gebhart/patrepeval huggingface dataset:
An overview of protein-folding techniques: issues and perspectives (2005)

The importance of protein folding has been recognised for many years. Almost a half century ago, Linus Pauling discovered two quite simple, regular arrangements of amino acids--the alpha-helix and the beta-sheet that are found in almost every protein. In the early 1960s, Christian Anfinsen showed that the proteins actually "tie" themselves: If proteins become unfolded, they fold back into proper shape of their own accord; no shaper or folder is needed. The nature of the unfolded state plays a great role in understanding proteins. Alzheimer's disease, cystic fibrosis, mad cow disease, and many cancers are inherited emphysema. Recent discoveries show that all these apparently unrelated diseases result from protein folding gone wrong. Theoretical and computational studies have recently achieved noticeable success in reproducing various features of the folding mechanism of several small to medium-sized fast-folding proteins. This survey presents the state-of-the-art in protein structure prediction methods from a computer scientist perspective.
A novel multilayer micro-ring resonator based optical network on chip (2014)

International audience
Organometallic molecule-inorganic surface coordination and catalytic chemistry. In situ CPMAS NMR delineation of organoactinide adsorbate structure, dynamics, and reactivity (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganometallic molecule-inorganic surface coordination and catalytic chemistry. In situ CPMAS NMR delineation of organoactinide adsorbate structure, dynamics, and reactivityWilliam C. Finch, Ralph D. Gillespie, David Hedden, and Tobin J. MarksCite this: J. Am. Chem. Soc. 1990, 112, 17, 6221–6232Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/ja00173a009https://doi.org/10.1021/ja00173a009research-articleACS PublicationsRequest reuse permissionsArticle Views260Altmetric-Citations69LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A digital technique for combining frequency standards (1969)

A new technique for combining multiple frequency standards into a single timing reference based on the average of the frequency of each input is described, The uniqueness of this approach is that it is an all-digital scheme utilizing delay lines and high-speed logic elements currently available, The present and future applications ii of combiners are discussed, the requirements are highlighted, several digital solutions are briefly described, and the detailed block diagrams and characteristics of a particular general purpose combiner are presented. It is suggested that the optimum combiner include a stable quartz crystal oscillator with a frequency control feature, The output of this internal clock is digitally divided into several phases via a tapped delay line. Periodically, as a function of each input standard, the phase is stored in a register, Any time two consecutive samples for any input differ, an accumulator is incremented or decremented by one, and the frequency of the internal clock is correspondingly changed, Throughout, emphasis is placed on digital approaches to problems associated with combining frequency standards.
Diversity of the Angiogenic Phenotype in Non–Small Cell Lung Cancer (2006)

Angiogenesis is crucial for tumor biology. There are many mechanisms by which tumors induce angiogenesis. We hypothesize that each individual tumor develops a unique mechanism to induce angiogenesis, and that activation of a particular angiogenic pathway suppresses the evolution of alternative pathways. We characterized 168 human non-small cell lung cancer (NSCLC) specimens for levels of angiogenic factors (angiogenic CXC chemokines, basic fibroblast growth factor, and vascular endothelial growth factor). We also induced lung tumor formation in A/J mice by injecting the tobacco carcinogen NNK. We dissected individual lung tumors and measured expression of angiogenic factors from three distinct families using real-time PCR. Finally, we controlled the angiogenic milieu using in vivo models to determine the resultant phenotype of the angiogenic factors expressed by NSCLC cells. Human tumors displayed marked variation in the expression of angiogenic factors. Individual mouse tumors, even from within the same mouse, displayed variability in their pattern of expression of angiogenic factors. In a sponge model of angiogenesis using murine lung cancer cells, implanting LLC cells with an angiogenic factor suppressed the expression of other angiogenic factors in implanted sponges. This suppressive effect was not seen in vitro. We conclude that lung cancer tumors evolve a unique and dominant angiogenic phenotype. Once an angiogenic pathway is activated, it may allow for tumor growth to proceed in the absence of a selection pressure to activate a second pathway.
Augmentation of neutrophil-mediated erythrocyte lysis by cells derived in vitro from human monocytes (1987)

