gebhart/patrepeval huggingface dataset:
Arabidopsis Membrane-anchored Ubiquitin-fold (MUB) Proteins Localize a Specific Subset of Ubiquitin-conjugating (E2) Enzymes to the Plasma Membrane (2011)

The covalent attachment of ubiquitin (Ub) to various intracellular proteins plays important roles in altering the function, localization, processing, and degradation of the modified target. A minimal ubiquitylation pathway uses a three-enzyme cascade (E1, E2, and E3) to activate Ub and select target proteins for modification. Although diverse E3 families provide much of the target specificity, several factors have emerged recently that coordinate the subcellular localization of the ubiquitylation machinery. Here, we show that the family of membrane-anchored ubiquitin-fold (MUB) proteins recruits and docks specific E2s to the plasma membrane. Protein interaction screens with Arabidopsis MUBs revealed that interacting E2s are limited to a well defined subgroup that is phylogenetically related to human UbcH5 and yeast Ubc4/5 families. MUBs appear to interact noncovalently with an E2 surface opposite the active site that forms a covalent linkage with Ub. Bimolecular fluorescence complementation demonstrated that MUBs bind simultaneously to the plasma membrane via a prenyl tail and to the E2 in planta. These findings suggest that MUBs contribute subcellular specificity to ubiquitylation by docking the conjugation machinery to the plasma membrane.
A Redox Economical Synthesis of Bioactive 6,12-Guaianolides (2013)

Syntheses of two 6,12-guaianolide analogs are reported within. The scope of the tandem allylboration/lactonization chemistry is expanded to provide a functionalized allene-yne-containing α-methylene butyrolactone that undergoes a Rh(I)-catalyzed cyclocarbonylation reaction to afford a 5-7-5 ring system. The resulting cycloadducts bear a structural resemblance to other NF-κB inhibitors such as cumambrin A and indeed were shown to inhibit NF-κB signaling and cancer cell growth.
Recent developments and future directions in mathematical programming (1992)

Recent advances in mathematical programming methodology have included: development of interior methods competing with the simplex method, improved simplex codes, vastly improved performance for mixed-integer programming using strong linear programming formulations, and a renewed interest in decomposition. In addition, use of vector and parallel processing has improved performance and influenced algorithmic developments. Application areas have been expanding from the traditional refinery planning and distribution models to include finance, scheduling, manufacturing, manpower planning, and many others. We see the acceleration of better methods and improved codes moving together with faster, lower-cost, and more interesting hardware into a variety of application areas, thereby opening up new demands for greater function of optimization codes. These new functions might include, for example, more powerful nonlinear codes, decomposition techniques taking advantage of network and other problem-dependent structures, and mixed-integer capability in quadratic and general nonlinear problems.Stochastic scenario programming and multitime-period problems are becoming solvable and open up applications and algorithmic challenges. The IBM Optimization Subroutine Library has helped to accelerate these changes but will have to continue to change and expand in ways that are touched upon in this paper.
Gene for spiralin, the major membrane protein of the helical mollicute Spiroplasma citri: cloning and expression in Escherichia coli (1985)

A library of cloned Spiroplasma citri genomic sequences was constructed by incorporating HindIII digestion fragments into the plasmid vector pBR328. Immunological screening allowed the identification of a recombinant plasmid containing the gene for spiralin, the major membrane protein of S. citri. The spiralin produced by the Escherichia coli transformant was characterized by immunological detection with monoclonal antibody after Western blotting of two-dimensional (isoelectric focusing and sodium dodecyl sulfate-polyacrylamide) electrophoresis gels and by partial proteolytic mapping. The gene for spiralin occurred within a 6.5-kilobase-pair cloned DNA fragment. Spiralin in E. coli was produced regardless of the orientation of the insert within the pBR328 vector. A spiroplasmal DNA sequence which acted as a promoter in E. coli was cloned along with the structural spiralin gene which is expressed in E. coli from that sequence.
Succinct indexable dictionaries with applications to encoding <i>k</i> -ary trees, prefix sums and multisets (2007)

