gebhart/patrepeval huggingface dataset:
In Multiple Myeloma Clonotypic CD38 − /CD19 + /CD27 + Memory B Cells Recirculate Through Bone Marrow, Peripheral Blood and Lymph Nodes (2004)

It is believed that myeloma cells are derived from a germinal center (GC) or post GC B cell. The GC B cell can differentiate into both a memory B cell and a plasma cell (PC). In this study, we investigated the recirculating potential of memory B cells clonally related to the myeloma PC (termed clonotypic). The V(H)DJ(H) immunoglobulin gene rearrangement of the myeloma clone was identified for 10 myeloma patients and allele-specific oligonucleotides (ASO) IgH RT-PCR assays were designed for each patient. Memory B cells (CD38- /CD19+ /CD27+) and their subsets defined by the monoclonal antibodies CD62L, CCR6, CXCR4, CXCR5, CCR7 were flow-sorted as single cells and analyzed by ASO RT-PCR analysis. In addition, aspirated peripheral lymph nodes (PLN) of 7 myeloma patients in complete or partial remission were analyzed for the presence of clonotypic cells. Circulating clonotypic memory B cells were identified in PBMNC of 7/10 patients and both CD62L positive and negative clonotypic memory B cells were identified. Furthermore, comparable frequencies of clonotypic cells were found in the CCR6 +/- and CXCR4 +/- memory B cell subsets, whereas all clonotypic memory and later stage B cells were CXCR5 positive. In accordance with their immunophenotype, clonotypic memory B-cells were identified in peripheral blood, bone marrow and PLNs. Clonotypic memory B-cells were present in the majority of myeloma patients and seem to have the same diverse recirculating/homing capacity as normal memory B cells.
Busulfan-based regimens and allogeneic bone marrow transplantation in patients with myelodysplastic syndromes (1993)

Preparative regimens containing busulfan (BU) followed by allogeneic bone marrow transplantation (BMT) were used in 27 consecutive patients with myelodysplastic syndromes (MDS). The median age was 33 years (range, 4 to 54). Ten were female and 17 male. Sixteen patients had primary MDS, 11 other patients had antecedent hematologic diseases or developed MDS after cytotoxic and/or radiation therapy. Six patients had leukemic transformation and received antileukemic therapy before BMT. Pre-BMT cytogenetic studies showed complex chromosomal abnormalities in 13 patients, a simple abnormality in 5 patients, and normal chromosome in 8 patients. Three BU-based preparative regimens were used: 1 patient received BU 4 mg/kg orally (PO) daily for 4 days and cyclophosphamide (CY) 50 mg/kg intravenously (IV) daily for 4 days (BUCY-4); 24 patients received BU 4 mg/kg PO daily for 4 days, cytosine arabinoside (ara-C) 2 g/m2 IV every 12 hours for 4 doses, and CY 60 mg/kg IV daily for 2 days (BAC); and 2 patients with preceding Fanconi anemia received BU 2 mg/kg PO daily for 4 days followed by total lymphoid irradiation of 5 Gy. Seventeen of 27 patients are alive with no evidence of disease. Ten patients have died: 2 from hepatic veno-occlusive disease, 3 from sepsis, 1 from a cerebral bleed, 1 from a massive gastrointestinal (GI) bleed associated with acute graft-versus-host disease, 1 from hemolytic uremic syndrome with adult respiratory distress syndrome, 1 from bronchiolitis obliterans, and the only patient who did not engraft died from acute myeloid leukemia. Regimen-related toxicities (RRT) include GI tract (diarrhea, 14; stomatitis, 11), liver (9), cardiac (1), and skin (5). Patients who received a genotypically matched marrow graft had a significantly better disease-free survival (DFS) than patients who received a nongenotypic marrow graft (P = .02). The Kaplan-Meier analysis projects an overall DFS of 56% +/- 13% and 78% +/- 10% for patients who received a genotypically matched marrow graft. With the exception of a child who did not engraft, there was no relapse of MDS or leukemia. Excellent DFS, acceptable RRT, and the ease of administration are advantages of this regimen.
DETERMINANTS OF PORT SELECTION (2007)

This paper explores the main factors adopted when shippers and shipping companies select their import/export and transshipment ports. In the present study, 38 port selection indices were chosen from the previous research and field interviews. The scores of the 38 items were collected by questionnaire survey to the three major maritime/port market players: shipper, liners and container terminal operators. In order to analyze the different priorities imposed on the port selection factors by the three market players, an one-way ANOVA technique has been employed. As a consequence, this research shows the different recognitions about port service attributes among service suppliers and demanders. In addition, the 38 items have been categorized into seven key factors through an exploratory factor analysis. An one-way ANOVA was employed again to analyze the perspective differences for the port selection factors among the market players. The results show that there exit significant differences among the players assessing the importance of the following port choice factors: hinterland and terminal basic condition; shipping liners’ operations and terminal operations.
The cloning of a self-replicating RNA molecule. (1968)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Joint Depth Map and Color Consistency Estimation for Stereo Images with Different Illuminations and Cameras (2012)

