gebhart/patrepeval huggingface dataset:
A double bifilar magneto-resistor for earth's field detection (1987)

This paper describes a new structure for a magneto-resistive thin-film field sensor. It is made up of two long folded serpentine sensor elements with an overlay double-serpentine bias conductor which is shifted with respect to the sensor pattern. This achieves effective biassing from a square-wave drive current. The device is assessed both theoretically and experimentally and found to be acceptable as an earth's field detector.
Solution structure of GOPC PDZ domain and its interaction with the C‐terminal motif of neuroligin (2006)

Abstract GOPC (Golgi‐associated PDZ and coiled‐coil motif‐containing protein) represents a PDZ domain‐containing protein associated with the Golgi apparatus, which plays important roles in vesicular trafficking in secretory and endocytic pathways. GOPC interacts with many other proteins, such as the Wnt receptors Frizzled 8 and neuroligin via its PDZ domain. Neuroligin is a neural cell‐adhesion molecule of the post‐synapse, which binds to the presynapse molecule neurexin to form a heterotypic intercellular junction. Here we report the solution structure of the GOPC PDZ domain by NMR. Our results show that it is a canonical class I PDZ domain, which contains two α‐helices and six β‐strands. Using chemical shift perturbation experiments, we further studied the binding properties of the GOPC PDZ domain with the C‐terminal motif of neuroligin. The observations showed that the ensemble of the interaction belongs to fast exchange with low affinity. The 3D model of the GOPC PDZ domain/neuroligin C‐terminal peptide complex was constructed with the aid of the molecular dynamics simulation method. Our discoveries provide insight into the specific interaction of the GOPC PDZ domain with the C‐terminal peptide of Nlg and also provide a general insight about the possible binding mode of the interaction of Nlg with other PDZ domain‐containing proteins.
High-performance embedded SOI DRAM architecture for the low-power supply (2000)

This paper presents the high-performance DRAM array and logic architecture for a sub-1.2-V embedded silicon-on-insulator (SOI) DRAM. The degradation of the transistor performance caused by boosted wordline voltage level is distinctly apparent in the low voltage range. In our proposed stressless SOI DRAM array, the applied electric field to the gate oxide of the memory-cell transistor can he relaxed. The crucial problem that the gate oxide of the embedded-DRAM process must be thicker than that of the logic process can be solved. As a result, the performance degradation of the logic transistor can be avoided without forming the gate oxides of the memory-cell array and the logic circuits individually. In addition, the data retention characteristics can be improved. Secondly, we propose the body-bias-controlled SOI-circuit architecture which enhances the performance of the logic circuit at sub-1.2-V power supply voltage, Experimental results verify that the proposed circuit architecture has the potential to reduce the gate-delay time up to 30% compared to the conventional one. This proposed architecture could provide high performance in the low-voltage embedded SOI DRAM.
Synthesis of a 10 000 Member 1,5-Benzodiazepine-2-one Library by the Directed Sorting Method (2000)

The solid-phase synthesis of a 10,000 member combinatorial library of 1,5-benzodiazepine-2-one derivatives is reported. The 3-amino-1,5-benzodiazepine-2-one scaffold was prepared in solution, and the benzamide nitrogen was used as a point of attachment to the resin. The 5-aniline and 3-amine were then used as points of diversity. A 10,000 member library was synthesized using the Irori directed sorting system, and after analysis of a representative sample from the library, the Irori system was used to remove the compounds of lower purity.
Scene completion using millions of photographs (2007)

What can you do with a million images? In this paper we present a new image completion algorithm powered by a huge database of photographs gathered from the Web. The algorithm patches up holes in images by finding similar image regions in the database that are not only seamless but also semantically valid. Our chief insight is that while the space of images is effectively infinite, the space of semantically differentiable scenes is actually not that large. For many image completion tasks we are able to find similar scenes which contain image fragments that will convincingly complete the image. Our algorithm is entirely data-driven, requiring no annotations or labelling by the user. Unlike existing image completion methods, our algorithm can generate a diverse set of results for each input image and we allow users to select among them. We demonstrate the superiority of our algorithm over existing image completion approaches.
Mix-and-Match Tuning for Self-Supervised Semantic Segmentation (2017)

