gebhart/patrepeval huggingface dataset:
Insulin-Like Growth Factor I/Somatomedin-C: A Rapid Isolation Procedure with FPLC (1985)

Insulin-like growth factor I (IGF I)/somatomedin-C (SM-C) was purified from lyophilized human serum by acid-ethanol extraction. The extract was precipitated with acetone-ethanol. The precipitate was purified by Sephadex G-50 chromatography. The protein peak within a molecular weight range of 5000-10 000 was further purified with FPLC-reversed phase chromatography using a Pep RPC HR 5/5 column (Pharmacia) with a solvent system of acetonitrile (CH3CN) and 0.1% trifluoroacetic acid (TFA) in water. The purification of IGF I was monitored by radioimmunoassay for SM-C. Purity was established by analytical isoelectric focusing and by SDS polyacrylamide gel electrophoresis. Analytical isoelectric focusing showed one single protein band with an apparent pI of 8.3 +/- 0.1. SDS polyacrylamide gel electrophoresis showed also one single protein band with an apparent molecular weight of 7000. Biological activity was demonstrated by measuring the (3H)thymidine incorporation into DNA of cultured arterial smooth muscle cells.
Learning from massive noisy labeled data for image classification (2015)

Large-scale supervised datasets are crucial to train convolutional neural networks (CNNs) for various computer vision problems. However, obtaining a massive amount of well-labeled data is usually very expensive and time consuming. In this paper, we introduce a general framework to train CNNs with only a limited number of clean labels and millions of easily obtained noisy labels. We model the relationships between images, class labels and label noises with a probabilistic graphical model and further integrate it into an end-to-end deep learning system. To demonstrate the effectiveness of our approach, we collect a large-scale real-world clothing classification dataset with both noisy and clean labels. Experiments on this dataset indicate that our approach can better correct the noisy labels and improves the performance of trained CNNs.
Ultrasonic instruments and devices : references for modern instrumentation, techniques, and technology (1999)

E.P. Papadakis, Preface. A.J. Gellman, E.P. Papadakis, N.J. Goldfine, S.R. Ringlee, W. Lord, S. Udpa, A. Ballato, and R. Stern, The Process of Technology Transfer and Commercialization: Several Essays on TT, Marketing, and Finance. E.P. Papadakis, C.G. Oakley, A.R. Selfridge, and B. Maxfield, Fabrication and Characterization of Transducers. F.S. Hickernell, Surface Acoustic Wave Devices: Macro-Success Through Micro-Seisms. J.R. Vig and A. Ballato, Frequency Control Devices. R.S. Gilmore, Industrial Ultrasonic Imaging/Microscopy. B.B. Chick, Research Instruments and Systems. Subject Index.
Building Nanostructures by Controlled Manipulation of Single Atoms and Molecules with the Scanning Tunneling Microscope (1995)

Abstract Our present experiences in manipulating single atoms and molecules on solid surfaces by using the tip of a scanning tunneling microscope (STM) are reviewed. The construction and performance characteristics of our temperature variable STM is shortly described, which allows investigations in the temperature range between 15 and 300 K. As example for horizontal manipulation, in which the adatoms or admolecules are pulled along the surface by the STM tip, and the formation of man‐made surface structures, the formation of the letters ‘F’ and ‘U’, which form the logo of our university is presented. The adspecies used in these experiments are CO molecules and the substrate a Cu(211) surface. An example of vertical manipulation, in which an adparticle is picked up by the tip, carried to another place and released back to the surface, concerns Xe on the same substrate. The latter technique allows also to vary the chemical composition of the tip apex in a well‐defined manner. Consequences in imaging the surface with tips of different compositions are presented and discussed. Finally, STM observations of ordered high density phases of CO on the Cu(211) substrate are discussed.
On the Mechanism of Mitochondrial Uncoupling Protein 1 Function (2005)

