gebhart/patrepeval huggingface dataset:
Deeply Supervised Salient Object Detection with Short Connections (2017)

Recent progress on saliency detection is substantial, benefiting mostly from the explosive development of Convolutional Neural Networks (CNNs). Semantic segmentation and saliency detection algorithms developed lately have been mostly based on Fully Convolutional Neural Networks (FCNs). There is still a large room for improvement over the generic FCN models that do not explicitly deal with the scale-space problem. Holisitcally-Nested Edge Detector (HED) provides a skip-layer structure with deep supervision for edge and boundary detection, but the performance gain of HED on saliency detection is not obvious. In this paper, we propose a new saliency method by introducing short connections to the skip-layer structures within the HED architecture. Our framework provides rich multi-scale feature maps at each layer, a property that is critically needed to perform segment detection. Our method produces state-of-the-art results on 5 widely tested salient object detection benchmarks, with advantages in terms of efficiency (0.08 seconds per image), effectiveness, and simplicity over the existing algorithms.
Release of O-Linked Sugar Chains from Glycoproteins with Anhydrous Hydrazine and Pyridylamination of the Sugar Chains with Improved Reaction Conditions1 (1992)

A method for preparation of pyridylamino (PA-) derivatives of O-linked sugar chains from glycoproteins was developed. A glycopeptide containing O-linked Gal beta 1-3GalNAc was prepared from fetuin and treated with anhydrous hydrazine followed by N-acetylation of free amino groups. Sugar chains released were pyridylaminated with improved reaction conditions and excess reagents were removed by gel filtration. Gal beta 1-3GalNAc-PA obtained together with PA-Gal as a by-product was quantified by HPLC. Conditions for the hydrazine treatment were investigated and the treatment at 40 degrees C for 350 h gave the best results for releasing O-linked sugar chains. The total yield of Gal beta 1-3GalNAc-PA from the glycopeptide was 53% under the established conditions and that of PA-Gal was 18%. The present method was applied to a glycoprotein, and the expected PA-O-linked sugar chains were obtained. Under these conditions, N-linked sugar chains were also released.
A CD-1 mouse model of infection with <i>Staphylococcus aureus</i>: Influence of gender on infection with MRSA and MSSA isolates (2000)

Staphylococcus aureus is an important pathogen of humans and other animals, causing bacteremia, abscessation, toxemia, and other infectious diseases. An animal model using CD-1 mice was developed to study the pathogenesis of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA). When inoculated into the CD-1 mouse model, it was shown that both MSSA isolates, (HR 78 and CSA-1) and MRSA isolates (MRSA 456 and MRSA 457) led to chronic infection of the kidney. Female CD-1 mice inoculated with MRSA 456 proved to be more susceptible to infection and mortality than their male counterparts. Castrated mice became more susceptible to infection than intact male mice, suggesting a hormonal involvement in the infection process.
Positron Emission Tomography Reporter Genes and Reporter Probes: Gene and Cell Therapy Applications (2012)

Positron emission tomography (PET) imaging reporter genes (IRGs) and PET reporter probes (PRPs) are amongst the most valuable tools for gene and cell therapy. PET IRGs/PRPs can be used to non-invasively monitor all aspects of the kinetics of therapeutic transgenes and cells in all types of living mammals. This technology is generalizable and can allow long-term kinetics monitoring. In gene therapy, PET IRGs/PRPs can be used for whole-body imaging of therapeutic transgene expression, monitoring variations in the magnitude of transgene expression over time. In cell or cellular gene therapy, PET IRGs/PRPs can be used for whole-body monitoring of therapeutic cell locations, quantity at all locations, survival and proliferation over time and also possibly changes in characteristics or function over time. In this review, we have classified PET IRGs/PRPs into two groups based on the source from which they were derived: human or non-human. This classification addresses the important concern of potential immunogenicity in humans, which is important for expansion of PET IRG imaging in clinical trials. We have then discussed the application of this technology in gene/cell therapy and described its use in these fields, including a summary of using PET IRGs/PRPs in gene and cell therapy clinical trials. This review concludes with a discussion of the future direction of PET IRGs/PRPs and recommends cell and gene therapists collaborate with molecular imaging experts early in their investigations to choose a PET IRG/PRP system suitable for progression into clinical trials.
Nontransgenic Genome Modification in Plant Cells (2010)

