gebhart/patrepeval huggingface dataset:
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the<i>Saccharomyces sensu stricto</i>Genus (2011)

High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), S. kudriavzevii (IFO 1802(T) and ZP 591), and S. mikatae (IFO 1815(T)), and describe their comparison to the genomes of S. cerevisiae and S. paradoxus. The new sequences, derived by assembling millions of short DNA sequence reads together with previously published Sanger shotgun reads, have vastly greater long-range continuity and far fewer gaps than the previously available genome sequences. New gene predictions defined a set of 5261 protein-coding orthologs across the five most commonly studied Saccharomyces yeasts, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses. To facilitate experimental investigations, we generated genetically marked, stable haploid strains for all three of these Saccharomyces species. These nearly complete genome sequences and the collection of genetically marked strains provide a valuable toolset for comparative studies of gene function, metabolism, and evolution, and render Saccharomyces sensu stricto the most experimentally tractable model genus. These resources are freely available and accessible through www.SaccharomycesSensuStricto.org.
Phase <scp>II</scp> Clinical Trials (2010)

Abstract Phase II trials are conducted to evaluate the drug's activity for patients with a particular disease or condition and to determine the level of short‐term side effects and possible risks associated with the use of the drug. The drug is further evaluated in randomized phase III trials where it is compared with the current standard treatment in a larger number of patients when preliminary evidence of effectiveness is found in these phase II trials. Phase II trials are single‐armed studies that investigate the antidisease activity of the new therapeutic regimen.
Escherichia coli Subtilase Cytotoxin (2010)

Subtilase cytotoxin (SubAB) is the prototype of a new AB(5) toxin family produced by a subset of Shiga toxigenic Escherichia coli (STEC) strains. Its A subunit is a subtilase-like serine protease and cytotoxicity for eukaryotic cells is due to a highly specific, single-site cleavage of BiP/GRP78, an essential Hsp70 family chaperone located in the endoplasmic reticulum (ER). This cleavage triggers a severe and unresolved ER stress response, ultimately triggering apoptosis. The B subunit has specificity for glycans terminating in the sialic acid N-glycolylneuraminic acid. Although its actual role in human disease pathogenesis is yet to be established, SubAB is lethal for mice and induces pathological features overlapping those seen in the haemolytic uraemic syndrome, a life-threatening complication of STEC infection. The toxin is also proving to be a useful tool for probing the role of BiP and ER stress in a variety of cellular functions.
Potent Inhibition of Steroid Sulfatase Activity by 3-<i>O</i>-Sulfamate 17α-Benzyl(or 4‘-<i>tert</i>-butylbenzyl)estra-1,3,5(10)-trienes:  Combination of Two Substituents at Positions C3 and C17α of Estradiol (1999)

Steroid sulfates are precursors of hormones that stimulate androgen- and estrogen-dependent cancers. Thus, steroid sulfatase, the enzyme that catalyzes conversion of DHEAS and E1S to the corresponding unconjugated steroids DHEA and E1, appears to be one of the key enzymes regulating the level of active androgenic and estrogenic steroids. Since 17alpha-substituted benzylestradiols and 3-O-sulfamate estrone (EMATE) represent two families of steroid sulfatase inhibitors that probably act through different mechanisms, we synthesized compounds 3-O-sulfamate 17alpha-benzylestradiol (4) and 3-O-sulfamate 17alpha-(tert-butylbenzyl)estradiol (5) that contain two kinds of substituents on the same molecule. In our enzymatic assay using a homogenate of human embryonal (293) cells transfected with steroid sulfatase, compounds 4 and 5 were found to be more potent inhibitors than already known steroid sulfatase inhibitors that have only a C17alpha-substituent or only a C3-sulfamate group (EMATE). The IC50 values of 4 and 5 were, respectively, 0.39 and 0.15 nM for the transformation of E1S to E1 and 4.1 and 1.4 nM for the transformation of DHEAS to DHEA. Compound 5 inhibited the steroid sulfatase activity in intact transfected (293) cell culture assays by inactivating the enzyme activity. Compound 5 also inactivates the steroid sulfatase activity at lower concentration than EMATE in microsomes of transfected (293) cells. In this assay, an excess of natural substrate E1S protects enzyme against inactivation by 5 or EMATE. Furthermore, the unsulfamoylated analogue of 5, compound 3, did not inactivate the steroid sulfatase.
What can we learn from molecular dynamics simulations for GPCR drug design? (2014)

Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this article we focus on the application of molecular dynamics (MD) simulations in GPCR drug discovery programs. Typical application scenarios of MD simulations and their scope and limitations will be described on the basis of two selected case studies, namely the binding of small molecule antagonists to the human CC chemokine receptor 3 (CCR3) and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3 (hM3R).
Bacterial and biochemical tests for assessing chemical toxicity in the aquatic environment: A review (1983)

This review describes the use of biochemical and microbial tests to assess the toxicity of aquatic pollutants. Biochemical assays include the use of enzymes (dehydrogenase, ATPases, and others), luminescence, and ATP for measuring chemical toxicity in the aquatic environment. Bacterial tests also can serve as a tool for toxicity testing. These tests are based on measurement of growth inhibition or viability of bacteria and alteration of bacterial metabolism. These tests are relatively simple, rapid, and inexpensive as compared to fish bioassays.
Teaching Engineering with an On-line Student-centred Environment (2001)

The multi-media-rich content associated with the Internet delivers a suite of information media such as video, sound, animations, diagrams and graphs to a student audience. The effectiveness, however, of internet-related technology for the purposes of education, is still not well understood. This paper investigates how the new Internet-based tools can be used to nurture learning at various levels by enhancing teaching with the support of a student-centred learning environment. This paper reports on the experience of using WebLearn, within which student learning is linked to learning objectives at identified learning levels. This ensures that the learning material and activities are coordinated to achieve the desired outcomes. WebLearn greatly facilitates this student learning strategy. The learning taxonomies are illustrated with an Engineering subject as an example. Other features of WebLearn, such as instant feedback and assessment content and administration, and their impact on learning are also described.
Selective focusing of different ion species produced by magnetically insulated ion beam diodes (1985)

Research in light-ion-driven inertial-confinement fusion is emphasizing high-voltage, nonprotonic ions to obtain improved magnetic stiffness. Target preheat by coaccelerated proton impurities is a serious concern. A method is described which should essentially eliminate protonic preheat for applied magnetic field, magnetically insulated (applied-B) ion diodes. Briefly, the charge state of the principal ion species is changed by passing through a thin foil in the applied magnetic field. Due to the change in canonical angular momentum, the ions’ closest approach to the axis of an axisymmetric diode is different from that of the proton contaminant. This difference provides effective separation of protons from the principal species.
Simple Heat Switch for Low Temperature Use (1963)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation J. G. Dash, J. Siegwarth; Simple Heat Switch for Low Temperature Use. Rev. Sci. Instrum. 1 November 1963; 34 (11): 1276–1277. https://doi.org/10.1063/1.1718213 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioReview of Scientific Instruments Search Advanced Search |Citation Search
Drugs for a new millennium (1999)

A millennium, a century, even a decade is a long time-frame for speculation about anything. Advances in biomedical research in the last few decades have been so extraordinary and escalating at an ever-accelerating pace that any prophecy is a risky proposition. However, it is possible to divine the big, unanswered questions and envisage ways in which they might reasonably be approached in the next few decades, a task which I will try to essay. So many drugs treat so many different medical conditions that a detailed and comprehensive coverage would probably be tiresome. Instead, I will address certain broad themes and diseases that offer both immense challenges and great potential for advances. Rather than review detailed experimental issues, I will confine myself to the 'big picture' issues, providing examples of specific research only in a few instances drawing largely from areas I know best.
Accurate prediction of term birth weight from prospectively measurable maternal characteristics. (1999)

Individual term birth weight can be accurately predicted in normal gravidas using routinely measurable maternal characteristics. Birth weight estimates using our equation are both prospectively derivable from the beginning of the third trimester and more accurate than any previously devised algorithms, including those that incorporate fetal ultrasonographic data. Our equation can also identify pregnancies at risk for fetal macrosomia so that the timing and mode of delivery may be prospectively modified to minimize peripartum risks to both fetus and mother.
The Effects of Child Abuse on Preschool Children's Play (1999)

Play is essential for preschool children's normal development and emotional wellbeing. Because play is sensitive to environmental conditions, an abusive or neglectful home environment can adversely affect the child's play development. Although the detrimental effects of physical, sexual, or emotional abuse and neglect are well-documented, few studies have investigated the play of abused children. This paper aims to critically examine the literature and describe the reported effects of child abuse and neglect on preschool children's play. This analysis highlights the need for early childhood professionals to be better informed about the effects of child abuse on young children.
Supply chain management in an uncertain economic climate: a UK perspective (2011)