Native uncoupling protein 1 (UCP 1) was purified from rat mitochondria by hydroxyapatite chromatography and identified by peptide mass mapping and tandem mass spectrometry. Native and expressed UCP 1 were reconstituted into liposomes, and proton flux through UCP 1 was shown to be fatty acid-dependent and GDP-sensitive. To investigate the mechanism of action of UCP 1, we determined whether hydrophilic modification of the omega-carbon of palmitate effected its transport function. We show that proton flux was greater through native UCP 1-containing proteoliposomes when facilitated by less hydrophilically modified palmitate (palmitate > omega-methoxypalmitate > omega-hydroxypalmitate with little or no proton flux due to glucose-O-omega-palmitate or undecanesulfonate). We show that non-proton-dependent charge transfer was greater when facilitated by less hydrophilically modified palmitate (palmitate/undecanesulfonate > omega-methoxypalmitate > omega-hydroxypalmitate, with no non-proton-dependent charge transfer flux due to glucose-O-omega-palmitate). We show that the GDP-inhibitable oxygen consumption rate in brown adipose tissue mitochondria was reversed by palmitate (as expected) but not by glucose-O-omega-palmitate. Our data are consistent with the model that UCP 1 flips long-chain fatty acid anions and contradict the "cofactor" model of UCP 1 function.
GridLAB-D Technical Support Document: Residential End-Use Module Version 1.0 (2008)

1.0 Introduction The residential module implements the following end uses and characteristics to simulate the power demand in a single family home: • Water heater • Lights • Dishwasher • Range • Microwave • Refrigerator • Internal gains (plug loads) • House (heating/cooling loads) The house model considers the following four major heat gains/losses that contribute to the building heating/cooling load: 1. Conduction through exterior walls, roof and fenestration (based on envelope UA) 2. Air infiltration (based on specified air change rate) 3. Solar radiation (based on CLTD model and using tmy data) 4. Internal gains from lighting, people, equipment and other end use objects. The Equivalent Thermal Parameter (ETP) approach is used to model the residential loads and energy consumption. The following sections describe the modeling assumptions for each of the above end uses and the details of power demand calculations in the residential module.
Ultra-low-power domain-specific multimedia processors (2002)

Programmability is an important requirement for portable computing and communication devices that must be flexible enough to accommodate a variety of multimedia services and communication capabilities. However, compared to dedicated, application-specific solutions, programmable devices often incur significant performance and power penalties. We present a hybrid architecture template that can be used to implement ultra-low-power programmable processors for signal processing applications.
Interaction of palladium(0) complexes with allylic acetates, allyl ethers, allyl phenyl chalcogenides, allylic alcohols, and allylamines. Oxidative addition, condensation, disproportionation, and .pi.-complex formation (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteraction of palladium(0) complexes with allylic acetates, allyl ethers, allyl phenyl chalcogenides, allylic alcohols, and allylamines. Oxidative addition, condensation, disproportionation, and .pi.-complex formationTakakazu YamamotoTakakazu YamamotoMore by Takakazu Yamamoto, Mitsuru AkimotoMitsuru AkimotoMore by Mitsuru Akimoto, Osamu SaitoOsamu SaitoMore by Osamu Saito, and Akio YamamotoAkio YamamotoMore by Akio YamamotoCite this: Organometallics 1986, 5, 8, 1559–1567Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/om00139a009https://doi.org/10.1021/om00139a009research-articleACS PublicationsRequest reuse permissionsArticle Views1574Altmetric-Citations110LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Regulation of CSF‐1 receptor expression (1997)

