gebhart/patrepeval huggingface dataset:
Tet-On Systems For Doxycycline-inducible Gene Expression (2016)

The tetracycline-controlled Tet-Off and Tet-On gene expression systems are used to regulate the activity of genes in eukaryotic cells in diverse settings, varying from basic biological research to biotechnology and gene therapy applications. These systems are based on regulatory elements that control the activity of the tetracycline-resistance operon in bacteria. The Tet-Off system allows silencing of gene expression by administration of tetracycline (Tc) or tetracycline-derivatives like doxycycline (dox), whereas the Tet-On system allows activation of gene expression by dox. Since the initial design and construction of the original Tet-system, these bacterium-derived systems have been significantly improved for their function in eukaryotic cells. We here review how a dox-controlled HIV-1 variant was designed and used to greatly improve the activity and dox-sensitivity of the rtTA transcriptional activator component of the Tet-On system. These optimized rtTA variants require less dox for activation, which will reduce side effects and allow gene control in tissues where a relatively low dox level can be reached, such as the brain.
The borrowdale volcanic series of the dunnerdale fells, lancashire (1956)

Abstract In the Dunnerdale Fells, south‐west of Coniston, Lancashire, a succession of tuffs, andesites and rhyolites, over 8,000 ft. thick, forming the lower part of the Borrowdale Volcanic Series, has been mapped. These rocks are overlain with marked unconformity by the Coniston Limestone Series, which dips steeply south‐eastwards and oversteps most of the Borrowdale succession in a south‐westerly direction. The Borrowdale Series is affected by two major periods of earth‐movements, the earlier of pre‐Caradoc and the later of Devonian age. The general dip of the Borrowdale Series is eastwards. It shows little folding but is traversed by large tear‐faults with northerly trend. An important belt of faulting closely follows the outcrop of the Coniston Limestone and includes reversed faults. Both sets of faults appear to be of Devonian age.
Vi polysaccharide of <i>Salmonella typhi</i> targets the prohibitin family of molecules in intestinal epithelial cells and suppresses early inflammatory responses (2004)

Vi capsular polysaccharide (Vi) was first identified as a virulence antigen of Salmonella typhi, the causative agent of typhoid fever in humans; it renders S. typhi resistant to phagocytosis and the action of serum complement. However, the role of Vi during the infection of intestinal epithelium with S. typhi is not completely understood. We show here that Vi can interact with a model human intestinal epithelial cell line, Caco-2, through a cell-surface-associated molecular complex containing two major proteins of 30 and 35 kDa and a minor protein of approximately 68 kDa. The two major proteins were identified as the putative tumor suppressor molecule, prohibitin, and its closely related homolog, B cell receptor-associated protein 37. These two proteins were enriched in lipid rafts, and Vi readily associated with these membrane microdomains. Engagement of Caco-2 cells with Vi inhibited their ability to produce an inflammatory response upon infection with Vi(-) S. typhi. Consistent with this effect, infection of Caco-2 cells with Vi(+) S. typhi produced less IL-8 compared with Vi(-) S. typhi. Cells treated with Vi showed reduced extracellular signal-regulated kinase phosphorylation in response to infection with Vi(-) S. typhi or stimulation with phorbol 12-myristate 13-acetate, suggesting that the mitogen-activated protein kinase pathway might be a target for Vi-mediated inhibition of inflammatory responses. These findings reveal a crucial role for Vi in the modulation of early inflammatory responses during infection with S. typhi. This kind of a modulation could play a significant role in the establishment of infection by S. typhi.
Interface magnetism in 3d/5d multilayers probed by X-ray magnetic circular dichroism (2003)

X-ray magnetic circular dichroism measurements have been performed on Fe/W, Fe/Ir and Co/Pt magnetic multilayers at 10 K. Considerable induced magnetic moments were probed for the nonmagnetic W (less-than-half-filled 5d shell) and Ir, Pt (more-than-half-filled 5d shell). It was found that W couples antiferromagnetically and Ir, Pt ferromagnetically to the 3d layers. Moreover, the spin and orbital magnetic moments for W couple in parallel contrary to what is expected form the third Hund's rule. In this case, the electronic band structure formation results in apparent violations of atomistic properties. This shows that unusual induced magnetic behavior of 5d elements may appear in layered structures.
A monolithic CMOS 10 MHz DPLL for burst-mode data retiming (1990)

