gebhart/patrepeval huggingface dataset:
Perceptual Losses for Real-Time Style Transfer and Super-Resolution (2016)

We consider image transformation problems, where an input image is transformed into an output image. Recent methods for such problems typically train feed-forward convolutional neural networks using a \emph{per-pixel} loss between the output and ground-truth images. Parallel work has shown that high-quality images can be generated by defining and optimizing \emph{perceptual} loss functions based on high-level features extracted from pretrained networks. We combine the benefits of both approaches, and propose the use of perceptual loss functions for training feed-forward networks for image transformation tasks. We show results on image style transfer, where a feed-forward network is trained to solve the optimization problem proposed by Gatys et al in real-time. Compared to the optimization-based method, our network gives similar qualitative results but is three orders of magnitude faster. We also experiment with single-image super-resolution, where replacing a per-pixel loss with a perceptual loss gives visually pleasing results.
Arachidonic, eicosapentaenoic, and biosynthetically related fatty acids in the seed lipids from a primitive gymnosperm, Agathis robusta (1999)

The fatty acid composition of the seeds from Agathis robusta, an Australian gymnosperm (Araucariaceae), was determined by a combination of chromatographic and spectrometric techniques. These enabled the identification of small amounts of arachidonic (5,8,11,14-20:4) and eicosapentaenoic (5,8,11,14,17-20:5) acids for the first time in the seed oil of a higher plant. They were apparently derived from gamma-linolenic (6,9,12-18:3) and stearidonic (6,9,12,15-18:4) acids, which were also present, via chain elongation and desaturation, together with other expected biosynthetic intermediates [bis-homo-gamma-linolenic (8,11,14-20:3) and bishomo-stearidonic (8,11,14,17-20:4) acids]. Also present were a number of C20 fatty acids, known to occur in most gymnosperm families, i.e., 5,11-20:2, 11,14-20:2 (bishomo-linoleic), 5,11,14-20:3 (sciadonic), 11,14,17-20:3 (bishomo-alpha-linolenic), and 5,11,14,17-20:4 (juniperonic) acids. In contrast to most other gymnosperm seed lipids analyzed so far, A. robusta seed lipids did not contain C18 delta5-desaturated acids [i.e., 5,9-18:2 (taxoleic), 5,9,12-18:3 (pinolenic), or 5,9,12,15-18:4 (coniferonic)]. These structures support the simultaneous existence of delta6- and delta5-desaturase activities in A. robusta seeds. The delta6-ethylenic bond is apparently introduced into C18 polyunsaturated acids, whereas the delta5-ethylenic bond is introduced into C20 polyunsaturated acids. A general metabolic pathway for the biosynthesis of unsaturated fatty acids in gymnosperm seeds is proposed. When compared to Bryophytes, Pteridophytes (known to contain arachidonic and eicosapentaenoic acids), and species from other gymnosperm families (without such acids), A. robusta appears as an "intermediate," with the C18 delta6-desaturase/C18-->C20 elongase/C20 delta5-desaturase system in common with the former subphyla, and the unsaturated C18-->C20 elongase/C20 delta5-desaturase system specific to gymnosperms. The following hypothetical evolutionary sequence for the C18 delta6/delta5-desaturase class in gymnosperm seeds is suggested: delta6 (initial)-->delta6/delta5 (intermediate)-->delta5 (final).
DO HUMAN T‐LYMPHOTROPHIC VIRUSES (HTLVs) AND OTHER ENVELOPED VIRUSES INDUCE AUTOIMMUNITY IN MULTIPLE SCLEROSIS? (1987)

A virally induced autoimmune reaction may be important in the pathogenesis of multiple sclerosis. The role that glycolipids and myelin basic protein presented to the virus may play in this process is considered. The most likely cells to be the source of autoantigens are neurons, myelin and oligodendrocytes. Viral infection of class II-expressing cells and association of the viral envelope autoantigens and the class II molecules could trigger an autoimmune reaction. It is suggested that for MS to develop following a virus infection the virus will need to cause expression of class II antigens on brain cells as well as fulfill the same role as an antigen presenting cell. The part which T-lymphotrophic viruses (HTLVs) and other enveloped viruses may play in this phenomenon is discussed.
Gas assisted etching of copper with focused ion beams (1999)

