gebhart/patrepeval huggingface dataset:
Latent high molecular weight complex of transforming growth factor beta 1. Purification from human platelets and structural characterization. (1988)

Human transforming growth factor beta 1 (TGF-beta 1) was purified as a latent high Mr complex from human platelets by a six-step procedure. Analysis by sodium dodecyl sulfate (SDS)-gel electrophoresis under reducing conditions revealed that the complex was composed of at least three components with apparent Mr values of 13,000, 40,000, and 125,000-160,000. The 13-kDa subunit was part of a disulfide-bonded dimer and was identified by amino acid sequencing as TGF-beta 1. The 40-kDa subunit was identified as the amino-terminal part of the TGF-beta 1 precursor lacking the hydrophobic signal sequence. Partial sequencing of the 125-160-kDa protein revealed that it is distinct from known proteins. The 40-kDa and the 125-160-kDa subunits are linked by disulfide bonds, forming a complex with an apparent Mr of 210,000 on SDS gels under nonreducing conditions. Experiments with partial reduction revealed that each complex contains two 40-kDa components linked by disulfide bonds; in addition, the dimer is disulfide-linked to one 125-160-kDa binding protein. TGF-beta 1 binds noncovalently to the 210-kDa complex, and in bound form, TGF-beta 1 is inactive. Incubations of the latent form of TGF-beta 1 at extreme pH values, in 0.02% SDS or in 8 M urea, lead to activation of TGF-beta 1, whereas the complex was resistant to treatment with 5 M NaCl or heat (3 min at 95 degrees C).
LIM Kinase-mediated Cofilin Phosphorylation during Mitosis Is Required for Precise Spindle Positioning (2007)

The interaction of astral microtubules with cortical actin networks is essential for the correct orientation of the mitotic spindle; however, little is known about how the cortical actin organization is regulated during mitosis. LIM kinase-1 (LIMK1) regulates actin dynamics by phosphorylating and inactivating cofilin, an actin-depolymerizing protein. LIMK1 activity increases during mitosis. Here we show that mitotic LIMK1 activation is critical for accurate spindle orientation in mammalian cells. Knockdown of LIMK1 suppressed a mitosis-specific increase in cofilin phosphorylation and caused unusual cofilin localization in the cell cortex in metaphase, instability of cortical actin organization and astral microtubules, irregular rotation and misorientation of the spindle, and a delay in anaphase onset. Similar results were obtained by treating the cells with a LIMK1 in hibitor peptide or latrunculin A or by overexpressing a non-phosphorylatable cofilin(S3A) mutant. Furthermore, localization of LGN (a protein containing the repetitive Leu-Gly-Asn tripeptide motifs), an important regulator of spindle orientation, in the crescent-shaped cortical regions was perturbed in LIMK1 knockdown cells. Our results suggest that LIMK1-mediated cofilin phosphorylation is required for accurate spindle orientation by stabilizing cortical actin networks during mitosis.
Learning-based Query Performance Modeling and Prediction (2012)

Accurate query performance prediction (QPP) is central to effective resource management, query optimization and query scheduling. Analytical cost models, used in current generation of query optimizers, have been successful in comparing the costs of alternative query plans, but they are poor predictors of execution latency. As a more promising approach to QPP, this paper studies the practicality and utility of sophisticated learning-based models, which have recently been applied to a variety of predictive tasks with great success, in both static (i.e., fixed) and dynamic query workloads. We propose and evaluate predictive modeling techniques that learn query execution behavior at different granularities, ranging from coarse-grained plan-level models to fine-grained operator-level models. We demonstrate that these two extremes offer a tradeoff between high accuracy for static workload queries and generality to unforeseen queries in dynamic workloads, respectively, and introduce a hybrid approach that combines their respective strengths by selectively composing them in the process of QPP. We discuss how we can use a training workload to (i) pre-build and materialize such models offline, so that they are readily available for future predictions, and (ii) build new models online as new predictions are needed. All prediction models are built using only static features (available prior to query execution) and the performance values obtained from the offline execution of the training workload. We fully implemented all these techniques and extensions on top of Postgre SQL and evaluated them experimentally by quantifying their effectiveness over analytical workloads, represented by well-established TPC-H data and queries. The results provide quantitative evidence that learning-based modeling for QPP is both feasible and effective for both static and dynamic workload scenarios.
Micro-electro-mechanical systems (MEMS) for WDM optical-crossconnect networks (2003)

