gebhart/patrepeval huggingface dataset:
Typical 2‐Cys peroxiredoxins – modulation by covalent transformations and noncovalent interactions (2009)

2-Cys peroxiredoxins are peroxidases devoid of prosthetic groups that mediate in the defence against oxidative stress and the peroxide activation of signaling pathways. This dual capacity relies on the high reactivity of the conserved peroxidatic and resolving cysteines, whose modification embraces not only the usual thiol-disulfide exchange but also higher oxidation states of the sulfur atom. These changes are part of a complex system wherein the cooperation with other post-translational modifications - phosphorylation, acetylation - may function as major regulatory mechanisms of the quaternary structure. More importantly, modern proteomic approaches have identified the oxyacids at cysteine residues as novel protein targets for unsuspected post-translational modifications, such as phosphorylation that yields the unusual sulfi(o)nic-phosphoryl anhydride. In this article, we review the biochemical attributes of 2-Cys peroxiredoxins that, in combination with complementary studies of forward and reverse genetics, have generated stimulating molecular models to explain how this enzyme integrates into cell signaling in vivo.
Structural geology of the Rub' Al‐Khali Basin, Saudi Arabia (2016)

Abstract The Rub' Al‐Khali basin lies below a Quaternary sand sea, and the structural evolution from the Late Precambrian to Neogene is known only from reflection seismic, gravity, and magnetic data, and wells. Gravity and magnetic data show north‐south and northwest‐southeast trends, matching mapped Precambrian faults. The deepest structures imaged on reflection seismic data are undrilled Precambrian rifts filled with layered strata at depths up to 13 km. The distribution of Ediacaran‐Cambrian Ara/Hormuz mobile salt is restricted to an embayment in the eastern Rub' Al‐Khali. The Precambrian rifts show local inversion and were peneplained at base Phanerozoic. A broad crustal‐scale fold (Qatar Arch) developed in the Carboniferous and amplified in the Late Triassic, separating subbasins in the west and east Rub' Al‐Khali. A phase of kilometer‐scale folding occurred in the Late Cretaceous, coeval with thrusting and ophiolite obduction in eastern Oman. These folds trend predominantly north‐south, oblique to the northwesterly shortening direction, and occasionally have steep fault zones close to their axial surfaces. The trend and location of these folds closely matches the Precambrian lineaments identified in this study, demonstrating preferential reactivation of basement structures. Compression along the Zagros suture reactivated these folds in the Neogene, this time the result of highly oblique, north‐northeast to south‐southwest shortening. Cretaceous‐Tertiary fold style is interpreted as transpression with minor strain partitioning. Permian, Jurassic, and Eocene evaporite horizons played no role in the structural evolution of the basin, but the Eocene evaporites caused widespread kilometer‐scale dissolution collapse structures in the basin center.
A Balanced-to-Balanced In-Phase Filtering Power Divider With High Selectivity and Isolation (2018)

In this paper, a balanced-to-balanced in-phase filtering power divider (FPD) is proposed, which can realize a two-way equal power division with high selectivity and isolation. The design of the proposed FPD is primarily based on microstrip/slotline transition structures and slotline T-junction. A U-type microstrip feed line integrated with a stepped-impedance slotline resonator is adopted at the input and output ports, which makes the differential-mode (DM) responses independent of the common-mode (CM) ones. Meanwhile, superior DM transmission and CM suppression are achieved intrinsically, thereby simplifying the design procedure significantly. By employing slotline resonators loaded with resistors, the isolation between the two output ports can be improved greatly. In addition, a DM passband with a sharp filtering performance is realized by introducing the microstrip stub-loaded resonators (SLRs). By changing the electrical length of the open stub of the SLR, the fractional bandwidth is controllable. In order to verify the feasibility of the proposed design method, two prototype circuits of the proposed FPDs with different bandwidths are fabricated and measured. Good agreement between the simulation and measurement results is observed.
Electrically tunable Nd 3+ -doped fibre laserusing nematic liquid crystals (1995)

An intracavity wavelength filter formed by a nematic liquid crystal cell is used to tune the wavelength of a fibre laser. The tuning range of the device is 17 nm and the tuning rate is 8 nm/V.
The future for weed control and technology (2013)

