gebhart/patrepeval huggingface dataset:
Directionality in FLP protein-promoted site-specific recombination is mediated by DNA-DNA pairing. (1986)

The 2 mu plasmid of the yeast Saccharomyces cerevisiae encodes a site-specific recombination system consisting of plasmid-encoded FLP protein and two recombination sites on the plasmid. The recombination site possesses a specific orientation, which is determined by an asymmetric 8-base pair spacer sequence separating two 13-base pair inverted repeats. The outcome or directionality of site-specific recombination is defined by the alignment of two sites in the same orientation during the reaction. Sites containing point mutations or 1-base pair insertions or deletions within the spacer generally undergo recombination with unaltered sites at reduced levels. In contrast, recombination between the two identical mutant sites (where homology is restored) proceeds efficiently in all cases. Sites containing spacer sequences of 10 base pairs or more are nonfunctional under all conditions. A recombination site in which 5 base pairs are changed to yield an entirely symmetrical spacer sequence again recombines efficiently, but only with an identical site. This reaction, in addition, produces a variety of new products which can only result from random alignment of the two sites undergoing recombination, i.e. the reaction no longer exhibits directionality. These and other results demonstrate that both the efficiency and directionality of site-specific recombination is dependent upon homology between spacer sequences of the two recombining sites. This further implies that critical DNA-DNA interactions between the spacer region of the two sites involved in the reaction occur at some stage during site-specific recombination in this system. The specific spacer sequence itself appears to be unimportant as long as homology is maintained; thus, these sequences are probably not involved in recognition by FLP protein.
A learning agent for wireless news access (2000)

We describe a user interface for wireless information devices, specifically designed to facilitate learning about users' individual interests in daily news stories. User feedback is collected unobtrusively to form the basis for a content-based machine learning algorithm. As a result, the described system can adapt to users' individual interests, reduce the amount of information that needs to be transmitted, and help users access relevant information with minimal effort.
Error Resilient Video Coding Using Redundant Pictures (2008)

This paper presents several error resilient video coding methods based on redundant pictures. We combine redundant picture coding with reference picture selection and reference picture list reordering to prevent error propagation in motion compensated video coding. A hierarchical redundant picture allocation method is employed to make a tradeoff between error resilience and coding efficiency. For improved end-to-end rate-distortion performance in packet loss environment, three adaptive redundant picture allocation methods are further developed, utilizing characteristics of the input video content. Simulation results show that the adaptive redundant picture coding methods can achieve average luma peak-signal-to-noise improvements up to 3.5 dB compared to the loss-aware rate distortion optimized intra macroblock refresh algorithm implemented in the H.264/AVC Joint Model (JM). The proposed redundant picture coding methods are standard-compliant and do not introduce any additional end-to-end delay, therefore suit for low-delay applications such as video telephony and video conferencing. Due to the good error resilience performance, some of the proposed redundant picture coding methods have been adopted and integrated into the JM.
Redox-driven switching in pseudorotaxanes (2009)

Two donor–acceptor thread-like compounds incorporating viologen (V2+) units and 1,5-dihydroxynaphthalene (DNP) stations have been prepared. Their ability to form self-assembled charge-transfer (CT) complexes with cucurbit[8]uril (CB[8]) is evidenced by UV-Vis and NMR spectroscopies, as well as by mass spectrometry. Binding studies show the formation of 1 : 1 and 2 : 1 complexes between CB[8] and a thread-like compound containing two viologen units, while only a 1 : 1 inclusion complex was observed between CB[8] and a thread-like compound containing only a single viologen unit. The switching behavior of the threads within their pseudorotaxane frameworks was investigated by using cyclic voltammetry (CV) and UV-Vis spectroscopy.
Learning latent semantic relations from clickthrough data for query suggestion (2008)