We consider the indexable dictionary problem, which consists of storing a set S ⊆ {0,…, m − 1} for some integer m while supporting the operations of rank( x ), which returns the number of elements in S that are less than x if x ∈ S , and −1 otherwise; and select( i ), which returns the i th smallest element in S . We give a data structure that supports both operations in O (1) time on the RAM model and requires B( n, m ) + o ( n ) + O (lg lg m ) bits to store a set of size n , where B( n, m ) = ⌊lg ( m / n )⌋ is the minimum number of bits required to store any n -element subset from a universe of size m . Previous dictionaries taking this space only supported (yes/no) membership queries in O (1) time. In the cell probe model we can remove the O (lg lg m ) additive term in the space bound, answering a question raised by Fich and Miltersen [1995] and Pagh [2001]. We present extensions and applications of our indexable dictionary data structure, including: —an information-theoretically optimal representation of a k -ary cardinal tree that supports standard operations in constant time; —a representation of a multiset of size n from {0,…, m − 1} in B( n, m + n ) + o ( n ) bits that supports (appropriate generalizations of) rank and select operations in constant time; and + O (lg lg m ) —a representation of a sequence of n nonnegative integers summing up to m in B( n, m + n ) + o ( n ) bits that supports prefix sum queries in constant time.
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences (2009)

Users can access the EpiSearch from our web server http://curie.utmb.edu/episearch.html.
Oxidative burst in lipopolysaccharide-activated human alveolar macrophages is inhibited by interleukin-9 (2002)

Interleukin (IL)-9 is known to regulate many cell types involved in T-helper type 2 responses classically associated with asthma, including B- and T-lymphocytes, mast cells, eosinophils and epithelial cells. In contrast, target cells mediating the effects of IL-9 in the lower respiratory tract remain to be identified. Therefore, the authors evaluated the activity of IL-9 on human alveolar macrophages (AM) from healthy volunteers. AM preincubated with IL-9 before lipopolysaccharide (LPS) stimulation exhibited a decreased oxidative burst, as previously shown with IL-4. The inhibitory effect of IL-9 was abolished by anti-hIL-9R alpha monoclonal antibody, and presence of IL-9 receptors on AM was demonstrated by immunofluorescence. Both IL-4 and IL-9 failed to modulate tumour necrosis factor-alpha, IL-8 and IL-10 release by LPS-stimulated AM. However, several observations suggested that IL-9 and IL-4 act through different mechanisms: 1) interferon-gamma antagonised the IL4- but not the IL-9-mediated inhibition of AM oxidative burst; 2) expression of CD14 was downregulated by IL-4 but not by IL-9 and 3) production of tumour growth factor-beta by activated AM was potentiated by IL-9 and not by IL4, and was required for the IL-9-mediated inhibition of AM oxidative burst. These observations provide additional information concerning the activity of interleukin-9 in the lung, related to inflammatory or fibrosing lung processes.
Outcome Measures in Acute Stroke Trials (2000)

There is no consensus on the level of outcome to be used, the method of measurement to be used, or the most appropriate timing of the assessment. It is recommended that future studies should include extended/instrumental activities and advanced mobility as components of the primary outcome measure, with outcome assessment being undertaken at 6 months. New initiatives in developing stroke-specific outcomes may address some of the current problems in the assessment of stroke outcomes
Resistant and Test-Based Outlier Rejection: Effects on Gaussian One- and Two-Sample Inference (1997)

Resistant and sequential test-based procedures for the detection of multiple outliers are compared in Gaussian one- and two-sample problems. Subsequent to statistical rejection of putative outliers, operating characteristics of hypothesis tests applied to samples that are outlier-free may differ from their nominal values. Outlier rejection rules may be calibrated, however, to control the rate of erroneous outlier labeling in pure Gaussian samples. The small-sample behavior of resistant location and scale estimators used in outlier detection is examined through simulation, yielding new formulas for calibration of boxplot-based and shorth-based outlier-rejection rules. Effects of different outlier criteria and calibration rubrics on postrejection hypothesis tests are compared in a variety of contamination settings and real-world examples. Tests conducted subsequent to calibrated rejection have approximately nominal operating characteristics whether or not outliers are present. The selection of an outlier criterion can have an impact on inference and thus becomes a potential component of model uncertainty. Properly calibrated tools should be widely available so that this component of uncertainty becomes better understood; we describe public-domain software implementing a variety of detection techniques.
Efficient Parallel Algorithm for Robot Inverse Dynamics Computation (1986)

