gebhart/patrepeval huggingface dataset:
The Historic Pattern of U.S Corn Yields, Any Implications for 2012? (2012)

historic-pattern-of-us-cor-1.htmlThe U.S. average corn yield was below trend value in both 2010 and 2011.Market sentiment seems to be that such a pattern reduces the odds of a below-trend average yield in 2012.That sentiment raises the interesting issue of what, if anything can be learned from the historical pattern of U.S. average corn yields that would be useful in anticipating yields in any particular year?Here we examine the pattern of yields from 1960 through 2011 (Figure 1).
Specification of regional intestinal stem cell identity during <i>Drosophila</i> metamorphosis (2014)

In the adult Drosophila midgut the bone morphogenetic protein (BMP) signaling pathway is required to specify and maintain the acid-secreting region of the midgut known as the copper cell region (CCR). BMP signaling is also involved in the modulation of intestinal stem cell (ISC) proliferation in response to injury. How ISCs are able to respond to the same signaling pathway in a regionally different manner is currently unknown. Here, we show that dual use of the BMP signaling pathway in the midgut is possible because BMP signals are only capable of transforming ISC and enterocyte identity during a defined window of metamorphosis. ISC heterogeneity is established prior to adulthood and then maintained in cooperation with regional signals from surrounding tissue. Our data provide a conceptual framework for how other tissues maintained by regional stem cells might be patterned and establishes the pupal and adult midgut as a novel genetic platform for identifying genes necessary for regional stem cell specification and maintenance.
Orthogonal Persistence in a Heterogeneous Distributed Object-Oriented Environment (1994)

This paper describes the major issues in the design and implementation of orthogonal persistence in IK. A single and uniform programming paradigm is used to manipulate objects in a persistent and distributed environment. Object references can be freely passed during remote invocations or stored persistently. IK supports orthogonal persistence with type inheritance. Objects are stored persistently when reachable from an Eternal Root, regardless of their type. For programmers, objects are created and manipulated uniformly, independently of the time they persist. Persistent objects are dynamically grouped at run-time into clusters to encapsulate fine-grain language level objects into coarser-grain entities. We present a novel approach to integrate object clustering, naming and garbage collection in persistent systems, and present experimental results.
The missing link (2002)

Using a participatory design process, we created three prototype augmented laboratory notebooks that provide the missing link between paper, physical artifacts and on-line data. The final a-book combines a graphics tablet and a PDA. The tablet captures writing on the paper notebook and the PDA acts as an "interaction lens" or window between physical and electronic documents. Our approach is document-centered, with a software architecture based on layers of physical and electronic information.
Oracle 10g grid & real application clusters : oracle 10g grid computing with rac (2004)

Covering all areas of Oracle Grid computing, this guide is indispensable for any Oracle DBA who is charged with configuring and implementing Oracle11g Grid with server blades. This comprehensive manual presents a complete method for the installation, configuration and design of Oracle Grid and 11g RAC. It supplies expert internals of shared disk technology, raw devices and RAID, and exposes the internal configuration methods for server blades. Also demonstrated is the use of Oracle Grid using the Enterprise Manager Grid control utility.
Pyrrolo[1,4]benzodiazepine antitumor antibiotics: relationship of DNA alkylation and sequence specificity to the biological activity of natural and synthetic compounds (1988)

