gebhart/patrepeval huggingface dataset:
ppGpp-dependent Stationary Phase Induction of Genes on Salmonella Pathogenicity Island 1 (2004)

We have examined expression of the genes on Salmonella pathogenicity island 1 (SPI1) during growth under the physiologically well defined standard growth condition of Luria-Bertani medium with aeration. We found that the central regulator hilA and the genes under its control are expressed at the onset of stationary phase. Interestingly, the two-component regulatory genes hilC/hilD, sirA/barA, and ompR, which are known to modulate expression from the hilA promoter (hilAp) under so-called "inducing conditions" (Luria-Bertani medium containing 0.3 m NaCl without aeration), acted under standard conditions at the stationary phase induction level. The induction of hilAp depended not on RpoS, the stationary phase sigma factor, but on the stringent signal molecule ppGpp. In the ppGpp null mutant background, hilAp showed absolutely no activity. The stationary phase induction of hilAp required spoT but not relA. Consistent with this requirement, hilAp was also induced by carbon source deprivation, which is known to transiently elevate ppGpp mediated by spoT function. The observation that amino acid starvation elicited by the addition of serine hydroxamate did not induce hilAp in a RelA(+) SpoT(+) strain suggested that, in addition to ppGpp, some other alteration accompanying entry into the stationary phase might be necessary for induction. It is speculated that during the course of infection Salmonella encounters various stressful environments that are sensed and translated to the intracellular signal, ppGpp, which allows expression of Salmonella virulence genes, including SPI1 genes.
Adaptive crosstalk cancellation and laser frequency drift compensation in dense WDM networks (1995)

Two variations of the LMS algorithm are proposed to cancel received linear crosstalk in dense WDM networks. Analysis and simulations show that with the addition of a few photodetectors, channel spacing requirements can be reduced by over 50 percent. Simulations using a demultiplexer with Gaussian bandpass characteristics show that a 2.5 dB signal-to-crosstalk-plus-noise ratio can be increased to over 35 dB. The decision-directed algorithm will work with OOK data or any intensity modulation scheme which uses the absence of light as one symbol. The decision-directed algorithm makes assumptions on the desired laser frequency so it can accommodate only limited laser drift. A second cancellation algorithm uses pilot tones added to each laser signal in order to cancel the crosstalk. It will work with analog or digital intensity-modulated data and will automatically configure itself to account for laser drift. Both algorithms are blind in that they do not require training sequences for initialization. Analysis shows that weights derived from pilot tones are nearly optimum for canceling crosstalk for the data. Simulations of both algorithms are presented. Finally both algorithms are shown to be capable of canceling nonlinear beating terms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of H<sub>2</sub>O<sub>2</sub> on homogeneous gas phase NO reduction reaction with NH<sub>3</sub> (1982)

Abstract To study the effect of H 2 O 2 on NO reduction with NH 3 , the homogeneous gas phase reaction of NH 3 NOH 2 O 2 O 2 was investigated in a Pyrex flow reactor over the temperature range from 500°C to 600°C under one atmospheric pressure. H 2 O 2 accelerated the NO reduction by NH 3 and caused it to be induced at a temperature of 500°C. In the absence of O 2 , NOx reduction ratio of more than 90% was obtained for NH 3 /NO5 and H 2 O 2 /NO1 at 550°C. In the presence of O 2 or an excess of H 2 O 2 , two side reactions, which cause the NOx reduction ratio to decrease, occur. One of the side reactions is NO oxidation with H 2 O 2 . It was found experimentally that NO 2 inhibited NO reduction and that H 2 O 2 was an NO oxidizing agent, as well as an NH 3 decomposing agent. The other side reaction was the formation of NO and NO 2 , which resulted from the oxidation of NH 3 with O 2 . Under the conditions of our experiments, the amount of O 2 in our reaction system was extremely high compared to the amounts of NO, NH 3 and H 2 O 2 in the system. Thus NO x was assumed to be produced by the oxidation of the NO reducing radicals, which were produced by the reaction of NH 3 with H 2 O 2 .
Small Signaling Peptides in <i>Arabidopsis</i> Development: How Cells Communicate Over a Short Distance (2012)