Zinc finger nucleases (ZFNs) are a powerful tool for genome editing in eukaryotic cells. ZFNs have been used for targeted mutagenesis in model and crop species. In animal and human cells, transient ZFN expression is often achieved by direct gene transfer into the target cells. Stable transformation, however, is the preferred method for gene expression in plant species, and ZFN-expressing transgenic plants have been used for recovery of mutants that are likely to be classified as transgenic due to the use of direct gene-transfer methods into the target cells. Here we present an alternative, nontransgenic approach for ZFN delivery and production of mutant plants using a novel Tobacco rattle virus (TRV)-based expression system for indirect transient delivery of ZFNs into a variety of tissues and cells of intact plants. TRV systemically infected its hosts and virus ZFN-mediated targeted mutagenesis could be clearly observed in newly developed infected tissues as measured by activation of a mutated reporter transgene in tobacco (Nicotiana tabacum) and petunia (Petunia hybrida) plants. The ability of TRV to move to developing buds and regenerating tissues enabled recovery of mutated tobacco and petunia plants. Sequence analysis and transmission of the mutations to the next generation confirmed the stability of the ZFN-induced genetic changes. Because TRV is an RNA virus that can infect a wide range of plant species, it provides a viable alternative to the production of ZFN-mediated mutants while avoiding the use of direct plant-transformation methods.
Body charge related transient effects in floating body SOI NMOSFETs (2002)

The transient operation of submicrometer floating body SOI NMOSFETs is studied and measured down to a nanosecond time scale. We emphasize the role of the overall hole charge in the body of the device, for a global understanding of the transient phenomena: drain current overshoot or undershoot, memory effect, dynamic instabilities... . This charge integrates the device history, with a strongly bias dependent time constant, and influences the drain current, mainly by electrostatic action. The resulting transient current instability has to be considered to avoid anomalous circuit operation.
Angiogenesis: An update and potential drug approaches (Review) (2009)

The therapeutic potential of targeting tumor endothelium and vascular supply is now widely recognized to treat different diseases. One such disease is cancer; where endothelial cells are actively proliferating to support the tumor growth. Solid tumors cannot grow beyond the size of a few millimeters without inducing the proliferation of endothelium and formation of new blood vessels. Hence it is crucial to search for new agents that selectively block tumor blood supply. These include anti-angiogenic molecules, vascular disrupting agents or endothelial disrupting agents. The anti-angiogenic molecules such as monoclonal antibodies and tyrosine kinase inhibitors disrupt endothelial cell survival mechanisms and new blood vessel formation, and vascular disrupting agents for instance ligand-directed and small molecules can be used to disrupt the already existing abnormal vasculature that support tumors by targeting their dysmorphic endothelial cells. The recent advances in this area of research have identified a variety of investigational agents which are currently in clinical development at various stages and some of these candidates are already approved in cancer treatment. This report will review some of the recent developments and most significant advances in this field and outline future challenges and directions.
An experimental basis for revising the graphic rating scale for pain (1984)

Seven subjects judged the differences between electrocutaneous shocks and words from two category rating lists describing those sensations in each of two differences estimation experiments. The electrocutaneous shocks used for the two experiments were 10 suprathreshold shock intensities determined separately for each subject. There were two distinct 7-word category rating lists. Both lists shared 6 common words; however, the seventh word made the rational ordering of the two lists different. Magnitude scales of meaning for the category rating words and sensory scales for the electrocutaneous shock intensities were determined for each of the two experiments for each subject using conjoint measurement analysis. Comparisons of the sensory scales for electrocutaneous shock between the two difference estimation experiments for each subject showed that they judged the electrocutaneous shocks similarly with the two words lists. This allowed for comparisons between the scales of meaning for the words from the category rating lists. The two word lists were not equivalent. There was substantial agreement among the subjects on characteristic spacings of quantitative values for the category rating items. These results suggest that clinical ratings scales used for analgesimetry should not assume homogeneity of spacing of category items. A scale incorporating our subjects' common understanding is presented.
Use of Anticoagulants and Antiplatelet Agents in Stable Outpatients with Coronary Artery Disease and Atrial Fibrillation. International CLARIFY Registry (2015)