MEMS (micro-electro-mechanical systems) have shown promise for optical crossconnects in WDM networks. We describe various MEMS optical-switching technologies, their successes in implementing important optical-networking functionalities, and future perspectives.
Discovery and Pharmacology of a Novel Class of Diacylglycerol Acyltransferase 2 Inhibitors (2015)

DGAT2 plays a critical role in hepatic triglyceride production, and data suggests that inhibition of DGAT2 could prove to be beneficial in treating a number of disease states. This article documents the discovery and optimization of a selective small molecule inhibitor of DGAT2 as well as pharmacological proof of biology in a mouse model of triglyceride production.
Linear multiuser detectors for synchronous code-division multiple-access channels (1989)

Under the assumptions of symbol-synchronous transmissions and white Gaussian noise, the authors analyze the detection mechanism at the receiver, comparing different detectors by their bit error rates in the low-background-noise region and by their worst-case behavior in a near-far environment where the received energies of the users are not necessarily similar. Optimum multiuser detection achieves important performance gains over conventional single-user detection at the expense of computational complexity that grows exponentially with the number of users. It is shown that in the synchronous case the performance achieved by linear multiuser detectors is similar to that of optimum multiuser detection. Attention is focused on detectors whose linear memoryless transformation is a generalized inverse of the matrix of signature waveform crosscorrelations, and on the optimum linear detector. It is shown that the generalized inverse detectors exhibit the same degree of near-far resistance as the optimum multiuser detectors. The optimum linear detector is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wood Anatomy of Mangifera indica L. (Anacardiaceae) (2006)

The wood anatomy of Mangifera indica belonging to the species of Anacardiaceae native to Bangladesh was described. The species of this family was distinctive in having growth rings, thin-to thick-walled, nonseptate libriform fibres, vessels with simple perforation plate and nonvestures intervessel pittings. Paratracheal axial parenchyma was vasicentric, lozenge-aliform and confluent. Axial parenchyma band more than 3 cells wide and in marginal or in seemingly marginal bands. 3-4 cells per axial parenchyma was dominantly present. Ray height was less than 1㎜, Body ray cells were procumbent with one row of upright and square marginal cells. More than one prismatic crystals of about the same size was present in upright or square ray cells.
Uniquely Altered DNA Replication Fidelity Conferred by an Amino Acid Change in the Nucleotide Binding Pocket of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (1999)

Arginine 72 in human immunodeficiency virus type 1 reverse transcriptase (RT), a highly conserved residue among retroviral polymerases and telomerases, forms part of the binding pocket for the nascent base pair. We show here that replacement of Arg(72) by alanine strongly alters fidelity in a highly unusual manner. R72A reverse transcriptase is a frameshift and base substitution antimutator polymerase whose increased fidelity results both from increased nucleotide selectivity and from a decreased ability to extend mismatched primer termini. Thus, Arg(72)-substrate interactions in wild-type human immunodeficiency virus type 1 RT can stabilize incorrect nucleotides allowing misinsertion and promoting extension of mismatched and perhaps misaligned template-primers. In contrast to the higher fidelity at most sites, R72A RT is highly error-prone for misincorporations opposite template T in the sequence context: 5'-CTGG. Surprisingly, this results mostly from a 1200-fold increase in the apparent K(m) for correct dAMP incorporation. Thus, Arg(72) interactions with substrate are critical for the stability of the correct T.dAMP base pair when the 5'-CTGG sequence is present in the binding pocket for the nascent base pair. Collectively, the data show that a mutant polymerase may yield higher than normal average replication fidelity, yet paradoxically place specific sequences at very high risk of mutation.
Reactivity of Secondary Metal−Alkyls in Catalytic Propene Polymerization:  How Dormant Are “Dormant Chains”? (2005)