A first-order digital phase locked loop (DPLL) that can acquire phase lock from the highly jittered preamble of a burst-mode, Manchester-coded, 10-Mb/s data packet using information acquired from only three transistors is described. A 16-stage delay line locked to a 10-MHz reference clock is embedded in the DPLL. This allows 3.125-ns phase steps to be generated without a high-speed clock. Implemented in a 1.75- mu m CMOS technology, the DPLL circuit occupies 4 mm/sup 2/ of silicon and consumes 125 mW from a 5-V supply.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Nitrite in Meat (1992)

Another way of expressing 200 ppm is to say it is 1 pound of sodium nitrite in 5,000 pounds of meat. Effective June 15,1978, the USDA changed the curing procedures of “pumped” bacon as follows: the use of sodium nitrate and potassium nitrate is prohibited; the level of ingoing sodium nitrite shall be 120 ppm (or 148 ppm potassium nitrite); the level of ingoing sodium ascorbate (vitamin C) or sodium erythorbate (isoascorbate) shall be 550 ppm. According to USDA surveys, these changes have resulted in bacon that does not form nitrosamines when cooked at 340° F for 3 minutes on each side. These three changes apply only to pumped bacon and do not apply to dry cured bacon.
1,8-Diazabicyclo[6.6.6]eicosa-4,11,17-triyne: a flexible cage for protons, copper(I) and silver(I) (1999)

X-Ray structure analysis of the diprotonated cage of 3 and its silver(I) and copper(I) complexes reveals in all three cases the in,in conformation and a significant shortening of the intrabridgehead distance from 5.05 Å in 3 to 4.85 Å for 3·2H+, 4.23 Å for 3·Cu+ and 4.61 Å for 3·Ag+.
Blocking Probability Analysis of Circuit-Switched Networks With Long-Lived and Short-Lived Connections (2013)

We consider a circuit-switched network with nonhierarchical alternate routing and trunk reservation involving two types of connections that are modeled as long-lived and short-lived calls. The long-lived calls can be reserved well in advance, and the short-lived calls are provided on demand. Therefore, we assume that the long-lived calls have strict priority over the short-lived ones. We develop approximations for the estimation of the blocking probability based on the quasi-stationary approach in two ways. One uses the Erlang fixed-point approximation (EFPA), and the other uses the overflow priority classification approximation (OPCA). We compare the results of the approximations with simulation results and discuss the accuracy of the approximations under different system parameters, such as ratio of offered load, number of links per trunk, maximum allowable number of deflections, and trunk reservation. We also discuss the robustness of the quasi-stationary approximation to the ratio of the mean holding times of the long-lived and short-lived calls as well as that of EFPA and OPCA to the shape of the holding time distribution. Finally, we demonstrate that OPCA can be applied to a large network such as the Coronet.
Development of surrogate endpoint biomarkers for clinical trials of cancer chemopreventive agents: relationships to fundamental properties of preinvasive (intraepithelial) neoplasia. (1994)

