gebhart/patrepeval huggingface dataset:
Evidence for allosteric coupling between the ribosome and repressor binding sites of a translationally regulated mRNA (1990)

Escherichia coli ribosomal protein S4 is a translational repressor regulating the expression of four ribosomal genes in the alpha operon. In vitro studies have shown that the protein specifically recognizes an unusual mRNA pseudoknot secondary structure which links sequences upstream and downstream of the ribosome binding site for rpsM (S13) [Tang, C. K., & Draper, D. E. (1989) Cell 57, 531]. We have prepared fusions of the rpsM translational initiation site and lacZ that allows us to detect repression in cells in which overproduction of S4 repressor can be induced. Twenty-five mRNA sequence variants have been introduced into the S13-lacZ fusions and the levels of translational repression measured. Sets of compensating base changes confirm the importance of the pseudoknot secondary structure for translational repression. An A residue in a looped, single-stranded sequence is also required for S4 recognition and may contact S4 directly. Comparison of translational repression levels and S4 binding constants for the set of mRNA mutations show that nine mutants are repressed much more weakly than predicted from their affinity for S4; in extreme cases no repression can be detected for variants with unchanged S4 binding. We suggest that the mRNA contains functionally distinct ribosome and repressor binding sites that are allosterically coupled. Mutations can relieve translational repression by disrupting the linkage between the two sites without altering S4 binding. This proposal assigns to the mRNA a more active role in mediating translational repression than found in other translational repression systems.
Synthesis and applications of MOF-derived porous nanostructures (2017)

Metal organic frameworks (MOFs) represent a class of porous material which is formed by strong bonds between metal ions and organic linkers. By careful selection of constituents, MOFs can exhibit very high surface area, large pore volume, and excellent chemical stability. Research on synthesis, structures and properties of various MOFs has shown that they are promising materials for many applications, such as energy storage, gas storage, heterogeneous catalysis and sensing. Apart from direct use, MOFs have also been used as support substrates for nanomaterials or as sacrificial templates/precursors for preparation of various functional nanostructures. In this review, we aim to present the most recent development of MOFs as precursors for the preparation of various nanostructures and their potential applications in energy-related devices and processes. Specifically, this present survey intends to push the boundaries and covers the literatures from the year 2013 to early 2017, on supercapacitors, lithium ion batteries, electrocatalysts, photocatalyst, gas sensing, water treatment, solar cells, and carbon dioxide capture. Finally, an outlook in terms of future challenges and potential prospects towards industrial applications are also discussed.
Deflector based on frustrated total internal reflection of light (1977)

A description is given of a linear light deflector based on multiple total internal reflection. A nematic MBBA liquid crystal is used to frustrate the total reflection. The results are given of a study of the voltage dependence of the switching time.
Issues related to development of new antiseizure treatments (2013)

This report represents a summary of the discussions led by the antiseizure treatment working group of the International League Against Epilepsy (ILAE)/American Epilepsy Society (AES) Working Groups joint meeting in London (London Meeting). We review here what is currently known about the pharmacologic characteristics of current models of refractory seizures, both for adult and pediatric epilepsy. In addition, we address how the National Institute of Neurological Disorders and Stroke (NINDS)-funded Anticonvulsant Screening Program (ASP) is evolving to incorporate appropriate animal models in the search for molecules that might be sufficiently novel to warrant further pharmacologic development. We also briefly address what we believe is necessary, going forward, to achieve the goal of stopping seizures in all patients, with a call to arms for funding agencies, the pharmaceutical industry, and basic researchers.
Quantitative and qualitative differences in subcutaneous adipose tissue stores across lipodystrophy types shown by magnetic resonance imaging (2007)

Semi-automated MRI-based adipose tissue quantification indicates differences between various lipodystrophy types in these studied clinical cases and is a potentially useful tool for extended quantitative phenomic analysis of genetic metabolic disorders. Further studies with a larger sample size are essential for confirming these preliminary findings.
Neural tube defects and neuroepithelial cell death in Tulp3 knockout mice (2001)