Cells of the mononuclear phagocyte lineage possess receptors for macrophage colony-stimulating factor (CSF-1) encoded by the c-fms protooncogene and respond to CSF-1 with increased survival, growth, differentiation, and reversible changes in function. The c-fms gene is itself a macrophage differentiation marker. In whole mount analyses of mRNA expression in embryos, c-fms is expressed at very high levels on placental trophoblasts. It is detectable on individual cells in the yolk sac around 8.5 to 9 days postcoitus, appears on isolated cells in the head of the embryo around 9.5 dpc, and appears on numerous cells throughout the embryo by day 10.5. The extent of c-fms expression is much greater than for other macrophage-specific genes including lysozyme and a macrophage-specific protein tyrosine phosphatase. Our studies of the cis-acting elements of the c-fms promoter have indicated a key role for collaboration between the macrophage-specific transcription factor, Pu. 1, which functions in determining the site of transcription initiation, and other members of the Ets transcription factor family. This is emerging as a common pattern in macrophage specific promoters. We have shown that two PU box elements alone can function as a macrophage-specific promoter. The activity of both the artifical promoter and the c-fms promoter is activated synergistically by coexpression of Pu. 1 and another Ets factor, c-Ets-2. A 3.5kb c-fms exon 2 promoter (but not the 300bp proximal promoter) is also active in a wide diversity of tumor cell lines. The interesting exception is the melanoma cell line K1735, in which the promoter is completely shut down and expression of c-fms causes growth arrest and cell death. The activity of the exon 2 promoter in these nonmacrophages is at least as serum responsive as the classic serum-responsive promoter of the c-fos gene. It is further inducible in nonmacrophages by coexpression of the c-fms product. Unlike other CSF-1/c-fms-responsive promoters, the c-fms promoter is not responsive to activated Ras even when c-Ets-2 is coexpressed. In most lines, production of full length c-fms is prevented by a downstream intronic terminator, but in Lewis lung carcinoma, read-through does occur, and expression of both c-fms and other macrophage-specific genes such as lysozyme and urokinase becomes detectable in conditions of serum deprivation. Mol Reprod Dev 46:46–53, 1997. © 1997 Wiley-Liss, Inc.
Compressive force promotes Sox9, type II collagen and aggrecan and inhibits IL-1β expression resulting in chondrogenesis in mouse embryonic limb bud mesenchymal cells (1998)

The initial modeling and subsequent development of the skeleton is controlled by complex gene-environment interactions. Biomechanical forces may be one of the major epigenetic factors that determine the form and differentiation of skeletal tissues. In order to test the hypothesis that static compressive forces are transduced into molecular signals during early chondrogenesis, we have developed a unique three-dimensional collagen gel cell culture system which is permissive for the proliferation and differentiation of chondrocytes. Mouse embryonic day 10 (E10) limb buds were microdissected and dissociated into cells which were then cultured within a collagen gel matrix and maintained for up to 10 days. Static compressive forces were exerted onto these cultures. The time course for expression pattern and level for cartilage specific markers, type II collagen and aggrecan, and regulators of chondrogenesis, Sox9 and IL-1beta, were analyzed and compared with non-compressed control cultures. Under compressive conditions, histological evaluation showed an apparent acceleration in the rate and extent of chondrogenesis. Quantitatively, there was a significant 2- to 3-fold increase in type II collagen and aggrecan expression beginning at day 5 of culture and the difference was maintained through 10 days of cultures. Compressive force also causes an elevated level of Sox9, a transcriptional activator of type II collagen. In contrast, the expression and accumulation of IL-1beta, a transcriptional repressor of type II collagen was down-regulated. We conclude that static compressive forces promote chondrogenesis in embryonic limb bud mesenchyme, and propose that the signal transduction from a biomechanical stimuli can be mediated by a combination of positive and negative effectors of cartilage specific extracellular matrix macromolecules.
Sequence requirement for hand-in-hand interaction in formation of RNA dimers and hexamers to gear φ29 DNA translocation motor (1999)

Translocation of DNA or RNA is a ubiquitous phenomenon. One intricate translocation process is viral DNA packaging. During maturation, the lengthy genome of dsDNA viruses is translocated with remarkable velocity into a limited space within the procapsid. We have revealed that phi29 DNA packaging is accomplished by a mechanism similar to driving a bolt with a hex nut, which consists of six DNA-packaging pRNAs. Four bases in each of the two pRNA loops are involved in RNA/RNA interactions to form a hexagonal complex that gears the DNA translocating machine. Without considering the tertiary interaction, in some cases only two G/C pairs between the interacting loops could provide certain pRNAs with activity. When all four bases were paired, at least one G/C pair was required for DNA packaging. The maximum number of base pairings between the two loops to allow pRNA to retain wild-type activity was five, whereas the minimum number was five for one loop and three for the other. The findings were supported by phylogenetic analysis of seven pRNAs from different phages. A 75-base RNA segment, bases 23-97, was able to form dimer, to interlock into the hexamer, to compete with full-length pRNA for procapsid binding, and therefore to inhibit phi29 assembly in vitro. Our result suggests that segment 23-97 is a self-folded, independent domain involved in procapsid binding and RNA/RNA interaction in dimer and hexamer formation, whereas bases 1-22 and 98-120 are involved in DNA translocation but dispensable for RNA/RNA interaction. Therefore, this 75-base RNA could be a model for structural studies in RNA dimerization.
Flip-chip packaging using micromachined conductive polymer bumps and alignment pedestals for MOEMS (1999)