The tissue changes offering the greatest immediate potential for development as surrogate endpoint biomarkers (SEBs) to be used in Phase II trials of cancer chemopreventive agents are those derived from the microscopic tissue changes pathologists use to make the diagnosis of preinvasive (intraepithelial) neoplasia. These changes comprise four categories: proliferative index, ploidy, nuclear morphometry (size, shape, texture, and pleomorphism), and nucleolar morphometry (number, size, shape, position, and pleomorphism). Computer-assisted image analysis (CIA) permits dozens of additional morphometric parameters to be developed. Other categories of candidate SEBs are: DNA and chromosomal structural changes associated with genomic instability, activation of oncogenes and inactivation of tumor suppressor genes, structural changes in differentiated molecules, and aberrations of growth factor/receptor structure and function. Self-perpetuating DNA breakage with secondary mutator mutations in genomic stability genes is a major mechanism by which the genomic instability characteristic of neoplasia occurs, and from which stem other basic neoplastic properties, including clonal evolution, along multiple pathways of genetic variation that are stochastically determined, continuously increasing proliferation, rate and extent of phenotypic heterogeneity. SEBs resulting from genomic instability include homogeneously staining regions, double minute chromosomes, micronuclei, dicentrics, gene amplification, loss of heterozygosity, and alterations in chromosome number. Newly developed assays for detecting genomic instability include comparative genomic hybridization using fluorescence in situ hybridization on > 20 micron-thick sections monitored by confocal laser scanning microscopy, assays for microsatellite instability, and restriction landmark genomic scanning. These assays offer promise for detecting the earliest molecular changes of neoplasia in normal-appearing epithelium prior to the onset of the dysplastic phase of intraepithelial neoplasia.
Evaluation of Chemical Mechanical Planarization Capability of Titan™ Wafer Carrier on Silicon Oxide (2017)

Chemical mechanical polishing (CMP) has emerged as a critical technique for the manufacture of complex integrated circuits to achieve low surface roughness and high degree of planarization. In part ...
对佛教体验的再思考：皈依与神迹——佛教体验的“家族相似性”特征 (2005)

佛教中的体验与家庭相似性关联何在,为之辩护的论题包括两部分:(1)与其他方式相比,把皈依概念和神迹概念纳入体验概念可以使我们对佛教体验形成一种更为恰当的观点,而这一观点能够表明佛教的宣称与科学的经验主义的宣称之间的区别(前提1-10);(2)关于界定体验之所是的家族相似性理念,本文结论是,皈依与神迹是对佛教中的体验所作出的非实在论的家族相似性定义中的两个要素(前提11-13).
A simple method for measuring complex acoustic impedance of biological tissues using a used quartz rod as a transmission line (2002)

The authors have developed a simple method of measuring the complex acoustic impedance of small biological materials for use as a tactile sensor in the field of endoscopic ultrasonography. Previous methods are too bulky for use in endoscopy. The reflection coefficient was measured by varying the distance between the end face of the transmission line and the surface of the sample. The real part of the impedance was calculated form the maximum and minimum values of the reflected signal and the imaginary part of the impedance was calculated for the distance. An experiment was conducted at 5 MHz using a 10-cm 2-mm diameter fused quartz rod. The experiment results show that the impedance can be measured with an accuracy of 5%.
<i>COD::CIF::Parser</i>: an error-correcting CIF parser for the Perl language (2015)

A syntax-correcting CIF parser, <i>COD::CIF::Parser</i>, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on <i>COD::CIF::Parser</i>, the <i>cod-tools</i> package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The <i>cod-tools</i> package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.
Studies on the source of urinary cholesterol in the normal human male (1981)

The aim of the present study was to obtain information on the source of urinary cholesterol in normal men of various age groups (22-25, 37-42, greater than 63 yrs). Aliquots of 24-hr urine samples were fractionated by ultracentrifugation. Between 10-20% of the total cholesterol in urine (measured by gas-liquid chromatography) separately sedimented after 2 x 10(4) g-min and after 4 x 10(5) g-min of centrifugation. However, an average of more than 50% of the total sedimented after 6 x 10(6) g-min and only 10-20% of total cholesterol remained in this supernatant. These results indicate that most of the cholesterol in urine of normal males is a component of a light particulate fraction. Little difference was seen in the distribution of urinary cholesterol among the various age groups examined The 4 x 10(5) g-min supernatant from 24-hour total urine samples was recentrifuged at 10(5) g for 60 min. The resulting pellet (100 P) was assayed for protein, total cholesterol and phospholipid. The cholesterol was 12-14% esterified. A molar ratio of total cholesterol to phospholipid of 1 to 0.8 was calculated. Assay of the 100 P fraction for marker enzymes showed an activity pattern characteristic for plasma membranes. Fractionation of the 100 P proteins by electrophoresis and separation of the 100 P phospholipids by thin-layer chromatography revealed patterns clearly different from those of human red cell plasma membrane. Electron micrographs of the 100 P fraction revealed an appearance similar to that of deteriorated membranes. The results suggest that most of the cholesterol in urine of the adult human male is present as a component of membranes derived from endogenous cells of the urogenital system.
Effect of Melatonin on Age Associated Changes in Guinea Pig Bladder Function (2007)