Neutrophilic polymorphonuclear leukocytes (PMNs) were incubated with opsonized zymosan and lysed human erythrocytes (RBCs) as measured by a 51Cr release method. Conversely, myeloperoxidase (MPO)-negative hydrogen peroxide (H2O2)-generating cells, derived in vitro from human monocytes (monocyte-derived cells (MDCs), were ineffective per se but capable of augmenting the lysis by PMNs. The lysis by PMNs and PMNs plus MDCs was inhibited by catalase, azide, taurine, and alanine, consistent with the requirement for hypochlorous acid (HOCl). As detected under conditions similar to those used for lytic assays, MDCs failed to produce HOCl but augmented the HOCl recovery from the PMN-RBC system. Moreover, when the extent of the lysis was plotted as a function of the HOCl recovery, a positive linear relationship was found. Although the actual size of the H2O2 extracellular pool could not be measured because of the inexistence of a reliable assay to probe our cytolytic model without perturbing the equilibrium of the system, the results presented suggest that MDCs enhance the PMN-mediated lysis by improving the HOCl production, presumably by supplying extra amounts of H2O2 to be handled by PMN MPO. In fact, the events mediated by MDCs could be reproduced by using an appropriate H2O2-generating enzymatic system (glucose-glucose oxidase). The present study provides direct evidence for the possibility of cooperation between MPO-positive and MPO-negative phagocytes in exerting functions (HOCl production and, in turn, cytolysis) possibly relevant to the outcome of inflammatory processes.
A damping ring design for the SLAC next linear collider (2002)

In this paper, we describe the design of the main damping rings and the positron pre-damping ring for the SLAC Next Linear Collider, a future linear collider with a center-of-mass energy of 0.5 to 1.5 TeV. The rings will operate at an energy of 2 GeV with a maximum repetition rate of 180 Hz. The normalized extracted beam emittances are /spl gamma//spl epsiv//sub x/=3 mm-mrad and /spl gamma//spl epsiv//sub y/=0.03 mm-mrad. To provide the necessary damping, the rings must damp multiple trains of bunches. Thus, the beam current is large, roughly 1 A. We will present the optical layout, magnet designs, and RF systems, along with the dynamic aperture and required alignment tolerances; collective effects will be discussed in another paper.
The Effect of Amorphization Conditions on the Measured Activation of Source Drain Extension Implants (2008)

Un‐patterned wafers were processed using low‐dose Indium or medium‐dose Germanium pre‐amorphization implants (PAI) followed by p‐type dopant implants of BF2 or carborane (CBH). The wafers were then annealed by RTA (spike), laser anneal (LSA) or combination of LSA and spike. Active dopant distributions calculated from SIMS and sheet resistance measurements compared favorably with those determined by differential Hall, which is a challenging technique for shallow profiles. The trends in B diffusion behavior and activation are discussed in relation to the different implant damage budgets, damage evolution during the anneals and presence of fluorine. In particular, for low thermal budget LSA only anneals, CBH implants appear to give higher activation than BF2 due to the absence of fluorine.
Role of P225 and the C136‐C201 disulfide bond in tissue plasminogen activator (1998)

The protease domain of tissue plasminogen activator (tPA), a key fibrinolytic enzyme, was expressed in Escherichia coli with a yield of 1 mg per liter of media. The recombinant protein was titrated with the Erythrina caraffa trypsin inhibitor (ETI) and characterized in its interaction with plasminogen and the natural inhibitor plasminogen activator inhibitor-1 (PAI-1). Analysis of the catalytic properties of tPA using a library of chromogenic substrates carrying substitutions at P1, P2, and P3 reveals a strong preference for Arg over Lys at P1, unmatched by other serine proteases like thrombin or trypsin. In contrast to these proteases and plasmin, tPA shows little or no preference for Pro over Gly at P2. A specific inhibition of tPA by Cu2+ was discovered. The divalent cation presumably binds to H188 near D189 in the primary specificity pocket and inhibits substrate binding in a competitive manner with a Kd = 19 microM. In an attempt to engineer Na+ binding and enhanced catalytic activity in tPA, P225 was replaced with Tyr, the residue present in Na+-dependent allosteric serine proteases. The P225Y mutation did not result in cation binding, but caused a significant loss of specificity (up to 100-fold) toward chromogenic substrates and plasminogen and considerably reduced the inhibition by PAI-1 and ETI. Interestingly, the P225Y substitution enhanced the ability of Cu2+ to inhibit the enzyme. Elimination of the C136-C201 disulfide bond, that is absent in all Na+-dependent allosteric serine proteases, significantly enhanced the yield (5 mg per liter of media) of expression in E. coli, but caused no changes in the properties of the enzyme whether residue 225 was Pro or Tyr. These findings point out an unanticipated crucial role for residue 225 in controlling the catalytic activity of tPA, and suggest that engineering of a Na+-dependent allosteric enhancement of catalytic activity in this enzyme, must involve substantial changes in the region homologous to the Na+ binding site of allosteric serine proteases.
Toward personalized management in bladder cancer: the promise of novel molecular taxonomy (2017)

Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer. The current review is an update on the above advances and their significant implications on the future of bladder cancer patient management.
On identifiability, maximum-likelihood, and novel HOS based criteria (1990)