To sustain plants' postembryonic growth and development in a structure of cells fixed in cell walls, a tightly controlled short distance cell-cell communication is required. The focus on phytohormones, such as auxin, has historically overshadowed the importance of small peptide signals, but it is becoming clear that secreted peptide signals are important in cell-cell communication to coordinate and integrate cellular functions. However, of the more than 1000 potential secreted peptides, so far only very few have been functionally characterized or matched to a receptor. Here, we will describe our current knowledge on how small peptide signals can be identified, how they are modified and processed, which roles they play in Arabidopsis thaliana development, and through which receptors they act.
Patterning Graphene through the Self-Assembled Templates: Toward Periodic Two-Dimensional Graphene Nanostructures with Semiconductor Properties (2010)

Periodic graphene nanostructures are fabricated via patterning graphene through the self-assembled monolayers of monodisperse colloidal microspheres. The resulting structures exhibit promising electronic properties featuring high conductivities and ON-OFF ratios up to 10. The apparent advantages of the presented method are the possibilities of fabricating periodic graphene nanostructures with different periodicities, ranging from ∼100 nm to several μm, and also varying the periodicity and the neck width independently. The use of the presented method yields graphene nanostructures with variable electronic properties.
New Optimization Methods for Modern Machine Learning (2017)

Modern machine learning systems pose several new statistical, scalability, privacy and ethical challenges. With the advent of massive datasets and increasingly complex tasks, scalability has especially become a critical issue in these systems. In this thesis, we focus on fundamental challenges related to scalability, such as computational and communication efficiency, in modern machine learning applications. The underlying central message of this thesis is that classical statistical thinking leads to highly effective optimization methods for modern big data applications. The first part of the thesis investigates optimization methods for solving large-scale nonconvex Empirical Risk Minimization (ERM) problems. Such problems have surged into prominence, notably through deep learning, and have led to exciting progress. However, our understanding of optimization methods suitable for these problems is still very limited. We develop and analyze a new line of optimization methods for nonconvex ERM problems, based on the principle of variance reduction. We show that our methods exhibit fast convergence to stationary points and improve the state-of-the-art in several nonconvex ERM settings, including nonsmooth and constrained ERM. Using similar principles, we also develop novel optimization methods that provably converge to second-order stationary points. Finally, we show that the key principles behind our methods can be generalized to overcome challenges in other important problems such as Bayesian inference. The second part of the thesis studies two critical aspects of modern distributed machine learning systems — asynchronicity and communication efficiency of optimization methods. We study various asynchronous stochastic algorithms with fast convergence for convex ERM problems and show that these methods achieve near-linear speedups in sparse settings common to machine learning. Another key factor governing the overall performance of a distributed system is its communication efficiency. Traditional optimization algorithms used in machine learning are often ill-suited for distributed environments with high communication cost. To address this issue, we dis- cuss two different paradigms to achieve communication efficiency of algorithms in distributed environments and explore new algorithms with better communication complexity.
Temporal and Spatial Patterns of Accumulation of the Transcript of <i>Myo</i>-Inositol-1-Phosphate Synthase and Phytin-Containing Particles during Seed Development in Rice1 (1999)

Myo-inositol-1-phosphate (I[1]P) synthase (EC 5.5.1.4) catalyzes the reaction from glucose 6-phosphate to I(1)P, the first step of myo-inositol biosynthesis. Among the metabolites of I(1)P is inositol hexakisphosphate, which forms a mixed salt called phytin or phytate, a storage form of phosphate and cations in seeds. We have isolated a rice (Oryza sativa L.) cDNA clone, pRINO1, that is highly homologous to the I(1)P synthase from yeast and plants. Northern analysis of total RNA showed that the transcript accumulated to high levels in embryos but was undetectable in shoots, roots, and flowers. In situ hybridization of developing seeds showed that the transcript first appeared in the apical region of globular-stage embryos 2 d after anthesis (DAA). Strong signals were detected in the scutellum and aleurone layer after 4 DAA. The level of the transcript in these cells increased until 7 DAA, after which time it gradually decreased. Phytin-containing particles called globoids appeared 4 DAA in the scutellum and aleurone layer, coinciding with the localization of the RINO1 transcript. The temporal and spatial patterns of accumulation of the RINO1 transcript and globoids suggest that I(1)P synthase directs phytin biosynthesis in rice seeds.
Rapid Covalent Modification of Silicon Oxide Surfaces through Microwave-Assisted Reactions with Alcohols (2016)