In this communication, we report on the direct measurement of dormant chain concentration and of the relative reactivity of authentic primary and secondary Zr-polymeryls toward propene, ethene, and H2 under practical conditions for a new highly regio- and stereoselective postmetallocene polymerization catalyst with controlled kinetic behavior. The results, in particular, confirm the poor reactivity toward propene of secondary M-polymeryls and the possible accumulation of dormant chains in propene homopolymerization.
A Systematic Approach to Blocking Convolutional Neural Networks (2016)

Convolutional Neural Networks (CNNs) are the state of the art solution for many computer vision problems, and many researchers have explored optimized implementations. Most implementations heuristically block the computation to deal with the large data sizes and high data reuse of CNNs. This paper explores how to block CNN computations for memory locality by creating an analytical model for CNN-like loop nests. Using this model we automatically derive optimized blockings for common networks that improve the energy efficiency of custom hardware implementations by up to an order of magnitude. Compared to traditional CNN CPU implementations based on highly-tuned, hand-optimized BLAS libraries,our x86 programs implementing the optimal blocking reduce the number of memory accesses by up to 90%.
Kidney iron status in passive Heymann nephritis and the effect of an iron-deficient diet. (1996)

In the study presented here, the iron status in the kidney in passive Heymann nephritis, a complement-dependent model of membranous nephropathy, was examined. To examine whether the effect of immune injury on iron status has a pathogenic role, the effect of an iron-deficient diet was also determined. Injection of the anti-Fx1A antibody (10 mg/100 g body wt) in Sprague-Dawley rats resulted in no change in the serum iron level, a marked increase in the urinary excretion rate of iron, a marked increase in non-heme iron content of kidney cortex, and a marked increase in the non-heme iron level in tubules. These increases in iron were prevented by feeding the rats an iron-deficient diet. In the rats fed a normal iron diet and injected with anti-Fx1A-lgG, there was no significant change in the non-heme iron level in glomeruli. However, an iron-deficient diet resulted in a significant decrease in the non-heme iron level in glomeruli, compared with its respective control. In addition, an iron-deficient diet significantly reduced urinary protein excretion rate (Day 5: iron-replete, 68 +/- 12 mg/24 h, N = 12; iron-deficient, 36 +/- 11, N = 10, P < 0.05) in the complement-dependent immune phase of the glomerular injury. Taken together, these data indicate a marked alteration in the iron status in the kidney and suggest an important role of iron in glomerular injury of passive Heymann nephritis.
Electrical properties of low-temperature epitaxial doped Si thin films fabricated by using a sputtering-type electron cyclotron resonance plasma (2001)

The electrical properties of Sb-doped n+ epitaxial Si films have been investigated. These films were fabricated at low temperatures of below 515 °C and at a conventional base pressure of 5×10-7 Torr using a sputtering-type electron cyclotron resonance plasma. It was found that the Sb dopants in the target were almost wholly incorporated into lattice sites of epilayers and the Hall mobility of the epilayers grown at 515 °C was comparable to that of the bulk Si. A reverse current density as low as 1×10-8 A cm-2 was obtained by a direct deposition of an n+ epilayer on a p-type substrate, which suggests the formation of a high-quality interface between the epilayer and the substrate. The precise control of the deposition gas pressure, substrate potential and substrate temperature was found to be very important for the fabrication of high-quality epilayers. Heavily B-doped p+ epilayers were also fabricated at a substrate temperature of 515 °C. The B dopant was wholly incorporated into the epitaxial layers, but annealing at temperatures of more than 700 °C was required to electrically activate the B dopant. The electrical activation mechanism has been discussed and it has been inferred that the B dopant occupied interstitial sites in the as-grown epilayers.
Effects of rosemary extracts and major constituents on lipid oxidation and soybean lipoxygenase activity (1992)

Rosemary ( Rosemarinus officinalis L.) leaves were extracted with three different solvents, namely hexane, acetone and methanol. A reverse‐phase high‐performance liquid chromatography system in combination with a mass detector was used to quantitate the content of carnosol, carnosic acid and ursolic acid in the rosemary extracts. All rosemary extracts showed strong inhibitory effects on lipid oxidation and soybean lipoxygenase activity.
Multiplexed, High Density Electrophysiology with Nanofabricated Neural Probes (2011)