The DNA alkylation and sequence specificity of a group of natural and synthetic pyrrolo-[1,4]benzodiazepines [P(1,4)Bs] were evaluated by using an exonuclease III stop assay, and the results were compared with in vitro and in vivo biological potency and antitumor activity. The P(1,4)B antibiotics are potent antitumor agents produced by various Actinomycetes, which are believed to mediate their cytotoxic effects by covalent bonding through N-2 of guanine in the minor groove of DNA. In this article we describe the results of a sensitive DNA alkylation assay using exonuclease III which permits both estimation of the extent of DNA modification as well as location of the precise guanines to which the drugs are covalently bound. Using this assay, we have evaluated a series of natural and synthetic compounds of the P(1,4)B class for their ability to bind to DNA and also determined their DNA sequence preference. The compounds included in this study are P(1,4)Bs carrying different substituents in the aromatic ring, having varying degrees of saturation in the five-membered ring, or differing in the stereochemistry at C-11a. These same compounds were evaluated for in vitro cytotoxic activity against B16 melanoma cells, for potency in vivo in B6D2F1 mice (LD50), and for antitumor activity (ILSmax) against P388 leukemia cells. A good correlation was found between extent of DNA alkylation and in vitro and in vivo potency. Furthermore, on the basis of electronic and steric considerations, it was possible to rationalize why those compounds that showed negligible biological activity were unable to bond covalently to DNA. Last, we have determined that the degree of saturation in the five-membered ring of the P(1,4)Bs has a significant effect on the DNA bonding reactivity and biological activity of this class of compounds.
Characterization Of Polaroid's DMP-128 Holographic Recording Photopolymer (1988)

The fundamental holographic properties of Polaroid's DMP-128 have been measured. Diffraction efficiencies over 90% have been obtained with an index modulation of 0.033. It was found that the diffraction efficiency could be reduced from 90% to less than 10% by the use of an index matching fluid. When the index matching fluid was allowed to evaporate, the diffraction efficiency returned to its original value. This observation suggests that the index modulation produced in the photopolymer is due to tiny cracks or voids formed in the polymer.
Randomized Sequence Databases for Tandem MassSpectrometry Peptide and Protein Identification (2005)

Tandem mass spectrometry (MS/MS) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. Many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." False positive identification rates for these criteria can vary substantially with changing organisms under study, growth conditions, sequence databases, experimental protocols, and instrumentation; therefore, study-specific methods are needed to estimate the accuracy (false positive rates) of these peptide and protein identifications. We present and evaluate methods for estimating false positive identification rates based on searches of randomized databases (reversed and reshuffled). We examine the use of separate searches of a forward then a randomized database and combined searches of a randomized database appended to a forward sequence database. Estimated error rates from randomized database searches are first compared against actual error rates from MS/MS runs of known protein standards. These methods are then applied to biological samples of the model microorganism Shewanella oneidensis strain MR-1. Based on the results obtained in this study, we recommend the use of use of combined searches of a reshuffled database appended to a forward sequence database as a means providing quantitative estimates of false positive identification rates of peptides and proteins. This will allow researchers to set criteria and thresholds to achieve a desired error rate and provide the scientific community with direct and quantifiable measures of peptide and protein identification accuracy as opposed to vague assessments such as "high confidence."
Vitamin C for preventing and treating the common cold (2007)

The failure of vitamin C supplementation to reduce the incidence of colds in the normal population indicates that routine mega-dose prophylaxis is not rationally justified for community use. But evidence suggests that it could be justified in people exposed to brief periods of severe physical exercise or cold environments.
Prostaglandin E2 Protects Gastric Mucosal Cells from Apoptosis via EP2 and EP4 Receptor Activation (2003)

Prostaglandin E(2) (PGE(2)) has a strong protective effect on the gastric mucosa in vivo; however, the molecular mechanism of a direct cytoprotective effect of PGE(2) on gastric mucosal cells has yet to be elucidated. Although we reported previously that PGE(2) inhibited gastric irritant-induced apoptotic DNA fragmentation in primary cultures of guinea pig gastric mucosal cells, we show here that PGE(2) inhibits the ethanol-dependent release of cytochrome c from mitochondria. Of the four main subtypes of PGE(2) receptors, we also demonstrated, using subtype-specific agonists, that EP(2) and EP(4) receptors are involved in the PGE(2)-mediated protection of gastric mucosal cells from ethanol-induced apoptosis. Activation of EP(2) and EP(4) receptors is coupled with an increase in cAMP, for which a cAMP analogue was found here to inhibit the ethanol-induced apoptosis. The increase in cAMP is known to activate both protein kinase A (PKA) and phosphatidylinositol 3-kinase pathways. An inhibitor of PKA but not of phosphatidylinositol 3-kinase blocked the PGE(2)-mediated protection of cells from ethanol-induced apoptosis, suggesting that a PKA pathway is mainly responsible for the PGE(2)-mediated inhibition of apoptosis. Based on these results, we considered that PGE(2) inhibited gastric irritant-induced apoptosis in gastric mucosal cells via induction of an increase in cAMP and activation of PKA, and that this effect was involved in the PGE(2)-mediated protection of the gastric mucosa from gastric irritants in vivo.
How Powerful is Adiabatic Quantum Computation? (2008)

