gebhart/patrepeval huggingface dataset:
A Leucine Zipper-Like Domain Is Essential for Dimerization and Encapsidation of Bluetongue Virus Nucleocapsid Protein VP4 (1998)

The bluetongue virus (BTV) minor protein VP4, with molecular mass of 76 kDa, is one of the seven structural proteins and is located within the inner capsid of the virion. The protein has a putative leucine zipper near the carboxy terminus of the protein. In this study, we have investigated the functional activity of this putative leucine zipper by a number of approaches. The putative leucine zipper region (amino acids [aa] 523 to 551) was expressed initially as a fusion protein by using the pMAL vector of Escherichia coli, which expresses a maltose binding monomeric protein. The expressed fusion protein was purified by affinity chromatography, and its size was determined by gel filtration chromatography. Proteins of two sizes, 51 and 110 kDa, were recovered, one equivalent to the monomeric form and the other equivalent to the dimeric form of the fusion protein. To prove that the VP4-derived sequence was responsible for dimerization of this protein, a mutated fusion protein was created in which a VP4 leucine residue (at aa 537) within the zipper was replaced by a proline residue. Analyses of the mutated protein demonstrated that the single mutation indeed prevented dimerisation of the protein. The dimeric nature of VP4 was further confirmed by using purified full-length BTV-10 VP4 recovered from recombinant baculovirus-expressing BTV-10 VP4-infected insect cells. Using chemical cross-linking and gel filtration chromatography, we documented that the native VP4 indeed exists as a dimer in solution. Subsequently, Leu537 was replaced by either a proline or an alanine residue and the full-length mutated VP4 was expressed in the baculovirus system. By sucrose density gradient centrifugation and gel filtration chromatography, these mutant forms of VP4 were shown to lack the ability to form dimers. The biological significance of the dimeric forms of VP4 was examined by using a functional assay system, in which the encapsidation activity of VP4 into core-like particles (CLPs) was studied (H. LeBlois, T. French, P. P. C. Mertens, J. N. Burroughs, and P. Roy, Virology 189:757-761, 1992). We demonstrated conclusively that dimerization of VP4 was essential for encapsidation by CLPs.
Selective atomic layer deposition of zirconia on copper patterned silicon substrates using ethanol as oxygen source as well as copper reductant (2013)

The authors report a new chemical approach for the selective atomic layer deposition of ultrathin layers of zirconium oxide (ZrO2) on copper patterned silicon surfaces. Instead of using common atomic layer deposition (ALD) oxygen sources such as water, oxygen, or ozone, the authors use ethanol, which serves as oxygen source for the ALD on the silicon side and as effective reducing agent on the copper side, thereby selectively depositing ZrO2 film on the silicon surface of the substrate without any deposition on copper up to at least 70 ALD cycles. The resulting ZrO2 nanofilm is found to be an effective copper diffusion barrier at temperatures at least up to 700 °C.
Diagnostic Tests for Agents of Community-Acquired Pneumonia (2011)

Lower respiratory infections are the major cause of death due to infectious disease in the United States and worldwide. Most forms of community-acquired pneumonia (CAP) are treatable, and there is consensus that the selection of antimicrobial agents is notably simplified if the pathogen is defined. The rich history of CAP studies in the prepenicillin era showed that an etiologic diagnosis was established in >90% of cases, but the 2009 data from Medicare indicate that a probable pathogen is now detected in <10% according to a review of the records of >17,000 patients hospitalized with CAP. This review addresses the issue of the state of the art of microbiological studies of CAP in terms of the realities of current-day practice. Unfortunately, the desire for better data to achieve pathogen-directed treatment clashes with a multitude of harsh realities, including cost, Centers for Medicare and Medicaid Services (CMS) requirements for antibiotics to be administered within 6 h of disease onset, guidelines that discourage any microbiological studies in most cases, belief in empiricism that is well supported by at least 1 prospective study, the decline of microbiological analysis standards in most laboratories, and the devastating impact of the Clinical Laboratory Improvement Amendments (CLIA) regulations that led to the demise of "the house staff laboratory" and the distancing of microbiological analysis from the site of care. Microbiological principles are reviewed, with emphasis on specimen source, pathogenic potential of isolates, concentrations, impact of antecedent antibiotics, and the "Washington criteria" for expectorated sputum. The recommendation is that the high-quality microbiological analysis that is still achieved in some places should be retained but that to advance the field on the basis of the contemporary realities, two goals should be adopted: First is the broad use of antigen tests for Streptococcus pneumoniae and Legionella pneumophila with interpretation by clinical staff under the CLIA waiver for low-complexity tests. The second and more ambitious recommendation is the adoption of molecular techniques, with particular emphasis on nucleic acid detection, which is rapid and sensitive and has already been developed for virtually all recognized pulmonary pathogens. This may be the ultimate solution for many laboratories, and it is likely to have selected use.
Semiconductor electrodes. 27. The p- and n-gallium arsenide-N,N'-dimethyl-4,4'-bipyridinium system. Enhancement of hydrogen evolution on p-gallium arsenide and stabilization of n-gallium arsenide electrodes (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSemiconductor electrodes. 27. The p- and n-gallium arsenide-N,N'-dimethyl-4,4'-bipyridinium system. Enhancement of hydrogen evolution on p-gallium arsenide and stabilization of n-gallium arsenide electrodesFu-Ren F. Fan, Benjamin Reichman, and Allen J. BardCite this: J. Am. Chem. Soc. 1980, 102, 5, 1488–1492Publication Date (Print):February 1, 1980Publication History Published online1 May 2002Published inissue 1 February 1980https://pubs.acs.org/doi/10.1021/ja00525a003https://doi.org/10.1021/ja00525a003research-articleACS PublicationsRequest reuse permissionsArticle Views173Altmetric-Citations29LEARN 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
New insights into repeat instability (2010)

