gebhart/patrepeval huggingface dataset:
Identification of Human Embryonic Progenitor Cell Targeting Peptides Using Phage Display (2013)

Human pluripotent stem (hPS) cells are capable of differentiation into derivatives of all three primary embryonic germ layers and can self-renew indefinitely. They therefore offer a potentially scalable source of replacement cells to treat a variety of degenerative diseases. The ability to reprogram adult cells to induced pluripotent stem (iPS) cells has now enabled the possibility of patient-specific hPS cells as a source of cells for disease modeling, drug discovery, and potentially, cell replacement therapies. While reprogramming technology has dramatically increased the availability of normal and diseased hPS cell lines for basic research, a major bottleneck is the critical unmet need for more efficient methods of deriving well-defined cell populations from hPS cells. Phage display is a powerful method for selecting affinity ligands that could be used for identifying and potentially purifying a variety of cell types derived from hPS cells. However, identification of specific progenitor cell-binding peptides using phage display may be hindered by the large cellular heterogeneity present in differentiating hPS cell populations. We therefore tested the hypothesis that peptides selected for their ability to bind a clonal cell line derived from hPS cells would bind early progenitor cell types emerging from differentiating hPS cells. The human embryonic stem (hES) cell-derived embryonic progenitor cell line, W10, was used and cell-targeting peptides were identified. Competition studies demonstrated specificity of peptide binding to the target cell surface. Efficient peptide targeted cell labeling was accomplished using multivalent peptide-quantum dot complexes as detected by fluorescence microscopy and flow cytometry. The cell-binding peptides were selective for differentiated hPS cells, had little or no binding on pluripotent cells, but preferential binding to certain embryonic progenitor cell lines and early endodermal hPS cell derivatives. Taken together these data suggest that selection of phage display libraries against a clonal progenitor stem cell population can be used to identify progenitor stem cell targeting peptides. The peptides may be useful for monitoring hPS cell differentiation and for the development of cell enrichment procedures to improve the efficiency of directed differentiation toward clinically relevant human cell types.
A functional genomic analysis of cell morphology using RNA interference (2003)

Using RNAi, we identified genes that influence cytoskeletal organization and morphology in two distinct cell types. Some genes exhibited similar RNAi phenotypes in both cell types, while others appeared to have cell-type-specific functions, in part reflecting the different mechanisms used to generate a round or a flat cell morphology.
A human Ro/SS-A autoantigen is the homologue of calreticulin and is highly homologous with onchocercal RAL-1 antigen and an aplysia "memory molecule". (1990)

The Ro/SS-A (Ro) autoantigens consist of at least four immunologically distinct proteins which are recognized by autoantibodies typically found in sera from patients with primary Sjogren's syndrome and in subsets of patients with lupus erythematosus. We recently isolated a 1.9-kb human cDNA clone which encodes one of these Ro autoantigens. Synthetic oligonucleotides corresponding to the human Ro sequence were used to amplify the homologous gene from a murine B cell cDNA library using the polymerase chain reaction. The mouse cDNA-encoded amino acid sequence was found to be 94% homologous to the human Ro sequence and is 100% homologous to murine calreticulin, a high affinity calcium-binding protein which resides in the endoplasmic and sarcoplasmic reticulum. The amino acid sequence of rabbit calreticulin is 92% homologous to both murine calreticulin and human Ro. Onchocerca volvulus and Drosophila melanogaster also have molecules that are highly homologous to human Ro. In addition, human Ro has a molecular mass, isoelectric point, and significant amino acid sequence similar to the Aplysia californica snail neuronal protein 407. These homologies suggest that this Ro protein has a very basic cellular function(s) which may in part involve calcium binding.
Generation of complement C3 and expression of cell membrane complement inhibitory proteins by human bronchial epithelium cell line (2000)

Local generation of complement C3 and expression of cell membrane CIP by human bronchial epithelium and its modulation by proinflammatory cytokines might be an additional regulatory mechanism of local airway defence and may affect airway function and epithelial integrity in health and disease.
Modulation of endothelial cell hemostatic properties by tumor necrosis factor. (1986)

Tumor necrosis factor/cachectin (TNF) is a mediator of the septic state, which involves diffuse abnormalities of coagulation throughout the vasculature. Since previous studies have shown that endothelial cells can play an active role in coagulation, we wished to determine whether TNF could modulate endothelial cell hemostatic properties. Incubation of purified recombinant TNF with cultured endothelial cells resulted in a time- and dose-dependent acquisition of tissue factor procoagulant activity. Concomitant with enhanced procoagulant activity, TNF also suppressed endothelial cell cofactor activity for the anticoagulant protein C pathway; both thrombin-mediated protein C activation and formation of functional activated protein C-protein S complex on the cell surface were considerably attenuated. Comparable concentrations of TNF (half-maximal affect at approximately 50 pM) and incubation times (half-maximal affect by 4 h after addition to cultures) were required for each of these changes in endothelial cell coagulant properties. This unidirectional shift in cell surface hemostatic properties favoring promotion of clot formation indicates that, in addition to leukocyte procoagulants, endothelium can potentially be instrumental in the pathogenesis of the thrombotic state associated with inflammatory and malignant disorders.
Fault-tolerant quantum error detection (2017)