We analyze the computational power and limitations of the recently proposed ‘quantum adiabatic evolution algo-rithm’. 1.
From Bent to Linear Uranium Metallocenes:  Influence of Counterion, Solvent, and Metal Ion Oxidation State (2006)

Reactions of Cp*2UCl2 with a slight excess of Me3SiI or Me3SiOTf in acetonitrile provide convenient routes to Cp*2UI2 (1) or Cp*2U(OTf)2 (2) (Cp* = η-C5Me5; OTf = OSO2CF3), which were isolated with excellent yields. Crystals of the bent metallocenes Cp*2UI2(NCR) (R = Me (3), tBu (4)) have been obtained by addition of excess RCN to a toluene solution of 1. The triflate analogue Cp*2U(OTf)2(NCMe) (5) contains monodentate OTf ligands. Treatment of Cp*2UMe2 with 2 equiv of HNEt3BPh4 in acetonitrile led to the immediate formation of [Cp*2U(NCMe)5][BPh4]2 (6). The 1H NMR spectra of 1 and 2 in acetonitrile are similar to that of 6, indicating the presence of the dicationic species [Cp*2U(NCMe)5][X]2 [X = I (7), OTf (8)] in this solvent. Compounds 6−8 are the first linear metallocenes of an f-element and exhibit an unprecedented structure with auxiliary donor ligands in the equatorial plane parallel to the cyclopentadienyl rings. When treated with Me3SiOTf, the uranium(III) species Cp*2UCl2Na(thf)2 did not afford the trivalent complex Cp*2U(OTf) (9) but gave crystals of the dimeric uranium(IV) “ate” compound [Cp*2U(OTf)3Na(thf)2]2·2(CH2)4O (10·2(CH2)4O). The first organouranium(III) triflate, 9, was isolated in 90% yield from the reaction of U(OTf)3 with 2 equiv of KCp* in thf. Dissolution of Cp*2UI(py) in acetonitrile gave the adduct Cp*2UI(NCMe)2 (11), which, like its cerium analogue, adopts a bent sandwich structure in its crystalline form. The 1H NMR spectra of 11 and Cp*2U(OTf)(NCMe)2 are similar in benzene and acetonitrile, suggesting that the trivalent linear metallocene [Cp*2U(NCMe)5][X] (X = I or OTf) is not present in pure acetonitrile. These observations are confirmed by the addition of 3 equiv or excess MeCN to a solution of [Cp*2U(thf)2][BPh4] in thf, which afforded the stable [Cp*2U(NCMe)3][BPh4] as the sole product.
Interconnect IP node for future system-on-chip designs (2003)

An interconnect IP (intellectual Property) node architecture for flexible on-chip communication is introduced. This architecture is targeted for communication in future gigatransistor SoC (System-on-Chip) designs. The interconnect IP will be used as a testing platform when the efficiency of network topologies and routing schemes are investigated for the on-chip environment. The interconnect node uses packet based communication and forms a reusable component itself. The node is constructed from a collection of parameterized and reusable hardware blocks, which include components such as FIFO buffers, routing controllers and standardized interface wrappers. A node can be tuned to fulfill the desired characteristics of communication by selecting the internal architecture properly.
Pregabalin in the discontinuation of long-term benzodiazepine use: a case-series (2008)