This review is both a retrospective (what have we missed?) and prospective (where are we going?) examination of weed control and technology, particularly as it applies to herbicide-resistant weed management (RWM). Major obstacles to RWM are discussed, including lack of diversity in weed management, unwillingness of many weed researchers to conduct real integrated weed management research or growers to accept recommendations, influence or role of agrichemical marketing and governmental policy and lack of multidisciplinary research. We then look ahead to new technologies that are needed for future weed control in general and RWM in particular, in areas such as non-chemical and chemical weed management, novel herbicides, site-specific weed management, drones for monitoring large areas, wider application of 'omics' and simulation model development. Finally, we discuss implementation strategies for integrated weed management to achieve RWM, development of RWM for developing countries, a new classification of herbicides based on mode of metabolism to facilitate greater stewardship and greater global exchange of information to focus efforts on areas that maximize progress in weed control and RWM. There is little doubt that new or emerging technologies will provide novel tools for RMW in the future, but will they arrive in time?
INCREASED SWELLING RESULTS IN POOR OUTCOME AFTER ANKLE ARTHRITIS SURGERY (2018)

Patients often comment on swelling after foot and ankle surgery. However the relationship between swelling and outcome (pain and function) has not previously been outlined. A recent study by Pinsker and Daniels demonstrated that while swelling was rated as important by patients it was rarely included in outcome scores. The purpose of this paper was to determine the relationship between swelling and outcome after ankle fusion or replacement. A secondary purpose was to determine how this relationship changed in time, how swelling score changed before and after surgery, and determine differences in swelling score between total ankle replacement (TAR), open ankle arthrodesis (OAA) and arthroscopic ankle arthrodesis (AAA).The COFAS prospective ankle arthritis database enrolls patients in 4 centers undergoing surgery by one of 6 surgeons since 2002. The MODEMS outcomes package from AAOS was used, with the validated ankle osteoarthritis score (AOS) score being used to assess outcomes in the pain and disability d...
On the (Im)possibility of Preserving Utility and Privacy in Personalized\n Social Recommendations (2010)

With the recent surge of social networks like Facebook, new forms of\nrecommendations have become possible -- personalized recommendations of ads,\ncontent, and even new social and product connections based on one's social\ninteractions. In this paper, we study whether "social recommendations", or\nrecommendations that utilize a user's social network, can be made without\ndisclosing sensitive links between users. More precisely, we quantify the loss\nin utility when existing recommendation algorithms are modified to satisfy a\nstrong notion of privacy called differential privacy. We propose lower bounds\non the minimum loss in utility for any recommendation algorithm that is\ndifferentially private. We also propose two recommendation algorithms that\nsatisfy differential privacy, analyze their performance in comparison to the\nlower bound, both analytically and experimentally, and show that good private\nsocial recommendations are feasible only for a few users in the social network\nor for a lenient setting of privacy parameters.\n
Traffic engineering with BGP (2009)

Distributed under a Creative Commons license. This paper will give an overview of how to connect reliably to the Internet using con-nections to multiple Internet Service Providers (ISPs). Since there are numerous possible ways for packets to enter and leave our own network in such a setup, a network oper-ator might want to control this behavior as best as possible for several reasons. We will discuss how to achieve this goal. 1
Structure and conformational cycle of a bacteriophage-encoded chaperonin (2020)

Abstract Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa . ɸEL, an evolutionary distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeF x revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionary more ancient chaperonin prior to acquisition of the encapsulation mechanism.
Variable effects of retinoids on two pigmenting human melanoma cell lines. (1982)

Two melanoma cell lines, each derived from a different patient with metastatic disease, were very similar in their appearance, their growth characteristics, and their tendency to differentiate and to pigment in culture as they become confluent. These lines, UCT-Mel 1 and UCT-Mel 2, were used to study the effects of retinoic acid and other derivatives of vitamin A. When added to UCT-Mel 1 cells, retinoids had only a modest effect on plasminogen activator release and were without measurable effect on morphology, growth, or tyrosinase synthesis. In contrast, when added to UCT-Mel 2 cells, retinoids appeared to induce a more differentiated state evident as an inhibition of cell proliferation and the assumption of a dendritic morphology. Paradoxically, however, retinoids caused a striking inhibition of the density-dependent intracellular accumulation of tyrosinase and melanin that was taken to represent spontaneous in vitro differentiation. Culture of UCT-Mel 2 cells in the presence of retinoic acid resulted in initial inhibition followed by marked stimulation of cellular plasminogen activator release. The data suggest that the manner in which retinoids exert their effects on cells in vitro does not depend on the histological origin of the tumor cells being studied but on the innate responsiveness of that particular cell line to the retinoid or compound in question.
Comparative Analysis of Methods for Assessment of Circulating Endothelial Progenitor Cells (2006)