The tubby-like protein 3 (Tulp3) gene has been identified as a member of a small novel gene family which is primarily neuronally expressed. Mutations in two of the family members, tub and tulp1, have been shown to cause neurosensory disorders. To determine the in vivo function of Tulp3, we have generated a germline mutation in the mouse Tulp3 gene by homologous recombination. Embryos homozygous for the Tulp3 mutant allele exhibit failure of neural tube closure, and die by embryonic day 14.5. Failure of cranial neural tube closure coincided with increased neuroepithelial apoptosis specifically in the hindbrain and the caudal neural tube. In addition, the number of betaIII-tubulin positive cells is significantly decreased in the hindbrain of Tulp3(-/-) embryos. These results suggest that disruption of the Tulp3 gene affects the development of a neuronal cell population. Interestingly, some Tulp3 heterozygotes also manifest embryonic lethality with neuroepithelial cell death. Our results demonstrate that the Tulp3 gene is essential for embryonic development in mice.
Distributed Clock Synchronization over Wireless Networks: Algorithms and Analysis (2006)

We analyze the spatial smoothing algorithm of Solis, Borkar and Kumar [1] for clock synchronization over multi-hop wireless networks. In particular, for a model of a random wireless network we show that with high probability the error variance is O(1) as the number of nodes in the network increases. This provides support for the feasibility of time-based computing n large wireless networks. We also provide bounds on the settling time of a distributed algorithm.
Striae Distensae (Stretch Marks) and Different Modalities of Therapy (2009)

The therapeutic strategies are numerous, and no single modality has been far more consistent than the rest. The long-term future of treatment strategies is encouraging with the advance in laser technologies.
Alignment of transtibial prostheses based on rollover shape principles (2003)

The authors examined the roll-over shape alignment hypothesis, which states that prosthetic feet are aligned by matching their roll-over shapes with an "ideal" shape. The "ideal" shape was considered to be the roll-over shape of the able-bodied foot-ankle system. An alignment algorithm and computational alignment system were developed to set trans-tibial alignments based on this hypothesis. Three prosthetic feet with considerably different roll-over shapes were either aligned using the alignment system or not aligned (i.e. used previous foot's alignment), and then were aligned by a team of prosthetists. No significant differences were found between roll-over shapes aligned by the computational alignment system and those based on standard clinical techniques (p = 0.944). Significant differences were found between the "no alignment" shapes and the prosthetist alignment shapes (p = 0.006), and between the "no alignment" shapes and the computational alignment system shapes (p = 0.024). The results of the experiment support the hypothesis that the goal of alignment is to match the prosthetic foot's roll-over shape, as closely as possible, with an "ideal" shape. The hypothesis is also supported by its ability to explain the results of previous studies. Using an "ideal" roll-over shape or surface as a goal for prosthetic alignment could lead to a priori alignment, eliminating the need for alignment hardware in some cases. Being able to build the alignment into a prosthesis without special hardware could be beneficial in low-income countries and in the fabrication of lightweight prostheses for the elderly.
High-frequency characteristics of a quantum well diode (2002)

High-frequency characteristics of a quantum well (QW) diode with thermionic electron transport are reported. The frequency-dependent admittance of the QW diode is obtained using a rigorous self-consistent small-signal analysis. The frequency dependencies of the QW diode capacitance and conductance are governed by a characteristic time of the recharging of the QW, which depends strongly on temperature and device structural parameters. Experimental data on conductance and capacitance of the QW diode as functions of temperature and frequency can be used to extract the parameters of the QW, such as QW recombination velocity and ionization energy.
Optoelectronic Substrate With High-Aspect-Ratio Optical Through-Hole for Chip-to-Chip Interconnects (2011)