For a given query raised by a specific user, the Query Suggestion technique aims to recommend relevant queries which potentially suit the information needs of that user. Due to the complexity of the Web structure and the ambiguity of users' inputs, most of the suggestion algorithms suffer from the problem of poor recommendation accuracy. In this paper, aiming at providing semantically relevant queries for users, we develop a novel, effective and efficient two-level query suggestion model by mining clickthrough data, in the form of two bipartite graphs (user-query and query-URL bipartite graphs) extracted from the clickthrough data. Based on this, we first propose a joint matrix factorization method which utilizes two bipartite graphs to learn the low-rank query latent feature space, and then build a query similarity graph based on the features. After that, we design an online ranking algorithm to propagate similarities on the query similarity graph, and finally recommend latent semantically relevant queries to users. Experimental analysis on the clickthrough data of a commercial search engine shows the effectiveness and the efficiency of our method.
Nerve injuries sustained during warfare (2012)

The outcomes of 261 nerve injuries in 100 patients were graded good in 173 cases (66%), fair in 70 (26.8%) and poor in 18 (6.9%) at the final review (median 28.4 months (1.3 to 64.2)). The initial grades for the 42 sutures and graft were 11 good, 14 fair and 17 poor. After subsequent revision repairs in seven, neurolyses in 11 and free vascularised fasciocutaneous flaps in 11, the final grades were 15 good, 18 fair and nine poor. Pain was relieved in 30 of 36 patients by nerve repair, revision of repair or neurolysis, and flaps when indicated. The difference in outcome between penetrating missile wounds and those caused by explosions was not statistically significant; in the latter group the onset of recovery from focal conduction block was delayed (mean 4.7 months (2.5 to 10.2) vs 3.8 months (0.6 to 6); p = 0.0001). A total of 42 patients (47 lower limbs) presented with an insensate foot. By final review (mean 27.4 months (20 to 36)) plantar sensation was good in 26 limbs (55%), fair in 16 (34%) and poor in five (11%). Nine patients returned to full military duties, 18 to restricted duties, 30 to sedentary work, and 43 were discharged from military service. Effective rehabilitation must be early, integrated and vigorous. The responsible surgeons must be firmly embedded in the process, at times exerting leadership.
Mapping of DFNB12, a gene for a non-syndromal autosomal recessive deafness, to chromosome 10q21-22 (1996)

We report here, the localization of a new recessive non-syndromal deafness gene (DFNB12) to 10q21-22 by linkage analysis, of a Sunni family. Affected individuals suffer from congenital profound sensorineural hearing loss. A maximum LOD score of 6.40 (theta = 0.00) was obtained with locus D10S535. Analysis of patients carrying recombinations mapped the gene distal to D10S529 and proximal to D10S532, delineating an interval between 11 and 15 cM. Three deaf mouse mutants Jackson circler (jc), Waltzer (v) and Ames waltzer (av) have been localized to the homologous murine region on chromosome 10. Each of these mouse mutants is a candidate mouse model for the DFNB12-associated hearing impairment.
Additional Data for Preliminary Cost Estimation (1994)

Experience has shown that the relative variation in the unit rates of constituents of construction with change in time is never uniform. Because of this, a structural system or scheme which is economical at any given time may not always remain so. For accuracy, it is therefore essential to consider the prevailing unit rates of constituents for cost estimation. With this aim in mind, quantities of constituents in an interior grid of an overall structure using the reinforced concrete beam and slab system are shown in Table 10.1 for different design parameters. The same information, for the reinforced concrete flat slab and waffle slab systems, is shown in Tables 10.2 and 10.3 respectively, while for the prestressed concrete beam and reinforced concrete slab system it is exhibited in Table 10.4.
Special Relativity: An Introduction with 200 Problems and Solutions (2019)

This textbook develops Special Relativity in a systematic way and offers the unique feature of having more than 200 problems with detailed solutions to empower students to gain a real understanding of this core subject in physics. This new edition has been thoroughly updated and has new sections on relativistic fluids, relativistic kinematics and on four-acceleration. The problems and solution section has been significantly expanded and short history sections have been included throughout the book. The approach is structural in the sense that it develops Special Relativity in Minkowski space following the parallel steps as the development of Newtonian Physics in Euclidian space. A second characteristic of the book is that it discusses the mathematics of the theory independently of the physical principles, so that the reader will appreciate their role in the development of the physical theory. The book is intended to be used both as a textbook for an advanced undergraduate teaching course in Special Relativity but also as a reference book for the future. In that respect it is linked to an online repository with more than 200 problems, carefully classified according to subject area and solved in detail, providing an independent problem book on Special Relativity. .
The Resting Place of Innovation (2009)