Using flip-chip bonding techniques with micromachined conductive polymer bumps and passive alignment techniques with electroplated side alignment pedestal bumps, a prototype microoptoelectromechanical systems (MOEMS) structure for optical input/output (I/O) couplers has been designed, fabricated and characterized. A top MOEMS substrate has through holes, contact metal pads, and side alignment pedestals with electroplated NiFe to align GaAs metal-semiconductor-metals (MSMs). Conductive polymer bumps have been formed on contact metal pads of GaAs MSMs using thick photoresist bump-holes as molding patterns. A diced GaAs photodetectors die with micromachined conductive polymer bumps was aligned to the side alignment pedestals and flip-chip bonded onto the substrate. This conductive polymer flip-chip bonding technique allowed a very low contact resistance (/spl sim/10 m/spl Omega/), a lower bonding temperature (/spl sim/170/spl deg/C), and simple processing steps. The GaAs MSM photodetectors flip-chip mounted on the top of OE-MCM substrate showed a low dark current of about 10 nA and a high responsivity of 0.33 A/W.
Isolation of Monomeric and Dimeric Secreted MD-2 (2008)

Potent cell activation by endotoxin requires sequential protein-endotoxin and protein-protein interactions involving lipopolysaccharide-binding protein, CD14, MD-2, and Toll-like receptor 4 (TLR4). MD-2 plays an essential role by bridging endotoxin (E) recognition initiated by lipopolysaccharide-binding protein and CD14 to TLR4 activation by presenting endotoxin as a monomeric E.MD-2 complex that directly and potently activates TLR4. Secreted MD-2 (sMD-2) exists as a mixture of monomers and multimers. Published data suggest that only MD-2 monomer can interact with endotoxin and TLR4 and support cell activation, but the apparent instability of MD-2 has thwarted efforts to more fully separate and characterize the individual species of sMD-2. We have taken advantage of the much greater stability of sMD-2 in insect culture medium to fully separate sMD-2 monomer from dimer by gel sieving chromatography. At low nanomolar concentrations, the sMD-2 monomer, but not dimer, reacted with a monomeric complex of E.sCD14 to form monomeric E.MD-2 and activate HEK293/TLR4 cells. The monomer, but not dimer, also reacted with the ectodomain of TLR4 with an affinity comparable with the picomolar affinity of E.MD-2. These findings demonstrate directly that the monomeric form of sMD-2 is the active species both for reaction with E.CD14 and TLR4, as needed for potent endotoxin-induced TLR4 activation.
Efficient genotype compression and analysis of large genetic variation datasets (2015)

ABSTRACT The economy of human genome sequencing has catalyzed ambitious efforts to interrogate the genomes of large cohorts in search of new insight into the genetic basis of disease. This manuscript introduces Genotype Query Tools (GQT) as a new indexing strategy and toolset that addresses an analytical bottleneck by enabling interactive analyses based on genotypes, phenotypes and sample relationships. Speed improvements are achieved by operating directly on a compressed genotype index without decompression. GQT’s data compression ratios increase favorably with cohort size and relative analysis performance improves in kind. We demonstrate substantial performance improvements over state-of-the-art tools using datasets from the 1000 Genomes Project (46 fold), the Exome Aggregation Consortium (443 fold), and simulated datasets of up to 100,000 genomes (218 fold). Furthermore, we show that this indexing strategy facilitates population and statistical genetics measures such as principal component analysis and burden tests. Based on its computational efficiency and by complementing existing toolsets, GQT provides a flexible framework for current and future analyses of massive genome datasets.
Dymaxion++: A Directive-Based API to Optimize Data Layout and Memory Mapping for Heterogeneous Systems (2014)