Purpose: The incidence of urinary incontinence increases with age but the cause and effect relationship between aging and altered bladder function is poorly understood. It was suggested that melatonin can ameliorate negative effects induced by aging by its free radical scavenging activity and its ability to decrease oxidative stress. We investigated the changes in bladder function evoked by aging and the possible benefits of melatonin treatment on age related bladder disturbances. Materials and Methods: Bladder function was assessed using cystometry in conscious, freely moving female guinea pigs. Animals were grouped according to age as young adults (4 months old) and senescents (18 to 20 months old). A group of senescent animals were treated with 2.5 mg kg(-1) day(-1) melatonin for 21 days. Results: Aging led to increased detrusor activity, as demonstrated by short micturition intervals, decreased bladder capacity and spontaneous contractions during the filling phase. During the voiding phase aged animals showed lower micturition pressures than young adults. Melatonin counteracted the cystometric changes in senescent animals and restored micturition parameters to those of young adults. Conclusions: These results show that in guinea pigs aging induces detrusor overactivity. Melatonin treatment improved age induced changes in bladder function. If similar effects can be demonstrated in humans, melatonin treatment may be a new approach to decrease the impact of age related bladder disorders.
A reverse engineering methodology to reconstruct hierarchical data flow diagrams for software maintenance (2003)

The methodology used to define a reverse engineering process that has been employed in an enhancement maintenance operation on a Pascal software system is described. Attention is focused on the methodology used to produce, from code, a hierarchy of data-flow diagrams (DFDs) at different levels of abstraction. DFDs are produced in the high-level design phase of a software production process using transform analysis. It is shown that DFD production by reverse engineering is useful in maintenance, not only for the software comprehension phase, but also for suggesting and supporting restructuring activities during the development of maintenance operations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Characterization of a prostaglandin‐like metabolite of linolenic acid produced by a flaxseed extract (1978)

Abstract One of the products formed upon incubation of linolenic acid ( cis 9,12,15‐octadecatrienoic acid) with an extract of flaxseed acetone powder has been characterized as 8‐[2‐( cis ‐pent‐2′‐enyl)‐3‐oxo‐ cis ‐cyclopent‐4‐enyl]octanoic acid. The cyclopentenone ring structure of this acid is analogous to that of the A‐type prostaglandins produced in mammalian systems.
Watch your language! (1998)

Sure, object orientation is unnatural-computer programming in any language is. We must rely on good principles, good tools, and good languages. This author tells L. Hatton to blame C++ and its culture for the bad rap against OO, and to look elsewhere for a workable OO language. He suggests comparing C to a better OOP language. In his view, Eiffel fosters a culture embodying the best tendencies of OOP Most importantly, Eiffel offers programmers the ability to specify formally, at the implementation level, the behavior of a class. Several companies have reported that such specifications, written in Eiffel, can greatly improve the reliability of large scale software systems.
Large scale genotype–phenotype correlation analysis based on phylogenetic trees (2007)

We provide two methods for identifying changes in genotype that are correlated with changes in a phenotype implied by phylogenetic trees. The first method, VENN, works when the number of branches over which the change occurred are modest. VENN looks for genetic changes that are completely penetrant with phenotype changes on a tree. The second method, CCTSWEEP, allows for a partial matching between changes in phenotypes and genotypes and provides a score for each change using Maddison's concentrated changes test. The mutations that are highly correlated with phenotypic change can be ranked by score. We use these methods to find SNPs correlated with resistance to Bacillus anthracis in inbred mouse strains. Our findings are consistent with the current biological literature, and also suggest potential novel candidate genes.
Point-of-care, portable microfluidic blood analyzer system (2012)

