gebhart/patrepeval huggingface dataset:
Ptychographic coherent diffractive imaging of weakly scattering specimens (2010)

Applying iterative phase retrieval schemes to ptychographic data, i.e. diffraction patterns collected with a localized illumination probe from overlapping regions of a specimen, has enabled the investigation of extended specimens previously inaccessible by other coherent x-ray diffractive imaging methods. While the technique had initially been limited by the requirement of precise knowledge of the illumination function, recent algorithmic developments allow now the simultaneous reconstruction of both the probe and the object. However, these new approaches suffer from an inherent ambiguity, which affects especially the case of weakly scattering specimens. We present new schemes to circumvent this problem and introduce new tools for obtaining information about the scattering behaviour of weak phase objects already during data collection. The new techniques are experimentally demonstrated for a data set taken on Magnetospirillum gryphiswaldense. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.
Reclaiming space from duplicate files in a serverless distributed file system (2003)

The Farsite distributed file system provides availability by replicating each file onto multiple desktop computers. Since this replication consumes significant storage space, it is important to reclaim used space where possible. Measurement of over 500 desktop file systems shows that nearly half of all consumed space is occupied by duplicate files. We present a mechanism to reclaim space from this incidental duplication to make it available for controlled file replication. Our mechanism includes: (1) convergent encryption, which enables duplicate files to be coalesced into the space of a single file, even if the files are encrypted with different users' keys; and (2) SALAD, a Self-Arranging Lossy Associative Database for aggregating file content and location information in a decentralized, scalable, fault-tolerant manner. Large-scale simulation experiments show that the duplicate-file coalescing system is scalable, highly effective, and fault-tolerant.
Triphenylbutanamines: Kinesin Spindle Protein Inhibitors with in Vivo Antitumor Activity (2012)

The human mitotic kinesin Eg5 represents a novel mitotic spindle target for cancer chemotherapy. We previously identified S-trityl-l-cysteine (STLC) and related analogues as selective potent inhibitors of Eg5. We herein report on the development of a series of 4,4,4-triphenylbutan-1-amine inhibitors derived from the STLC scaffold. This new generation systematically improves on potency: the most potent C-trityl analogues exhibit K(i)(app) ≤ 10 nM and GI(50) ≈ 50 nM, comparable to results from the phase II clinical benchmark ispinesib. Crystallographic studies reveal that they adopt the same overall binding configuration as S-trityl analogues at an allosteric site formed by loop L5 of Eg5. Evaluation of their druglike properties reveals favorable profiles for future development and, in the clinical candidate ispinesib, moderate hERG and CYP inhibition. One triphenylbutanamine analogue and ispinesib possess very good bioavailability (51% and 45%, respectively), with the former showing in vivo antitumor growth activity in nude mice xenograft studies.
Real-time hand-tracking with a color glove (2009)

Articulated hand-tracking systems have been widely used in virtual reality but are rarely deployed in consumer applications due to their price and complexity. In this paper, we propose an easy-to-use and inexpensive system that facilitates 3-D articulated user-input using the hands. Our approach uses a single camera to track a hand wearing an ordinary cloth glove that is imprinted with a custom pattern. The pattern is designed to simplify the pose estimation problem, allowing us to employ a nearest-neighbor approach to track hands at interactive rates. We describe several proof-of-concept applications enabled by our system that we hope will provide a foundation for new interactions in modeling, animation control and augmented reality.
High-Affinity GD2-Specific CAR T Cells Induce Fatal Encephalitis in a Preclinical Neuroblastoma Model (2017)

The GD2 ganglioside, which is abundant on the surface of neuroblastoma cells, is targeted by an FDA-approved therapeutic monoclonal antibody and is an attractive tumor-associated antigen for cellular immunotherapy. Chimeric antigen receptor (CAR)-modified T cells can have potent antitumor activity in B-cell malignancies, and trials to harness this cytolytic activity toward GD2 in neuroblastoma are under way. In an effort to enhance the antitumor activity of CAR T cells that target GD2, we generated variant CAR constructs predicted to improve the stability and the affinity of the GD2-binding, 14G2a-based, single-chain variable fragment (scFv) of the CAR and compared their properties <i>in vivo</i> We included the E101K mutation of GD2 scFv (GD2-E101K) that has enhanced antitumor activity against a GD2<sup>+</sup> human neuroblastoma xenograft <i>in vivo</i> However, this enhanced antitumor efficacy <i>in vivo</i> was concomitantly associated with lethal central nervous system (CNS) toxicity comprised of extensive CAR T-cell infiltration and proliferation within the brain and neuronal destruction. The encephalitis was localized to the cerebellum and basal regions of the brain that display low amounts of GD2. Our results highlight the challenges associated with target antigens that exhibit shared expression on critical normal tissues. Despite the success of GD2-specific antibody therapies in the treatment of neuroblastoma, the fatal neurotoxicity of GD2-specific CAR T-cell therapy observed in our studies suggests that GD2 may be a difficult target antigen for CAR T-cell therapy without additional strategies that can control CAR T-cell function within the CNS. <i>Cancer Immunol Res; 6(1); 36-46. ©2017 AACR</i>.
Synthesis of Polyamide Nucleic Acids (Pnas), Pna /Dna-Chimeras and Phosphonic Ester Nucleic Acids (Phonas) (1997)