There has been a growing trend in using heterogeneous systems with CPUs and GPUs to solve diverse compute problems. However, high application performance on these platforms relies on efficient memory accesses. For many applications, CPUs and GPUs prefer different memory mappings and data structure layouts. This in turn requires developers to use device-specific strategies for memory access optimizations. Achieving both code and performance portability becomes a challenge for heterogeneous computing. This paper proposes a directive-based API, Dymaxion++, which enables programmers to optimize memory access patterns across devices with a simple interface. Use of Dymaxion++ requires only minimal modifications to existing codes with a small set of pragma extensions. The current framework augments the original Dymaxion framework with a clean abstraction backed by a source-to-source code translator. Dymaxion++ also provides additional programming features to map data structures to GPU's hybrid memory spaces (e.g. texture and constant memory) for different uses. Additionally, data layout transformation is enabled while exchanging data between GPU scratchpad and device memory as well as between system memory and device memory.
A Convenient Synthesis of the Pyrrolo[3,2-c]quinoline Core of Martinelline Alkaloids (2002)

The tricyclic core of the martinellines has been synthesised stereoselectively in two steps, using 1,3-dipolar cycloaddition of azomethine ylides as a key step.
Interleukin‐10 production in malignant melanoma: Preferential detection of IL‐10‐secreting tumor cells in metastatic lesions (1996)

IL-10 mRNA expression and protein production in established melanoma cell lines and freshly cultured primary and metastatic melanoma cells was examined. The in situ distribution of IL-10 in native melanoma tissue was also investigated by immunohistochemistry in primary tumors, metastases, benign melanocytic nevi and normal skin of healthy persons and melanoma patients. IL-10 mRNA, but not IL-10 protein in the culture supernatant, was found in 1 of 4 cultured melanoma cells of primary tumors, while 3 of 6 melanoma-metastasis-derived cultures expressed both IL-10 mRNA and protein. No IL-10 was detected in skin biopsies of healthy volunteers or in the healthy skin of melanoma patients; nor was IL-10 found in congenital nevi. In only 1 of the 11 examined primary malignant melanomas was IL-10 immunoreactivity detected within the cytoplasm of cells in the tumor. On the other hand, 4 of 9 metastases clearly displayed scattered IL-10+ cells. In all sections with IL-10-positive cells, the cells were positive for HMB-45. No co-expression of CD3 and IL-10 was observed. The data suggest that melanoma cells themselves are the main origin of IL-10 in tumor specimens in vivo. The preferential expression of IL-10 in metastatic lesions and in cultured cells from metastases might indicate an increased spreading potential of IL-10-secreting melanoma-cell clones. © 1996 Wiley-Liss, Inc.
Neural network control of functional neuromuscular stimulation systems: computer simulation studies (1995)

A neural network control system has been designed for the control of cyclic movements in Functional Neuromuscular Stimulation (FNS) systems. The design directly addresses three major problems in FNS control systems: customization of control system parameters for a particular individual, adaptation during operation to account for changes in the musculoskeletal system, and attaining resistance to mechanical disturbances. The control system was implemented by a two-stage neural network that utilizes a combination of adaptive feedforward and feedback control techniques. A new learning algorithm was developed to provide rapid customization and adaptation. The control system was evaluated in a series of studies on a computer simulated musculoskeletal model. The model of electrically stimulated muscle used in the study included nonlinear recruitment, linear dynamics, and multiplicative nonlinear torque-angle and torque-velocity scaling factors. The skeletal model consisted of a one-segment planar system with passive constraints on joint movement. Results of the evaluation have demonstrated that the control system can provide automated customization of the feedforward controller parameters for a given musculoskeletal system. It can account for changes in the musculoskeletal system by adapting the feedforward controller parameters on-line and it can resist the effects of mechanical disturbances. These results suggest that this design may be suitable for the control of FNS systems and other dynamic systems.