Deep convolutional networks for semantic image segmentation typically require large-scale labeled data, e.g. ImageNet and MS COCO, for network pre-training. To reduce annotation efforts, self-supervised semantic segmentation is recently proposed to pre-train a network without any human-provided labels. The key of this new form of learning is to design a proxy task (e.g. image colorization), from which a discriminative loss can be formulated on unlabeled data. Many proxy tasks, however, lack the critical supervision signals that could induce discriminative representation for the target image segmentation task. Thus self-supervision's performance is still far from that of supervised pre-training. In this study, we overcome this limitation by incorporating a "mix-and-match" (M&amp;M) tuning stage in the self-supervision pipeline. The proposed approach is readily pluggable to many self-supervision methods and does not use more annotated samples than the original process. Yet, it is capable of boosting the performance of target image segmentation task to surpass fully-supervised pre-trained counterpart. The improvement is made possible by better harnessing the limited pixel-wise annotations in the target dataset. Specifically, we first introduce the "mix" stage, which sparsely samples and mixes patches from the target set to reflect rich and diverse local patch statistics of target images. A "match" stage then forms a class-wise connected graph, which can be used to derive a strong triplet-based discriminative loss for fine-tuning the network. Our paradigm follows the standard practice in existing self-supervised studies and no extra data or label is required. With the proposed M&amp;M approach, for the first time, a self-supervision method can achieve comparable or even better performance compared to its ImageNet pre-trained counterpart on both PASCAL VOC2012 dataset and CityScapes dataset.
Suppression of T-Lymphocyte Activation and Chemotaxis by the Adenylate Cyclase Toxin ofBordetella pertussis (2008)

The adenylate cyclase toxin (CyaA) released by Bordetella pertussis is an essential virulence factor for colonization of the host. This toxin inhibits migration and activation of phagocytes, thereby preventing bacterial killing. In addition, CyaA interferes with the initiation of adaptive immunity by misdirecting dendritic cell differentiation to a suppressive rather than stimulatory phenotype. Here we show that CyaA directly affects adaptive responses by catalyzing cyclic AMP (cAMP) production in peripheral blood lymphocytes. Treatment with CyaA resulted in profound impairment of T-lymphocyte activation and chemotaxis. These effects resulted from inhibition of T-cell antigen receptor and chemokine receptor signaling via a cAMP/protein kinase A (PKA)-dependent pathway. A comparison of the activities of CyaA on T-cell and macrophage activation and migration revealed that the biological effects of the toxin were paralleled by inhibition of the activation of mitogen-activated protein (MAP) kinases, highlighting the conclusion that the ubiquitous and evolutionarily conserved MAP kinase modules are common targets of the PKA-mediated immunosuppressant activities of CyaA and underlining the potential of cAMP-elevating toxins as a means of evasion of immunity by bacterial pathogens.
Putative nuclear localization signals (NLS) in protein transcription factors (1994)