Considers estimation and classification problems for a stretch of stationary data containing a non-Gaussian linear process and additive Gaussian noise of unknown covariance (AGN/UC). To allow general noncausal and nonminimum phase (NC/NMP) ARMA models, and develop estimation and classification schemes which are immune to AGN/UC higher-order statistics (HOS) are resorted to. Time-domain optimality criteria are discussed which employ a finite set of sample cumulant lags, while the frequency-domain criteria involve sample polyspectral lags.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ChemInform Abstract: ORGANOPHOSPHOR‐ENAMINE 4. MITT. ENAMINTHIOPHOSPHONATE, HERST. UND VERSUCHE EINER VERWENDUNG BEI DER SYNTH. VON ALPHA,BETA‐UNGESAETTIGEN KETONEN (1972)

Abstract Alkinyl‐thiophosphonate (I) addieren die Amine (II) glatt zu den entsprechenden Enaminen (III), deren Stereochemie untersucht wird.
Carbon Starvation Can Induce Energy Deprivation and Loss of Fermentative Capacity in <i>Saccharomyces cerevisiae</i> (2003)

ABSTRACT Seven different strains of Saccharomyces cerevisiae were tested for the ability to maintain their fermentative capacity during 24 h of carbon or nitrogen starvation. Starvation was imposed by transferring cells, exponentially growing in anaerobic batch cultures, to a defined growth medium lacking either a carbon or a nitrogen source. After 24 h of starvation, fermentative capacity was determined by addition of glucose and measurement of the resulting ethanol production rate. The results showed that 24 h of nitrogen starvation reduced the fermentative capacity by 70 to 95%, depending on the strain. Carbon starvation, on the other hand, provoked an almost complete loss of fermentative capacity in all of the strains tested. The absence of ethanol production following carbon starvation occurred even though the cells possessed a substantial glucose transport capacity. In fact, similar uptake capacities were recorded irrespective of whether the cells had been subjected to carbon or nitrogen starvation. Instead, the loss of fermentative capacity observed in carbon-starved cells was almost surely a result of energy deprivation. Carbon starvation drastically reduced the ATP content of the cells to values well below 0.1 μmol/g, while nitrogen-starved cells still contained approximately 6 μmol/g after 24 h of treatment. Addition of a small amount of glucose (0.1 g/liter at a cell density of 1.0 g/liter) at the initiation of starvation or use of stationary-phase instead of log-phase cells enabled the cells to preserve their fermentative capacity also during carbon starvation. The prerequisites for successful adaptation to starvation conditions are probably gradual nutrient depletion and access to energy during the adaptation period.
Undergraduate Students' Beliefs about Engineering Problem Solving (2016)

Abstract Background Problem solving is considered to be a central activity of engineering practice. While some studies have shown how various beliefs affect students' abilities to solve problems, studies are needed that explicitly examine the beliefs and assumptions students bring to the problem‐solving process. Purpose/Hypothesis The purpose of this qualitative research was to describe students' engineering problem‐solving processes and develop a conceptual model that illustrates students' beliefs about problem solving. Our research question was, What beliefs do students have about engineering problem solving? Design/Method We analyzed data from retrospective semistructured interviews carried out after a problem‐solving session. We interviewed nine engineering students about the processes they used to solve the problems and the assumptions and beliefs that guided their problem solving. We then used grounded theory to identify and analyze statements from the interviews and to develop a conceptual model of student beliefs. Results The resulting model has five major categories: the problem‐solving process itself, the role of classroom problems, the role of workplace problems, personal characteristics that affect problem solving, and resources that assist problem solving. Students identify a sharp distinction between classroom problems and workplace problems. Conclusions Our conceptual model provides an initial framework for understanding how students' beliefs affect their approaches to engineering problems. In contrast to stage models, our model shows that students' epistemic beliefs about problem solving are contextual. Future work is needed to understand the limits and extend the applicability of our model.
The ShapeLock system adapted to intragastric and transgastric surgery (2007)

Endoluminal and transgastric surgical procedures present challenges for current endoscopes and instruments which, especially when retroflexed, are too flexible and do not permit transmission of adequate force. The USGI TransPort is a multilumen surgical access system designed to enable endosurgical therapy. ShapeLock technology allows the TransPort to have either a flexible or a rigid state. In flexible mode, the TransPort is introduced and steered to a precise location. It is then locked by squeezing a handle, to provide a rigid platform for therapeutic procedures. A new device for tissue grasping and approximation, the g-Prox, has been designed for use with the TransPort, and this new endosurgical system has been tested in a series of intragastric and transgastric procedures in pigs and human cadavers. The experiments demonstrated the potential for using the TransPort platform to improve flexible endoluminal and transluminal procedures, including intragastric and transgastric fundoplication, cholecystectomy, gastric restriction, and gastric full-thickness incision closure.
Transparent ceramic scintillators for gamma-ray spectroscopy and radiography (2010)