With the implementation of copper instead of aluminum as the metallization layer in high performance integrated circuits, the use of gas assisted etching of copper for focused ion beam (FIB) based failure analysis and circuit rewiring becomes important. In the present study the effects of exposing a copper substrate with a mixture of chlorine (Cl2) and anhydrous ammonia (NH3) during ion bombardment have been investigated. The exposure of the copper surface to Cl2 or to NH3/Cl2 mixtures leads to the formation of a reaction layer. The thickness of this layer and its texture depends on the FIB parameters such as ion beam dwell time, Cl2 pressure, and the NH3 to Cl2 flux ratio. In addition, the experiments indicate that the formation of the reaction layer is enhanced in areas that have been previously exposed (i.e., damaged) with the ion beam. The etch yield shows a strong dependence on the ion beam dwell time and the gas flux. For short dwell times and low NH3 and Cl2 flux a 12-fold increase over physical sputtering could be achieved. With increasing Cl2 flux the etch rate decreased and the maximum in the etch yield shifted to longer dwell times, indicating a change in the rate limiting step of the ion induced reaction sequence.
Identification and Screening of Individuals at Increased Risk for Pancreatic Cancer with Emphasis on Known Environmental and Genetic Factors and Hereditary Syndromes (2016)

Despite recent diagnostic and therapeutic advances, pancreatic cancer still carries a poor prognosis. Screening high-risk individuals is a relatively new concept with regards to pancreatic cancer but is an area of intense study. Significant effort has been invested in identifying risk factors for pancreatic cancer. Risk factors for pancreatic cancer can be classified into three broad categories: demographic, environmental (host), and hereditary (genetic) predisposition. This manuscript will review the risk factors and genetic syndromes associated with increased risk of developing pancreatic cancer, the role of genetic testing in the evaluation of high-risk patients, the available serologic and imaging tests that can be used to screen these individuals, and will summarize the available literature on attempts at pancreatic cancer screening to date.
Superantigen-Induced Regulatory T Cells Display Different Suppressive Functions in the Presence or Absence of Natural CD4+CD25+ Regulatory T Cells In Vivo (2003)

Repeated exposures to both microbial and innocuous Ags in vivo have been reported to both eliminate and tolerize T cells after their initial activation and expansion. The remaining tolerant T cells have been shown to suppress the response of naive T cells in vitro. This feature is reminiscent of natural CD4(+)CD25(+) regulatory T cells. However, it is not known whether the regulatory function of in vivo-tolerized T cells is similar to the function of natural CD4(+)CD25(+) regulatory T cells. In this study, we demonstrate that CD4(+)CD25(+) as well as CD4(+)CD25(-) T cells isolated from mice treated with superantigen three consecutive times to induce tolerance were functionally comparable to natural CD4(+)CD25(+) regulatory T cells, albeit more potent. The different subpopulations of in vivo-tolerized CD4(+) T cells efficiently down-modulated costimulatory molecules on dendritic cells, and their suppressive functions were strictly cell contact dependent. Importantly, we demonstrate that conventional CD4(+)CD25(-) T cells could also be induced to acquire regulatory functions by the same regimen in the absence of natural regulatory T cells in vivo, but that such regulatory cells were functionally different.
Chromosomal Double-Strand Breaks Induce Gene Conversion at High Frequency in Mammalian Cells (1997)

Double-strand breaks (DSBs) stimulate chromosomal and extrachromosomal recombination and gene targeting. Transcription also stimulates spontaneous recombination by an unknown mechanism. We used Saccharomyces cerevisiae I-SceI to stimulate recombination between neo direct repeats in Chinese hamster ovary (CHO) cell chromosomal DNA. One neo allele was controlled by the dexamethasone-inducible mouse mammary tumor virus promoter and inactivated by an insertion containing an I-SceI site at which DSBs were introduced in vivo. The other neo allele lacked a promoter but carried 12 phenotypically silent single-base mutations that create restriction sites (restriction fragment length polymorphisms). This system allowed us to generate detailed conversion tract spectra for recipient alleles transcribed at high or low levels. Transient in vivo expression of I-SceI increased homologous recombination 2,000- to 10,000-fold, yielding recombinants at frequencies as high as 1%. Strikingly, 97% of these products arose by gene conversion. Most products had short, bidirectional conversion tracts, and in all cases, donor neo alleles (i.e., those not suffering a DSB) remained unchanged, indicating that conversion was fully nonreciprocal. DSBs in exogenous DNA are usually repaired by end joining requiring little or no homology or by nonconservative homologous recombination (single-strand annealing). In contrast, we show that chromosomal DSBs are efficiently repaired via conservative homologous recombination, principally gene conversion without associated crossing over. For DSB-induced events, similar recombination frequencies and conversion tract spectra were found under conditions of low and high transcription. Thus, transcription does not further stimulate DSB-induced recombination, nor does it appear to affect the mechanism(s) by which DSBs induce gene conversion.
Lead cleavage sites in the core structure of group I intron-RNA (1993)