We demonstrate the method of a rapid covalent modification of silicon oxide surfaces with alcohol-containing compounds with assistance by microwave reactions. Alcohol-containing compounds are prevalent reagents in the laboratory, which are also relatively easy to handle because of their stability against exposure to atmospheric moisture. The condensation of these alcohols with the surfaces of silicon oxides is often hindered by slow reaction kinetics. Microwave radiation effectively accelerates this condensation reaction by heating the substrates and/or solvents. A variety of substrates were modified in this demonstration, such as silicon oxide films of various thicknesses, glass substrates such as microscope slides (soda lime), and quartz. The monolayers prepared through this strategy demonstrated the successful formation of covalent surface modifications of silicon oxides with water contact angles of up to 110° and typical hysteresis values of 2° or less. An evaluation of the hydrolytic stability of these monolayers demonstrated their excellent stability under acidic conditions. The techniques introduced in this article were successfully applied to tune the surface chemistry of silicon oxides to achieve hydrophobic, oleophobic, and/or charged surfaces.
Mechanism of geometric nonlinearity in a nonprismatic and heterogeneous microbeam resonator (2017)

Implementation of geometric nonlinearity in microelectromechanical systems (MEMS) resonators offers a flexible and efficient design to overcome the limitations of linear MEMS by utilizing beneficial nonlinear characteristics not attainable in a linear setting. Integration of nonlinear coupling elements into an otherwise purely linear microcantilever is one promising way to intentionally realize geometric nonlinearity. Here, we demonstrate that a nonlinear, heterogeneous microresonator system, consisting of a silicon microcantilever with a polymer attachment exhibits strong nonlinear hardening behavior not only in the first flexural mode but also in the higher modes (i.e., second and third flexural modes). In this design, we deliberately implement a drastic and reversed change in the axial vs bending stiffness between the Si and polymer components by varying the geometric and material properties. By doing so, the resonant oscillations induce the large axial stretching within the polymer component, which effectively introduces the geometric stiffness and damping nonlinearity. The efficacy of the design and the mechanism of geometric nonlinearity are corroborated through a comprehensive experimental, analytical, and numerical (finite element) analysis on the nonlinear dynamics of the proposed system.
Evolution of a trusted B3 window system prototype (2003)

The early issues, obstacles, and ultimate achievements of Phase II of the US DARPA Advanced Computing Systems project to develop a proof-of-concept prototype for a B3 X-Window system on a TMach base are described. The present work defines initial project goals, presents an overview of X, and describes system objectives. The major implications of meeting the B3 trust criteria and the constraints of building the Trusted X prototype on the TMach system (itself a prototype) are described. The reader is led through the process of Trusted X evolution from an initial architecture requiring a large and complex TCB to an architecture based on task polyinstantiation greatly simplifying the TCB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Application of Molecular Spectroscopy in the Mid-Infrared Region to the Determination of Glucose and Cholesterol in Whole Blood and in Blood Serum (1997)

The feasibility of applying molecular spectroscopy in the mid-infrared region to the quantitation of glucose and cholesterol in whole blood and in blood serum was examined by measuring the samples in the dry state on a polyethylene carrier. The partial least-squares (PLS) algorithm was employed to set up the calibration models. Analysis was performed by normalizing the spectra to a standard area. Evidence that this approach is warranted was obtained through experiments where potassium thiocyanate served as the internal standard. The following average PRESS 1/2 values (PRESS stands for prediction residual error sum of squares) emerged from the calibration: glucose, 22.3 mg/dL; cholesterol, 31.3 mg/dL. Such errors are comparable with those achieved in attenuated total reflectance (ATR) measurements. The calibration models set up for blood serum samples fit better than those for whole blood samples. If the procedure of sample application onto the carrier is improved, the method may work well for the determination of glucose and cholesterol in whole blood and in blood serum.
Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene. (1993)