Quantum computers will eventually reach a size at which quantum error correction becomes imperative. Quantum information can be protected from qubit imperfections and flawed control operations by encoding a single logical qubit in multiple physical qubits. This redundancy allows the extraction of error syndromes and the subsequent detection or correction of errors without destroying the logical state itself through direct measurement. We show the encoding and syndrome measurement of a fault-tolerantly prepared logical qubit via an error detection protocol on four physical qubits, represented by trapped atomic ions. This demonstrates the robustness of a logical qubit to imperfections in the very operations used to encode it. The advantage persists in the face of large added error rates and experimental calibration errors.
Wavefront sensing and the irradiance transport equation (1990)

Phase retrieval has recently been experimentally demonstrated, using the irradiance transport equation. We show that this equation provides a unified description for incoherent wavefront sensing methods, bringing new insights and opening new prospects in this area.
Potentially Macrocyclic Peptidyl Boronic Acids as Chymotrypsin Inhibitors (1997)

The possibility of forming a peptide boronate adduct in a serine protease active site that mimics the first tetrahedral intermediate in the peptide hydrolysis mechanism was explored with the complex boronic acid analogs 7, 8-OH, and 8-NH(2)(). In these structures, the P(1) and P(2) residues and the P(1)'-P(3)' residues are connected through the P(2) and P(1)' side chains, to encourage formation of the diester or amide-ester adducts via macrocyclization. These inhibitors were assembled from suitably protected derivatives of 2,4-diaminobutanoic acid or 2,4-diaminopentanoic acid (11), borophenylalanine (12), aspartic acid, malic acid or the substituted malic acid analog 13, and Leu-Arg dipeptide. Stereoselective syntheses were developed for the (S,S)-2,4-diaminopentanoate 11 and for the (S,S)-beta-isobutylmalate 13 derivatives. The complex peptidyl boronates 7 (K(i) = 26 nM) and 8-OH (68 nM) are potent inhibitors of alpha-chymotrypsin; however, the affinity of 7 is neither time- nor pH-dependent, and it is only moderately greater than that found for comparison compounds like 8-H (114 nM), 9 (356 nM), and 10 (219 nM) that cannot cyclize or form a diester adduct.
Towards a Synthetic Chloroplast (2011)

Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.
[Colon cancer: what is new in 2004?]. (2004)

Two thousand and three was a particularly dense year for publications and communications on therapy for colon cancer summarizing the real advance performed in this field. The last ten years allowed a rapid evolution for colon chemotherapy with a switch from 5-FU modulated by leucovorin to poly-chemotherapy (fluoropyrimidines with oxaliplatin or irinotecan) integrated into therapeutic strategies, where surgery had a place more and more important in metastatic patients. In correlation with these advances, median survival of patient with metastatic colorectal cancer is between 17 and 22 months. Targeted therapeutics with monoclonal antibody such as EGF inhibitors (cetuximab) or VEGF inhibitors (bevacizumab) had for the first time demonstrated efficacy with encouraging results in randomised trials. In adjuvant situation, LV5FU2 is less toxic than monthly FUFOL and no statistically significant difference could be detected in disease-free or overall survival between the two schedules. Oxaliplatin combined with 5 fluorouracil and leucovorin (FOLFOX4) is the first combination to demonstrate significant superiority over 5 fluorouracil and leucovorin in adjuvant treatment of colorectal cancer. Fluorouracil-based adjuvant chemotherapy benefited to patients with stage II or III colon cancer with microsatellite-stable tumours or tumour exhibiting low-frequency microsatellite instability but may be not those with tumours exhibiting high-frequency microsatellite instability (MSI). These data need to be confirmed by prospective studies before changing our therapeutic references. The number of lymph nodes analyzed for colon cancer staging is itself a prognostic variable on outcome. Laparoscopic surgery of colon cancer is demonstrated as a feasible and safe procedure. Shrinkage of tumours after administration of preoperative chemotherapy and availability of ablative techniques (radiofrequency and cryotherapy) now allow to treat with curative intent metastases initially considered as non-resectable.
Dry Low NOx Combustion Systems for GE Heavy-Duty Gas Turbines (1996)

General Electric began development of Dry Low NOx (DLN) systems in the mid-1970s and operated its first DLN system in 1981 (Reference 1). Subsequent to that, further development was done (Reference 2) prior to commercial introduction.
Inhibition of Growth of HIV by Human Natural Interferon In Vitro (1988)