Tolerance, dependence, and adverse effects on cognitive functions are well known consequences of long-term use of benzodiazepines (BDZ), especially at high doses; this raises thorny therapeutic problems in their discontinuation. One promising pharmacological agent in BDZ discontinuation might be the newer antiepileptic, pregabalin (PGB), which has already successfully been tested in the treatment of anxiety disorders. We report on a series of four women with long-term, high-dose dependence on BDZ, who were treated with PGB at doses of 225-600 mg. All four patients discontinued BDZ successfully in 3-7 weeks. Moreover, they had an impressive reduction of their previous anxiety levels under BDZ. In addition, the patients showed a clinically significant amelioration in their cognitive functioning. The side effects of PGB were mild and transient, persisting only during the first 2 weeks of treatment. Although our findings are preliminary, they suggest that PGB might be one of the most promising of the newer agents in the treatment of BDZ dependence.
Structural and dynamic membrane properties of .alpha.-tocopherol and .alpha.-tocotrienol: Implication to the molecular mechanism of their antioxidant potency (1993)

d-alpha-Tocopherol and d-alpha-tocotrienol are two vitamin E constituents having the same aromatic chromanol "head" but different hydrocarbon "tails". alpha-Tocotrienol has been shown to be more potent in protecting against free radical-induced oxidative stress than alpha-tocopherol. Simple models of phospholipid membrane systems were used to investigate the mechanism of the antioxidant potency of alpha-tocotrienol in terms of its effects on membrane order and reorientation dynamics. Chemiluminescence and fluorescence measurements demonstrated that alpha-tocotrienol exhibits significantly greater peroxyl radical scavenging potency than alpha-tocopherol in phosphatidylcholine liposomes, whereas both antioxidants have identical activity in hexane. This suggests that the antioxidant potency of alpha-tocotrienol requires the membrane environment. When alpha-tocopherol and alpha-tocotrienol were examined for their effects on phospholipid molecular order using conventional ESR spin labeling with 5- and 16-position-labeled doxylstearic acid, although both vitamin E constituents disordered the gel phase and stabilized the liquid-crystalline phase, no differences were observed between the effects of the two compounds. A slightly greater increase (19% vs 15%) in ordering of the liquid-crystalline state due to alpha-tocopherol, however, was discerned in noninvasive 2H NMR experiments. The difference is most noticeable near C10-C13 positions of the phospholipid chain, possibly suggesting alpha-tocotrienol is located closer to the membrane surface. Saturation-transfer ESR, furthermore, revealed that on the time scale tau c = 10(-7)-10(-3) s the rates of rotation about the long molecular axis and of the wobbling motion of the axis are modified to differing extents by the two forms of the vitamin E.(ABSTRACT TRUNCATED AT 250 WORDS)
Carbon nanotube growth for GHz devices (2004)

Horizontally oriented single walled carbon nanotubes are grown with CVD between lithographically defined catalyst sites. Single walled carbon nanotubes up to 60 /spl mu/m in length are grown using methane as the feedstock. The nanoparticle catalyst is deposited from a newly developed aqueous solution requiring only photoresist and optical lithography. Carbon nanotube Y-junctions are also observed and characterized.
Decomposition of Uncertainty in Bayesian Deep Learning for Efficient and Risk-sensitive Learning (2017)

Bayesian neural networks with latent variables are scalable and flexible probabilistic models: They account for uncertainty in the estimation of the network weights and, by making use of latent variables, can capture complex noise patterns in the data. We show how to extract and decompose uncertainty into epistemic and aleatoric components for decision-making purposes. This allows us to successfully identify informative points for active learning of functions with heteroscedastic and bimodal noise. Using the decomposition we further define a novel risk-sensitive criterion for reinforcement learning to identify policies that balance expected cost, model-bias and noise aversion.
Functional effects of naturally occurring <i>KCNJ11</i> mutations causing neonatal diabetes on cloned cardiac K<sub>ATP</sub> channels (2005)

