gebhart/patrepeval huggingface dataset:
“Sleeping Beauty”: Quiescence in<i>Saccharomyces cerevisiae</i> (2004)

The cells of organisms as diverse as bacteria and humans can enter stable, nonproliferating quiescent states. Quiescent cells of eukaryotic and prokaryotic microorganisms can survive for long periods without nutrients. This alternative state of cells is still poorly understood, yet much benefit is to be gained by understanding it both scientifically and with reference to human health. Here, we review our knowledge of one "model" quiescent cell population, in cultures of yeast grown to stationary phase in rich media. We outline the importance of understanding quiescence, summarize the properties of quiescent yeast cells, and clarify some definitions of the state. We propose that the processes by which a cell enters into, maintains viability in, and exits from quiescence are best viewed as an environmentally triggered cycle: the cell quiescence cycle. We synthesize what is known about the mechanisms by which yeast cells enter into quiescence, including the possible roles of the protein kinase A, TOR, protein kinase C, and Snf1p pathways. We also discuss selected mechanisms by which quiescent cells maintain viability, including metabolism, protein modification, and redox homeostasis. Finally, we outline what is known about the process by which cells exit from quiescence when nutrients again become available.
Detection of Hepatitis C Virus RNA in Formalin-Fixed, Paraffin-Embedded Thin-Needle Liver Biopsy Specimens (2003)

We examined the feasibility of detecting hepatitis C virus (HCV) RNA in formalin-fixed, paraffin-embedded (FFPE) specimens obtained by thin-needle biopsy (TNB). Specimens obtained by large-needle biopsy (LNB) and unfixed frozen tissue served as controls. A total of 23 biopsy specimens, 13 obtained by TNB and 10 by LNB, from 20 patients with chronic hepatitis C were included in the study. HCV RNA was detected by nested reverse transcription-polymerase chain reaction (RT-PCR). HCV RNA was found in FFPE archival specimens obtained by TNB (11 [85%]) or LNB (7 [70%]). The sensitivity was similar in unfixed tissue in which HCV RNA was found in 7 (88%) of 8 TNB specimens and 6 (86%) of 7 LNB specimens. The detection of HCV RNA did not seem to be affected by storage of the paraffin blocks, the presence of advanced fibrosis and cirrhosis, or fragmentation of the core cylinder. TNB yields enough qualitative suitable material to detect HCV RNA by RT-PCR.
Generalization of Microdischarge Scaling Laws for All Gases at Atmospheric Pressure (2017)

The failure of traditional breakdown theories to predict breakdown voltage Vb for microscale gaps motivates studies for more accurate approaches. We generalize scaling laws previously derived for argon at atmospheric pressure to model any gas at atmospheric pressure for gap distances from 100 nm to 30 μm and perform a matched asymptotic analysis to derive simple analytic equations for Vb at critical limits. We obtain excellent agreement between numerical solutions, analytic equations, particle-in-cell simulations, and experimental data. Furthermore, we assess the relative contributions of field emission and Townsend discharge for gaps larger than 100 nm, demonstrating that the field emission contribution exceeds the Townsend contribution for gap distances smaller than several microns. For example, with argon, nickel electrodes, and a field enhancement factor of 55, the field emission contribution exceeds the Townsend contribution below 10 μm.
Understanding the limitations of causally and totally ordered communication (1993)

Causally and totally ordered communication support (CATOCS) has been proposed as important to provide as part of the basic building blocks for constructing reliable distributed systems. In this paper, we identify four major limitations to CATOCS, investigate the applicability of CATOCS to several classes of distributed applications in light of these limitations, and the potential impact of these facilities on communication scalability and robustness. From this investigation, we find limited merit and several potential problems in using CATOCS. The fundamental difficulty with the CATOCS is that it attempts to solve problems at the communication level in violation of the well-known "end-to-end" argument.
Enhanced giant magneto-impedance effect in soft ferromagnetic amorphous ribbons with pulsed laser deposition of cobalt ferrite (2013)

