruitment to inflammatory sites in Balb/c mice.
An Analysis of Author Contribution Patterns in Eclipse Foundation Project Source Code (2011)

Collaborative development is a key tenet of open source software, but if not properly understood and managed, it can become a liability. We examine author contribution data for the newest revision of 251,633 Java source files in 592 Eclipse projects. We use this observational data to analyze collaboration patterns within files, and to explore relationships between file size, author count, and code authorship. We calculate author entropy to characterize the contributions of multiple authors to a given file, with an eye toward understanding the degree of collaboration and the most common interaction patterns.
Fatigue Severity Scale (FSS) (1989)

Fatigue Severity Scale (FSS) includes nine items that extracted from the 28 items of fatigue questionnaire to measure changes in fatigue level and severity, in particular for patients with medical and neurologic disease as multiple sclerosis and systemic lupus erythematous. Each item was rated on 7-point Likert scale where 1 indicates Strongly Disagree and 7 indicates Strongly Agree.
Monolithic 2-18 GHz low loss, on-chip biased PIN diode switches (1995)

Two state-of-the-art monolithic GaAs PIN diode switches have been designed, fabricated and tested. These single-pole double-throw (SPDT) switches exhibit insertion losses of 1.15/spl plusmn/0.15 dB over a 2-18 GHz band, which is an unprecedented performance in loss and flatness for monolithic wideband switches incorporating on-chip bias networks. Isolation and return loss are greater than 43 dB and 12 dB, respectively, and the input port power handling is 23 dBm at 1-dB insertion loss compression. These performance characteristics were measured at a nominal bias setting of -8 V, which corresponds to 3.7 mA of series diode bias current and a total dc power consumption of 55 mW. The input power at the third-order interception is 40 dBm. The switches can handle up to 31 dBm (1.25 W) at a higher bias of -18 V and 9.3 mA.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>