Abstract We have recognized about ten distinct forms of strongly basic hexapeptides, containing at least four arginines and lysines, characteristic of nuclear proteins among all eukaryotic species, including yeast, plants, flies and mammals. These basic hexapeptides are considered to be different versions of a core nuclear localization signal, NLS. Core NLSs are present in nearly all nuclear proteins and absent from nearly all “nonassociated” cytoplasmic proteins that have been investigated. We suggest that the few (∼ 10%) protein factors lacking a typical NLS core peptide may enter the nucleus via their strong crosscomplexation with their protein factor partners that possess a core NLS. Those cytoplasmic proteins found to possess a NLS‐like peptide are either tightly associated with cell membrane proteins or are integral components of large cytoplasmic protein complexes. On the other hand, some versions of core NLSs are found in many cell membrane proteins and secreted proteins. It is hypothesized that in these cases the N‐terminal hydrophobic signal peptide of extracellular proteins and the internal hydrophobic domains of transmembrane proteins are stronger determinants for their subcellular localization. The position of core NLSs among homologous nuclear proteins may or may not be conserved; however, if lost from an homolgous site it appears elsewhere in the protein. This search provides a set of rules to our understanding of the nature of core nuclear localization signals: (1) Core NLS are proposed to consist most frequently of an hexapeptide with 4 arginines and lysines; (2) aspartic and glutamic acid residues as well as bulky amino acids (F, Y, W) need not to be present in this hexapeptide; (3) acidic residues and proline or glycine that break the α‐helix are frequently in the flanking region of this hexapeptide stretch; (4) hydrophobic residues ought not to be present in the core NLS flanking region allowing for the NLS to be exposed on the protein. In this study we attempt to classify putative core NLS from a wealth of nuclear protein transcription factors from diverse species into several categories, and we propose additional core NLS structures yet to be experimentally verified. © 1994 Wiley‐Liss, Inc.
Ligand‐induced endocytosis of the asialoglycoprotein receptor: evidence for heterogeneity in subunit oligomerization (1998)

The hepatic asialoglycoprotein receptor, a non‐covalent hetero‐oligomer of two subunits, is a constitutively cycling endocytic receptor. However, the ligand asialoorosomucoid caused downregulation of up to 40% of surface binding sites and a twofold increase in internalization rate. This was not the result of receptor crosslinking, since monovalent ligands had the same effect. Ligand binding thus appears to transmit a signal to the cytosolic portion of the receptor not unlike in signaling receptors. The two subunits were endocytosed at different average rates lower than that of ligand, indicating heterogeneity in oligomer formation and potentially in ligand specificity.
Epitaxial two dimensional aluminum films on silicon (111) by ultra-fast thermal deposition (2012)

Aluminum thin films are known for their extremely rough surface, which is detrimental for applications such as molecular electronics and photonics, where protrusions cause electrical shorts or strong scattering. We achieved atomically flat Al films using a highly non-equilibrium approach. Ultra-fast thermal deposition (UFTD), at rates &amp;gt;10 nm/s, yields RMS roughness of 0.4 to 0.8 nm for 30–50 nm thick Al films on variety of substrates. For UFTD on Si(111) substrates, the top surface follows closely the substrate topography (etch pits), indicating a 2D, layer-by-layer growth. The Al film is a mixture of (100) and (111) grains, where the latter are commensurate with the in-plane orientation of the underlying Si (epitaxy). We show the use of these ultra-smooth Al films for highly reproducible charge-transport measurements across a monolayer of alkyl phosphonic acid as well as for plasmonics applications by directly patterning them by focused ion beam to form a long-range ordered array of holes. UFTD is a one-step process, with no need for annealing, peeling, or primer layers. It is conceptually opposite to high quality deposition methods, such as MBE or ALD, which are slow and near-equilibrium processes. For Al, though, we find that limited diffusion length (and good wetting) is critical for achieving ultra-smooth thin films.
Astrocytes Directly Influence Tumor Cell Invasion and Metastasis In Vivo (2013)

Brain metastasis is a defining component of tumor pathophysiology, and the underlying mechanisms responsible for this phenomenon are not well understood. Current dogma is that tumor cells stimulate and activate astrocytes, and this mutual relationship is critical for tumor cell sustenance in the brain. Here, we provide evidence that primary rat neonatal and adult astrocytes secrete factors that proactively induced human lung and breast tumor cell invasion and metastasis capabilities. Among which, tumor invasion factors namely matrix metalloprotease-2 (MMP-2) and MMP-9 were partly responsible for the astrocyte media-induced tumor cell invasion. Inhibiting MMPs reduced the ability of tumor cell to migrate and invade in vitro. Further, injection of astrocyte media-conditioned breast cancer cells in mice showed increased invasive activity to the brain and other distant sites. More importantly, blocking the preconditioned tumor cells with broad spectrum MMP inhibitor decreased the invasion and metastasis of the tumor cells, in particular to the brain in vivo. Collectively, our data implicate astrocyte-derived MMP-2 and MMP-9 as critical players that facilitate tumor cell migration and invasion leading to brain metastasis.
The Leidenfrost Point: Experimental Study and Assessment of Existing Models (1999)