Self-splicing of group I introns requires divalent metal ions to promote catalysis as well as for the correct folding of the RNA. Lead cleavage has been used to probe the intron RNA for divalent metal ion binding sites. In the conserved core of the intron, only two sites of Pb2+ cleavage have been detected, which are located close to the substrate binding sites in the junction J8/7 and at the bulged nucleotide in the P7 stem. Both lead cleavages can be inhibited by high concentrations of Mg2+ and Mn2+ ions, suggesting that they displace Pb2+ ions from the binding sites. The RNA is protected from lead cleavage by 2'-deoxyGTP, a competitive inhibitor of splicing. The two major lead induced cleavages are both located in the conserved core of the intron and at phosphates, which had independently been demonstrated to interact with magnesium ions and to be essential for splicing. Thus, we suggest that the conditions required for lead cleavage occur mainly at those sites, where divalent ions bind that are functionally involved in catalysis. We propose lead cleavage analysis of functional RNA to be a useful tool for mapping functional magnesium ion binding sites.
A New Approach to Jacobian Formulation for a Class of Multi-Section Continuum Robots (2006)

We introduce a new method for synthesizing kinematics and Jacobian relationships for an important class of continuous backbone “continuum” robots. The resulting Jacobians enable task and shape control by relating work space (Cartesian) coordinates to actuator inputs (tendon lengths, pneumatic pressures, etc.), via robot shape coordinates. The approach, which is applicable to a wide class of existing continuum robots, also features the capability of including extension, as well as bending, of individual sections. The approach is also shown to produce correct results for orientation, in contrast to previously published approaches. Results of a real-time implementation of the method on a multisection continuum manipulator are reported.
Systemic gene therapy: biodistribution and long-term expression of a transgene in mice. (1995)

We have investigated the in vivo efficacy of a systemic gene transfer method, which combines a liposomal delivery system (DLS liposomes) with episomally replicative DNA plasmids to effect long-term expression of a transgene in cells. A single i.v. injection of a plasmid DNA vector containing the luciferase gene as a marker was administered with the DLS liposomes in BALB/c mice. The luciferase gene and its product were found in all mouse tissues tested as determined by PCR analysis and immunohistochemistry. Luciferase activity was also detected in all tissues tested and was present in lung, liver, spleen, and heart up to 3 months postinjection. In contrast to the nonepisomal vectors tested (pRSV-luc and pCMVintlux), human papovavirus (BKV)-derived episomal vectors showed long-term transgene expression. We found that these episomal vectors replicated extrachromosomally in lung 2 weeks postinjection. Results indicated that transgene expression in specific tissues depended on the promoter element used, DNA/liposome formulation, dose of DNA per injection, and route of administration.
Autophagosome Supports Coxsackievirus B3 Replication in Host Cells (2008)

Recent studies suggest a possible takeover of host antimicrobial autophagy machinery by positive-stranded RNA viruses to facilitate their own replication. In the present study, we investigated the role of autophagy in coxsackievirus replication. Coxsackievirus B3 (CVB3), a picornavirus associated with viral myocarditis, causes pronounced intracellular membrane reorganization after infection. We demonstrate that CVB3 infection induces an increased number of double-membrane vesicles, accompanied by an increase of the LC3-II/LC3-I ratio and an accumulation of punctate GFP-LC3-expressing cells, two hallmarks of cellular autophagosome formation. However, protein expression analysis of p62, a marker for autophagy-mediated protein degradation, showed no apparent changes after CVB3 infection. These results suggest that CVB3 infection triggers autophagosome formation without promoting protein degradation by the lysosome. We further examined the role of the autophagosome in CVB3 replication. We demonstrated that inhibition of autophagosome formation by 3-methyladenine or small interfering RNAs targeting the genes critical for autophagosome formation (ATG7, Beclin-1, and VPS34 genes) significantly reduced viral replication. Conversely, induction of autophagy by rapamycin or nutrient deprivation resulted in increased viral replication. Finally, we examined the role of autophagosome-lysosome fusion in viral replication. We showed that blockage of the fusion by gene silencing of the lysosomal protein LAMP2 significantly promoted viral replication. Taken together, our results suggest that the host's autophagy machinery is activated during CVB3 infection to enhance the efficiency of viral replication.
UGRP1, a Uteroglobin/Clara Cell Secretory Protein-Related Protein, Is a Novel Lung-Enriched Downstream Target Gene for the T/EBP/NKX2.1 Homeodomain Transcription Factor (2001)