Extracellular electrode arrays can reveal the neuronal network correlates of behavior with single-cell, single-spike, and sub-millisecond resolution. However, implantable electrodes are inherently invasive, and efforts to scale up the number and density of recording sites must compromise on device size in order to connect the electrodes. Here, we report on silicon-based neural probes employing nanofabricated, high-density electrical leads. Furthermore, we address the challenge of reading out multichannel data with an application-specific integrated circuit (ASIC) performing signal amplification, band-pass filtering, and multiplexing functions. We demonstrate high spatial resolution extracellular measurements with a fully integrated, low noise 64-channel system weighing just 330 mg. The on-chip multiplexers make possible recordings with substantially fewer external wires than the number of input channels. By combining nanofabricated probes with ASICs we have implemented a system for performing large-scale, high-density electrophysiology in small, freely behaving animals that is both minimally invasive and highly scalable.
Markup meets middleware (2003)

We describe a distributed system architecture that supports the integration of different front-office trading systems with middle and back-office systems, each of which have been procured from different vendors. The architecture uses a judicious combination of object-oriented middleware and markup languages. In this combination an object request broker implements reliable trade data transport. Markup languages, particularly XML, are used to address data integration problems. We show that the strengths of middleware and markup languages are complementary and discuss the benefits of deploying middleware and markup languages in a synergistic manner.
The constitution of a progesterone response element. (1993)

Progesterone receptors (PRs) recognize and bind to DNA in a sequence-specific manner. To define the sequence-specific determinants of PR binding to DNA, we employed a detailed series of target elements and analyzed both PR binding in vitro and PR-mediated activation of a reporter gene in vivo. These elements represent point substitution or insertion mutants of a progesterone response element derived from the mouse mammary tumor virus (MMTV). Substitution of a G for the first T in the 15-base pair (bp) MMTV progesterone response element core sequence, GTTACAAACTGTTCT, increases PR-DNA binding in vitro. All other tested mutations within this sequence either had no effect or decreased PR binding. From these analyses, we infer an optimal PR recognition sequence, -7RGNACANRNTGTNCY+7, composed of hexameric half-sites separated by precisely 3 bp and exhibiting dyad symmetry. Limited substitution of a suboptimal base for an optimal base, as in the wild type MMTV element, can be tolerated, but further suboptimal substitutions significantly decrease binding by PR. The identity of 1 bp within the hexameric half-site, position +/- 5, is unconstrained. Transition mutations, but not transversions, are permitted at position +/- 7. Here the hydrogen bond acceptor of the N-7 position of the purine ring may be involved in receptor recognition, since this feature is shared by the permitted substitutions. Insertion of a single base pair between the half-sites abolishes detectable binding, suggesting that the spatial orientation of the DNA binding domains of the monomeric receptor subunits are fixed by dimerization of the receptor. This pattern of sequence-specific recognition parallels that previously inferred for the glucocorticoid receptor, indicating that the two receptors may be unable to distinguish individual target sites. Each of the mutant response elements was also assessed for its ability to confer progestin responsiveness to a truncated MMTV promoter when introduced into a PR-containing cell line. Elements exhibiting strong receptor binding in vitro were fully inducible, whereas poorly inducible or uninducible elements displayed little or no recognition by receptor in vitro. However, some elements, though poorly bound in vitro, still activated transcription in vivo in response to hormone. In certain cases activation was as good as that seen with the wild type element. Further examination of in vitro receptor binding by this class of mutant elements using higher levels of baculovirus-expressed receptor revealed that many were indeed recognized by receptor, albeit with a lower affinity than the wild type sequence.(ABSTRACT TRUNCATED AT 400 WORDS)
Long-term left ventricular echocardiographic follow-up of SHR and WKY rats: effects of hypertension and age (2004)

