gebhart/patrepeval huggingface dataset:
Non‐parametric multivariate analyses of changes in community structure (1993)

Abstract In the early 1980s, a strategy for graphical representation of multivariate (multi‐species) abundance data was introduced into marine ecology by, among others, Field, et al. (1982). A decade on, it is instructive to: (i) identify which elements of this often‐quoted strategy have proved most useful in practical assessment of community change resulting from pollution impact; and (ii) ask to what extent evolution of techniques in the intervening years has added self‐consistency and comprehensiveness to the approach. The pivotal concept has proved to be that of a biologically‐relevant definition of similarity of two samples, and its utilization mainly in simple rank form, for example ‘sample A is more similar to sample B than it is to sample C’. Statistical assumptions about the data are thus minimized and the resulting non‐parametric techniques will be of very general applicability. From such a starting point, a unified framework needs to encompass: (i) the display of community patterns through clustering and ordination of samples; (ii) identification of species principally responsible for determining sample groupings; (iii) statistical tests for differences in space and time (multivariate analogues of analysis of variance, based on rank similarities); and (iv) the linking of community differences to patterns in the physical and chemical environment (the latter also dictated by rank similarities between samples). Techniques are described that bring such a framework into place, and areas in which problems remain are identified. Accumulated practical experience with these methods is discussed, in particular applications to marine benthos, and it is concluded that they have much to offer practitioners of environmental impact studies on communities.
Brain Tumor Signs and Symptoms: Analysis of Primary Health Care Records From the UKCCS (2009)

On average, cases consulted more often than controls between birth and diagnosis/pseudodiagnosis with brain tumor signs and symptoms. Their consultation rate with >or=1 suggestive symptom escalated in the 2 years before diagnosis. Symptom prevalence was higher among cases than controls, a relative difference of 3.29 times as many consultations with >or=1 suggestive symptom (95% confidence interval [CI]: 2.82-3.83) and 7.01 as many with more than 1 (95% CI: 5.38-9.13). In each 6-month period in the 4 years before diagnosis, cases had at least twice as many consultations with >or=1 suggestive symptom (20.81 times as many in the 6 months before diagnosis [95% CI: 14.29-30.30]) and 2-3 times more records of suggestive symptoms (28.35 times more in the 6 months before diagnosis [95% CI: 19.05-42.19]). Symptoms rarely or not observed among control children included head tilt, odd head movements, odd posture, back or neck stiffness, and unsteadiness without obvious cause. CONCLUSION Key to identifying the 1 child among many who merits prompt investigation is recognition of unusual symptoms, or specific symptom patterns.
Characterization of a continuous T-cell line susceptible to the cytopathic effects of the acquired immunodeficiency syndrome (AIDS)-associated retrovirus. (1985)

We have developed a continuous human T-cell line (A3.01) for the study of acquired immunodeficiency syndrome (AIDS)-associated retrovirus that mimics normal peripheral blood lymphocytes in susceptibility to viral cytopathic effect without the need for cell activation or conditioned medium. Following infection, substantial quantities of virus are produced during a 3- to 5-day period; the associated killing of cells can be monitored in a microtiter assay as a function of virus input. Southern blot hybridization of infected cellular DNAs indicated that no gross alteration occurred in the restriction maps of the proviral DNA during the transfer of virus to and its passage in A3.01 cells. This cell system offers an alternative to other AIDS retrovirus cell systems because it permits the monitoring of viral cytopathic effects.
Genetic instability and increased mutational load: which diagnostic tool best direct patients with cancer to immunotherapy? (2017)

The occurrence of high rates of somatic mutations in cancer is believed to correspond to increased frequency of neo-epitope formation and tumor immunogenicity. Thus, classification of patients with cancer according to degree a somatic hyper-mutational status could be proposed as a predictive biomarker of responsiveness to immunotherapy with immune checkpoint inhibitors. Here, we discuss the suitable and reliable tests easily adoptable in clinical practice to assess somatic mutational status in patients with advanced cancer.
Recombinant human thrombopoietin (Mpl ligand) enhances proliferation of erythroid progenitors (1995)