We have grown a 50 nm thick magnetic layer of cobalt ferrite (CFO) on two Co-based amorphous ribbons of compositions Co65Fe4Ni2Si15B14 (type I) and Co69Fe4Ni1Mo2B12Si12 (type II) by a pulsed laser deposition technique. A comparative study of the influence of this CFO layer on the giant magneto-impedance (GMI) effect and field sensitivity (η) of the ribbons is presented. Our results reveal that the presence of the CFO layer enhanced both the GMI ratio and the field sensitivity of the ribbons. Relative to the plain ribbons, the GMI ratio and field sensitivity of the CFO-coated ribbons increased by 97% and 42% for type I and by 34% and 50% for type II, respectively. The enhanced effects are attributed to the modifications on the ribbon surface and closure of magnetic flux paths due to the CFO layer.
Nonenzymatic Polyubiquitination of Expressed Proteins (2014)

Ubiquitination is one of the most ubiquitous posttranslational modifications in eukaryotes and is involved in various cellular events such as proteasomal degradation and DNA repair. The overwhelming majority of studies aiming to understand ubiquitination and deubiquitination have employed unanchored ubiquitin chains and mono-ubiquitinated proteins. To shed light on these processes at the molecular level, it is crucial to have facile access to ubiquitin chains linked to protein substrates. Such conjugates are highly difficult to prepare homogenously and in workable quantities using the enzymatic machinery. To address this formidable challenge we developed new chemical approaches to covalently attach ubiquitin chains to a protein substrate through its Cys residue. A key aspect of this approach is the installation of acyl hydrazide functionality at the C-terminus of the proximal Ub, which allows, after ubiquitin chain assembly, the introduction of various reactive electrophiles for protein conjugation. Employing α-globin as a model substrate, we demonstrate the facile conjugation to K48-linked ubiquitin chains, bearing up to four ubiquitins, through disulfide and thioether linkages. These bioconjugates were examined for their behavior with the USP2 enzyme, which was found to cleave the ubiquitin chain in a similar manner to unanchored ones. Furthermore, proteasomal degradation study showed that di-ubiquitinated α-globin is rapidly degraded in contrast to the mono-ubiquitinated counterpart, highlighting the importance of the chain lengths on proteasomal degradation. The present work opens unprecedented opportunities in studying the ubiquitin signal by enabling access to site-specifically polyubiquitinated proteins with an increased size and complexity.
Detection of CD44 splice variants in formalin‐fixed, paraffin‐embedded specimens of human skin cancer (1997)

The standard form of CD44 (CD44s) and CD44 isoforms, containing sequences encoded by one or several of 10 different variant CD44 exons (v1-v10), are thought to play a crucial role in the growth and metastasis of certain human tumors. Recently, monoclonal antibodies (mAbs) directed against all CD44 isoforms (panCD44), or against epitopes encoded by specific variant exons (CD44v) have been developed, which unfortunately only stain cryopreserved tissues. We wished to develop a technique to unmask chemically CD44s and CD44v epitopes in paraffin-embedded specimens of human skin cancers, so that they would be accessible for these mAbs. To address this issue, CD44s and CD44v expression was compared in cryopreserved and in formalin-fixed, paraffin-embedded biopsies obtained from the same basal cell carcinomas (BCC), squamous cell carcinomas (SCC), primary malignant melanomas (PMM) and metastatic malignant melanomas (MMM). Formalin-fixed tumors were deparaffinized and treated briefly with an antigen retrieval fluid (TUFTM) at 95 degrees C or left untreated. In untreated paraffin-embedded tissues, no CD44s or CD44v staining was detected. In contrast, in antigen retrieval fluid-treated biopsies CD44s and CD44v expression was identical to that in cryopreserved specimens of the same tumor with the exception of mAbs detecting v7/8 and v10. We conclude that antigen retrieval unmasks certain epitopes in formalin-fixed, paraffin-embedded tissues, thus facilitating future research on the relevance of CD44s and CD44v expression for human skin carcinogenesis.
P4‐135: Inclusion criteria and cognitive responses to optimize trials in Alzheimer's disease (2015)