We report high-aspect-ratio optical through-holes fabricated in optoelectronic substrates for chip-to-chip optical interconnections. They are used for transmitting optical signals vertically through the optoelectronic substrate. They consist of cladding layer and cores that are 50 μm in diameter. Their lengths are 1.2 mm equal to the thickness of the substrate. This small diameter enables the optical through-holes to achieve low-loss optical coupling with a polymer optical waveguide. This thickness of the optoelectronic substrate accommodates embedded capacitor integration under CPUs. The capacitor will improve power supply to the CPU and co-planarity for both package level and board level assembly. We have evaluated the optical characteristics of the high-aspect-ratio optical through holes. We have measured optical loss and crosstalk. Optical coupling dependencies of alignment offset for the optical through-holes are also evaluated to clear the effects of misalignment. The optical loss of core-cladding optical through-hole was 1.3 dB that was 2.9 dB better than that of only one kind of transparent resin and 3.8 dB better than that of a vacant drilled hole. The narrowest 1-dB coupling tolerance was +/− 12 μm from the transmitter optical through-hole to the optical waveguide. Total optical loss was estimated to be 6.8 dB from a vertical-cavity surface-emitting laser through 100-mm polymer waveguide with two 45°-ended mirrors to a photodiode.
The Mutant Form of Lamin A that Causes Hutchinson-Gilford Progeria Is a Biomarker of Cellular Aging in Human Skin (2007)

Hutchinson-Gilford progeria syndrome (HGPS, OMIM 176670) is a rare disorder characterized by accelerated aging and early death, frequently from stroke or coronary artery disease. 90% of HGPS cases carry the LMNA G608G (GGC>GGT) mutation within exon 11 of LMNA, activating a splice donor site that results in production of a dominant negative form of lamin A protein, denoted progerin. Screening 150 skin biopsies from unaffected individuals (newborn to 97 years) showed that a similar splicing event occurs in vivo at a low level in the skin at all ages. While progerin mRNA remains low, the protein accumulates in the skin with age in a subset of dermal fibroblasts and in a few terminally differentiated keratinocytes. Progerin-positive fibroblasts localize near the basement membrane and in the papillary dermis of young adult skin; however, their numbers increase and their distribution reaches the deep reticular dermis in elderly skin. Our findings demonstrate that progerin expression is a biomarker of normal cellular aging and may potentially be linked to terminal differentiation and senescence in elderly individuals.
Tribeca: a system for managing large databases of network traffic (1998)

The engineers who analyze traffic on high bandwidth networks must filter and aggregate either recorded traces of network packets or live traffic from the network itself. These engineers perform operations similar to database queries, but cannot use conventional data managers because of performance concerns and a semantic mismatch between the analysis operations and the operations supported by commercial DBMSs. Traffic analysis does not require fast random access, transactional update, or relational joins. Rather, it needs fast sequential access to a stream of traffic records and the ability to filter, aggregate, define windows, demultiplex, and remultiplex the stream. Tribeca is an extensible, stream-oriented DBMS designed to support network traffic analysis. It combines ideas from temporal and sequence databases with an implementation optimized for databases stored on high speed ID-1 tapes or arriving in real time from the network. The paper describes Tribeca&apos;s query language, executo...
Creating, changing, and recovering community: an introduction to the annual conference edition of the British Association for South Asian Studies (2010)

The 23rd Annual Conference of the British Association for South Asian Studies (BASAS) took place at the University of Edinburgh, 30 March–1 April 2009. The conference was convened by Crispin Bates ...
Gas-Surface Interactions Basic Thermodynamics and Recent Work on Sticking (1990)

In this ehapter an introduetion is provided to two aspeets of gas-solid interaetions: classical and statistieal thermo dyn ami es of adsorption, and the quantum theory of stieking. The thermodynamies of adsorption finds applieations prineipally, but not exclusively, to physisorption systems. Many chemisorption systems widely studied are irreversible; an equilibrium pressure is never measured. This does not mean that desorption of ehemisorbed material is not studied. It is, but in an irreversible way, by temperature programmed desorption, for example. Thermodynamies is eoneerned with eertain maeroseopie properties of matter in equilibrium, pressure, volume, entropy, free energy, enthalpy, for example. The laws of thermodynamies lead only to relations among them so that a certain experimental input is required to enable these quantities to be calculated. Electrochemical cells provide a well-known example. Measurements of the cell EMF and its temperature coefficient give the Gibbs free energy change and the entropy change, respectively, in the cell reaction. From these, the enthalpy change is calculated from G = H TS, and calorimetry is avoided. In this chapter we consider how calorimetric determination of the enthalpy of (physical) adsorption is avoided in favor of measuring the temperature dependence of the equilibrium pressure. On the other hand, for chemisorption, calorimetric determination of the enthalpy change seems to be essential for most systems, and a detailed feasibility study of a single-crystal calorimeter has been made.(l)
The Role Of Modelling And Simulation In Design-Build Projects (2006)