ATP-sensitive K+ (K(ATP)) channels are hetero-octamers of inwardly rectifying K+ channel (Kir6.2) and sulphonylurea receptor subunits (SUR1 in pancreatic beta-cells, SUR2A in heart). Heterozygous gain-of-function mutations in Kir6.2 cause neonatal diabetes, which may be accompanied by epilepsy and developmental delay. However, despite the importance of K(ATP) channels in the heart, patients have no obvious cardiac problems. We examined the effects of adenine nucleotides on K(ATP) channels containing wild-type or mutant (Q52R, R201H) Kir6.2 plus either SUR1 or SUR2A. In the absence of Mg2+, both mutations reduced ATP inhibition of SUR1- and SUR2A-containing channels to similar extents, but when Mg2+ was present ATP blocked mutant channels containing SUR1 much less than SUR2A channels. Mg-nucleotide activation of SUR1, but not SUR2A, channels was markedly increased by the R201H mutation. Both mutations also increased resting whole-cell K(ATP) currents through heterozygous SUR1-containing channels to a greater extent than for heterozygous SUR2A-containing channels. The greater ATP inhibition of mutant Kir6.2/SUR2A than of Kir6.2/SUR1 can explain why gain-of-function Kir6.2 mutations manifest effects in brain and beta-cells but not in the heart.
Observations of Plasma Line Splitting in the Ionospheric Incoherent Scatter Spectrum (2008)

Wide-bandwidth ionospheric incoherent scatter (IS) spectra obtained using the Arecibo IS radar show the occurrence of a split in the plasma line (i.e., two plasma lines) when the plasma frequency is close to the second harmonic of the electron gyrofrequency. This split is predicted in the IS theory for a magnetized plasma, but observations have never been reported. Here we present the experimental results and theoretical calculations supporting the observations. These results may assist in understanding the behavior of Langmuir waves in the magnetized plasma and are a validation of what historically was a somewhat controversial aspect of the IS theory.
Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an Antagonist (2007)

Prostanoids play important physiological roles in the cardiovascular and immune systems and in pain sensation in peripheral systems through their interactions with eight G-protein coupled receptors. These receptors are important drug targets, but development of subtype specific agonists and antagonists has been hampered by the lack of 3D structures for these receptors. We report here the 3D structure for the human DP G-protein coupled receptor (GPCR) predicted by the MembStruk computational method. To validate this structure, we use the HierDock computational method to predict the binding mode for the endogenous agonist (PGD2) to DP. Based on our structure, we predicted the binding of different antagonists and optimized them. We find that PGD2 binds vertically to DP in the TM1237 region with the alpha chain toward the extracellular (EC) region and the omega chain toward the middle of the membrane. This structure explains the selectivity of the DP receptor and the residues involved in the predicted binding site correlate very well with available mutation experiments on DP, IP, TP, FP, and EP subtypes. We report molecular dynamics of DP in explicit lipid and water and find that the binding of the PGD2 agonist leads to correlated rotations of helices of TM3 and TM7, whereas binding of antagonist leads to no such rotations. Thus, these motions may be related to the mechanism of activation.
How (not) to Train your Generative Model: Scheduled Sampling, Likelihood, Adversary? (2015)

Modern applications and progress in deep learning research have created renewed interest for generative models of text and of images. However, even today it is unclear what objective functions one should use to train and evaluate these models. In this paper we present two contributions. Firstly, we present a critique of scheduled sampling, a state-of-the-art training method that contributed to the winning entry to the MSCOCO image captioning benchmark in 2015. Here we show that despite this impressive empirical performance, the objective function underlying scheduled sampling is improper and leads to an inconsistent learning algorithm. Secondly, we revisit the problems that scheduled sampling was meant to address, and present an alternative interpretation. We argue that maximum likelihood is an inappropriate training objective when the end-goal is to generate natural-looking samples. We go on to derive an ideal objective function to use in this situation instead. We introduce a generalisation of adversarial training, and show how such method can interpolate between maximum likelihood training and our ideal training objective. To our knowledge this is the first theoretical analysis that explains why adversarial training tends to produce samples with higher perceived quality.