Expansion of tandem repeat sequences is responsible for more than 20 human diseases. Several cis elements and trans factors involved in repeat instability (expansion and contraction) have been identified. However no comprehensive model explaining large intergenerational or somatic changes of the length of the repeating sequences exists. Several lines of evidence, accumulated from different model studies, indicate that transcription through repeat sequences is an important factor promoting their instability. The persistent interaction between transcription template DNA and nascent RNA (RNA•DNA hybrids, R loops) was shown to stimulate genomic instability. Recently, we demonstrated that cotranscriptional RNA•DNA hybrids are preferentially formed at GC-rich trinucleotide and tetranucleotide repeat sequences in vitro as well as in human genomic DNA. Additionally, we showed that cotranscriptional formation of RNA•DNA hybrids at CTG•CAG and GAA•TTC repeats stimulate instability of these sequences in both E. coli and human cells. Our results suggest that persistent RNA•DNA hybrids may also be responsible for other downstream effects of expanded trinucleotide repeats, including gene silencing. Considering the extent of transcription through the human genome as well as the abundance of GC-rich and/or non-canonical DNA structure forming tandem repeats, RNA•DNA hybrids may represent a common mutagenic conformation. Hence, R loops are potentially attractive therapeutic target in diseases associated with genomic instability.
Luspatercept improves hemoglobin levels and blood transfusion requirements in a study of patients with β-thalassemia (2019)

β-thalassemia is a hereditary disorder with limited approved treatment options; patients experience anemia and its complications, including iron overload. The study aim was to determine whether luspatercept could improve anemia and disease complications in patients with β-thalassemia. This open-label, nonrandomized, uncontrolled study consisted of a 24-week dose-finding and expansion stage (initial stage) and a 5-year extension stage, currently ongoing. Sixty-four patients were enrolled; 33 were non-transfusion dependent (mean hemoglobin, <10.0 g/dL; <4 red blood cell [RBC] units transfused per 8 weeks), and 31 were transfusion dependent (≥4 RBC units per 8 weeks). Patients received 0.2 to 1.25 mg/kg luspatercept subcutaneously every 21 days for ≥5 cycles (dose-finding stage) and 0.8 to 1.25 mg/kg (expansion cohort and 5-year extension). The primary end point was erythroid response, defined as hemoglobin increase of ≥1.5 g/dL from baseline for ≥14 consecutive days (without RBC transfusions) for non-transfusion-dependent patients or RBC transfusion burden reduction ≥20% over a 12-week period vs the 12 weeks before treatment for transfusion-dependent patients. Eighteen non-transfusion-dependent patients (58%) receiving higher dose levels of luspatercept (0.6-1.25 mg/kg) achieved mean hemoglobin increase ≥1.5 g/dL over ≥14 days vs baseline. Twenty-six (81%) transfusion-dependent patients achieved ≥20% reduction in RBC transfusion burden. The most common grade 1 to 2 adverse events were bone pain, headache, and myalgia. As of the cutoff, 33 patients remain on study. In this study, a high percentage of β-thalassemia patients receiving luspatercept had hemoglobin or transfusion burden improvements. These findings support a randomized clinical trial to assess efficacy and safety. This study was registered at www.clinicaltrials.gov as #NCT01749540 and #NCT02268409.
Investigation into the Operating Characteristics of a “Microarc” Atmospheric-Pressure Glow Discharge (1979)