The effect of human natural interferons (IFN) alpha, beta, and gamma on the replication of human immunodeficiency virus (HIV) strain LAV in T cell lines TALL-1 and CCRF-CEM and peripheral blood lymphocytes (PBL) was studied. The growth of TALL-1 was moderately sensitive to these IFN, whereas that of CCRF-CEM was resistant to them. The progeny virus yield of LAV in TALL-1 at the time of its peak was reduced to 10% of the control level at IFN-alpha, beta, and gamma concentrations of 3, 11, and 23 IU/ml, respectively. These concentrations of IFN-alpha, beta, and gamma did not affect the cell growth. In CCRF-CEM, IFN-alpha, beta, and gamma at the concentration of 50, 60, and 76 IU/ml reduced the progeny virus to 10% of the control level. The virus growth in PBL was more sensitive to IFN than that in CCRF-CEM. The progeny virus yield was reduced to 10% of the control level by IFN-alpha and beta concentrations of 5 IU/ml and less than 5 IU/ml, respectively.
Extracting Story Units in Sports Video Based on Unsupervised Video Scene Clustering (2006)

Many sports videos such as archery, diving and tennis have repetitive structure patterns. They are reliable clues to generate highlights, summarization and automatic annotation. In this paper, we present a novel approach to analyze these structure patterns in sports video to extract story units. First, an unsupervised scene clustering method for sports video is adopted to automatically categorize the video shots into several disparate scenes. Then, the clustering results are modeled by a transition matrix. Finally, the key scene shots are detected to analyze the structure patterns and extract the story units. Experimental results on several types of broadcast sports video demonstrate that our approach is effective
Encyclopedia of cancer (1996)

Since the publication of the first edition of the of Cancer, an amazing amount of new information has been disseminated in the field of cancer research. This second edition strives to capture the advances occurring in the etiology, prevention, and treatment of cancer, from basic science to clinical application. By providing concise expositions on a broad range of topics, the Encyclopedia is an excellent resource for those seeking information beyond their specific areas of expertise. Written by a distinguished panel of authors, entries cover a variety of aspects of cancer such as oncology, immunology, epidemiology, gene therapy, oncogenes/tumor suppressor genes, and pharmacology. This outstanding reference is essential for anyone involved in the study or treatment of cancer. It covers various aspects of cancer, segueing from basic science to clinical topics. It includes an additional volume to incorporate all the new advances in the etiology, prevention, and treatment of cancer made since the first edition. It includes a convenient organization which employs standard entry format for quick and easy reference. Extensive cross-referencing provides reader with broader range of knowledge. The contributions are solicited from among the top names in a variety of fields.
Deep Ordinal Regression Network for Monocular Depth Estimation (2018)

Monocular depth estimation, which plays a crucial role in understanding 3D scene geometry, is an ill-posed problem. Recent methods have gained significant improvement by exploring image-level information and hierarchical features from deep convolutional neural networks (DCNNs). These methods model depth estimation as a regression problem and train the regression networks by minimizing mean squared error, which suffers from slow convergence and unsatisfactory local solutions. Besides, existing depth estimation networks employ repeated spatial pooling operations, resulting in undesirable low-resolution feature maps. To obtain high-resolution depth maps, skip-connections or multilayer deconvolution networks are required, which complicates network training and consumes much more computations. To eliminate or at least largely reduce these problems, we introduce a spacing-increasing discretization (SID) strategy to discretize depth and recast depth network learning as an ordinal regression problem. By training the network using an ordinary regression loss, our method achieves much higher accuracy and faster convergence in synch. Furthermore, we adopt a multi-scale network structure which avoids unnecessary spatial pooling and captures multi-scale information in parallel. The proposed deep ordinal regression network (DORN) achieves state-of-the-art results on three challenging benchmarks, i.e., KITTI [16], Make3D [49], and NYU Depth v2 [41], and outperforms existing methods by a large margin.
Dual-Energy CT–Based Monochromatic Imaging (2012)

Virtual monochromatic images synthesized from dual-energy CT data have the potential to reduce beam-hardening artifacts and to provide quantitative measurements. If there is no desire to obtain material-specific information or to correct for metal or beam-hardening artifacts from the dual-energy data, however, it is better to perform a conventional single-energy scan at the optimal tube potential.
New Nanostructured Li2S/Silicon Rechargeable Battery with High Specific Energy (2010)