Successful software-intensive systems are generally quite innovative, as evidenced by their success. Although their architectures will, over time, converge to a stable point, this does not mean that innovation stops. Rather, for any such system to remain vibrant and relevant, innovation much proceed simultaneously at many levels.
Structure‐reactivity relation for polymines and derivatives in activated ester hydrolysis (1984)

Abstract Three polymeric amines, poly(1‐aminoethylene) (polyvinylamine) (PVNH 2 ) and linear and branched poly(iminoethylene)s (polyethylene(imines)) (1‐PEI and b‐PEI) as well as their dodecyl (D) and imidazolylmethyl (Im) substituted derivatives were used for the hydrolysis of p ‐nitrophenyl acetate (PNPA), 4‐acetoxy‐3‐nitrobenzoic acid (ANBA) and some of their homologues in order to elucidate the relations between their overall structures and their catalytic activities. In each series polymers of similar degree of substitution were compared, namely PVNH 2 ‐D18 and PVNH 2 ‐D18‐Im16; b‐PEI‐D20 and b‐PEI‐D20‐Im18; 1‐PEI‐D20 and 1‐PEI‐D20‐Im16. The degree of branching of b‐PEI was 41%. All reactions were carried out at 28,7°C in aqueous solution, and followed spectrometrically. Using a catalyst concentration in large excess with respect to the substrate concentration (10 −4 mol · l −1 ) the reactions were found to obey pseudo‐first order kinetics. By plotting log [Substrate] against time, k 2 (cat) and consequently k 2 rate constantes were evaluated. For each series of polymers, k 2 increases considerably by dodecyl substitution (hydrophobic‐), imidazolylmethyl substitution (catalytic‐) and by the use of a charged substrate (electrostatic effects). At similar degree of substitution the catalytic activity is always in the following order: l‐PEI < PVNH 2 < b‐PEI. Using the method of Kosower‐Mikes the polarity of the microenvironment of l‐PEI and b‐PEI was found to be almost equal. Substitution of l‐PEI with ethyl or 2‐diethylaminoethyl side groups (40% substitution) modifies only slightly the catalytic effect of l‐PEI. It is, therefore, concluded that the primary amino groups of the side chains in b‐PEI are reponsible for its much higher reactivity than that of l‐PEI and PVNH 2 . Experiments with [Substrate] > [Catalyst] were carried out with b‐PEI, b‐PEI‐D20‐lm18 and l‐PEI‐D20‐Im16. Under these conditions the reactions follow Michaelis‐Menten kinetics and permit the comparison of the complexation constant and rate constant of hydrolysis for the three systems. In the case of b‐PEI hydrolysis, reactions towards PNPA carried out at different temperatures, indicate a low enthalpy of activation, Δ H ≠ = −196 j · mol K −1 is strongly negative. On the contrary the enthalpy and entropy of complexation are low, indicating low hydrophobic effects.
Who You Are by way of What You Are: Behavioral Biometric Approaches to Authentication (2014)

We present our work in behavioral biometrics employed in the emerging contexts of gesture-based interfaces. We discuss novel approaches to authentication in signature, multi-touch gesture, and full body in-air gesture. Our work addresses security in these contexts not only in term of technical performance but also in terms of pleasurable interactions between user and system. We highlight opportunities to reframe security topics through ‘natural’ interactions. We also raise questions as to how to evaluate the usability of such approaches and how to incorporate these considerations into the evaluation of overall security. 1. MOTIVATIONS Recent advances in user interface technology have remarkably transformed the way we interact with computing devices and the form factors of computing devices themselves. However, the
Management of the Difficult Adult Airway With Special Emphasis on Awake Tracheal Intubation (1991)

