gebhart/patrepeval huggingface dataset:
Probing the Stereochemistry of E. coli 3-Deoxy-d-arabino-heptulosonate 7-Phosphate Synthase (Phenylalanine-Sensitive)-Catalyzed Synthesis of KDO 8-P Analogues (2000)

The five-carbon phosphorylated monosaccharide analogues, D-arabinose 5-phosphate, D-ribose 5-phosphate, and 2-deoxy-D-ribose 5-phosphate, were separately condensed with (Z)- and (E)-[3-(2)H]-phosphoenolpyruvate (PEP) in the presence of Escherichia coli 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH 7-P) synthase (phe) to give in the case of (Z)-[3-(2)H]-PEP (3S)-[3-(2)H]-3-deoxy-D-manno-octulosonate 8-phosphate, (3S)-[3-(2)H]-3-deoxy-D-altro-octulosonate 8-phosphate, and (3S)-[3-(2)H]-3,5-dideoxy-D-altro-octulosonate 8-phosphate, respectively, whereas incubation with (E)-[3-(2)H]-PEP gives the corresponding (3R)-monosaccharides. These results are in complete agreement with the observed facial selectivity of DAH 7-P synthase for its normal substrates D-erythrose 4-phosphate and PEP and provide direct evidence that DAH 7-P synthase (phe) catalyzes the si face addition of the C3 of PEP to the re face of C1 of the phosphorylated monosaccharides tested. Products formed by DAH 7-P synthase (phe)-catalyzed condensation of (Z)- and (E)-[3-F]-PEP with E 4-P were completely characterized by (1)H and (19)F NMR analysis for the first time. Results of our studies suggest that disappearence of the double bond between C2 and C3 of PEP and formation of a bond between C3 of PEP and C1 of the phosphorylated monosaccharide tested occur in concert during the DAH 7-P synthase-catalyzed condensation reaction.
Genome hypomethylation and activation of MAGE genes in tumor cells (2004)

Genome hypomethylation is a common feature of human cancers. We have shown previously that this epigenetic alteration in tumors is accompanied by the ectopic activation of a group of germline-specific genes, including gene MAGE-A1, whose repression in normal somatic tissues relies on DNA methylation. MAGE-A1 has a CpG-rich promoter, which unlike classical CpG-rich promoters, is methylated in most healthy tissues in the adult. Its expression in both male germ cells and tumor cells is associated with extensive demethylation of a restricted region of less than 3 Kb centered around the transcription initiation site. The other parts of the locus are only partially unmethylated in tumors. The process leading to this site-specific hypomethylation does not appear to be due to a permanent demethylating activity targeted to the 5' region of MAGE-A1, as in vitro methylated MAGE-A1 sequences do not undergo demethylation after being stably transfected in cells that normally express the gene. These cells however, contain transcriptional activators that protect the 5' region of the gene against remethylation , since unmethylated MAGE-A1 transgenes undergo remethylation at all CpGs except those located within the 5' region. These observations suggest that the site-specific hypomethylation in the 5' region of MAGE-A1 results from a sequence of two distinct processes: a transient DNA demethylation process, followed by a persistent site-specific protection of this region against remethylation. We are now searching to identify the DNA methyltransferases that are normally involved in maintaining the MAGE-A1 gene methylated. Knock-down experiments using anti-sense oligonucleotides suggest that DNMT1 plays a dominant role in this process.
Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns (2023)