A novel gene that is down-regulated in lungs of T/ebp/Nkx2.1-null mouse embryos has been identified using a suppressive-subtractive hybridization method. The gene product is a secreted protein, forms a homodimer, and exhibits an amino acid sequence similar to that seen in the uteroglobin/Clara cell secretory protein family of proteins. This gene, designated Ugrp1 (uteroglobin-related protein 1), consists of three exons and two introns and produces three transcripts by alternative splicing. The Ugrp1 gene was localized by fluorescence in situ hybridization to mouse chromosome 18 at region 18C-D; this region is homologous with human 5q31-34, where one of the asthma susceptibility genes has been assigned. UGRP1 mRNA is predominantly expressed in the lung, with low levels of expression in the thyroid. Expression in the lung is detectable as early as embryonic day 12.5 and increases markedly by embryonic day 16.5. In T/ebp/Nkx2.1-null embryo lungs, UGRP1 expression was significantly reduced as assessed by RT-PCR analysis. Cotransfection assays using a T/EBP/NKX2.1 expression construct with Ugrp1 promoter-luciferase reporter constructs confirmed that T/EBP/NKX2.1 regulates Ugrp1 gene activity at the transcriptional level. Thus, Ugrp1 is a downstream target gene for the T/EBP/NKX2.1 homeodomain transcription factor. Changes in UGRP1 mRNA levels in lungs from antigen-sensitized mice suggest the possible involvement of UGRP1 in inflammation.
High-gain direct-drive target design for laser fusion (2000)

A new laser fusion target concept is presented with a predicted energy gain of 127 using a 1.3 MJ KrF laser. This energy gain is sufficiently high for an economically attractive fusion reactor. X rays from high- and low-Z materials are used in combination with a low-opacity ablator to spatially tune the isentrope, thereby providing both high fuel compression and a reduction of the ablative Rayleigh–Taylor instability.
METH-1, a Human Ortholog of ADAMTS-1, and METH-2 Are Members of a New Family of Proteins with Angio-inhibitory Activity (1999)

We have studied two related proteins that contain a repeated amino acid motif homologous to the anti-angiogenic type 1 repeats of thrombospondin-1 (TSP1). Complete sequence analysis revealed no other similarities with TSP1, but identified unique signal sequences, as well as metalloprotease and disintegrin-like domains in the NH(2) termini. We named these proteins METH-1 and METH-2 due to the novel combination of metalloprotease and thrombospondin domains. Overall amino acid sequence identity between METH-1 and METH-2 is 51. 7%, yet transcript distribution revealed non-overlapping patterns of expression in tissues and cultured cell lines. To characterize these proteins functionally, we isolated full-length cDNAs, produced recombinant protein, and generated antisera to the recombinant proteins. Both METH-1 and METH-2 represent single copy genes, which encode secreted and proteolytically processed proteins. METH proteins suppressed fibroblast growth factor-2-induced vascularization in the cornea pocket assay and inhibited vascular endothelial growth factor-induced angiogenesis in the chorioallantoic membrane assay. Suppression of vessel growth in both assays was considerably greater than that mediated by either thrombospondin-1 or endostatin on a molar basis. Consistent with an endothelial specific response, METH-1 and METH-2 were shown to inhibit endothelial cell proliferation, but not fibroblast or smooth muscle growth. We propose that METH-1 and METH-2 represent a new family of proteins with metalloprotease, disintegrin, and thrombospondin domains. The distinct distribution of each gene product suggests that each has evolved distinct regulatory mechanisms that potentially allow for fine control of activity during distinct physiological and pathological states.
Purification, cDNA cloning, functional expression, and characterization of a 26-kDa endogenous mammalian carboxypeptidase inhibitor. (1995)