Long-term follow-up of left ventricular (LV) function using echocardiography has not been reported and, in this study, was carried out in normotensive (WKY) rats and spontaneously hypertensive rats (SHR). In 10 WKY rats and SHR, LV diastolic and systolic diameter (LVEDD and LVSD), shortening fraction (SF), and weight (LVW) were determined at 8, 15, 20, 35, and 80 wk of age. The ratio of early to late mitral flow and mitral annulus velocity (VE/VA and Em/Am), isovolumic relaxation time (IVRT), deceleration time of the E wave (DTE), Tei index, and mitral flow propagation velocity (Vp) were measured. No difference in LVEDD was found between SHR and WKY rats; however, LVEDD was increased at 80 wk in both strains. SF decreased slightly in old WKY rats. LVW progressively increased from 20 to 80 wk in both strains and was greater in SHR. VE/VA and Em/Am decreased at 80 wk in WKY rats. LV relaxation (IVRT, Tei index, and Vp) was progressively impaired in SHR compared with WKY rats. LV compliance (DTE) was altered in old SHR. Echocardiography permitted a long follow-up of LV function in SHR and WKY rats. Ventricular relaxation was impaired early in the life of SHR and progressed with aging. Furthermore, LV compliance was altered, but systolic function remained unchanged, in old SHR. In contrast, relaxation and SF were only slightly altered in old WKY rats, suggesting that pressure-related changes in LV function were the dominant features in the SHR.
Moving Past Markovnikov's Rule (2001)

A broadened application of Markovnikov's rule is proposed that virtually eliminates the common exceptions that cause students difficulty. Alkene addition mechanisms can be an excellent case study showing how empirical rules evolve into more advanced theories.
Unsaturated Phospholipid Acyl Chains Are Required To Constitute Membrane Binding Sites for Factor VIII (1998)

Membranes containing phosphatidyl-L-serine (PS) and phosphatidylethanolamine (PE) greatly enhance the function of the enzymatic cofactor factor VIII. The mechanisms of enhanced function involve condensation of enzyme (factor IXa), activated cofactor (factor VIIIa), and substrate (factor X) at a common location and, most dramatically, activation of the assembled enzyme-cofactor complex. We asked whether unsaturated phospholipid (PL) acyl chains are necessary to constitute factor VIII binding sites or to activate the factor VIIIa-factor IXa complex. We found that membranes composed of saturated, dimyristoyl phospholipids had 20-fold fewer factor VIII binding sites and that these sites supported less than 5% normal activity of the factor VIIIa-factor IXa complex. Thrombin-activated factor VIII bound to a similar number of membrane sites, and thrombin activation did not reduce the affinity for saturated membranes more than 2-fold so that the loss of functional activity is due to a requirement of the factor VIIIa-factor IXa complex for unsaturated acyl chains that exceeds the requirement for factor VIII binding alone. Replacement of dimyristoyl-PS, -PE, or -PC individually with the corresponding unsaturated phospholipid restored 75%, 60%, and 15%, respectively, of factor VIII binding sites but less than 10% of factor VIIIa-factor IXa activating activity. Lyso-PS did not support binding of factor VIII or function of the factor VIIIa-factor IXa complex even when PE and phosphatidylcholine contained unsaturated acyl chains. We conclude that the sn-2 acyl chain of PS and unsaturated phospholipid acyl chains are chemical requirements for constitution of fully functional factor VIII binding sites on phospholipid membranes.
From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System (1992)

Up-to-date third edition which presents a coherant description of the nervous system from the perspective of modern work on molecular biology, cellular and developmental biology, biophysics, neurophysiology, neurochemistry and neuroanatomy. The scope of the book has been broadened with entirely new chapters on the biophysics and molecular biology of membrane channels, indirect mechanisms of synaptic transmission, the cellular and molecular biology of synaptic transmission, nervous system development, sensory receptors and systems, and motor systems. To accommodate this new information other subjects have been abbreviated or ammalgamated. Permeating the book are new concepts derived from experiments at the molecular level. Techniques such as patch clamping, gene cloning and expression, the use of monoclonal antibodies, and site-directed mutagenesis not only deepen but often simplify the presentation of topics related to signaling, synapse transmission, plasticity and development.