Abstract The synthesis of polyamide nucleic acids (PNAs) and derivatives thereof by different synthetic routes is described. The first strategy makes use of 9-Fluorenylmethoxycarbonyl (Fmoc)/monomethoxytrityl (Mmt) protected building blocks, whereas the second approach involves the use of Mmt/acyl protected monomers, which allows the preparation of PNADNA chimera. Additionally, a block coupling strategy is presented for the synthesis of novel phosphonic ester nucleic acids (PHONAs).
Synthesis of amino acids and related compounds. 6. New convenient synthesis of .alpha.-C-acylamino acids and .alpha.-amino ketones (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of amino acids and related compounds. 6. New convenient synthesis of .alpha.-C-acylamino acids and .alpha.-amino ketonesMamoru Suzuki, Tameo Iwasaki, Muneji Miyoshi, Kentaro Okumura, and Kazuo MatsumotoCite this: J. Org. Chem. 1973, 38, 20, 3571–3575Publication Date (Print):October 1, 1973Publication History Published online1 May 2002Published inissue 1 October 1973https://pubs.acs.org/doi/10.1021/jo00960a028https://doi.org/10.1021/jo00960a028research-articleACS PublicationsRequest reuse permissionsArticle Views1213Altmetric-Citations62LEARN 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
Pseudouridine Mapping in the Saccharomyces cerevisiae Spliceosomal U Small Nuclear RNAs (snRNAs) Reveals that Pseudouridine Synthase Pus1p Exhibits a Dual Substrate Specificity for U2 snRNA and tRNA (1999)

Pseudouridine (Psi) residues were localized in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Psi residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1, PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Psi content, only the loss of the Pus1p activity was found to affect Psi formation in spliceosomal UsnRNAs. Indeed, Psi44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Psi44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Psi content, formation of Psi residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism.
Nutritional management of replacement beef heifers: a review (1993)

Systems to produce replacement heifers to calve initially at 2 yr of age and at 12-mo intervals thereafter require integrated forage-animal management plans. The process of developing heifers as replacements must begin during the cow-calf production phase. Age and weight at puberty are affected by several factors, including breed of livestock. Generally, breeds of a larger size at maturity are older and heavier when reaching puberty. Heifers that are kept as replacements must be weaned at relatively heavy weights in comparison to their expected mature body size without becoming obese. Excessive adipose tissue in heifers during the preweaning phase may result in reduced subsequent performance of these animals. Several management techniques were reviewed that can be used both pre- and postweaning, including using anthelmintics, anabolic growth implants, and ionophores. Anabolic growth implants can increase heifer rates of gain and increase pelvic size. In addition, there are indications that these implants may alter mammary gland development, which may subsequently increase milk production. Ionophores were shown to increase growth rates, particularly in grazing heifers but more importantly to decrease age at puberty. Age and weight at puberty have been shown to be affected by level of nutrition. It is preferable for heifers to reach puberty one or two estrous cycles before the breeding season, and the breeding season for heifers should begin > or = 21 d before the breeding season of the mature cow herd. This time difference allows for the generally longer postpartum interval for primiparous cows than for multiparous cows. Because of the limited opportunities (every 12 mo) for cows to calve, optimum efficiency must be pursued.
Cell Surface Glycoconjugates and Carbohydrate-Binding Proteins: Possible Recognition Signals in Sensory Neurone Development (1986)