This study presents a detailed and thorough parametric study of the Leidenfrost point (LFP), which serves as the temperature boundary between the transition and film boiling regimes. Sessile drop evaporation experiments were conducted with acetone, benzene, FC-72, and water on heated aluminum surfaces with either polished, particle blasted, or rough sanded finishes to observe the influential effects of fluid properties, surface roughness, and surface contamination on the LFP. A weak relationship between surface energies and the LFP was observed by performing droplet evaporation experiments with water on polished copper, nickel, and silver surfaces. Additional parameters which were investigated and found to have negligible influence on the LFP included liquid subcooling, liquid degassing, surface roughness on the polished level, and the presence of polishing paste residues. The accumulated LFP data of this study was used to assess several existing models which attempt to identify the mechanisms which govern the LFP. The disagreement between the experimental LFP values and those predicted by the various models suggests that an accurate and robust theoretical model which effectively captures the LFP mechanisms is currently unavailable.
Shift-map image editing (2009)

Geometric rearrangement of images includes operations such as image retargeting, inpainting, or object rearrangement. Each such operation can be characterized by a shiftmap: the relative shift of every pixel in the output image from its source in an input image. We describe a new representation of these operations as an optimal graph labeling, where the shift-map represents the selected label for each output pixel. Two terms are used in computing the optimal shift-map: (i) A data term which indicates constraints such as the change in image size, object rearrangement, a possible saliency map, etc. (ii) A smoothness term, minimizing the new discontinuities in the output image caused by discontinuities in the shift-map. This graph labeling problem can be solved using graph cuts. Since the optimization is global and discrete, it outperforms state of the art methods in most cases. Efficient hierarchical solutions for graph-cuts are presented, and operations on 1M images can take only a few seconds.
Study on the growth of biaxially aligned yttria-stabilized zirconia films during ion beam assisted deposition (1997)

(001)-oriented and in-plane aligned yttria-stabilized zirconia (YSZ) thin films were synthesized on Ni–Cr alloy substrates by ion beam assisted deposition. It was found that it is not the 〈111〉 axial channel but the {110} plane channel that will always follow the direction of the bombarding ion beam and will result in the in-plane aligned structure of the YSZ films. At 55° incident angle, the bombarding ion beam is in the {110} plane channel and the 〈111〉 axial channel simultaneously; this produces the optimal biaxial alignment of YSZ films. On YSZ single crystalline substrates or textured YSZ layers, growth of YSZ films will not be controlled by the bombarding ion beam; rather, but the films continue to grow along the lattice orientation of the substrate. The formation of the biaxial alignment is an evolutionally selected process by ion beam selective bombardment. YSZ grains of (001) orientation are resputtered less than other oriented grains under ion beam bombardment, which causes the (001) orientation to emerge from initial random orientations evolutionally. About a 1000 Å-M20 thickness is needed to develop the alignment. The roughness of the substrate has no obvious influence on the alignment within several hundred Å. Increasing the substrate temperature tends to reduce the (001) orientation and to promote the (111) orientation along the substrate normal. Postannealing of the YSZ films fabricated at ambient temperature can improve the crystalline structure.
The Histone-Like Protein Hlp Is Essential for Growth of Streptococcus pyogenes: Comparison of Genetic Approaches To Study Essential Genes (2011)