Recent advances in MEMS technology have provided an opportunity to develop microfluidic devices with enormous potential for portable, point-of-care, low-cost medical diagnostic tools. Hand-held flow cytometers will soon be used in disease diagnosis and monitoring. Despite much interest in miniaturizing commercially available cytometers, they remain costly, bulky, and require expert operation. In this article, we report progress on the development of a battery-powered handheld blood analyzer that will quickly and automatically process a drop of whole human blood by real-time, on-chip magnetic separation of white blood cells (WBCs), fluorescence analysis of labeled WBC subsets, and counting a reproducible fraction of the red blood cells (RBCs) by light scattering. The whole blood (WB) analyzer is composed of a micro-mixer, a special branching/separation system, an optical detection system, and electronic readout circuitry. A droplet of un-processed blood is mixed with the reagents, i.e. magnetic beads and fluorescent stain in the micro-mixer. Valve-less sorting is achieved by magnetic deflection of magnetic microparticle-labeled WBC. LED excitation in combination with an avalanche photodiode (APD) detection system is used for counting fluorescent WBC subsets using several colors of immune-Qdots, while counting a reproducible fraction of red blood cells (RBC) is performed using a laser light scatting measurement with a photodiode. Optimized branching/channel width is achieved using Comsol Multi-Physics™ simulation. To accommodate full portability, all required power supplies (40v, ±10V, and +3V) are provided via step-up voltage converters from one battery. A simple onboard lock-in amplifier is used to increase the sensitivity/resolution of the pulse counting circuitry.
Infant Methemoglobinemia: The Role of Dietary Nitrate in Food and Water (2005)

Infants for whom formula may be prepared with well water remain a high-risk group for nitrate poisoning. This clinical report reinforces the need for testing of well water for nitrate content. There seems to be little or no risk of nitrate poisoning from commercially prepared infant foods in the United States. However, reports of nitrate poisoning from home-prepared vegetable foods for infants continue to occur. Breastfeeding infants are not at risk of methemoglobinemia even when mothers ingest water with very high concentrations of nitrate nitrogen (100 ppm).
How Real Should Virtual Characters Be (2006)

In recent years 3D virtual characters have become more common\nin desktop interfaces, particularly in gaming and entertainment\napplications. In this paper we describe how augmented reality\n(AR) technology can be used to bring virtual characters into the\nreal world and compare AR characters to other types of virtual\ncharacters. We have developed a handheld AR educational\napplication in which a virtual character teaches users about art\nhistory. We present results from a user study that explores how\nrealistic the character needs to be for it to be an effective and\nengaging educational tool and if augmented reality offers benefits\nfor this type of application.
Trinucleotide Cap Analogue Bearing a Locked Nucleic Acid Moiety: Synthesis, mRNA Modification, and Translation for Therapeutic Applications (2021)

The synthesis of a new trinucleotide cap analogue containing a locked nucleic acid (LNA) moiety such as m<sup>7(LNA)</sup>G(5')ppp(5')A<sub>m</sub>pG and its molecular biology applications are described. The most appealing feature is that this new cap analogue outperforms the standard trinucleotide cap m<sup>7</sup>G(5')ppp(5')A<sub>m</sub>pG and the anti-reverse cap analogue m<sub>2</sub><sup>7,3'-<i>O</i></sup>G(5')ppp(5')G by a factor of 5 in terms of translational efficiency.
Organic‐Catalyst‐Mediated Cyclopropanation Reaction (2003)

Cyclopropanierung mit Ammoniumyliden überführt elektronenarme Alkene in einem katalytischen Prozess in guten Ausbeuten in trans-Cyclopropane (siehe Schema; EWG=Elektronen ziehende Gruppe). Die Reaktion lässt sich auch in einer hochenantioselektiven Version durchführen, wenn stöchiometrische Mengen eines chiralen tertiären Amins eingesetzt werden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2003/z50353_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.