Our goal was to find the combination of candidate biomarkers and cognitive endpoints to maximize statistical power and minimize cost of clinical trials of healthy elders at risk for cognitive decline due to Alzheimer's disease. 412 cognitively-normal participants were followed over 7 years. Nonlinear methods were used to estimate the longitudinal trajectories of several cognitive outcomes including delayed memory recall, executive function, processing speed, and several cognitive composites by subgroups selected on the basis of biomarkers, including APOE-ε4 allele carriers, CSF biomarkers (Aβ42, total tau and phosphorylated tau), and those with small hippocampi. Derived cognitive composites combining ADAS-cog scores with additional delayed memory recall and executive function components captured decline more robustly across biomarker groups than any measure of a single cognitive domain or ADAS-cog alone. Substantial increases in power resulted when including only participants positive for three or more biomarkers in simulations of clinical trials.
Experimental Testing and Validation of P-band Bi-static Remote Sensing of Soil Moisture in 137-138MHz Range (2016)

Remote sensing using readily available communication signal transmitted by ORBCOMM satellites at very high frequency (VHF) range (137-138MHz) is a promising method for detecting the root zone soil moisture content. The radio wave reflectivity of soil is strongly correlated to soil moisture content. Therefore, if we were able to measure the reflectivity, we might be able to estimate the soil moisture content. In this preliminary study, we analyze direct signal data from the satellites to investigate and verify communication channels in frequency range of interest and their characteristics (bandwidth, pattern, etc.). The analysis of direct signal data is also used for calibrating signal collection systems and compensating for the subtle differences of systems. After comparing the satellite geometry and spectrum from raw signal, we verified that ORBCOMM has 13 channels in our frequency range of interest. It was also verified that among these 13 channels, the channel with center frequency at 137.56MHz is a public channel shared by all satellites and is not suitable for reflectivity computation in that multiple satellites could be in sight by our antenna and the signal reflecting region cannot be determined. In our long duration (~12 hours) analysis, we observed the visible duration and period of the satellites. Conclusively, using ORBCOMM communication signal for sensing the soil moisture is viable. Further study is needed to build up model that relates soil moisture content to reflectivity and a lot of technical issues need to be resolved.
Handling asynchronous interrupts in a PL/1‐like language (1974)

Abstract A method of handling asynchronous interrupts, which are defined to be events, in a highlevel, block‐structured language is described. The language facilities are based on PL/1 conditions. The functions of an interrupt handler and its relationship with the execution time support for the language are defined and discussed. The development of the facilities being presented is also described. Solutions to design problems and implemenation details are stated. The use and benefits of the mechanism are discussed.
Toxicology in the Fast Lane: Application of High-Throughput Bioassays to Detect Modulation of Key Enzymes and Receptors (2009)

BackgroundLegislation at state, federal, and international levels is requiring rapid evaluation of the toxicity of numerous chemicals. Whole-animal toxicologic studies cannot yield the necessary throughput in a cost-effective fashion, leading to a critical need for a faster and more cost-effective toxicologic evaluation of xenobiotics.ObjectivesWe tested whether mechanistically based screening assays can rapidly provide information on the potential for compounds to affect key enzymes and receptor targets, thus identifying those compounds requiring further in-depth analysis.MethodsA library of 176 synthetic chemicals was prepared and examined in a high-throughput screening (HTS) manner using nine enzyme-based and five receptor-based bioassays.ResultsAll the assays have high Z′ values, indicating good discrimination among compounds in a reliable fashion, and thus are suitable for HTS assays. On average, three positive hits were obtained per assay. Although we identified compounds that were previously shown to inhibit a particular enzyme class or receptor, we surprisingly discovered that triclosan, a microbiocide present in personal care products, inhibits carboxylesterases and that dichlone, a fungicide, strongly inhibits the ryanodine receptors.ConclusionsConsidering the need to rapidly screen tens of thousands of anthropogenic compounds, our study shows the feasibility of using combined HTS assays as a novel approach toward obtaining toxicologic data on numerous biological end points. The HTS assay approach is very useful to quickly identify potentially hazardous compounds and to prioritize them for further in-depth studies.
ChemInform Abstract: Quesnoin (I), a Novel Pentacyclic ent‐Diterpene from 55 Million Years Old Oise Amber (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.
Oxidation of 2-Mercaptobenzoheterazoles by Dimethyldioxirane. A New Method for a Synthesis of C-2 Substituted Benzimidazole, Benzoxazole, and Benzothiazole Derivatives (1994)

New and efficient reactions in which 2-mercaptobenzoheterazoles are
 selectively converted by dimethyldioxirane, under mild experimental
 conditions, to several C-2 substituted benzoimidazole, benzoxazole, and
 benzothiazole derivatives are reported.
Tumbling Objects Using a Multi-fingered Robot. (1991)