Selection of possible targets for vaccine and drug development requires an understanding of the physiology of bacterial pathogens, for which the ability to manipulate expression of essential genes is critical. For Streptococcus pyogenes (the group A streptococcus [GAS]), an important human pathogen, the lack of genetic tools for such studies has seriously hampered research. To address this problem, we characterized variants of the inducible Ptet cassette, in both sense and antisense contexts, as tools to regulate transcription from GAS genes. We found that although the three-operator Ptet construct [Ptet(O)3] had low uninduced expression, its induction level was low, while the two-operator construct [Ptet(O)2] was inducible to a high level but showed significant constitutive expression. Use of Ptet(O)3 in the chromosome allowed us to demonstrate previously that RNases J1 and J2 are required for growth of GAS. Here we report that the uninduced level from the chromosomally inserted Ptet(O)2 construct was too high for us to observe differential growth. For the highly expressed histone-like protein (Hlp) of GAS, neither chromosomal insertion of Ptet(O)2 or Ptet(O)3 nor their use on a high-copy-number plasmid to produce antisense RNA specific to hlp resulted in adequate differential expression. However, by replacing the ribosome binding site of hlp with an engineered riboswitch to control translation of Hlp, we demonstrated for the first time that this protein is essential for GAS growth.
A novel Channel Boost Capacitance (CBC) cell technology with low program disturbance suitable for fast programming 4 Gbit NAND flash memories (2002)

This paper describes a novel Channel Boost Capacitance (CBC) cell technology suitable for highly scaled and fast-programming NAND flash memories. The CBC cell realizes a very high channel boost ratio in self-boosted programming without additional gate control, and drastically improves program disturbance with decreasing design rule, especially less than 0.2 /spl mu/m-rule. This memory cell is essential for realizing highly scaled, and fast-progamming NAND flash memories of 4 Gbit and beyond.
Targeted gene therapies: tools, applications, optimization (2012)

Many devastating human diseases are caused by mutations in a single gene that prevent a somatic cell from carrying out its essential functions, or by genetic changes acquired as a result of infectious disease or in the course of cell transformation. Targeted gene therapies have emerged as potential strategies for treatment of such diseases. These therapies depend upon rare-cutting endonucleases to cleave at specific sites in or near disease genes. Targeted gene correction provides a template for homology-directed repair, enabling the cell's own repair pathways to erase the mutation and replace it with the correct sequence. Targeted gene disruption ablates the disease gene, disabling its function. Gene targeting can also promote other kinds of genome engineering, including mutation, insertion, or gene deletion. Targeted gene therapies present significant advantages compared to approaches to gene therapy that depend upon delivery of stably expressing transgenes. Recent progress has been fueled by advances in nuclease discovery and design, and by new strategies that maximize efficiency of targeting and minimize off-target damage. Future progress will build on deeper mechanistic understanding of critical factors and pathways.
Using Loran-C for Automatic Vehicle Monitoring* (1982)

The knowledge of the location and status of vehicles in a fleet greatly enhances the command and control capability of that fleet. Significant operational and economical benefits can be derived. Among the factors contributing to the delay in responding to any emergency, whether it is a heart attack, burglary in progress, severe auto accident, or a special cargo or passenger vehicle needing assistance, is determining the exact location of the incident and dispatching the closest available assistance. In both rural and urban situations, Automatic Vehicle Monitoring (AVM) systems in conjunction with an effective Command and Control (C2) system can reduce this delay. AVM provides economic benefits to people and cargo transport fleets (buses, taxis, trucks) by dispatching closest available units and providing most direct routings. These benefits are available to both government and private sectors. This article will review briefly the development of AVM systems, describe characteristics of some existing systems, focusing on Loran based systems, and provide some scenarios illustrating the use of AVM systems.
An informed source separation system for speech signals (2011)

In two previous papers, we proposed an audio Informed Source Separation (ISS) system which can achieve the separation of I > 2 musical sources from linear instantaneous stationary stereo (2-channel) mixtures, based on audio signal's natural sparsity, pre-mix source signals analysis, and side-information embedding (within the mix signal). In the present paper and for the first time, we apply this system to mixtures of (up to seven) simultaneous speech signals. Compared to the reference MPEG-4 Spatial Audio Object Coding system, our system pro- vides much cleaner separated speech signals (consistently 10- 20 dB higher Signal to Interference Ratios), revealing strong potential for audio conference applications.