Ferns and lycophytes, now known as monilophytes, have received scant molecular attention in comparison to angiosperms. The advent of high-throughput technologies allowed an advance towards a greater knowledge of their elusive genomes. In this work, proteomic analyses of heart-shaped gametophytes of two ferns were performed: the apomictic species Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. In total, a set of 218 proteins shared by these two gametophytes were analyzed using the STRING database, and the proteome associated with metabolism, genetic information processing, and responses to abiotic stress is discussed. Specifi-cally, we report proteins involved in the metabolism of carbohydrates, lipids, and nucleotides, the biosynthesis of amino acids, and secondary compounds, energy, oxido-reduction, transcrip-tion, translation, protein folding, sorting and degradation, and responses to abiotic stress. Look-ing at the interactome of this set of proteins, it represents a total network composed of 218 nodes and 1,792 interactions, obtained mostly from databases and textmining. The interactions among the identified proteins of the ferns D. affinis and D. oreades, together with the description of their biological functions, might contribute to a better understanding of the function and develop-ment of ferns as well as to fill knowledge gaps in plant evolution.
Grocery Store Flexibility Management Using Model Predictive Control With\n Neural Networks (2020)

As more and more energy is produced from renewable energy sources (RES), the\nchallenge for balancing production and consumption is being shifted to\nconsumers instead of the power grid. This requires new and intelligent ways of\nflexibility management at individual building and district levels. To this end,\nthis paper presents a model based optimal control (MPC) algorithm embedded with\ndeep neural network for day-ahead consumption and production forecasting. The\nalgorithm is used to optimize a medium-sized grocery store energy consumption\nlocated in Finland. System was tested in a simulation tool utilising real-life\npower measurements from the grocery store. We report a $8.4\\%$ reduction in\ndaily peak loads with flexibility provided by a $20$ kWh battery. On the other\nhand, a significant benefit was not seen in trying to optimize with respect to\nthe energy spot price. We conclude that our approach is able to significantly\nreduce peak loads in a grocery store without additional operational costs.\n
Biometric Template Security (2008)

Biometric recognition offers a reliable solution to the problem of user authentication in identity management systems. With the widespread deployment of biometric systems in various applications, there are increasing concerns about the security and privacy of biometric technology. Public acceptance of biometrics technology will depend on the ability of system designers to demonstrate that these systems are robust, have low error rates, and are tamper proof. We present a high-level categorization of the various vulnerabilities of a biometric system and discuss countermeasures that have been proposed to address these vulnerabilities. In particular, we focus on biometric template security which is an important issue because, unlike passwords and tokens, compromised biometric templates cannot be revoked and reissued. Protecting the template is a challenging task due to intrauser variability in the acquired biometric traits. We present an overview of various biometric template protection schemes and discuss their advantages and limitations in terms of security, revocability, and impact on matching accuracy. A template protection scheme with provable security and acceptable recognition performance has thus far remained elusive. Development of such a scheme is crucial as biometric systems are beginning to proliferate into the core physical and information infrastructure of our society.
EyePointing (2019)

Interacting with objects from a distance is not only challenging in the real world but also a common problem in virtual reality (VR). One issue concerns the distinction between attention for exploration and attention for selection -- also known as the Midas-touch problem. Researchers proposed numerous approaches to overcome that challenge using additional devices, gaze input cascaded pointing, and using eye blinks to select the remote object. While techniques such as MAGIC pointing still require additional input for confirming a selection using eye gaze and, thus, forces the user to perform unnatural behavior, there is still no solution enabling a truly natural and unobtrusive device free interaction for selection. In this paper, we propose EyePointing: a technique which combines the MAGIC pointing technique and the referential mid-air pointing gesture to selecting objects in a distance. While the eye gaze is used for referencing the object, the pointing gesture is used as a trigger.
Increased Peripheral Nerve Excitability and Local Nav1.8 RNA Up-Regulation in Painful Neuropathy (2009)

Cuff entrapment injury resulted in significantly elevated axonal excitability and increased NaV1.8 immunoreactivity in rat sciatic nerves. The concomitant axonal accumulation of NaV1.8 mRNA may play a role in the pathogenesis of this model of neuropathic pain.
FRACTURES OF THE DISTAL ASPECT OF THE RADIUS (2003)