The recent demonstration of the occurrence in rat brain and other nonpancreatic tissues of carboxypeptidase A (CPA) gene transcripts without associated catalytic activity could be ascribed to the presence of a soluble endogenous protein inhibitor. This tissue carboxypeptidase inhibitor (TCI), detected by the inhibition of added bovine pancreatic CPA, was purified from rat brain. Peptides were obtained by partial proteolysis of purified TCI, a protein of approximately 30 kDa, and starting from their sequences, a full-length cDNA encoding a 223-amino acid protein containing three potential phosphorylation sites was cloned from a cDNA library. Its identity with TCI was shown by expression in Escherichia coli of a recombinant protein recognized by antibodies raised against native TCI and display characteristic CPA-inhibiting activity. TCI appears as a hardly reversible, non-competitive, and potent inhibitor of CPA1 and CPA2 (Ki approximately 3 nM) and mast-cell CPA (Ki = 16 nM) and inactive on various other proteases. This pattern of selectivity might be attributable to a limited homology of a 11-amino acid sequence with sequences within the activation segments of CPA and CPB known to interact with residues within their active sites. The widespread expression of TCI in a number of tissues (e.g., brain, lung, or digestive tract) and its apparently cytosolic localization point to a rather general functional role, e.g., in the control of cytosolic protein degradation.
Multifunctional polymeric micelles with folate-mediated cancer cell targeting and pH-triggered drug releasing properties for active intracellular drug delivery (2005)

A new type of multifunctional polymeric micelle drug carrier for active intracellular drug delivery was prepared and characterized in this study. The micelle is a nano-supramolecular assembly with a spherical core-shell structure, and its surface and core were modified with piloting molecules for cancer cells and pH-sensitive drug binding linkers for controlled drug release, respectively. In order to prepare such micelles, self-assembling amphiphilic block copolymers, folate-poly(ethylene glycol)-poly(aspartate hydrazone adriamycin) [Fol-PEG-P(Asp-Hyd-ADR)], were specially designed and synthesized by installing a molecular promoter to enhance intracellular transport, folate (Fol), at the end of the shell-forming PEG chain and conjugating the anticancer drug, adriamycin (ADR), to the side chain of the core-forming PAsp segment through an acid-sensitive hydrazone bond. Because folate-binding proteins (FBP) are selectively overexpressed on the cancer cell membranes, the folate-bound micelles (FMA) can be guided to the cancer cells in the body, and after the micelles enter the cells, hydrazone bonds are cleaved by the intracellular acidic environment (pH 5-6) so that the drug release profile of the micelles is controlled pH-dependently. In this regard, FBP-binding selectivity of the prepared FMA was evaluated by surface plasmon resonance (SPR) measurements. The tetrazolium dye method (MTT assay) using human pharyngeal cancer cells (KB cell) revealed that FMA significantly improved cell growth inhibitory activity in spite of a short exposure time due to the selective and strong interaction between folate molecules and their receptors. Subsequent flow cytometric analysis showed that cellular uptake of FMA significantly increased. Consequently, these findings would provide one of the most effective approaches for cancer treatment using intracellular environment-targeting supramolecular drug carriers.
A Simple Large-Scale Synthesis of Nearly Monodisperse Gold and Silver Nanoparticles with Adjustable Sizes and with Exchangeable Surfactants (2004)

Oleylamine-ligated gold and silver nanoparticles can be conveniently synthesized by reaction of tetrachloroauric acid or silver acetate with oleylamine in refluxing toluene, hexane, or 1,2-dichlorobenzene. The sizes of the colloids can be controlled with the solvent, reaction temperature, and reaction time. The gold nanoparticles spontaneously organize into micrometer-size colloidal crystals. Reactions of the gold and silver nanoparticles with aliphatic and carboxylic acid-functionalized thiols affords the ligand-exchanged nanoparticles as colloids that, depending on the surfactants, can be soluble in aqueous or nonaqueous solvents.
DRAM Using Crystalline Oxide Semiconductor for Access Transistors and Not Requiring Refresh for More Than Ten Days (2012)

We fabricated a dynamic random access memory (DRAM) using crystalline oxide semiconductor (OS) transistors and not requiring refresh for more than ten days. We call this memory a dynamic oxide semiconductor random access memory (DOSRAM). A crystalline oxide semiconductor is an In-Ga-Zn-oxide (IGZO) semiconductor and has a c-axis aligned crystal (CAAC) structure. A crystalline OS transistor has extremely low off-state current. The DOSRAM uses this device for access transistors, and can have a very long refresh cycle. A memory cell array made of a crystalline OS layer can be stacked on peripheral circuits made of a silicon (Si) semiconductor layer; thus, the area of the DOSRAM can be decreased.