The number and properties of endothelial progenitor cells (EPC) in disease states is of considerable interest due to the importance attributed to this distinct cell population. However, there has been no study comparing each of the methods employed in the same sampled individuals. Herein, we performed an analysis of several methods used for circulating EPC assessment and correlated them with humoral factors known to influence their numbers. Thirty-eight individuals (mean age of 34 +/- 9 years) were tested. Peripheral blood mononuclear cells were obtained and stained for FACS analysis with antibodies to CD34, CD45, CD133, and KDR and the remaining cells grown under endothelial cell conditions for assessment of colony-forming unit (CFU) numbers and adhesive properties. Levels of circulating vascular endothelial growth factor (VEGF), erythropoietin (EPO), and C-reactive protein (CRP) were determined and correlated with each of the EPC markers. CFU numbers did not correlate with CD34/KDR or CD34/CD133/KDR and negatively correlated with CD34/ CD133 numbers. CD34/KDR numbers correlated with CD34/CD133/KDR, but not with CD34/ CD133. Only CD34/KDR and CD34/CD133/KDR correlated with VEGF serum levels. The number of EPC adhering to fibronectin and endothelial cells correlated with CFU numbers and not with either of the EPC membrane markers. Current methods for quantitatively assessing numbers of circulating EPC are not correlated. VEGF serum levels are associated only with CD34/KDR and CD34/ CD133/KDR, whereas CFU numbers correlate with EPC functional properties. These findings may suggest that CD34/KDR is more appropriate for the definition of circulating EPC, whereas CFU numbers are more likely to reflect their ability to proliferate.
Moderate frequency of BRCA1 and BRCA2 germ-line mutations in Scandinavian familial breast cancer. (1997)

Previous studies of high-risk breast cancer families have proposed that two major breast cancer-susceptibility genes, BRCA1 and BRCA2, may account for at least two-thirds of all hereditary breast cancer. We have screened index cases from 106 Scandinavian (mainly southern Swedish) breast cancer and breast-ovarian cancer families for germ-line mutations in all coding exons of the BRCA1 and BRCA2 genes, using the protein-truncation test, SSCP analysis, or direct sequencing. A total of 24 families exhibited 11 different BRCA1 mutations, whereas 11 different BRCA2 mutations were detected in 12 families, of which 3 contained cases of male breast cancer. One BRCA2 mutation, 4486delG, was found in two families of the present study and, in a separate study, also in breast tumors from three unrelated males with unknown family history, suggesting that at least one BRCA2 founder mutation exists in the Scandinavian population. We report 1 novel BRCA1 mutation, eight additional cases of 4 BRCA1 mutations described elsewhere, and 11 novel BRCA2 mutations (9 frameshift deletions and 2 nonsense mutations), of which all are predicted to cause premature truncation of the translated products. The relatively low frequency of BRCA1 and BRCA2 mutations in the present study could be explained by insufficient screening sensitivity to the location of mutations in uncharacterized regulatory regions, the analysis of phenocopies, or, most likely, within predisposed families, additional uncharacterized BRCA genes.
Multifunctional behaviors of reconfigurable superbot robots (2007)

Superbot consists of Lego-like but autonomous robotic modules that can reconfigure into different systems for different tasks. Examples of configurable systems include rolling tracks or wheels (for efficient travel), spiders or centipedes (for climbing), snakes (for burrowing in ground), and climbers (for inspection and repair in space). This video shows several configurations and behaviors that are new for modular and reconfigurable robots. Each SuperBot module is a complete robotic system and has a power supply, micro- controllers, sensors, communication, three degrees of freedom, and six connecting faces (front, back, left, right, up and down) to dynamically connect to other modules. This design allows flexible bending, docking, and continuous rotation. A single module can move forward, back, left, right, flip-over, and rotate as a wheel. Modules can communication with each other for totally distributed control and can support arbitrary module reshuffling during their operation. The modules have both internal and external sensors for monitoring self-status and environmental parameters. They can form arbitrary configurations (graphs) and can control these configurations for different functionality such as locomotion, manipulation, and self-repair. This video shows the latest status the SuperBot modules and all these behaviors were made in just one week. The fact that SuperBot can achieve so much in so short a time demonstrates the unique value of modular, multifunctional and self-reconfigurable robots.
Computerized detection &amp; classification of ECG signals (2012)