Rechargeable lithium ion batteries are important energy storage devices; however, the specific energy of existing lithium ion batteries is still insufficient for many applications due to the limited specific charge capacity of the electrode materials. The recent development of sulfur/mesoporous carbon nanocomposite cathodes represents a particularly exciting advance, but in full battery cells, sulfur-based cathodes have to be paired with metallic lithium anodes as the lithium source, which can result in serious safety issues. Here we report a novel lithium metal-free battery consisting of a Li(2)S/mesoporous carbon composite cathode and a silicon nanowire anode. This new battery yields a theoretical specific energy of 1550 Wh kg(-1), which is four times that of the theoretical specific energy of existing lithium-ion batteries based on LiCoO(2) cathodes and graphite anodes (approximately 410 Wh kg(-1)). The nanostructured design of both electrodes assists in overcoming the issues associated with using sulfur compounds and silicon in lithium-ion batteries, including poor electrical conductivity, significant structural changes, and volume expansion. We have experimentally realized an initial discharge specific energy of 630 Wh kg(-1) based on the mass of the active electrode materials.
Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma. (2006)

Parallel analysis of gene copy numbers and expression levels by cDNA microarray in MM allowed efficient identification of genes whose expression levels are elevated because of increased copy number. This is the first time that MALT1 and BCL2 have been shown to be overexpressed and amplified in MM.
Specificity of the Binding of Synapsin I to Src Homology 3 Domains (2000)

Synapsins are synaptic vesicle-associated phosphoproteins involved in synapse formation and regulation of neurotransmitter release. Recently, synapsin I has been found to bind the Src homology 3 (SH3) domains of Grb2 and c-Src. In this work we have analyzed the interactions between synapsins and an array of SH3 domains belonging to proteins involved in signal transduction, cytoskeleton assembly, or endocytosis. The binding of synapsin I was specific for a subset of SH3 domains. The highest binding was observed with SH3 domains of c-Src, phospholipase C-gamma, p85 subunit of phosphatidylinositol 3-kinase, full-length and NH(2)-terminal Grb2, whereas binding was moderate with the SH3 domains of amphiphysins I/II, Crk, alpha-spectrin, and NADPH oxidase factor p47(phox) and negligible with the SH3 domains of p21(ras) GTPase-activating protein and COOH-terminal Grb2. Distinct sites in the proline-rich COOH-terminal region of synapsin I were found to be involved in binding to the various SH3 domains. Synapsin II also interacted with SH3 domains with a partly distinct binding pattern. Phosphorylation of synapsin I in the COOH-terminal region by Ca(2+)/calmodulin-dependent protein kinase II or mitogen-activated protein kinase modulated the binding to the SH3 domains of amphiphysins I/II, Crk, and alpha-spectrin without affecting the high affinity interactions. The SH3-mediated interaction of synapsin I with amphiphysins affected the ability of synapsin I to interact with actin and synaptic vesicles, and pools of synapsin I and amphiphysin I were shown to associate in isolated nerve terminals. The ability to bind multiple SH3 domains further implicates the synapsins in signal transduction and protein-protein interactions at the nerve terminal level.
Sorting and expansion of murine embryonic stem cell colonies using micropallet arrays (2008)

Isolation of cell colonies is an essential task in most stem cell studies. Conventional techniques for colony selection and isolation require significant time, labor, and consumption of expensive reagents. New microengineered technologies hold the promise for improving colony manipulation by reducing the required manpower and reagent consumption. Murine embryonic stem cells were cultured on arrays composed of releasable elements termed micropallets created from a biocompatible photoresist. Micropallets containing undifferentiated colonies were released using a laser-based technique followed by cell collection and expansion in culture. The micropallet arrays provided a biocompatible substrate for maintaining undifferentiated murine stem cells in culture. A surface coating of 0.025% gelatin was shown to be optimal for cell culture and collection. Arrays composed of surface-roughened micropallets provided further improvements in culture and isolation. Colonies of viable stem cells were efficiently isolated and collected. Colonies sorted in this manner were shown to remain undifferentiated even after collection and further expansion in culture. Qualitative and quantitative analyses of sorting, collection efficiency, and cell viability after release and expansion of stem cell colonies demonstrated that the micropallet array technology is a promising alternative to conventional sorting methods for stem cell applications.
A cost-based heterogeneous recovery scheme for distributed storage systems with RAID-6 codes (2012)

Modern distributed storage systems provide large-scale, fault-tolerant data storage. To reduce the probability of data unavailability, it is important to recover the lost data of any failed storage node efficiently. In practice, storage nodes are of heterogeneous types and have different transmission bandwidths. Thus, traditional recovery solutions that simply minimize the number of data blocks being read may no longer be optimal in a heterogeneous environment. We propose a cost-based heterogeneous recovery (CHR) algorithm for RAID-6-coded storage systems. We formulate the recovery problem as an optimization model in which storage nodes are associated with generic costs. We narrow down the solution space of the model to make it practically tractable, while still achieving the global optimal solution in most cases. We implement different recovery algorithms and conduct testbed experiments on a real networked storage system with heterogeneous storage devices. We show that our CHR algorithm reduces the total recovery time of existing recovery solutions in various scenarios.