It is shown that the time lower bound of computing the inverse dynamics of an n-link robot manipulator parallelly using p processors is O(k1 [n/p] + k2 [log<2 p]), where k1 and k2 are constants. A novel parallel algorithm for computing the inverse dynamics using the Newton-Euler equations of motion was developed to be implemented on a single-instruction-stream multiple-data-stream computer with p processors to achieve the time lower bound. When p = n, the proposed parallel algorithm achieves the Minsky's time lower bound O([log2 n]), whidc is the conjecture of parallel evaluation. The proposed p-fold parallel algorithm can be best described as consisting of p-parallel blocks with pipelined elements within each parallel block The results from the computations in the p blocks form a new homogeneous linear recurrence of size p, which can be computed using the recursive doubling algorithm. A modified inverse perfect shuffle interconnection scheme was suggested to interconnect the p processors. Furthermore, the proposed parallel algorithm is susceptible to a systolic pipelined architecture, requiring three floating-point operations per complete set of joint torques.
CARDS: Conjoint Adaptive Retroactive Database System (2002)

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
Reducing aliasing artifacts through resampling (2012)

Post-processing antialiasing methods are well suited for deferred shading because they decouple antialiasing from the rest of graphics pipeline. In morphological methods, the final image is filtered with a data-dependent filter. The filter coefficients are computed by analyzing the non-local neighborhood of each pixel. Though very simple and efficient, such methods have intrinsic quality limitations due to spatial undersampling and temporal aliasing. We explore an alternative formulation in which filter coefficients are computed locally for each pixel by supersampling geometry, while shading is still done only once per pixel.During pre-processing, each geometric subsample is converted to a single bit indicating whether the subsample is different from the central one. The ensuing binary mask is then used in the post-processing step to retrieve filter coefficients, which were precomputed for all possible masks. For a typical 8 subsamples, it results in a sub-millisecond performance, while improving the image quality by about 10 dB.To compare subsamples, we use a novel symmetric angular measure, which has a simple geometric interpretation. We propose to use this measure in a variety of applications that assess the difference between geometric samples (rendering, mesh simplification, geometry encoding, adaptive tessellation).
Proposed Ammeter Using Flux Quantization (1968)

The possibility is discussed of using flux quantization in superconductors as the basis of an ammeter and more generally as a fundamental standard of electromagnetic measurement. A particular design is proposed and in this context some of the fundamental design problems of this sort of instrument are considered. It is concluded that an instrument of this type could measure a current in terms of the flux quantum, length, and time to an accuracy approaching 1 part in 106. The limitations and advantages of the proposed instrument are discussed and comparisons are made with present current-measuring instruments and some conjectures are made of the future potential of flux quantization instruments of this kind.
Physiologic activation of T cells via the T cell receptor induces NF-kappa B (1991)

Abstract The transcription factor NF-kappa B has been implicated in the mitogen-induced expression of several genes that are critical for the immunologic function of T cells such as those encoding IL-2 and the IL-2R alpha chain (IL-2R alpha). We show here that NF-kappa B is induced in T cells activated by Ag, anti-CD3 antibody, or allogeneic stimulation. The induction of NF-kappa B via the TCR was dependent on protein kinase C. IL-2, which also activates IL-2R alpha expression and proliferation in T cells, was not able to induce NF-kappa B. TCR-mediated induction of NF-kappa B suggests a central role for this factor in activated T cells and also provides a mechanism for activation of latent HIV provirus during the normal immune response.
Manually flown windshear recovery technique (1990)