Fractures of the distal end of the radius are among the most common orthopaedic injuries, and treatment of these fractures has changed over the course of time. Many fractures of the distal radius are in fact relatively uncomplicated and are effectively treated by closed reduction and casting. However, fractures that are either unstable and/or involve the articular surfaces can jeopardize the integrity of the articular congruence and/or the kinematics of these articulations. The goal of the treating physician should then be to restore the functional anatomy by a method that does not compromise hand function. The fracture pattern, degree of displacement, the stability of the fracture, and the age and physical demands of the patient determine the best treatment option. Over the past 20 years, there has been a development of more sophisticated internal and external fixation techniques and devices for the treatment of displaced fractures of the distal radius. The use of percutaneous pin fixation, external fixation devices that permit distraction and palmar translation, low profile internal fixation plates and implants, arthroscopically-assisted reduction, and bone grafting techniques including bone graft substitutes all have contributed to improving fracture stability and outcome.
Generalized inverse multiplexing of switched ATM connections (2002)

Inverse multiplexing for ATM (IMA) has been standardized by the ATM Forum to provide a high-capacity logical link by grouping several lower-capacity physical links. IMA is intrinsically point-to-point, assumes congestion-free links, and only tolerates relatively constant differential delays between the links. In this paper, we generalize the notion of inverse multiplexing by introducing switching and buffering within the inverse multiplexed segment. The new scheme, which we call Switched Connection Inverse Multiplexing for ATM (SCIMA) allows to implement an N/spl times/N switch with ports operating at rate kR by using a kN/spl times/kN core ATM switch with ports of rate R. SCIMA executes demultiplexing on a selected set of virtual connections, dynamically distributes their traffic onto a group of switching paths, and performs egress re-assembly using an asynchronous method for differential delay compensation. The scheme is simple to implement, has low overhead, is robust in presence of cell loss within the switch, handles congestion, and tolerates wide variations in differential delays.
Incremental maintenance of views with duplicates (1995)

We study the problem of efficient maintenance of materialized views that may contain duplicates. This problem is particularly important when queries against such views involve aggregate functions, which need duplicates to produce correct results. Unlike most work on the view maintenance problem that is based on an algorithmic approach, our approach is algebraic and based on equational reasoning. This approach has a number of advantages: it is robust and easily extendible to new language constructs, it produces output that can be used by query optimizers, and it simplifies correctness proofs.We use a natural extension of the relational algebra operations to bags (multisets) as our basic language. We present an algorithm that propagates changes from base relations to materialized views. This algorithm is based on reasoning about equivalence of bag-valued expressions. We prove that it is correct and preserves a certain notion of minimality that ensures that no unnecessary tuples are computed. Although it is generally only a heuristic that computing changes to the view rather than recomputing the view from scratch is more efficient, we prove results saying that under normal circumstances one should expect, the change propagation algorithm to be significantly faster and more space efficient than complete recomputing of the view. We also show that our approach interacts nicely with aggregate functions, allowing their correct evaluation on views that change.
A mass transfer probe for measurements of cavitation activity in ultrasonic fields (1989)

A new type of probe was developed to evaluate the distribution of kinetic, thermal, and acoustic energy in an ultrasonically induced cavitation field. The probe is based on an electrochemical mass transfer technique for direct measurement of the flux of reactants to a surface. Cavitation was generated in a focused ultrasonic field at 1.58 MHz over a large range of focal intensities. Electrochemical measurements of the reduction of ferricyanide to ferrocyanide in a NaOH solution show that the focal area dimensions (as characterized by the cavitation activity) increased almost an order of magnitude in the presence of intense cavitation. The cavitation activity is attributed to fluid motion generated by cavitation-induced jets and microstreaming. A mathematical model is proposed to predict the mass transfer rate at the surface under cavitation conditions and to relate the mass transfer coefficient to the acoustic focal intensity. The concept of the mass transfer probe resulted from the author’s previous work in the study of the electrochemistry of metals in the presence of ultrasound [S. Perusich, Ph.D. thesis, University of Illinois at Urbana, Urbana, IL (1985)].
Multi-dip radon stack as an alternative to conventional stacking (1994)