The paper discusses the role of modelling and simulation techniques in large scale construction projects focusing on the opportunities and on the modelling challenges that are specific to this context of application.The paper argues that a methodology based on dynamic multi-process simulation models provides powerful decision support when assessing the performance implications of changes in the design and/or in the technology, as well as the impact of alternative courses of action during project execution.Dynamic multi-process simulation provides quantitative grounds for the understanding, analysis, and discussion among the project stakeholders, and creates the conditions for a concurrent engineering approach throughout the project's lifecycle, starting from the early stages of conceptual design.A simulation-based study, based on actual data from a construction project, is presented in the paper to illustrate these benefits.
Persistence of maternal antibody to chicken anaemia agent and its effect on the susceptibility of young chickens (1992)

Based on the incidence of anaemia, chicks derived from immune dams were shown to resist the parenteral challenge with chicken anaemia agent (CAA) until 14 days of age. Judging from thymic atrophy induced by the CAA-challenge, maternally-derived immunity of chicks against CAA infection persisted up to at least day 21. A very low level of maternal anti-CAA antibody seemed to be efficacious to the CAA-challenge. These results are discussed in relation to the significance of CAA anaemia under field conditions.
Cemented Carbides (1990)

Abstract Cemented carbides belong to a class of hard, wear-resistant, refractory materials in which the hard carbide particles are bound together, or cemented, by a soft and ductile metal binder. The performance of cemented carbide as a cutting tool lies between that of tool steel and cermets. Almost 50% of the total production of cemented carbides is used for nonmetal cutting applications. Their properties also make them appropriate materials for structural components, including plungers, boring bars, powder compacting dies and punches, high-pressure dies and punches, and pulverizing hammers. This article discusses the manufacture, microstructure, composition, classifications, and physical and mechanical properties of cemented carbides, as well as their machining and nonmachining applications. It examines the relationship between the workpiece material, cutting tool and operational parameters, and provides suggestions to simplify the choice of cutting tool for a given machining application. It also examines new tool geometries, tailored substrates, and the application of thin, hard coatings to cemented carbides by chemical vapor deposition and physical vapor deposition. It discusses the tool wear mechanisms and the methods available for holding the carbide tool. The article is limited to tungsten carbide cobalt-base materials.
Mast cell growth-enhancing activity (MEA) stimulates interleukin 6 production in a mouse bone marrow-derived mast cell line and a malignant subline. (1990)

A novel mast cell growth-enhancing activity (MEA/P40/interleukin 9 [IL-9]) purified from the conditioned medium of a murine interleukin 2 (IL-2)-dependent Mlsa-specific T-cell line (MLS4.2) was tested for its capacity to induce interleukin 6 (IL-6) production in a mouse bone marrow-derived factor-dependent mast cell line (L138.8A). This interleukin 3 (IL-3)/interleukin 4 (IL-4)/MEA-responsive cell line was demonstrated recently to express IL-6 mRNA and to secrete IL-6 when cultured with IL-3/IL-4. Now we were able to show that conditioned medium from L138.8A mast cells stimulated with MEA alone contained growth factor activity for the IL-6-dependent mouse hybridoma cell line 7TD1 that was completely blocked by the monoclonal anti-IL-6 antibody 6B4. A dose-response study including IL-3, IL-4, and MEA tested either alone or in different combinations revealed that among these growth factors MEA was the most potent inducer of IL-6 in L138.8A cells. Moreover, IL-4 but not IL-3 had a strong synergistic effect on MEA-induced IL-6 production. The autonomous malignant mast cell subline L138Cauto also showed enhanced IL-6 production when stimulated with MEA. Our findings indicate that MEA (IL-9) not only provides a proliferation signal, but also leads to a marked functional activation of responsive mast cells.
Flame lonization Detector Molar Responses for Methyl Esters of Some Polyfunctional Metabolic Acids (1968)