Details of the processes occurring during sample atomization from a “microarc” discharge have been studied photometrically, by use of high-speed color cinematography and through current-voltage waveforms. The microarc studied here is an atmospheric-pressure inert-gas glow discharge supported between 0.25 mm diameter tungsten wires; quiescent argon-1% H 2 provides reactive-sputtering conditions and improved behavior in the presence of oxygen impurities. Excitation temperatures of ca. 5000°K are measured for the argon glow. Samples of Na, Al, and Sr illustrate the influence of volatile, refractory, insulating, and electron-emitting sample properties on the temporal-spatial-electrical behavior of the discharge. The step-by-step events occurring in the discharge are described qualitatively and a variety of processes are invoked to explain sample volatilization, including sputtering, chemical reactions, and purely thermal effects. In the first stages of the discharge, instabilities are related to the placement and insulating character of deposits. With heating, electron emission becomes important in directing the discharge to or away from the sample; abnormal glow wandering and glow-to-arc transitions can ensue. Improved stability is achieved by uniformly depositing multi-element samples along the electrode, which localizes the initial discharge and promotes ablative cooling of the sample and electrode.
Interrelationship of Gene Expression, Polysome Prevalence, and Respiration during Ripening of Ethylene and/or Cyanide-Treated Avocado Fruit (1984)

Upon initiation of ripening in avocado fruit (Persea americana Mill. cv Hass) with 10 microliters/liter ethylene, polysome prevalence and associated poly(A)(+) mRNA increase approximately 3-fold early in the respiratory climacteric and drop off to preclimacteric levels at the peak of the respiratory climacteric. The increase in poly(A)(+) mRNA on polysomes early in the respiratory climacteric constitutes a generic increase in constitutive mRNAs. New gene expression associated with ripening is minimal but evident after 10 hours of ethylene treatment and continues to increase relative to constitutive gene expression throughout the climacteric. The respiratory climacteric can be temporally separated into two phases. The first phase is associated with a general increase in protein synthesis, whereas the second phase reflects new gene expression and accumulation of corresponding proteins which may be responsible for softening and other ripening characteristics. A major new message on polysomes that arises concomitantly with the respiratory climacteric codes for an in vitro translation product of 53 kilodaltons which is immunoprecipitated by antiserum against avocado fruit cellulase.Cyanide at 500 microliters/liter fails to affect the change in polysome prevalance or new gene expression associated with the ethylene-evoked climacteric in avocado fruit. Treatment of fruit with 500 microliters/liter cyanide alone initiates a respiratory increase within 4 hours, ethylene biosynthesis within 18 hours, and new gene expression akin to that educed by ethylene within 20 hours of exposure to cyanide.
Urokinase-Treatment of Fresh Laser Irradiation-Induced Vitreous Hemorrhage (1983)

Using a ruby laser, we induced vitreous hemorrhage in each eye of 12 rabbits. On the following day either 25,000 Ploug units of urokinase or saline were injected into the eyes of each rabbit. Urokinase did not accelerate the absorption of blood from the vitreous but prevented the development of severe vitreous fibrosis which replaced the hemorrhage in seven of the control eyes.
GATA3 mutations define a unique subtype of luminal‐like breast cancer with improved survival (2014)

GATA3 mutations mainly occur in patients with luminal-like breast cancer and have identifiable clinicopathologic and genetic characteristics, highlighting a subgroup of patients with breast cancer in whom limited therapy may be appropriate.
ChemInform Abstract: Ferroelectric WO3 Nanoparticles for Acetone Selective Detection. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Isolation of Human Fibrinogen of High Purity and in High Yield Using Polyethylene Glycol 1000 (1983)

Fibrinogen was isolated from human plasma using a polyethylene glycol 1000 fractionation procedure that eliminates problems of denaturation, degradation and contamination encountered with other procedures (1). The technique is simple, rapid, gives a high yield and gram amounts of fibrinogen can be readily obtained.
Probes of Hydrogen Tunneling with Horse Liver Alcohol Dehydrogenase at Subzero Temperatures (2001)