Abstract—In this paper, we propose a method that infers both accurate depth maps and color-consistent stereo images for radiometrically varying stereo images. In general, stereo matching and performing color consistency between stereo images are a chicken-and-egg problem since it is not a trivial task to simultaneously achieve both goals. Hence, we have developed an iterative framework in which these two processes can boost each other. First, we transform the input color images to log-chromaticity color space, from which a linear relationship can be established during constructing a joint pdf of transformed left and right color images. From this joint pdf, we can estimate a linear function that relates the corresponding pixels in stereo images. Based on this linear property, we present a new stereo matching cost by combining Mutual Information (MI), SIFT descriptor, and segment-based plane-fitting to robustly find correspondence for stereo image pairs which undergo radiometric variations. Meanwhile, we devise a Stereo Color Histogram Equalization (SCHE) method to produce color-consistent stereo image pairs, which conversely boost the disparity map estimation. Experimental results show that our method produces both accurate depth maps and color-consistent stereo images, even for stereo images with severe radiometric differences.
[Neurological consequences following perinatal asphyxia in preschool age children]. (2009)

Various groups have been addressing the question of whether perinatal asphyxia (PA) affects on newborn health and nervous system. It is widely accepted that severe PA causes motor and cognitive alterations and leads to a variety of brain disorders: cerebral palsy, epilepsy, mental retardation as well as psychiatric deficits. At the same time it was established, that large percentage of children, surviving PA didn't demonstrate apparent sequelae, but mild physical and mental delay in future. With the purpose of disclose further consequences of PA on child development, we examine 20 children (6 years old) surviving mild or moderate PA without severe neurological pathology. In most cases we revealed muscle tone disturbances, physical development and growth retardation, speech pathology in the form of dyslaliya and speech delay. Intact cognitive capacities in these children combine with limited information content. Our investigation discovered, that the presence of certain psychoneurological characteristics such as hyperexcitability, irritability, timidity, aggressiveness; reduced activity, concentration and motivation -- are the consequences of survived birth trauma. These characteristics producing undue fatiguability, inattention, restlessness and diminished working-capacity, can pose additional problems in education process. In the absence of individual approach without taking into account emotional and motivational peculiarities, this category of children could not completely realize their intact cognitive capacities and represent risk group for further mild retardation.
Efficient Query Processing for Large XML Data in Distributed Environments (2007)

We propose an efficient distributed query processing method for large XML data by partitioning and distributing XML data to multiple computation nodes. There are several steps involved in this method; however, we focused particularly on XML data partitioning and dynamic relocation of partitioned XML data in our research. Since the efficiency of query processing depends on both XML data size and its structure, these factors should be considered when XML data is partitioned. Each partitioned XML data is distributed to computation nodes so that the CPU load can be balanced. In addition, it is important to take account of the query workload among each of the computation nodes because it is closely related to the query processing cost in distributed environments. In case of load skew among computation nodes, partitioned XML data should be relocated to balance the CPU load. Thus, we implemented an algorithm for relocating partitioned XML data based on the CPU load of query processing. From our experiments, we found that there is a performance advantage in our approach for executing distributed query processing of large XML data.
Charge Injection and Photooxidation of Single Conjugated Polymer Molecules (2004)

The complex, coupled mechanisms of charge transfer and oxidative damage in organic electronic devices (such as organic light-emitting diodes (OLED), solar cells, etc.) have been elucidated by a new technique that combines single-molecule spectroscopy with charge injection from a metal electrode. The experiments employed a sandwich device architecture (Au/TPD/MEH-PPV:PMMA/SiO2/ITO), essentially a modified OLED with a charge-blocking layer (SiO2) to suppress charge injection at the ITO electrode. The fluorescence (photoluminescence) of isolated MEH-PPV conjugated polymer molecules imbedded in the device was observed to exhibit diverse time- and electrical bias-dependent effects. These include: (i) fluorescence quenching due to interactions between MEH-PPV and holes in the TPD hole-transport layer; (ii) fluorescence quenching, or "photobleaching", due to chemical defects at MEH-PPV generated by photooxidation; and (iii) a novel process, reductive "repair" of the oxidative chemical defects by externally injected carriers. These results demonstrate a very different mechanism for photobleaching of organic conjugated materials than is generally assumed to operate and, furthermore, suggest an intimate relationship among photobleaching, charge transport, and persistent photoconductivity in organic materials.
Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces (2006)

Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82(T) (DSM 14610(T)), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0.5x1.5-5.0 mum and were motile. Two strains belonging to one cluster (A2-181 and A2-183(T)) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1(T)) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194(T)) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1(T) gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183(T), A2-194(T), M72/1(T) and R. intestinalis L1-82(T) were 47.4, 41.4, 42.0 and 42.6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183(T)=DSM 16839(T)=NCIMB 14029(T)), Roseburia inulinivorans sp. nov. (type strain A2-194(T)=DSM 16841(T)=NCIMB 14030(T)) and Roseburia faecis sp. nov. (type strain M72/1(T)=DSM 16840(T)=NCIMB 14031(T)).
Reasoning about sets using redescription mining (2005)

Redescription mining is a newly introduced data mining problem that seeks to find subsets of data that afford multiple definitions. It can be viewed as a generalization of association rule mining, from finding implications to equivalences; as a form of conceptual clustering, where the goal is to identify clusters that afford dual characterizations; and as a form of constructive induction, to build features based on given descriptors that mutually reinforce each other. In this paper, we present the use of redescription mining as an important tool to reason about a collection of sets, especially their overlaps, similarities, and differences. We outline algorithms to mine all minimal (non-redundant) redescriptions underlying a dataset using notions of minimal generators of closed itemsets. We also show the use of these algorithms in an interactive context, supporting constraint-based exploration and querying. Specifically, we showcase a bioinformatics application that empowers the biologist to define a vocabulary of sets underlying a domain of genes and to reason about these sets, yielding significant biological insight.
Isolation of Neisseria meningitidis mutants deficient in class 1 (porA) and class 3 (porB) outer membrane proteins (1990)

The class 1 major outer membrane protein of Neisseria meningitidis is a serious candidate for a meningococcal vaccine. To facilitate studies on the function of this protein, mutants were isolated that lacked this protein or the structurally related class 3 protein. These mutants were obtained by using the antibody-dependent bactericidal action of the complement system. The class 1 protein-deficient strain grew normally in vitro, whereas growth of the class 3 protein-deficient strain was slightly retarded. The class 3 protein-deficient strain displayed increased resistance to the antibiotics tetracycline and cefsulodin, which is consistent with the proposed role of the protein as a pore-forming protein. The class 1 protein was purified to homogeneity from the class 3 protein-deficient strain. Lipid bilayer experiments revealed that this protein also formed pores. The class 1 protein pores were cation selective.
Egg sizes and differential egg counts in relation to sheep nematodes (1953)

1. The width and length of eggs of Haemonchus contortus, Cooperia curticei, Trichostrongylus axei, T. vitrinus, Bunostomum trigonocephalum, Chabertia ovina, Oesophagostomum venulosum and Ostertagia spp. were measured. 2. Frequency distributions of the linear dimensions of the eggs of each species are given, together with the frequencies calculated on the assumption that the distributions are normal. 3. A method of species differentiation based on egg measurements is described, the method being based upon the statistical chances of eggs of different species falling into particular size classes. 4. The application of the method and the construction of a classifying scale are described.
Synthesis of an Advanced Model of Zetekitoxin AB Focusing on the N‐Acylisoxazolidine Amide Structure Corresponding to C13–C17 (2014)

Abstract Zetekitoxin AB (ZTX) is a neurotoxin bearing a saxitoxin core structure together with a characteristic nine‐membered macrocyclic lactam involving a N ‐acylisoxazolidine moiety and a N ‐hydroxylcarbonylmethyl group. We describe a synthesis of an advanced model for ZTX bearing saxitoxin core structure with N ‐acylisoxazolidine moiety, i.e., C13–C17. In this synthesis, the isoxazolidine amide moiety of a ZTX analogue was constructed by reaction of an isoxazolidine with the carboxylic acid at C13 of STX, which was obtained by oxidation of the axially oriented alcohol at C13 2‐azaadamantane N ‐oxyl (AZADO) in the presence of NaClO and NaClO 2 . The 13 C NMR signal of C13 in the resulting ZTX analogue was discussed by comparison with the reported spectral data for natural product of ZTX.
Mechanisms of bone lesions in multiple myeloma and lymphoma (1997)

Thus, OAF produced locally by the tumor or the marrow microenvironment play an important role in the bone destruction seen in patients with hematologic malignancies.
A Fluorescent Probe Study of Plasminogen Activator Inhibitor-1 (1995)