An electrocardiogram (ECG) is a recorded representation of electrical activity of heart with respect to time. Being a very important diagnostic tool for determining various heart functions, computer based ECG interpretation is a computing system that records and automatically detects the variations in important parameters of a given ECG recording. These parameters are very critical for doctors while examining the condition of the heart of a patient. Identification of the specific area of the heart under problem and the extent of damage done are the basic areas which have been highlighted for proper diagnosis to save patient's life. This paper, proposes an approach to determine the values of the amplitude of P, QRS & T together with time durations (PR, RR, QRS, and QT). From these calculations, the heart condition whether it is normal or not, is determined along with amount of variation so that the cardiologist can recommend the amount of dosing required for the medicine for the ailment of the patient. It also classifies the ECG into seven major cardiac problems. In this thesis, we have introduced a curve mapping technique based on slope method to detect & classify the ECG signals into seven major cardiac problems. The accuracy rate arrived in the slope method ranges from 92% to 100%, for seven cardiac conditions with an overall average 96.57 %.
Genetic Variability of Smoking Persistence in African Americans (2020)

To date, most genetic association analyses of smoking behaviors have been conducted in populations of European ancestry and many of these studies focused on the phenotype that measures smoking quantity, i.e. cigarettes per day. Additional association studies in diverse populations with different linkage disequilibrium (LD) patterns and an alternate phenotype, such as total tobacco exposure which accounts for intermittent periods of smoking cessation within a larger smoking period as measured in large cardiovascular risk studies, can aid the search for variants relevant to smoking behavior. For these reasons, we undertook an association analysis using a genotyping array that includes 2100 genes to analyze smoking persistence in unrelated African-American participants from The Atherosclerosis Risk in Communities (ARIC) study. A locus located ~ 4 Kb downstream from the 3’ UTR of the Brain-Derived Neurotrophic Factor (BDNF) significantly influenced smoking persistence. In addition, independent variants rs12915366 and rs12914385 in the cluster of genes encoding nicotinic acetylcholine receptor subunits (CHRNA5-CHRNA3-CHRNB4) on 15q25.1 were also associated with the phenotype in this sample of African American subjects. To our knowledge, this is the first study to more extensively evaluate the genome in the African American population as a limited number of previous studies of smoking behavior in this population included evaluations of only single genomic regions.
GLUCOSE AND LACTATE TURNOVER IN MAN DURING REST AND EXERCISE STUDIED WITH SIMULTANEOUS INFUSION OF 14C-GLUCOSE AND 13C-LACTATE (1984)

Stanley, W. C.; Gertz, E. W.; Wianeski, J. A.; Neese, R. A.; Brooks, G. A. Author Information
Traveler's Value of Real-Time Transit Information (2009)

Intelligent transportation systems (ITS) have become common in public transit systems, particularly for the use of providing real-time transit information. For new implementations, it remains difficult predict and quantify system and user benefits of technology implementation. Although previous studies have quantified the operational benefits of real-time transit traveler information systems, a gap in knowledge exists around passenger benefits of such systems. The objective of this research was to create a refined method for evaluating transit rider benefits from real-time traveler information and predict subsequent changes in traveler behavior. The study was conducted on a rural university campus, isolating the impacts of the system from the multiple influences that often affect transportation in larger metropolitan areas. This study uniquely integrated transit system performance, pedestrian travel times, and traffic simulation to determine travel times and predict mode split. Findings indicated that reducing passenger waiting anxiety by proving estimates of the next buses arrival was the most significant measure of traveler benefit from such a system. While the benefits found were specific to the study site, the methodology can be used for other transit systems evaluating real-time technology investments in rural or urban environments.
Hyperfine structure of the 3d34s4p6G multiplet of atomic vanadium (2011)

The spectrum of atomic vanadium was recorded using high-resolution Fourier transform spectroscopy with optical bandpass filters in the wavelength range from 360 to 500 nm. Vanadium atoms are produced and excited in a hollow-cathode discharge. The main focus lies on the determination of the magnetic dipole hyperfine constants A of the lowest multiplet of odd parity, the 6G of the configuration 3d34s4p, the hyperfine structure (HFS) of which was unknown to date. The HFS of the lines, connecting this multiplet with the multiplets 3d34s5s 6F, 3d34s4d 6H and 3d34s4d 6G, was observed and analysed. New results are presented for all six levels belonging to 3d34s4p 6G as well as for seven high-lying levels belonging to 3d34s4d 6H and 3d34s4d 6G. The experimental results for the lowest multiplet of odd parity are compared with calculated magnetic dipole hyperfine constants which were estimated using the effective-operator formalism in the pure LS coupling case.
Klein Link Multiplicity and Recursion (2016)

The (m,n)-Klein links are formed by altering the rectangular representation of an (m,n)-torus link. Using the braid representation of a (m,n)-Klein link, we generalize a previous braid word result and show that the (m, 2m)-Klein link can be expressed recursively. Applying braid permutations, we determine a formula for the number of components for an (m,n)-Klein link and classify the Klein links that are equivalent to knots.