Dorsal root ganglion (DRG) neurones transmit cutaneous sensory information from the periphery to the dorsal horn of the spinal cord. Subpopulations of DRG neurones that subserve distinct sensory modalities project to discrete regions in the dorsal horn. The formation of specific sensory connections during development may involve cell-surface interactions with spinal cord cells. Molecules that are expressed on the surface of functional subpopulations of DRG and dorsal horn neurones have therefore been identified. Distinct subsets of DRG neurones express globo- or lactoseries carbohydrate differentiation antigens. The expression of defined carbohydrate structures correlates with the embryonic lineage, peptide phenotype and the central termination site of DRG neurones. Similar or identical glycoconjugates have been implicated in cellular interactions that contribute to preimplantation embryonic development. Small-diameter DRG neurones that project to the superficial dorsal horn express N-acetyllactosamine backbone structures that are potential ligands for beta-galactoside-specific binding proteins (lectins). Two lectins have been identified that are expressed early in development in the superficial dorsal horn. These complementary molecules may contribute to the development of sensory afferent projections in the spinal cord.
Involvement of Bone Morphogenetic Protein-4 (BMP-4) and Vgr-1 in morphogenesis and neurogenesis in the mouse (1991)

Bone Morphogenetic Protein-4 (BMP-4) and Vgr-1 are members of the TGF-beta gene family most closely related to the Drosophila Decapentaplegic and Xenopus Vg-1 genes. Members of this gene family have been implicated in diverse processes during embryogenesis including epithelial-mesenchymal interactions. Here, we use in situ hybridization to localize BMP-4 and Vgr-1 transcripts during murine development. BMP-4 mRNA is found in a variety of tissues. In the 8.5 days p.c. embryo, transcripts are localized to the mesoderm posterior to the last somite. Later gestation embryos show expression in developing limbs, the embryonic heart, the facial processes and condensed mesenchymal cells associated with early whisker follicle formation. In the developing central nervous system (CNS), BMP-4 expression is restricted to the floor of the diencephalon associated with pituitary development. In contrast, Vgr-1 transcripts are found along the anteroposterior axis of the CNS, in cells immediately adjacent to the floor plate and in the roof plate extending to the forebrain. Together, the data support the hypothesis that polypeptide growth factors of the TGF-beta superfamily play key roles in the initial stages of neurogenesis and organogenesis during murine development.
Oncogenic activity of cyclin D1 revealed through cooperation with Ha-ras: link between cell cycle control and malignant transformation. (1994)

Circumstantial evidence implicates the putative cell cycle regulator cyclin D1 in the process of malignant transformation. Overexpression of cyclin D1 is observed in mammary carcinomas as a result of gene amplification and in parathyroid adenomas and centrocytic B-cell lymphomas as a consequence of chromosomal rearrangements and juxtaposition of the cyclin D1 gene to strong transcriptional control elements. These findings suggest that deregulation of cyclin D1 expression may contribute to malignant transformation in these tumours. To date, however, an oncogenic potential of cyclin D1 has not been demonstrated and the mechanism of its oncogenic activation remains obscure although overexpression of the wild-type protein is likely. We report here that the overexpression of cyclin D1 induces transformation in primary rat embryo fibroblasts in cooperation with activated Ha-ras. Cyclin D1/Ha-ras transformed cells are immortalized, show anchorage independence and give rise to fibrosarcomas in nude mice. Our data directly demonstrate that cyclin D1 is a proto-oncogene that can be activated by transcriptional deregulation. Its previously demonstrated ability to interact with putative cell cycle regulators suggests that cyclin D1 defines a new class of proto-oncogenes.
Down-regulation of VEGF mRNA expression by 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) antisense oligonucleotides and investigation of non-target gene expression (2002)

We studied the properties of 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) oligonucleotides as antisense molecules. Compared to a phosphorothioate (PS) DNA and RNA heteroduplex, a duplex of an ENA/PS/ENA gapmer with RNA was a more effective substrate for RNase H-mediated cleavage. We designed ENA antisense oligonucleotides (AON) targeting human vascular endothelial growth factor (VEGF) mRNA. ENA AON with a cationic polymer considerably down-regulated VEGF mRNA expression, while no down-regulation by PS AON was observed. We also investigated the influence on the gene expression of genes other than VEGF by a gene database homology search and RT-PCR analysis. This method turned out to be an efficient approach to search for non-target genes sequence-specifically down-regulated by AON. In rat plasma, an ENA/PS/ENA gapmer was very stable after 24 hr, while a bridged nucleic acid (BNA) or locked nucleic acid (LNA) oligonucleotide and a PS oligonucleotide were half degraded in 4 hr. The high stability of ENA oligonucleotides in plasma would make ENA oligonucleotides ideal for in vivo studies.
Nanoscale Triboelectric-Effect-Enabled Energy Conversion for Sustainably Powering Portable Electronics (2012)