The windshear recovery technique described was developed following a thorough analysis of windshear related accidents and incidents. The recommended manually flown windshear recovery technique requires control of flight path by using maximum thrust and sufficient pitch attitude to establish a positive flight path or to minimize descent. This is done by pitching towards a target attitude of 15 degrees, using maximum rated thrust, and accepting lower than normal airspeeds during the recovery. The technique is relatively simple, easily recalled, generally applicable to all jet transports, and has been demonstrated to be effective in actual windshear encounters. The development and rationale for the recommended recovery technique are briefly outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Life History and Descriptions of the Immature Stages of the Planthopper Prokelisia crocea (Van Duzee) (Homoptera: Delphacidae) (1992)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Trichodermides A–E: New Peptaibols Isolated from the Australian Termite Nest-Derived Fungus <i>Trichoderma virens</i> CMB-TN16 (2018)

Chemical analysis of a fermentation of the Australian termite nest-derived fungus Trichoderma virens CMB-TN16 yielded five new acyclic nonapeptides, trichodermides A-E (1-5). Amino acid residues, configurations, and sequences were determined by a combination of spectroscopic (NMR and MS-MS) and chemical (C<sub>3</sub> Marfey's) methods. The trichodermides adhere to the sequence homology pattern common to Trichoderma 11 amino acid residue peptaibols; however, unlike other peptaibols the trichodermides do not exhibit antibacterial or antifungal activity and exhibit low to no cytotoxicity against mammalian cells. This variability in biological activity highlights the importance of knowing both planar structures and absolute configurations when interpreting structure-activity relationships.
Characterization of Inducible Nitric Oxide Synthase Expression in Human Airway Epithelium (1998)

Nitric oxide is an important mediator of inflammatory responses in the lung and a key regulator of pulmonary vascular and bronchomotor tone.We have shown that the inducible nitric oxide synthase (iNOS) isoform is continuously expressed in human airway epithelium at mRNA and protein/activity levels in vivo.However, removal of epithelial cells from the in vivo airway environment resulted in rapid loss of iNOS expression, which suggested that expression is dependent upon conditions and/or factors present in the airway.To investigate the mechanisms responsible for maintenance of expression in vivo, we evaluated regulation of iNOS expression in primary human airway epithelial cells.Interferon-y (IFNI' was sufficient for induction of iNOS in primary human airway epithelial cells (HAEC) in vitro, and interleukin-4 (IL-4) potentiated the expression through stabilization of iNOS mRNA.The IFN-y/IL-4-induced iNOS expression in HAEC was delayed in onset and prolonged with expression up to 1 week.Furthermore, transfer of overlying culture media [conditioned media (CM)] to other HAEC led to iNOS induction.Interestingly, IFN-y/IL-4 induction of iNOS was dependent on new protein synthesis, whereas CM induction of iNOS was not.IFN-,y and IL-4 activated signal transducers and activators of transcription (STAT1 and STAT6) in HAEC, but CM transfer to HAEC produced even higher levels of STAT1 activation than achieved by direct addition of cytokines.Thus, IFN-y/IL-4, which occurs in human lung lining fluid, led to iNOS expression in human airway epithelium through production of soluble mediators and stabilization of mRNA.
A framework for GPU-accelerated AES-XTS encryption in mobile devices (2011)

Attacks on data stored in mobile devices are increasingly getting more efficient and successful, especially with the use of advanced cryptanalysis techniques and high-tech systems. Encryption using the IEEE XTS-AES algorithm might be an attractive solution for this problem, but it comes with a significant impact on the performance of these limited-resources devices. The emergence of the potential Graphical Processing Units (GPUs), as a general purpose non-graphical computational power, has gained a great interest in both industry and academia. Recently, GPUs have presented higher performance for parallel programming than conventional CPUs while they continue gaining reduced cost. One important application area that can benefit from GPUs power is storage encryption in mobile devices. In this paper, we introduce a GPU-accelerated framework for storage encryption in mobile devices using the XTS-AES encryption algorithm. The Google's Android is targeted in this work as a mobile operating system.
Thermophoretic Deposition of Small Particles in the Modified Chemical Vapor Deposition (MCVD) Process (1980)