The b gene of maize encodes a transcriptional activator of anthocyanin pigment biosynthetic genes. Certain b alleles undergo paramutation: a unidirectional, heritable alteration of one allele caused by the presence of another allele. B-I (intensely pigmented plant) is always changed to B' (weakly pigmented plant) in the B'/B-I heterozygote, such that all progeny receive the B' allele. The "new" B', which was B-I in the previous generation, is weakly pigmented and fully capable of changing another B-I allele into B'. It was not previously known whether paramutation is associated with altered b expression, altered B protein function or both. Our results show that B' acts in trans to suppress the transcription of B-I, with transcription remaining low in subsequent generations, even when the original B' allele segregates away. The products of B-I and B' are equally capable of activating the transcription of their target genes, indicating they are functionally equivalent. Genomic restriction maps, DNA sequence and methylation of B' and B-I were compared. Despite dramatic differences in phenotype and transcription of B' and B-I, no evidence for rearrangements, changes in sequence or changes in methylation was found. These results provide no support for models involving "dominant negative" proteins, gene conversion or transposable element interactions. We suggest that b paramutation involves a physical interaction between the alleles that suppresses transcription and promotes a change in chromatin structure that is heritable.
On‐line identiﬁcation of further flavone <i>C</i>‐ and <i>O</i>‐glycosides from sugarcane (<i>Saccharum ofﬁcinarum</i> L., Gramineae) by HPLC‐UV‐MS (2006)

HPLC-UV-MS (APCI-MS/MS and CID/MS) was utilised for the identification of eight additional flavone glycosides from sugarcane (Saccharum officinarum L., Gramineae) extracts of bagasse, leaves and juice ('garapa'). Relevant information about substitution patterns was obtained through UV detection using post-column addition of shift reagents, while tandem MS provided structural information confirming the proposed structures of the C-glycosides vitexin, orientin, luteolin-8-C-(rhamnosylglucoside), 4',5'-dimethyl-luteolin-8-C-glycoside and the isomeric pair schaftoside-isoschaftoside, besides the O-glycosides tricin-7-O-neohesperidoside and tricin-7-O-glycoside.
Important issues regarding diode performance in radiation therapy applications (2002)

Diode detectors have found wide applications in radiation therapy due to their high spatial resolution, high sensitivity and ruggedness. Some of their limitations have been discussed in publications, such as sensitivity degradation with radiation, SSD and field size dependence. This paper addresses some important issues that may not be well recognized-diode impedance, directional dependence, accumulated dose effects.
MicroRNA miR-378 Regulates Nephronectin Expression Modulating Osteoblast Differentiation by Targeting GalNT-7 (2009)

MicroRNAs (miRNAs) are small fragments of single-stranded RNA containing 18-24 nucleotides, and are generated from endogenous transcripts. MicroRNAs function in post-transcriptional gene silencing by targeting the 3'-untranslated region (UTR) of mRNAs, resulting in translational repression. We have developed a system to study the role of miRNAs in cell differentiation. We have found that one of the miRNAs tested in our system (miR-378, also called miR-378*) plays a role in modulating nephronectin-mediated differentiation in the osteoblastic cell line, MC3T3-E1. Nephronectin is an extracellular matrix protein, and we have demonstrated that its over-expression enhanced osteoblast differentiation and bone nodule formation. Furthermore, we found that the nephronectin 3'-untranslated region (3'UTR) contains a binding site for miR-378. Stable transfection of MC3T3-E1 cells with miR-378 inhibited cell differentiation. MC3T3-E1 cells stably transfected with nephronectin exhibited higher rates of differentiation and nodule formation as compared with cells transfected with nephronectin containing the 3'UTR in the early stages of development, suggesting that endogenous miR-378 is present and active. However, in the later stages of MC3T3-E1 development, the differentiation rates were opposite, with higher rates of differentiation and nodule formation in the cells over-expressing the 3'UTR of nephronectin. This appeared to be the consequence of competition between nephronectin and UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7 or GalNT7) for miR-378 binding, resulting in increased GalNT7 activity, which in turn lead to increased nephronectin glycosylation and product secretion, thereby resulting in a higher rate of osteoblast differentiation.
MANET IP Header Compression (2013)