Purpose The purpose of the paper is to consider whether the benefits that construction organisations achieve by adopting a supply chain management approach to their specialist partners outweigh those that are derived from a market‐driven approach. Design/methodology/approach This editorial adopts a transaction economics perspective to evaluate the external environment facing contracting organisations within the UK, especially as a result of the recent economic downturn. One of the consequences of the reduced demand for construction work is that clients now prefer a market‐based approach to the procurement of their contractors; this assertion is supported by analysis of recently published survey data on client procurement approaches and price and cost data. Findings The transactional economic implications of these changes to the supplier/contractor relationship are presented for discussion. The research implications of this indicate that further empirical data is required on: the economic benefits of supply chain management, how the benefits are derived from the different sub markets that exist in construction, and the influence the external economic environment has upon the contractor/subcontractor transaction interface. Originality/value This work seeks to encourage researchers to empiricise the theoretical constructs of new institutional economics in line with the dynamics of the subcontracting/supplier market. In doing so, a better understanding of the economic factors that can influence the bilateral dependencies that exist between large and small organisations may result.
Control of Concrete Quality Through Statistics (1993)

The quality control of concrete is discussed, and the use of control charts of strength to detect any strength downturn or increase of variability, and pinpoint the cause of change, is described. Cusum control charts are described. The basic procedure of cusum analysis consists of subtracting a constant quantity from each test result and accumulating the differences as each result is obtained. The sum of the successive differences is called the cumulative sum or cusum, and a graph of cusums plotted in sequence of test is a cusum chart. It is noted that the use of cusum charts is not confined to the control of concrete strength. Other properties of concrete such as slump, air content or concrete temperature, can be charted in the same way.
An overview of the advantages and constraints of coded pattern projection techniques for autonomous navigation (2002)

The absolute necessity of obtaining 3D information of structured and unknown environments in autonomous navigation reduce considerably the set of sensors that can be used. The necessity to know, at each time, the position of the mobile robot with respect to the scene is indispensable. Furthermore, this information must be obtained in the least computing time. Stereo vision is an attractive and widely used method, but, it is rather limited to make fast 3D surface maps, due to the correspondence problem. The spatial and temporal correspondence among images can be alleviated using a method based on structured light. This relationship can be directly found codifying the projected light; then each imaged region of the projected pattern carries the needed information to solve the correspondence problem. We present the most significant techniques, used in recent years, concerning the coded structured light method.
Radical Interchange on the Part of Certain Alkyl Orthoformates<sup>1</sup> (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRadical Interchange on the Part of Certain Alkyl Orthoformates1Howard W. Post and Edwin R. EricksonCite this: J. Am. Chem. Soc. 1933, 55, 9, 3851–3854Publication Date (Print):September 1, 1933Publication History Published online1 May 2002Published inissue 1 September 1933https://doi.org/10.1021/ja01336a069RIGHTS & PERMISSIONSArticle Views57Altmetric-Citations11LEARN 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 InReddit PDF (260 KB) Get e-Alerts Get e-Alerts
CO2 laser-produced ripple patterns on Ni<i>x</i>P1−<i>x</i> surfaces (1977)

When CO2-laser pulses of ∼50 ns duration and intensity of ∼100–500 MW/cm2 are incident upon NixP1−x surfaces in oxygen-containing atmospheres, distinctive ’’ripple’’ patterns are etched into the surfaces. The ripple wave fronts are normal to the E field and vary in spacing from ∼λlaser at normal incidence to ∼0.5λlaser for π polarization at grazing incidence.
A NAND structured cell with a new programming technology for highly reliable 5 V-only flash EEPROM (1990)

A programming technology is proposed to improve the endurance and read retention characteristics of NAND-structured EEPROM cells programmed by Fowler-Nordheim tunneling of electrons. Erasing and writing are accomplished uniformly over the whole channel area instead of nonuniform erasing at the drain. To achieve programming over the whole channel area, a new device structure is also proposed. The high-voltage pulses can be easily generated on a chip from a single 5-V power supply because the direct current due to the avalanche breakdown does not flow. The gate length of the memory transistor is 1.0 &mu;m. Using 1.0 &mu;m rules, the cell size per bit is 11.7 &mu;m<sup>2</sup>
Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family (2012)