ISRCTN registry of clinical trials: ISRCTN43070564.
A Novel, Chemoselective and Efficient Microwave-Assisted Deprotection of Silyl Ethers with Selectfluor (2009)

A novel microwave-assisted, chemoselective and efficient method for the cleavage of silyl ethers (aliphatic and aromatic) catalyzed by Selectfluor is reported. A wide range of TBS-, TIPS-, and TBDPS-protected alkyl silyl ethers can be chemoselectively cleaved in high yield in the presence of aryl silyl ethers. The chemoselective deprotection of phenolic TBS ethers, and not the TIPS- or TBDPS-protected phenolic ethers, and the deprotection of silyl esters were also achieved under these reaction conditions. In addition, the transetherification and etherification of benzylic hydroxy groups in alcoholic solvents is observed.
Performance of MOSFETs with ultra thin ZrO/sub 2/ and Zr silicate gate dielectrics (2002)

In this paper, we report the transistor performance of both PMOS and NMOS fabricated with ZrO/sub 2/ and Zr-silicate gate dielectrics. These high-k films exhibit low leakage, low subthreshold swing (S), and good on-off characteristics. Good effective electron and hole mobilities were obtained. It was found that for Zr-silicate, a mobility closer to thermal SiO/sub 2/ was demonstrated due to the better interface with Si substrate.
The fragment assembly string graph (2005)

We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the reads and, in particular, present a novel linear expected time algorithm for transitive reduction in this context. The result demonstrates that the decomposition of reads into kmers employed in the de Bruijn graph approach described earlier is not essential, and exposes its close connection to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.
Rapid Sample Processing for LC-MS-Based Quantitative Proteomics Using High Intensity Focused Ultrasound (2008)

A new sample processing workflow that uses high intensity focused ultrasound to rapidly reduce and alkylate cysteines, digest proteins and then label peptides with (18)O was developed for quantitative proteomics applications. Each step was individually refined to minimize reaction times, peptide loses and undesired byproducts or modifications. When this novel workflow was used, mouse plasma proteins were successfully denatured, alkylated, in-solution digested, and (18)O-labeled in <10 min for subsequent analysis by liquid chromatography-electrospray ionization high resolution mass spectrometry. Performance was evaluated in terms of the number of mouse plasma peptides and proteins identified in a shotgun approach and the quantitative dynamic range. The results were compared with previously published results obtained using conventional sample preparation methods and were found to be similar. Advantages of the new method include greatly simplified and accelerated sample processing, as well as being readily amenable to automation.
Covalent Linkage of HIV-1 Trimers to Synthetic Liposomes Elicits Improved B Cell and Antibody Responses (2017)