Conventional velocity stack is performed after a hyperbolic moveout correction and straight summation of the data (CMP gathers). This process is equivalent to summing the data along hyperbolic paths. Although the Radon transform (RT) has never been designed to perform such operation as stacking, it is very interesting to note the basic definition of the forward generalized Radon transform (GRT) which is obtained by summing the original data along a path. If this path happens to be a hyperbolic one, then in principle, the forward GRT domain would indeed be equivalent to a velocity stack domain. And picking suitably in this transform domain should enable us to obtain an equivalent of a velocity stack. This is the idea that lays the foundation of the proposed method.
Automatic Ransomware Detection and Analysis Based on Dynamic API Calls Flow Graph (2017)

In recent cyber incidents, Ransom software (ransomware) causes a major threat to the security of computer systems. Consequently, ransomware detection has become a hot topic in computer security. Unfortunately, current signature-based and static detection model is often easily evadable by obfuscation, polymorphism, compress, and encryption. For overcoming the lack of signature-based and static ransomware detection approach, we have proposed the dynamic ransomware detection system using data mining techniques such as Random Forest (RF), Support Vector Machine (SVM), Simple Logistic (SL) and Naive Bayes (NB) algorithms for detecting known and unknown ransomware. We monitor the actual (dynamic) behaviors of software to generate API calls flow graphs (CFG) and transfer it in a feature space. Thereafter, data normalization and feature selection were applied to select informative features which are the best for discriminating between various categories of software and benign software. Finally, the data mining algorithms were used for building the detection model for judging whether the software is benign software or ransomware. Our experimental results show that our proposed system can be more effective to improve the performance for ransomware detection. Especially, the accuracy and detection rate of our proposed system with Simple Logistic (SL) algorithm can achieve to 98.2% and 97.6%, respectively. Meanwhile, the false positive rate also can be reduced to 1.2%.
Effect of molar ratios on strength, microstructure & embodied energy of metakaolin geopolymer (2021)

In this study, twenty-five geopolymer (GP) mixes were prepared by varying the alkaline solids to Metakaolin (MK) and sodium silicate to NaOH ratios from 0.1 to 0.5 and 0.2 to 1.0, respectively, thus giving a wide range of molar ratios of silica to alumina, sodium oxide to alumina and water to sodium oxide. The compressive strength of these GP mixes was determined for four curing schemes involving oven curing at 100oC for 24 h and three ambient curing with the curing ages of 3, 14, and 28 days. The test results revealed that for the manufacture of GP binder for structural applications of strength up to 90 MPa, the molar ratio of silica to alumina should be greater than 2.3, sodium oxide to alumina should be between 0.6 to 1.2, and water to sodium oxide should not exceed 12. The compressive strength of ambient cured GP mortar gets stabilized at 28 days of ambient curing. Experimental findings were also corroborated by GP microstructure analysis. The embodied energy of MK-based GP mortars, especially of high strength, is significantly less than the cement mortar of equivalent strength.
A comprehensive approach to expression of L1 loci (2016)

L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5΄ RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads. At least 99% of L1-related sequences found in RNA do not arise from the L1 promoter, instead representing pieces of L1 incorporated in other cellular RNAs. In any given cell type a relatively few active L1 loci contribute to the 'authentic' L1 transcripts that arise from the L1 promoter, with significantly different loci seen expressed in different tissues.
Development of a collaborative application in CSDL (2002)

Cooperative system programming deals with four topics: multiuser interfaces, coordination, shared workspace, and networking control. The goal of CSDL (Cooperative Systems Design Language) is to cover all these aspects. The authors present the development of a system in CSDL. The system allows a group of physically distributed users to edit a document concurrently. It permits sharing the single-user editor xedit by multiplexing the application's outputs to each participant, while inputs come from one user at a time. A simple floor control policy allows participants to designate who has that right. A detailed presentation of the coordination layer, and a discussion of system architecture are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Impact of short-term low-dose tamoxifen on molecular breast imaging background parenchymal uptake: a pilot study (2019)