A mutant recombinant plasminogen activator inhibitor 1 (PAI-1) was created (Ser-338-->Cys) in which cysteine was placed at the P9 position of the reactive center loop. Labeling this mutant with N,N'-dimethyl-N-(acetyl)-N'-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) ethylene diamine (NBD) provided a molecule with a fluorescent probe at that position. The NBD-labeled mutant was almost as reactive as wild type but was considerably more stable. Complex formation with tissue or urokinase type plasminogen activator (tPA or uPA), and cleavage between P3 and P4 with a catalytic concentration of elastase, all resulted in identical 13-nm blue shifts of the peak fluorescence emission wavelength and 6.2-fold fluorescence enhancements. Formation of latent PAI showed the same 13-nm spectral shift with a 6.7-fold fluorescence emission increase, indicating that the NBD probe is in a slightly more hydrophobic milieu. These changes can be attributed to insertion of the reactive center loop into the beta sheet A of the inhibitor in a manner that exposes the NBD probe to a more hydrophobic milieu. The rate of loop insertion due to tPA complexation was followed using stopped flow fluorimetry. This rate showed a hyperbolic dependence on tPA concentration, with a half-saturation concentration of 0.96 microM and a maximum rate constant of 3.4 s-1. These results demonstrate experimentally that complexation with proteases is presumably associated with loop insertion. The identical fluorescence changes obtained with tPa.PAI-1 and uPA.PAI-1 complexes and elastase-cleaved PAI-1 strongly suggest that in the stable protease-PAI-1 complex the reactive center loop is cleaved and inserted into beta sheet A and that this process is central to the inhibition mechanism.
A New FACS Approach Isolates hESC Derived Endoderm Using Transcription Factors (2011)

We show that high quality microarray gene expression profiles can be obtained following FACS sorting of cells using combinations of transcription factors. We use this transcription factor FACS (tfFACS) methodology to perform a genomic analysis of hESC-derived endodermal lineages marked by combinations of SOX17, GATA4, and CXCR4, and find that triple positive cells have a much stronger definitive endoderm signature than other combinations of these markers. Additionally, SOX17(+) GATA4(+) cells can be obtained at a much earlier stage of differentiation, prior to expression of CXCR4(+) cells, providing an important new tool to isolate this earlier definitive endoderm subtype. Overall, tfFACS represents an advancement in FACS technology which broadly crosses multiple disciplines, most notably in regenerative medicine to redefine cellular populations.
Diversity and Relatedness Among the Type I Interferons (2004)

Type I interferons (IFNs) include the IFN-alpha family of subtypes, IFN-beta, IFN-omega, IFN-tau, IFN-kappa, IFN-lambda, and IFN-zeta. IFN genes lack introns and encode secretory signal peptide sequences that are proteolytically cleaved prior to secretion from the cell. In contrast to the approximately 50% amino acid sequence identity among the human IFN-alpha subtypes, human IFN-alphas share approximately 22% identity with human IFN-beta and 37% identity with human IFN-omega. Many of the conserved residues among the type I IFNs are implicated in receptor recognition and structural integrity. This report provides an update on the gene annotations for the mouse and human IFN gene clusters on chromosome 4 and 9, respectively, with accompanying amino acid sequence alignments. Based on sequence identities, a phylogenic tree analysis for the different mammalian Type I IFNs is also presented, showing the high degree of relatedness among these IFNs. Notably, sequence alignment of the different human and mouse IFN promoter regions reveals different signature patterns for transcription factor binding sites, implying different inducers might differentially activate the transcription of the different IFNs.
Tyrosine Kinase Inhibition: An Approach to Drug Development (1995)

Protein tyrosine kinases (PTKs) regulate cell proliferation, cell differentiation, and signaling processes in the cells of the immune system. Uncontrolled signaling from receptor tyrosine kinases and intracellular tyrosine kinases can lead to inflammatory responses and to diseases such as cancer, atherosclerosis, and psoriasis. Thus, inhibitors that block the activity of tyrosine kinases and the signaling pathways they activate may provide a useful basis for drug development. This article summarizes recent progress in the development of PTK inhibitors and demonstrates their potential use in the treatment of disease.
Electrical Submersible Pumps in Subsea Completions (1991)

ABSTRACT Electrical Submersible Pumps (ESP's) are being utilised on production platforms as a method of artificial lift for enhanced recovery of oil. With more subsea fields being developed, it is apparent that there will be a demand for this technology in subsea completions. This paper presents the technical issues involved with the installation of ESP's in a subsea completion and describes a system for low cost installation and recovery of the ESP without the requirement to recover the tree. The system utilises existing workover equipment and techniques to provide a safe environment for atubing orcable suspended pump application.