We have demonstrated that a liposomal array of well-ordered trimers enhances B cell activation, germinal center formation, and the elicitation of tier-2 autologous neutralizing antibodies. Previously, we coupled well-ordered cleavage-independent NFL trimers via their C-terminal polyhistidine tails to nickel lipids integrated into the lipid bilayer. Despite favorable <i>in vivo</i> effects, concern remained over the potentially longer-term <i>in vivo</i> instability of noncovalent linkage of the trimers to the liposomes. Accordingly, we tested both cobalt coupling and covalent linkage of the trimers to the liposomes by reengineering the polyhistidine tail to include a free cysteine on each protomer of model BG505 NFL trimers to allow covalent linkage. Both cobalt and cysteine coupling resulted in a high-density array of NFL trimers that was stable in both 20% mouse serum and 100 mM EDTA, whereas the nickel-conjugated trimers were not stable under these conditions. Binding analysis and calcium flux with anti-Env-specific B cells confirmed that the trimers maintained conformational integrity following coupling. Following immunization of mice, serologic analysis demonstrated that the covalently coupled trimers elicited Env-directed antibodies in a manner statistically significantly improved compared to soluble trimers and nickel-conjugated trimers. Importantly, the covalent coupling not only enhanced gp120-directed responses compared to soluble trimers, it also completely eliminated antibodies directed to the C-terminal His tag located at the "bottom" of the spike. In contrast, soluble and noncovalent formats efficiently elicited anti-His tag antibodies. These data indicate that covalent linkage of well-ordered trimers to liposomes in high-density array displays multiple advantages <i>in vitro</i> and <i>in vivo</i><b>IMPORTANCE</b> Enveloped viruses typically encode a surface-bound glycoprotein that mediates viral entry into host cells and is a primary target for vaccine design. Liposomes with modified lipid head groups have a unique feature of capturing and displaying antigens on their surfaces, mimicking the native pathogens. Our first-generation nickel-based liposomes captured HIV-1 Env glycoprotein trimers via a noncovalent linkage with improved efficacy over soluble glycoprotein in activating germinal center B cells and eliciting tier-2 autologous neutralizing antibodies. In this study, we report the development of second-generation cobalt- and maleimide-based liposomes that have improved <i>in vitro</i> stability over nickel-based liposomes. In particular, the maleimide liposomes captured HIV-1 Env trimers via a more stable covalent bond, resulting in enhanced germinal center B cell responses that generated higher antibody titers than the soluble trimers and liposome-bearing trimers via noncovalent linkages. We further demonstrate that covalent coupling prevents release of the trimers prior to recognition by B cells and masks a nonneutralizing determinant located at the bottom of the trimer.
An oligopeptide permease responsible for the import of an extracellular signal governing aerial mycelium formation in Streptomyces coelicolor (1996)

Morphological differentiation in the filamentous bacterium Streptomyces coelicolor is believed to involve a mechanism of extracellular signalling that culminates with the formation of an aerial mycelium. We have identified a gene cluster designated bldK in which insertional and deletion mutations cause a block in aerial mycelium formation. Extracellular complementation experiments indicate that bldK defines a step in a cascade of extracellular signals; colonies of a bldK-mutant strain extracellularly complement bld261-mutant colonies, and are themselves extracellularly complemented by bldA- and bldH-mutant colonies. The bldK locus, which is located at 5 o'clock on the genetic map and within Asel fragment "N' on the physical map, consists of five adjacent open reading frames. These genes specify homologues of the subunits of the oligopeptide-permease family of ATP-binding cassette (ABC) membrane-spanning transporters. Because bldK mutations confer resistance to the toxic tripeptide bialaphos, it is inferred that BldK is an oligopeptide importer. We propose that the BldK transporter is responsible for the import of an extracellular signalling molecule produced under the control of the wild-type product of the bld261 gene. The BldK-imported signal, in turn, causes the production of a second extracellular signal molecule that depends on the products of bldA and bldH for its action.
Phase III Prospective Randomized Double-Blind Placebo-Controlled Trial of Plerixafor Plus Granulocyte Colony-Stimulating Factor Compared With Placebo Plus Granulocyte Colony-Stimulating Factor for Autologous Stem-Cell Mobilization and Transplantation for Patients With Non-Hodgkin's Lymphoma (2009)

Plerixafor and G-CSF were well tolerated and resulted in a significantly higher proportion of patients with non-Hodgkin's lymphoma achieving the optimal CD34+ cell target for transplantation in fewer apheresis days, compared with G-CSF alone.
Rhythmic cortical myoclonus in a case of HIV‐related encephalopathy (2003)

We describe a 66-year-old, HIV-seropositive patient presenting with ataxia and upper limb rhythmic myoclonus activated by postural maintenance. Electromyograph (EMG) recordings of the forearm muscles showed 50-msec bursts, with a frequency of 10 Hz, concurring with frontocentral electroencephalograph (EEG) rhythmic activity. Autoregressive spectral analysis applied to the EEG-EMG traces made it possible to detect significant coherence between the rhythmic EEG discharges and EMG bursts. The amplitude of the middle-latency somatosensory evoked potentials was increased. Long-latency reflexes were enhanced. On the basis of the electrophysiological findings, the movement disorder should be considered a rhythmic variant of cortical myoclonus. In our patient, HIV infection may have caused a dysfunction in the central nervous system pathways involving the cerebellum and sensorimotor cortex, similar to that occurring in genetically determined conditions characterised by cortical myoclonus.
SWNT−MWNT Hybrid Architecture for Proton Exchange Membrane Fuel Cell Cathodes (2008)