Pushing and tumbling operations (for example tipping a heavy object up on end by pushing it on one side) have good potential for improving the efficiency of robotic manipulation and for expanding the domains where the robot may be used, because robotic manipulators exploiting these operations need not grasp an object firmly and need not support its whole weight.
Polysulfonylamine XXVI. Ein polymeres Lithiumamid mit alternierend tetra‐ und hexakoordinierten Lithiumatomen: Kristallstruktur von Lithiumdimesylamid‐Monohydrat (1991)

Abstract LiN(SO 2 CH 3 ) 2 · H 2 O kristallisiert in der orthorhombischen Raumgruppe Cmc2 1 . Die Li‐Atome und die Wassermoleküle sind zu unendlichen Zickzack‐Ketten Li(2)OH 2 Li(1)OH 2 Li(2) verknüpft. Das Dimesylamid‐Anion fungiert als dreizähniger Brückenligand mit dem N‐Atom und je einem O‐Atom der beiden Sulfonylgruppen als Donoratomen. Außer von den Wassermolekülen wird jedes Li(1) von zwei N‐Atomen, jedes Li(2) von vier O‐Atomen aus vier verschiedenen Dimesylamid‐Gruppen koordiniert. Auf diese Weise erreicht Li(1) eine nahezu ideale tetraedrische (N 2 O 2 )‐Koordination, Li(2) eine verzerrt oktaedrische (O 6 )‐Koordination. Das Ergebnis des Koordinationsmusters ist ein Strang, dessen Repetiereinheit aus vier kondensierten Sechsringen besteht. Die Repetiereinheiten sind über Li(2) spiranartig verknüpft. Die Stränge sind über Wasserstoffbrücken dreidimensional quervernetzt. In der Repetiereinheit werden zwei extrem kurze (S  O)‐Bindungen (137 pm) beobachtet.
Regulation of Gonadotropin-Releasing Hormone (GnRH)-Receptor Gene Expression in Tilapia: Effect of GnRH and Dopamine1 (2004)

The present work was designed to study certain aspects of the endocrine regulation of gonadotropin-releasing hormone receptor (GnRH-R) in the pituitary of the teleost fish tilapia. A GnRH-R was cloned from the pituitary of hybrid tilapia (taGnRH-R) and was identified as a typical seven-transmembrane receptor. Northern blot analysis revealed a single GnRH-R transcript in the pituitary of approximately 2.3 kilobases. The taGnRH-R mRNA levels were significantly higher in females than in males. Injection of the salmon GnRH analog (sGnRHa; 5-50 microg/kg) increased the steady-state levels of taGnRH-R mRNA, with the highest response recorded at 25 microg/kg and at 36 h. At the higher dose of sGnRHa (50 microg/kg), taGnRH-R transcript appeared to be down-regulated. Exposure of tilapia pituitary cells in culture to graded doses (0.1-100 nM) of seabream (sbGnRH = GnRH I), chicken II (cGnRH II), or salmon GnRH (sGnRH = GnRH III) resulted in a significant increase in taGnRH-R mRNA levels. The highest levels of both LH release and taGnRH-R mRNA levels were recorded after exposure to cGnRH II and the lowest after exposure to sbGnRH. The dopamine-agonist quinpirole suppressed LH release and mRNA levels of taGnRH-R, indicating an inhibitory effect on GnRH-R synthesis. Collectively, these data provide evidence that GnRH in tilapia can up- regulate, whereas dopamine down-regulates, taGnRH-R mRNA levels.
Isolation of the mTOR Complexes by Affinity Purification (2011)

The mammalian Target Of Rapamycin (mTOR) protein is a central component of the essential and highly conserved signaling pathway that emerged as a critical effector in regulation of cell physiology. Biochemical studies defined mTOR as the protein kinase that exists at least in two distinct complexes. The first complex has been characterized as the nutrient-sensitive mTOR complex 1 that controls cell growth and cell size by regulating protein synthesis and autophagy. The second complex of mTOR has been defined as the component of growth factor signaling that functions as a major regulatory kinase of Akt/PKB. Here, we provide the detailed methods how to purify the functional complexes of mTOR by affinity purification. In the first part, we describe the purification of the distinct mTOR complexes by immunoprecipitation. Purification of the soluble mTOR complexes is explained in the second part of this chapter.
Liver x receptors stimulate lipogenesis in bovine mammary epithelial cell culture but do not appear to be involved in diet-induced milk fat depression in cows (2014)