The temperature dependence of steady-state kinetics has been studied with horse liver alcohol dehydrogenase (HLADH) using protonated and deuterated benzyl alcohol as substrates in methanol/water mixtures between +3 and -50 degrees C. Additionally, the competitive isotope effects, k(H)/k(T) and k(D)/k(T), were measured. The studies indicate increasing kinetic complexity for wild-type HLADH at subzero temperatures. Consistent with earlier findings at 25 degrees C [Bahnson et al. (1993) Biochemistry 31, 5503], the F93W mutant shows much less kinetic complexity than the wild-type enzyme between 3 and -35 degrees C. An analysis of noncompetitive deuterium isotope effects and competitive tritium isotope effects leads to the conclusion that the reaction of F93W involves substantial hydrogen tunneling down to -35 degrees C. The effect of methanol on kinetic properties for the F93W mutant was analyzed, showing a dependence of competitive KIEs on the NAD(+) concentration. This indicates a more random bi--bi kinetic mechanism, in comparison to an ordered bi-bi kinetic mechanism in water. Although MeOH also affects the magnitude of the reaction rates and, to some extent, the observed KIEs, the ratio of ln k(H)/k(T) to ln k(D)/k(T) for primary isotope effects has not changed in methanol, and we conclude little or no change in kinetic complexity. Importantly, the degree of tunneling, as shown from the relationship between the secondary k(H)/k(T) and k(D)/k(T) values, is the same in water and MeOH/water mixtures, implicating similar trajectories for H transfer in both solvents. In a recent study of a thermophilic alcohol dehydrogenase [Kohen et al. (1999) Nature 399, 496], it was shown that decreases in temperatures below a transition temperature lead to decreased tunneling. This arises because of a change in protein dynamics below a break point in enzyme activity [Kohen et al. (2000) J. Am. Chem. Soc. 122, 10738-10739]. For the mesophilic HLADH described herein, an opposite trend is observed in which tunneling increases at subzero temperatures. These differences are attributed to inherent differences in tunneling probabilities between 0 and 100 degrees C vs subzero temperatures, as opposed to fundamental differences in protein structure for enzymes from mesophilic vs thermophilic sources. We propose that future investigations of the relationship between protein flexibility and hydrogen tunneling are best approached using enzymes from thermophilic sources.
Design, Fabrication and Characterization of Micromirror Array for Display Application (1999)

Abstract A new design of micromachined mirror array for display purpose from Samsung Electronics is presented. Integrating multiple functions into a component and extensive use of photolithography make this design of mirror to be simple as well as easy to make. The prototype is fabricated in an array of 50 × 50 micromirrors. The size of mirror plate is 50 × 50μm2 and the gap between them is 3μm. The mirror plate is tilted by the electrostatic force, and the angle is designed to be 10°. Driving voltage for the finished micromirrors is 28v and the tilt angle is measured as 8.9°. The response time from the rest to full tilt and back to rest position takes about 20μs when it is driven at the natural frequency of 24.7kHz. In the reliability point of view, the importance of anti-stiction coating can not be over stressed. Without one, most of the mirrors couldn’t survive a few contacts with the substrate. However, when proper anti-stiction coating is applied and atmosphere is controlled to eliminate the humidity, 94.6% of micromirrors were still rocking after 1.15 × 1010 cycles. In a series of experiments, it was possible to show this new design of micromirror array could be used as a display device, when they are driven at a certain combination of addressing and bias signals. A variable character generation and PWM-type brightness control is successfully demonstrated.
A microRNA in a Multiple-Turnover RNAi Enzyme Complex (2002)

In animals, the double-stranded RNA-specific endonuclease Dicer produces two classes of functionally distinct, tiny RNAs: microRNAs (miRNAs) and small interfering RNAs (siRNAs). miRNAs regulate mRNA translation, whereas siRNAs direct RNA destruction via the RNA interference (RNAi) pathway. Here we show that, in human cell extracts, the miRNA let-7 naturally enters the RNAi pathway, which suggests that only the degree of complementarity between a miRNA and its RNA target determines its function. Human let-7 is a component of a previously identified, miRNA-containing ribonucleoprotein particle, which we show is an RNAi enzyme complex. Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells.
Long-Term Homeostasis of Extracellular Glutamate in the Rat Cerebral Cortex across Sleep and Waking States (2009)

Neuronal firing patterns, neuromodulators, and cerebral metabolism change across sleep-waking states, and the synaptic release of glutamate is critically involved in these processes. Extrasynaptic glutamate can also affect neural function and may be neurotoxic, but whether and how extracellular glutamate is regulated across sleep-waking states is unclear. To assess the effect of behavioral state on extracellular glutamate at high temporal resolution, we recorded glutamate concentration in prefrontal and motor cortex using fixed-potential amperometry in freely behaving rats. Simultaneously, we recorded local field potentials (LFPs) and electroencephalograms (EEGs) from contralateral cortex. We observed dynamic, progressive changes in the concentration of glutamate that switched direction as a function of behavioral state. Specifically, the concentration of glutamate increased progressively during waking (0.329 +/- 0.06%/min) and rapid eye movement (REM) sleep (0.349 +/- 0.13%/min). This increase was opposed by a progressive decrease during non-REM (NREM) sleep (0.338 +/- 0.06%/min). During a 3 h sleep deprivation period, glutamate concentrations initially exhibited the progressive rise observed during spontaneous waking. As sleep pressure increased, glutamate concentrations ceased to increase and began decreasing despite continuous waking. During NREM sleep, the rate of decrease in glutamate was positively correlated with sleep intensity, as indexed by LFP slow-wave activity. The rate of decrease doubled during recovery sleep after sleep deprivation. Thus, the progressive increase in cortical extrasynaptic glutamate during EEG-activated states is counteracted by a decrease during NREM sleep that is modulated by sleep pressure. These results provide evidence for a long-term homeostasis of extracellular glutamate across sleep-waking states.