Difficulty in managing the airway is the single most important cause of major anesthesia-related morbidity and mortality. Successful management of a difficult airway begins with recognizing the potential problem. All patients should be examined for their ability to open their mouth widely and for the structures visible upon mouth opening, the size of the mandibular space, and ability to assume the sniff position. If there is a good possibility that intubation and/or ventilation by mask will be difficult, then the airway should be secured while the patient is still awake. In order for an awake intubation to be successful, it is absolutely essential that the patient be properly prepared; otherwise, the anesthesiologist will simply fulfill a self-defeating prophecy. Once the patient is properly prepared, it is likely that any one of a number of intubation techniques will be successful. If the patient is already anesthetized and/or paralyzed and intubation is found to be difficult, many repeated attempts at intubation should be avoided because progressive development of laryngeal edema and hemorrhage will develop and the ability to ventilate the lungs via mask consequently may be lost. After several attempts at intubation, it may be best to awaken the patient, do a semielective tracheostomy, or proceed with the case using mask ventilation. In the event that the ability to ventilate via mask is lost and the patient's lungs still cannot be ventilated, TTJV should be instituted immediately. Tracheal extubation of a patient with a difficult airway over a jet stylet permits a controlled, gradual, and reversible (in that ventilation and reintubation is possible at any time) withdrawal from the airway. Significant advances in the management of the difficult airway have occurred in recent years. Eighty percent of the 127 references in this article were published after 1985. However, there is much more to learn with regard to recognition of the difficult airway, preparation of the patient for an awake intubation, new techniques of endotracheal intubation, and establishment of gas exchange in patients who cannot be intubated or ventilated by mask. As the anesthesiologist's ability to manage the difficult airway significantly improves, respiratory-related morbidity and mortality will decrease.
A three-dimensional fourth-order finite-difference time-domain scheme using a symplectic integrator propagator (2001)

A new explicit fourth-order finite-difference time-domain (FDTD) scheme for three-dimensional electromagnetic field simulation is proposed in this paper. A symplectic integrator propagator, which is also known as a decomposition of the exponential operator or a general propagation technique, is directly applied to Maxwell's equations in the scheme. The scheme is nondissipative and saves memory. The Courant stability limit of the scheme is 30% larger than that of the standard FDTD method. The perfectly matched layer absorbing boundary condition is applicable to the scheme. A specific eigenmode of a waveguide is successfully excited in the scheme. Stable and accurate performance is demonstrated by numerical examples.
The Urokinase Receptor (uPAR) Facilitates Clearance of Borrelia burgdorferi (2009)

The causative agent of Lyme borreliosis, the spirochete Borrelia burgdorferi, has been shown to induce expression of the urokinase receptor (uPAR); however, the role of uPAR in the immune response against Borrelia has never been investigated. uPAR not only acts as a proteinase receptor, but can also, dependently or independently of ligation to uPA, directly affect leukocyte function. We here demonstrate that uPAR is upregulated on murine and human leukocytes upon exposure to B. burgdorferi both in vitro as well as in vivo. Notably, B. burgdorferi-inoculated C57BL/6 uPAR knock-out mice harbored significantly higher Borrelia numbers compared to WT controls. This was associated with impaired phagocytotic capacity of B. burgdorferi by uPAR knock-out leukocytes in vitro. B. burgdorferi numbers in vivo, and phagocytotic capacity in vitro, were unaltered in uPA, tPA (low fibrinolytic activity) and PAI-1 (high fibrinolytic activity) knock-out mice compared to WT controls. Strikingly, in uPAR knock-out mice partially backcrossed to a B. burgdorferi susceptible C3H/HeN background, higher B. burgdorferi numbers were associated with more severe carditis and increased local TLR2 and IL-1beta mRNA expression. In conclusion, in B. burgdorferi infection, uPAR is required for phagocytosis and adequate eradication of the spirochete from the heart by a mechanism that is independent of binding of uPAR to uPA or its role in the fibrinolytic system.
Regulation of Inositol 1,4,5-Trisphosphate Receptors by cAMP Independent of cAMP-dependent Protein Kinase (2010)