Abstract Milk fat synthesis of ruminants can be inhibited by intermediates of ruminal fatty acid biohydrogenation including trans-10, cis-12 conjugated linoleic acid (CLA). These biohydrogenation intermediates signal a coordinated downregulation of genes involved in mammary FA synthesis, transport, and esterification. We have previously reported decreased mammary expression of sterol response element-binding protein 1 (SREBP1), SREBP1-activating proteins, and thyroid hormone-responsive spot 14 (S14) in the cow during diet-induced milk fat depression (MFD), and treatment with trans-10, cis-12 CLA. Liver x receptors (LXR) and retinoid x receptors (RXR) regulate lipogenesis and are known to bind polyunsaturated FA and LXR agonist increases lipid synthesis in mammary epithelial cell culture. The current studies investigated if biohydrogenation products of rumen origin inhibit mammary lipogenesis through LXR and/or RXR. Expression of LXRs was not different in lactating compared to nonlactating bovine mammary tissue, and expression of LXRs, RXRα, and selected LXR and RXR target genes was not changed in mammary tissue during diet-induced or CLA-induced MFD in the cow. In bovine mammary epithelial cell culture, LXR agonist stimulated lipogenesis and expression of LXRß, ATP-binding cassette 1 (ABCA1), SREBP1c, and S14, but LXR activation did not overcome CLA inhibition of lipogenesis and downregulation of LXRß, SREBP1c, and S14 expression. Lastly, expression of the LXR-regulated carbohydrate-responsive element-binding protein (ChREBP) was higher in lactating than nonlactating tissue and was decreased during CLA-induced MFD. We conclude that changes in mammary LXR expression in dairy cows are not involved in MFD and that trans-10, cis-12 CLA inhibition of lipogenesis and diet-induced MFD appears independent of direct LXR signaling.
Targeting ApoB as a therapeutic approach for the treatment of dyslipidemia: the potential role of mipomersen (2010)

AbstractClinical studies demonstrate that lowering LDL-C is associated with a decreased risk of cardiovascular disease. As such, LDL-C recommendations have been lowered over the last several years to keep in line with new clinical data. The currently available lipid-lowering modalities are insufficient to reach those goals for a small but significant percentage of the population. New lipid-lowering therapies that target a different pathway would therefore be of great utility in reaching these goals in high-risk individuals with severe hypercholesterolemia. Targeting efflux of lipids from the liver is an alluring pharmacological objective. Pharmacological inhibition of microsomal triglyceride transfer protein is highly efficacious at lowering LDL-C, but is associated with significant steatosis and fat malabsorption. Knockdown of ApoB, the protein required to produce VLDLs and LDLs, by antisense oligonucleotides is another approach for blocking the efflux of lipids from the liver. Studies in animal models and humans with high LDL-C levels suggest that blocking the synthesis of ApoB is not associated with the same degree of intestinal and hepatic side effects as observed with inhibitors of microsomal triglyceride transfer protein. Mipomersen, a sequence-specific antisense oligonucleotide targeting ApoB mRNA that is presently being tested in clinical trials, is a potentially useful adjunct therapy for individuals that are unable to reach their lipid-lowering goals with currently available lipid-lowering modalities.Keywords: antisense oligonucleotideApoBdyslipidemiaLDL-Cmipomersen
UV-exposed Bragg gratings for laser applications in silver-sodium ion-exchanged phosphate glass waveguides (2006)

High reflectivity Bragg gratings have been written by ArF excimer laser through a phase mask into IOG-1 hybrid phosphate glass. After grating exposure, a waveguide was fabricated by silver-sodium ion-exchange. Reflectivities around 80% at a wavelength of ~ 1535 nm were measured from the waveguide for both quasi-TE and -TM polarizations. Waveguide laser operation with the photowritten waveguide grating as another mirror was demonstrated. Output power of 3.8 mW with a pump power of 199 mW could be extracted from the laser configuration.