Molar responses, relative to CH2 = 100, were determined for methyl esters of some Krebs cycle and related acids. These experimentally determined values agreed well with responses predicted from general structural considerations. Comparison with data from another laboratory suggested that an apparent discrepancy was due to an anomalously low response for the internal hydrocarbon standard, and the ester responses were in fact comparable.
Bacillus thuringiensis Cry1Ca-resistant Spodoptera exigua lacks expression of one of four Aminopeptidase N genes (2005)

We have cloned and characterized four different midgut APN cDNAs from S. exigua. Expression analysis revealed the lack of expression of one of these APNs in the larvae of a Cry1Ca-resistant colony. Combined with previous evidence that shows the importance of APN in the mode of action of B. thuringiensis toxins, these results suggest that the lack of APN1 expression plays a role in the resistance to Cry1Ca in this S. exigua colony.
Common regions e.g. orf513 and antibiotic resistance: IS91-like elements evolving complex class 1 integrons (2006)

The ability of bacteria to procure, sometimes rearrange, and evince acquired DNA continues to impress us-even more so if this genetic plasticity involves the sequestering of antibiotic resistance genes. The acquisition of genes in bacteria is often facilitated by transposons, integrons and archetype insertion elements. Recently however, a new element, 'orf513', has been increasingly associated with class 1 integrons. Moreover, these 'complex' class 1 integrons can potentially mediate resistance to chloramphenicol, trimethoprim, aminoglycosides and tetracycline and may carry a range of beta-lactamase genes as well as the qnrA gene. Elements such as 'orf513' demonstrate IS91-like characteristics and will mobilize adjacent DNA via a process called rolling circle replication, and thus we have renamed them 'insertion sequence CRs' (ISCRs) to appropriately reflect their structure-function properties. In this article, we provide a brief description of these new and clinically important mobile elements, and how they are able to mobilize antibiotic resistance genes.
Femtosecond all-optical synchronization of an X-ray free-electron laser (2015)

Many advanced applications of X-ray free-electron lasers require pulse durations and time resolutions of only a few femtoseconds. To generate these pulses and to apply them in time-resolved experiments, synchronization techniques that can simultaneously lock all independent components, including all accelerator modules and all external optical lasers, to better than the delivered free-electron laser pulse duration, are needed. Here we achieve all-optical synchronization at the soft X-ray free-electron laser FLASH and demonstrate facility-wide timing to better than 30 fs r.m.s. for 90 fs X-ray photon pulses. Crucially, our analysis indicates that the performance of this optical synchronization is limited primarily by the free-electron laser pulse duration, and should naturally scale to the sub-10 femtosecond level with shorter X-ray pulses.
The amino acid sequence of the procoagulant- and prothrombin-binding domain isolated from staphylocoagulase. (1986)

The primary structure of the procoagulant- and prothrombin-binding domains, the 43- and 30-kDa fragments previously isolated from staphylocoagulase, has been determined by sequencing peptides derived from various chemical (CNBr and 2-(2-nitrophenylsulfenyl)-3-methyl-3-bromoindolenine) and enzymatic (trypsin and alpha-chymotrypsin) cleavages. Carboxypeptidase Y was also used to deduce the COOH-terminal sequence. The 43-kDa fragment contained 324 amino acids and had a calculated molecular weight of 38,098. It included the entire structure of the 30-kDa fragment located in the COOH-terminal portion (positions 126-324). The 43-kDa fragment had an unusual amino acid composition based on the sequence, in which the sum of Asp (28 residues), Asn (22), Glu (35), Gln (9), and Lys (52) residues accounted for more than 45% of the total. In addition, the frequent occurrence of repetitions of the various kinds of dipeptides was found along the whole sequence. Structural comparison of the NH2-terminal portion of the 43-kDa fragment of staphylocoagulase with that of streptokinase did not reveal any obvious sequence homologies. There was also no sequence homology with that of trypsin, alpha-chymotrypsin, and elastase.