Thermophoresis is conclusively established as the particulate deposition mechanism in the MCVD process by comparing experimental measurements and quantitative theoretical predictions. The deposition efficiency, E , is defined as the fraction of the silica in the gas stream (initially as SiCl 4 ) that is deposited. For normal MCVD operating conditions, the deposition efficiency is only a function of the equilibrium temperature, T e , at which the gas and walls equilibrate downstream of the torch and the temperature, T r , at which reaction occurs. The deposition efficiency is ∼0.8[1‐( T e / T r )]. It is determined that T e is a strong function of the torch traverse velocity, the traverse length, the temperature of the ambient environment, and the tube wall thickness but only a weak function of the gas flow rate. At high gas flow rates, the efficiency is limited by incomplete reaction.
Laser Doppler and time-varying speckle: a reconciliation (1996)

The techniques of laser Doppler and time-varying speckle can both be used to measure velocities. The two techniques have developed separately, and there has been little interchange of ideas between them. The essential equivalence of the two techniques for measuring line-of-sight velocities is demonstrated, and ways in which the two techniques might learn from each other are suggested.
ABility to rise independently from a chair during 6-month follow-up after unilateral and bilateral total knee replacement (2005)

We conclude that patients with unilateral total knee replacement gain independence earlier than patients with bilateral total knee replacement. However, for patients with bilateral total knee replacement eventually to gain independence, they should be prepared for a longer rehabilitation programme.
Route planning (1991)

Route planning is discussed as part of an avionics system. A very rapid route planning technique was developed based on the cellular automata (CA) paradigm. A CA consists of a 2-D, 3-D or higher-dimensional grid of cells. Each cell has either a real or virtual processor assigned to it, and communicates with neighboring cells to solve a variety of spatial-temporal problems. The route planner operates within a multidimensional cellular search space where there is a cost associated with travel through every cell. This cost is a weighted combination of many factors. To provide a dynamically adaptable level of resolution appropriate to the problem under consideration, a quadtree-based technique was developed. The basic route planning algorithm extends very naturally into the time dimension. >
Interfacial Properties of Poly(Caprolactone) and Derivatives (2004)

Abstract Monolayers of biodegradable polymers, poly(caprolactone) (PCL), poly(caprolactone) diol (PCL‐diol), and poly(caprolactone) triol (PCL‐triol) in the air/water interface were studied and characterized. The Langmuir–Blodgett technique was used for the monolayer transfer onto hydrophilic and hydrophobic solid substrates. The results obtained in both cases are dependent on the functional groups incorporated in the respective polymers. The surface energy (SE), and the polar and dispersion contributions, γp and γd, respectively, were obtained by wettability measurements. For polymeric spin‐casted thin films deposited over glass, the results also indicate an increment in the polymer hydrophilicity by hydroxyl groups insertion.
Design, Development and Implementation of ALU, RAM and ROM for 8051 Microcontroller on FPGA using VHDL (2013)

Reconfigurable systems offer a solution to solve complex problems by combining the speed of hardware with the flexibility of software to improve performance and system performance. Past three decades have seen the introduction of the technology that has radically changed the way one analyses and controls the world around them. A byproduct of Microprocessor development by Intel is the 8051 Microcontroller which finds its use in almost all walks of life. The Microcontrollers are not as well known to the general public, or even the technical community, as are the more glamorous Microprocessors. The public is however very well aware that "something" is responsible for all the Smart VCRs, clock radios, washers and dryers, video games, TVs etc. That "something" is nothing but the Microcontroller.
Spectrally Sliced WDM using a Single Femtosecond Source (1995)

Wavelength-division-multiplexed (WDM) networks are expected to play a major role in both long-haul communications as well as in the local loop (FTTL). One of the most pressing device issues for such systems is the question of an appropriate multi-wavelength source. Spectral slicing of broadband sources such as the ASE from Er-fiber amplifiers [1] or the supercontinuum generated from propagation of short pulses through fibers [2] has been suggested as WDM source. This approach provides precisely aligned channel wavelengths, but both the spectral slicing as well as the modulation is external to the laser cavity.