ClinicalTrials.gov NCT02979301 . Registered 01 December 2016.
New production in the warm waters of the tropical (1994)

The average depth-integrated rate of new production in the tropical Pacific Ocean was estimated from a calculation of horizontal and vertical nitrate balance over the region enclosed by the climatological 26oC isotherm. The net turbulent flux of nitrate into the region was computed in terms of the climatological net surface heat flux and the nitrate-temperature relationship at the base of the 26oC isotherm. The net advective transport of nitrate into the region was estimated using the mean nitrate distribution obtained from the analysis of historical data and previous results of a general circulation model of the tropical Pacific. The rate of new production resulting from vertical turbulent fluxes of nitrate was found to be similar in magnitude to that due to advective transport. Most (about 75%) of the advective input of nitrate was due to the horizontal transport of nutrient-rich water from the eastern equatorial region rather than from equatoriaupwelling. An average rate of new production of 14.5-16 g C rn -2 yr - was found for the warm waters of the tropicaPacific region. These values are in good agreement with previous estimates for this region and are almost five times less than is estimated for the eastern equatorial Pacific, where most of the nutrient upwelling occurs.
An encapsulating meta-molecule: U resonator containing spiral line (2014)

A new kind of planar metamaterial is investigated. It consists of meta-molecules where a first resonator encapsulates a second resonator. The near-field coupling between these resonators is the dominating effect determining the characteristics of the material and is discussed in detail at a physical level. The technique of encapsulating allows both to miniaturize the unit cell, which is advantageous with respect to making the material homogeneous, and to invoke strong coupling, which is advantageous for tuning the material.
Linearity Trade-offs in High-Voltage RF Switches for Antenna Tuning Applications (2020)

An analysis describing the harmonics distribution in a shunt aperture tuning RF switch operating in OFF mode is presented in the paper. The focus is put on the second and third harmonic power distribution as a function of geometry of an RF switch. The analytical findings are verified with measurements for which the two integrated circuits were manufactured in Infineon 130 nm RF switch technology. Both the analytical model and the measurements show, that there is a trade-off between the second and third harmonic depending on the geometry of the RF switch.
Crystal Structure and Magnetic Properties of Mn-Al-Ni Ferromagnetic Films (1991)

Mn 60-x Al 40 Ni x ternary films were prepared by dc magnetron sputtering and their crystallographic characteristics and magnetic properties were investigated. The ? phase was synthesized at Ni contents below 7 at%. The lattice constant a increased from 3.98 A to 4.12 A, and c decreased from 3.48 A to 3.21 A, as a result of increasing the Ni substitution. The M s of the ?-phase films increased with increasing Ni substitution up to an Ni content of a few percent. The maximum values for M s and Hc, 240 emu/cc and 2.9 kOe respectively, were obtained at an Ni content of 3 at%. The high H c was due to the increased asymmetry of the tetragonal structure. The magnetic anisotropy of ?-phase films was caused mainly by the preferential orientation of the c-axis of the tetragonal crystallites.
The Brazilian experience with biofuels (2007)

Abstract Brazil leads the world in ethanol production and ethanol use for fuel and the government has decided recently to implement a programme to blend biodiesel with diesel. In 2004, the government created the National Program for Production and Use of Biodiesel to reduce Brazil's dependence on imported diesel and to supply a fuel that has low environmental impact. The Program allows the use of 17 other oil sources for biodiesel production. This article describes the background to biodiesel and bioethanol production and use, details the Brazilian alcohol and biodiesel programmes, and examines the prospects for these biofuels and their potential effects on agriculture and oilseed crops.