Transparent ceramics have become available in useful sizes for a variety of applications within the past 15 years thanks to improved understanding of sintering phenomena on the nanoscale.1,2 While traditional ceramics may comprise single or multiple crystalline and amorphous mineral phases and are typically translucent or opaque to light, modern optically transparent ceramics are fully dense monoliths of micron-scale (or smaller) crystallites, in most cases formed from pure-phase cubic crystal structures. Fabrication of transparent ceramics begins with high-purity ceramic nanopowders, which are consolidated into a ‘green body’ by pressing or casting. The green body is sintered to near-full density, and the residual porosity is removed by processing the samples in a pressure vessel with high-pressure argon gas (hot isostatic pressing). A few commercial transparent ceramics are Lumicera lenses (a barium-based oxide made by Murata Mfg.), laser gain media—Nd:YAG (neodymium-doped yttrium aluminum garnet) is available from Konoshima—and transparent armor (aluminum oxynitride and spinel are available from Surmet and other vendors). As the manufacturing processes for transparent ceramics become better understood, industrial optical uses for these transparent materials with excellent mechanical robustness are likely to expand.
Chromosome numbers and pollen tetrad size in the Winteraceae (1955)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Urinary trypsin inhibitor efficiently inhibits urokinase production in tumor necrosis factor-stimulated cells. (1996)

We demonstrated that urinary trypsin inhibitor (UTI) efficiently inhibits soluble and tumor cell-associated plasmin activity and subsequently inhibits tumor cell invasion and metastasis. The effect of UTI on tumor necrosis factor-alpha (TNF)-induced stimulation of urokinase-type plasminogen activator (uPA) in cultured human umbilical vein endothelial cells (HUVEC) and in the promyeloid leukemia U937 cells was studied. uPA antigen was evaluated in the cell lysate and in the conditioned media by enzyme-linked immunosorbent assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis, and Western blot. TNF can promote the production of uPA in HUVEC and in U937 cells. The PKC inhibitors (H7, calphostin C, and staurosporine) inhibited TNF-induced uPA expression and secretion in a dose-dependent manner. Analysis of the expression of cell surface receptor-bound uPA by flow cytometry using uPA-specific MAb indicates that induction of uPA expression by TNF was inhibited when these cells were incubated with UTI. On the other hand, treatment of the cells with UTI alone failed to alter uPA production. UTI also reduced the secretion of uPA in TNF-treated cells. UTI was as effective as PKC inhibitors in inhibiting uPA expression by TNF. Incubation of the cells with UTI, however, had no effect on the ability of PMA to stimulate cell-associated uPA expression. These data suggest that UTI may influence the PKC-dependent protein kinase pathway in uPA expression. The study on intracellular pathways involved in UTI modulation of uPA will enhance our understanding of the role that UTI plays in uPA-mediated cellular invasion.
Corneal crosslinking with genipin, comparison with UV-riboflavin in ex-vivo model. (2012)

Corneal crosslinking was similar between UV-CLX and genipin with minimal toxicity to endothelial cells. Stiffened corneas by any method induced substancially higher IOP elevation when ocular volume is increased.
Annotated record of the detailed examination of Mn deposits observed from bottom photography taken during the INDOMED-1 expedition (1977)

35 km either side of the Pacific-Cocos spreading axis at 846'N, on crust 0.6 x 10SUP-6 years old, a pair of small seamounts rises 1.4 km above the faulted terrain of young abyssal hills. A high-resolution traverse made with the sonars and cameras of a deeply towed vehicle shows that the seamounts are inactive volcanoes, with concave side slopes that steepen upwards to 30, and then abruptly flatten at 2-4 km wide summits. Ledges of pillow basalt outcrop on the lower slopes, and form some talus slopes, but the superficial rock of the upper slopes appear to be mainly hyaloclastite. A transponder-navigated deep-tow survey at the summit area of the eastern seamount mapped an asymmetric caldera containing 3 pit craters, which have vertical walls and flat floors. Dredging across the caldera floor recovered hyaloclastite, angular fragments of primitive tholeiite, and manganese nodules. The paired seamounts probably had a common origin at a 'hot spot' on the spreading axis; continued to grow after they were split by sea-floor spreading; and became extinct and suffered summit collapse after they spread too far from their magma source.
Determination of Polyamines with Immobilized Beef Plasma Amine Oxidase (1980)

Beef plasma amine oxidase was immobilized on CNBr-activated Sepharose 4B. Properties of the immobilized enzyme were compared with those of the soluble enzyme. The thermo stability of the enzyme was slightly increased by immobilization. The immobilized enzyme which was packed into a column (0.6 × 1.8 cm) was completely stable during the repeated 100 times reactions at 37°C. Using two columns of different flow rates, small amounts of polyamines (0.005–0.04 μmol of spermine and 0.005–0.05 μmol of spermidine) could be assayed.