In HEK cells stably expressing type 1 receptors for parathyroid hormone (PTH), PTH causes a sensitization of inositol 1,4,5-trisphosphate receptors (IP(3)R) to IP(3) that is entirely mediated by cAMP and requires cAMP to pass directly from type 6 adenylyl cyclase (AC6) to IP(3)R2. Using DT40 cells expressing single subtypes of mammalian IP(3)R, we demonstrate that high concentrations of cAMP similarly sensitize all IP(3)R isoforms to IP(3) by a mechanism that does not require cAMP-dependent protein kinase (PKA). IP(3) binding to IP(3)R2 is unaffected by cAMP, and sensitization is not mediated by the site through which ATP potentiates responses to IP(3). In single channel recordings from excised nuclear patches of cells expressing IP(3)R2, cAMP alone had no effect, but it increased the open probability of IP(3)R2 activated by a submaximal concentration of IP(3) alone or in combination with a maximally effective concentration of ATP. These results establish that cAMP itself increases the sensitivity of all IP(3)R subtypes to IP(3). For IP(3)R2, this sensitization results from cAMP binding to a novel site that increases the efficacy of IP(3). Using stably expressed short hairpin RNA to reduce expression of the G-protein, G alpha(s), we demonstrate that attenuation of AC activity by loss of G alpha(s) more substantially reduces sensitization of IP(3)R by PTH than does comparable direct inhibition of AC. This suggests that G alpha(s) may also specifically associate with each AC x IP(3)R complex. We conclude that all three subtypes of IP(3)R are regulated by cAMP independent of PKA. In HEK cells, where IP(3)R2 selectively associates with AC6, G alpha(s) also associates with the AC x IP(3)R signaling junction.
Keratocan-deficient Mice Display Alterations in Corneal Structure (2003)

Keratocan (Kera) is a cornea-specific keratan sulfate proteoglycan (KSPG) in the adult vertebrate eye. It belongs to the small leucine-rich proteoglycan (SLRP) gene family and is one of the major components of extracellular KSPG in the vertebrate corneal stroma. The Kera gene is expressed in ocular surface tissues including cornea and eyelids during morphogenesis. Corneal KSPGs play a pivotal role in matrix assembly, which is accountable for corneal transparency. In humans, mutations of the KERA gene are associated with cornea plana (CNA2) that manifests decreases in vision acuity due to the flattened forward convex curvature of cornea. To investigate the biological role of the Kera gene and to establish an animal model for corneal plana, we generated Kera knockout mice via gene targeting. Northern and Western blotting and immunohistochemical analysis showed that no Kera mRNA or keratocan protein was detected in the Kera-/- cornea. The expression levels of other SLRP members including lumican, decorin, and fibromodulin were not altered in the Kera-/- cornea as compared with that of the wild-type littermates. Mice lacking keratocan have normal corneal transparency at the age of 12 months. However, they have a thinner corneal stroma and a narrower cornea-iris angle of the anterior segment in comparison to the wild-type littermates. As demonstrated by transmission electron microscopy, Kera-/- mice have larger stromal fibril diameters and less organized packing of collagen fibrils in stroma than those of wild type. Taken together, our results showed that ablation of the Kera gene resulted in subtle structural alterations of collagenous matrix and did not perturb the expression of other SLRPs in cornea. Keratocan thus plays a unique role in maintaining the appropriate corneal shape to ensure normal vision.
Selecting the best system in steady-state simulations using batch means (1995)

Suppose that we want to compare k different systems, where /spl mu//sub i/ denotes the steady state mean performance of system i. Our goal is to use simulation to pick the "best" system (i.e., the one with the largest or smallest steady state mean). To do this, we present some two stage procedures based on the method of batch means. Our procedures also construct multiple comparisons with the best (MCB) confidence intervals for /spl mu//sub i/-max/sub j/spl ne/i//spl mu//sub j/, i=1,...,k. Under the assumption of an indifference zone of (absolute or relative) width /spl delta/, we can show that asymptotically (as /spl delta//spl rarr/0 with the size of the batches proportional to 1//spl delta//sup 2/), the joint probability of correctly selecting the best system and of the MCB confidence intervals simultaneously containing /spl mu//sub i/-max/sub j/spl ne/i//spl mu//sub j/, i=1,...,k, is at least 1-/spl alpha/, where /spl alpha/ is prespecified by the user.
The mechanical properties of cement and loosening of the femoral component of hip replacements (1987)

Mechanical and biomechanical testing of a new bone cement suggests that improved load transfer to the proximal femur could be achieved with the combination of a cement having a lower modulus, a greater ductility and a lower creep resistance than polymethylmethacrylate and a suitably shaped femoral component.