A thin film of single-wall carbon nanotubes (SWNTs) and SWNT−multiwall carbon nanotube (MWNT) hybrids loaded with Pt have been evaluated as the cathode catalyst layer in proton exchange membrane fuel cells. The optimum Pt loading and thickness for SWNT films is found to be in the range of 20−100 µg Pt/cm2 and 0.3−1.4 µm, respectively. In this optimum range, Pt-SWNT thin films show excellent proton conductivity and are able to reach peak performance without additional nafion in the catalyst layer. Cathode-specific mass activity of Pt on a SWNT support is found to decrease as the Pt loading and thickness increase due to mass transfer limitations. Addition of Pt-MWNTs to Pt-SWNT thin films is found to increase the mass transport characteristics and cathode-specific mass activity. A SWNT−MWNT hybrid support shows three times higher mass activity than a SWNT support at about the same power output, and the optimum hybrid is found for a blend composed of 20−30 µgPt/cm2 on SWNTs and 5−10 µgPt/cm2 on MWNTs.
Anti-idiotypic antibodies to monoclonal antibody CO17-1A. (1986)

Anti-idiotypic antibodies (Ab2) raised during the course of monoclonal antibody (MAb) therapy against anti-colorectal carcinoma (CRC) MAb CO17-1A were characterized in 142 patients with carcinomas of the colon, rectum or pancreas. Ab2 comprised between 21 and 80% of the total human anti-mouse IgG antibodies in various patients, and up to 42 micrograms of Ab2 were isolated per ml serum. In one patient significant levels of Ab2 could be detected for greater than 770 days. Between 20 and 70% of Ab2 in various patients bound to the combining site of MAb CO17-1A and may therefore bear the internal image of the 17-1A tumor antigen. Furthermore, Ab2 isolated from different patients showed considerable cross-reactivities. A beneficial role of the Ab2 responses in the cancer patients who improved clinically following MAb immunotherapy is discussed in light of induction by Ab2 of anti-anti-idiotypic antibodies (Ab3) with tumor-binding activities.
Structural joins: a primitive for efficient XML query pattern matching (2003)

XML queries typically specify patterns of selection predicates on multiple elements that have some specified tree structured relationships. The primitive tree structured relationships are parent-child and ancestor-descendant, and finding all occurrences of these relationships in an XML database is a core operation for XML query processing. We develop two families of structural join algorithms for this task: tree-merge and stack-tree. The tree-merge algorithms are a natural extension of traditional merge joins and the multi-predicate merge joins, while the stack-tree algorithms have no counterpart in traditional relational join processing. We present experimental results on a range of data and queries using the TIMBER native XML query engine built on top of SHORE. We show that while, in some cases, tree-merge algorithms can have performance comparable to stack-tree algorithms, in many cases they are considerably worse. This behavior is explained by analytical results that demonstrate that, on sorted inputs, the stack-tree algorithms have worst-case I/O and CPU complexities linear in the sum of the sizes of inputs and output, while the tree-merge algorithms do not have the same guarantee.
Synthesis Of A Distamycin Analog - Tris(Meta-Benzamido) Compound (1987)

Distamycin analog I was prepared in order to examine its DNA binding properties. Thus, condensation of $3-O_2NC_6H_4COCl$ with $3-H_2NC_6H_4CO_2Me$ (II), sapon., acid chlorination, and recondensation with II gave $3-O_2NC_6H_4CONHC_6H_4CO_2Me$ (III). Sapon. of III, acid chlorination, condensation with $H_2NCH_2CH_2CN$, hydrolysis, hydrogenation, and formylation gave I.