The desire for DoD communications systems to converge on an all-IP infrastructure, fueled by the increased usage of net-centric IP applications at the tactical edge have pushed research in maximizing bandwidth efficiency amidst a shrinking allocation of RF spectrum. One method of providing increased bandwidth efficiency (especially with the desire to move to IPv6), is the use of IP header compression (IPHC) techniques such as IP header compression (RFC2507), RObust Header Compression (ROHC-RFC5225), and others, to compress headers. Although widely used in one-hop cellular networks, many IPHC schemes today are stateful in that they build hop-by-hop compression state per flow. Maintaining this per-hop state per flow, however, becomes increasingly difficult in MANET environments where next-hop information is constantly changing. In this paper, we propose a shared-state/stateless IP header compression scheme tailored to MANET environments called MANET IP Header Compression (MIPHC). We show that although MIPHC does not achieve the same load reduction as ROHC for single-hop wireless networks, there are gains in MANET environments due to lack of need to build compression context on a hop-by-hop basis. MIPHC can also be combined with other protocols to compress higher layer headers.
Lubricity of military jet fuels (1995)

In 1954, a corrosion inhibitor additive was required in JP-4, a wide cut gasoline type aviation turbine fuel, to alleviate corrosion carry-over from ground fuel systems to aircraft. The additive was blamed for fuel filtration problems and removed from the JP-4 specification in 1965. Almost immediately, the U.S. Air Force started experiencing lubricity problems with fuel pumps and controllers. Fuel controller tests showed that when a corrosion inhibitor was added to the fuel, the lubricity problem was alleviated. The effectiveness of the corrosion inhibitor additives as lubricity improvers was then studied. A variety of test methods evolved for use in evaluating the effectiveness of a corrosion inhibitor as a lubricity improver. In 1989, the ball-on-cylinder lubricity evaluator (BOCLE) test was added to MIL-I-25017, a military specification for fuel soluble corrosion inhibitor/lubricity improver, to determine lubricity effectiveness of the corrosion inhibitor additives. Since the revision of this specification, all corrosion inhibitor/lubricity improver additives on the qualified products list, QPL-25017, have been tested using the BOCLE. Due to aircraft engine redesign, MIL-T-25524, a thermally stable turbine fuel, recently required the addition of a lubricity additive. Concerns were raised to the effect that corrosion inhibitor/lubricity improver would have on the thermal stability ofmore » thermally stable turbine fuel. Recent jet fuel thermal oxidation tester and BOCLE evaluation of the additives in thermally stable turbine fuel addressed these concerns. 16 refs., 1 fig., 4 tabs.« less
Ultrasound-Guided Model Predictive Control of Needle Steering in Biological Tissue (2016)

In needle-based medical procedures, beveled tip flexible needles are steered inside soft tissue to reach the desired target locations. In this paper, we have developed an autonomous image-guided needle steering system that enhances targeting accuracy in needle insertion while minimizing tissue trauma. The system has three main components. First is a novel mechanics-based needle steering model that predicts needle deflection and accepts needle tip rotation as an input for needle steering. The second is a needle tip tracking system that determines needle deflection from the ultrasound images. The needle steering model employs the estimated needle deflection at the present time to predict needle tip trajectory in the future steps. The third component is a nonlinear model predictive controller (NMPC) that steers the needle inside the tissue by rotating the needle beveled tip. The MPC controller calculates control decisions based on iterative optimization of the predictions of the needle steering model. To validate the proposed ultrasound-guided needle steering system, needle insertion experiments in biological tissue phantoms are performed in two cases–with and without obstacle. The results demonstrate that our needle steering strategy guides the needle to the desired targets with the maximum error of 2.85[Formula: see text]mm.