Cyanuric acid hydrolases (AtzD) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an X-ray structural class. There has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. The present study has addressed those issues. First, the published enzyme reaction products of cyanuric acid hydrolase are incorrectly identified as biuret and carbon dioxide. The current study employed (13)C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to show that cyanuric acid hydrolase releases carboxybiuret, which spontaneously decarboxylates to biuret. This is significant because it revealed that homologous cyanuric acid hydrolases and barbiturases catalyze completely analogous reactions. Second, enzymes that had been annotated incorrectly in genome projects have been reassigned here by bioinformatics, gene cloning, and protein characterization studies. Third, the AtzD/barbiturase family has previously been suggested to consist of members of the amidohydrolase superfamily, a large class of metallohydrolases. Bioinformatics and the lack of bound metals both argue against a connection to the amidohydrolase superfamily. Lastly, steady-state kinetic measurements and observations of protein stability suggested that the AtzD/barbiturase family might be an undistinguished protein family that has undergone some resurgence with the recent introduction of industrial s-triazine compounds such as atrazine and melamine into the environment.
Hydrogen-bonding motifs in the solid-state structure of ferroceneboronic acid (2004)

At 180 K, the crystal structure of ferroceneboronic acid, [Fe(C5H5)(C5H6BO2)], consists of centrosymmetric [FcB(OH)2]2 dimers [Fc is (η5-C5H5)Fe(η5-C5H4)], formed by a pair of complementary O—H⋯O hydrogen-bonding interactions [O⋯H 1.97 Å and O⋯O 2.806 (3) Å]. The remaining two O-bound H atoms per [FcB(OH)2]2 moiety serve to link the dimeric units to adjacent dimers in a criss-cross fashion, very similar to that between hydrogen-bonded chains in solid Fe[η5-C5H4B(OH)2]2.
Microtubule nucleation: γ-tubulin and beyond (2006)

Centrosomes and their fungal equivalents, spindle pole bodies (SPBs), are the main microtubule (MT)-organizing centers in eukaryotic cells. Several proteins have been implicated in microtubule formation by centrosomes and SPBs, including microtubule-minus-end-binding proteins and proteins that bind along the length or stabilize the plus ends of microtubules. Recent work has improved our understanding of the molecular mechanisms of MT formation. In particular, it has shown that gamma-tubulin and its associated proteins play key roles in microtubule nucleation and spindle assembly in evolutionarily distant species ranging from fungi to mammals. Other work indicates that gamma-tubulin-mediated microtubule nucleation, although necessary, is not sufficient for mitotic spindle assembly but requires additional proteins that regulate microtubule nucleation independently of centrosomes.
Hybrid feature and decision level fusion of face and speech information for bimodal emotion recognition (2009)

A hybrid feature and decision level information fusion architecture is proposed for human emotion recognition from facial expression and speech prosody. An active buffer stores the most recent information extracted from face and speech. This buffer allows fusion of asynchronous information through keeping track of individual modality updates. The contents of the buffer will be fused at feature level; if their respective update times are close to each other. Based on the classifiers' reliability, a decision level fusion block combines results of the unimodal speech and face based systems and the feature level fusion based classifier. Experimental results on a database of 12 people show that the proposed fusion architecture performs better than unimodal classification, pure feature level fusion and decision level fusion.
Distinct roles for dystroglycan, β1 integrin and perlecan in cell surface laminin organization (2001)

Dystroglycan (DG) is a cell surface receptor for several extracellular matrix (ECM) molecules including laminins, agrin and perlecan. Recent data indicate that DG function is required for the formation of basement membranes in early development and the organization of laminin on the cell surface. Here we show that DG-mediated laminin clustering on mouse embryonic stem (ES) cells is a dynamic process in which clusters are consolidated over time into increasingly more complex structures. Utilizing various null-mutant ES cell lines, we define roles for other molecules in this process. In beta1 integrin-deficient ES cells, laminin-1 binds to the cell surface, but fails to organize into more morphologically complex structures. This result indicates that beta1 integrin function is required after DG function in the cell surface-mediated laminin assembly process. In perlecan-deficient ES cells, the formation of complex laminin-1 structures is defective, implicating perlecan in the laminin matrix assembly process. Moreover, laminin and perlecan reciprocally modulate the organization of the other on the cell surface. Taken together, the data support a model whereby DG serves as a receptor essential for the initial binding of laminin on the cell surface, whereas beta1 integrins and perlecan are required for laminin matrix assembly processes after it binds to the cell.
Expression of Matrix Metalloproteinase-2 and -9 and Their Inhibitors in Peripheral Blood Cells of Patients with Chronic Hepatitis C (2000)

Peripheral blood cell expression of MMP-2, MMP-9, and TIMP revealed no correlation with the circulating concentrations of these proteins. Only the circulating MMP-2/TIMP-1 ratio correlated to the histological degree of fibrosis in hepatitis C and should be further evaluated as a progression marker in patients with chronic liver disease.