Harvesting energy from our living environment is an effective approach for sustainable, maintenance-free, and green power source for wireless, portable, or implanted electronics. Mechanical energy scavenging based on triboelectric effect has been proven to be simple, cost-effective, and robust. However, its output is still insufficient for sustainably driving electronic devices/systems. Here, we demonstrated a rationally designed arch-shaped triboelectric nanogenerator (TENG) by utilizing the contact electrification between a polymer thin film and a metal thin foil. The working mechanism of the TENG was studied by finite element simulation. The output voltage, current density, and energy volume density reached 230 V, 15.5 μA/cm(2), and 128 mW/cm(3), respectively, and an energy conversion efficiency as high as 10-39% has been demonstrated. The TENG was systematically studied and demonstrated as a sustainable power source that can not only drive instantaneous operation of light-emitting diodes (LEDs) but also charge a lithium ion battery as a regulated power module for powering a wireless sensor system and a commercial cell phone, which is the first demonstration of the nanogenerator for driving personal mobile electronics, opening the chapter of impacting general people's life by nanogenerators.
A Novel, Highly Sensitive Antibody Allows for the Routine Detection of ALK -Rearranged Lung Adenocarcinomas by Standard Immunohistochemistry (2010)

Low levels of ALK protein expression is a characteristic feature of ALK-rearranged lung adenocarcinomas. However, a novel, highly sensitive IHC assay reliably detects lung adenocarcinomas with ALK rearrangements and obviates the need for fluorescence in situ hybridization analysis for the majority of cases, and therefore could be routinely applicable in clinical practice to detect lung cancers that may be responsive to ALK inhibitors.
Production of Infectious Hepatitis C Virus of Various Genotypes in Cell Cultures (2007)

A unique hepatitis C virus (HCV) strain JFH-1 has been shown to replicate efficiently in cell culture with production of infectious HCV. We previously developed a DNA expression system containing HCV cDNA flanked by two self-cleaving ribozymes to generate HCV particles in cell culture. In this study, we produced HCV particles of various genotypes, including 1a (H77), 1b (CG1b), and 2a (J6 and JFH-1), in the HCV-ribozyme system. The constructs also contain the secreted alkaline phosphatase gene to control for transfection efficiency and the effects of culture conditions. After transfection into the Huh7-derived cell line Huh7.5.1, continuous HCV replication and secretion were confirmed by the detection of HCV RNA and core antigen in the culture medium. HCV replication levels of strains H77, CG1b, and J6 were comparable, whereas the JFH-1 strain replicates at a substantially higher level than the other strains. To evaluate the infectivity in vitro, the culture medium of JFH-1-transfected cells was inoculated into naive Huh7.5.1 cells. HCV proteins were detected by immunofluorescence 3 days after inoculation. To evaluate the infectivity in vivo, the culture medium from HCV genotype 1b-transfected cells was inoculated into a chimpanzee and caused a typical course of HCV infection. The HCV 1b propagated in vitro and in vivo had sequences identical to those of the HCV genomic cDNA used for cell culture transfection. The development of culture systems for production of various HCV genotypes provides a valuable tool not only to study the replication and pathogenesis of HCV but also to screen for antivirals.
General atomic and molecular electronic structure system (1993)

Abstract A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley &amp; Sons, Inc.
Auto‐segmentation of normal and target structures in head and neck CT images: A feature‐driven model‐based approach (2011)

Our automated segmentation framework is able to segment anatomy in the head and neck region with high accuracy within a clinically-acceptable segmentation time.
Differentially Private Collaborative Learning for the IoT Edge (2019)

Collaborative learning based on training data contributed by many edge devices is a promising paradigm for implementing crowd intelligence. The collaboratively trained model generally provides superior classification performance due to the increased volume and expanded coverage of the training data. However, the data contribution may incur the concern of privacy breach. This paper presents the design of a privacy-preserving collaborative learning approach, in which the edge devices and the cloud train different stages of a deep neural network, and the data transmitted from an edge device to the honest-but-curious cloud is perturbed by Laplacian random noises to achieve e-differential privacy. We apply the proposed approach to a case study of collaboratively training a convolutional neural network for handwritten digit recognition. The results show that our approach maintains 99% and 96% classification accuracy in implementing privacy loss levels of e = 5 and e = 2, respectively.