We have studied the effects of recombinant human thrombopoietin (TPO, Mpl ligand) on human hematopoiesis in vitro. TPO alone did not support erythroid burst formation but, in the presence of erythropoietin, it enhanced erythroid burst formation from CD34+ bone marrow and cord blood cells. The burst-promoting activity (BPA) was stronger under 5% serum than 30% serum conditions. The direct nature of BPA effects was documented by replating studies of early erythroid bursts. The BPA of TPO was less than that of interleukin-3 but was comparable with that of granulocyte/macrophage colony-stimulating factor and steel factor. The soluble form of Mpl receptor inhibited burst enhancing effects of TPO, suggesting that the BPA effects of TPO are mediated through the Mpl receptor. These results further delineate the physiologic roles of TPO and may aid in the determination of the clinical usages of TPO.
Taking Cell-Matrix Adhesions to the Third Dimension (2001)

Adhesions between fibroblastic cells and extracellular matrix have been studied extensively in vitro, but little is known about their in vivo counterparts. Here, we characterized the composition and function of adhesions in three-dimensional (3D) matrices derived from tissues or cell culture. "3D-matrix adhesions" differ from focal and fibrillar adhesions characterized on 2D substrates in their content of alpha5beta1 and alphavbeta3 integrins, paxillin, other cytoskeletal components, and tyrosine phosphorylation of focal adhesion kinase (FAK). Relative to 2D substrates, 3D-matrix interactions also display enhanced cell biological activities and narrowed integrin usage. These distinctive in vivo 3D-matrix adhesions differ in structure, localization, and function from classically described in vitro adhesions, and as such they may be more biologically relevant to living organisms.
Microwave transformers, inductors and transmission lines implemented in an Si/SiGe HBT process (2001)

Experimental results are presented on microwave inductors, transformers, and transmission lines fabricated in an Si/SiGe heterojunction-bipolar-transistor process with standard metallization and a thick polyimide dielectric. Microstrip transmission lines with characteristic impedances from 44 to 73 /spl Omega/, Q's from 10 to 14, and insertion losses from 0.11 to 0.16 dB/mm at 10 GHz are presented. Conventional planar inductors with inductances from 0.5 to 15 nH and with peak Q's up to 22 are presented. Lateral transformers with a maximum available gain of better than -5 dB and a measured coupling coefficient (k) of 0.6 at 5.5 GHz and 0.4 up to 12.5 GHz are also discussed.
Inhibition of signal transducer and activator of transcription 3 activity results in down-regulation of Survivin following irradiation (2006)

Signal transducer and activator of transcription 3 (Stat3) and Survivin are constitutively up-regulated in various human tumor cells. We previously found Survivin to be significantly reduced in response to radiation in human umbilical vein endothelial cells (HUVEC) but not in tumor cell lines. In this study, we examined the effect of Stat3 on Survivin expression in irradiated HUVECs and breast cancer cells. We also studied how inhibition of Stat3 and Survivin activity affects cell survival and angiogenesis following irradiation. We determined that Survivin was significantly increased by overexpression of an active Stat3 (Stat3-C). Following irradiation, the level of phospho-Stat3 Tyr(705), but not phospho-Stat3 Ser(727), was reduced in HUVECs, whereas it remained unchanged in irradiated breast cancer cells. Correspondingly, Stat3 DNA-binding activity following irradiation was specifically down-regulated in HUVECs but not in breast cancer cells. Mutation of Tyr(705) abolished radiation-induced down-regulation of Survivin. Clonogenic and endothelial cell morphogenesis assays suggested that DN-Stat3 and DN-Survivin together resulted in the greatest radiosensitization of MDA-MB-231, decreasing angiogenesis and cell survival. In summary, Stat3 modulates Survivin, and both are potential therapeutic targets for radiation sensitization in breast cancer.
Blind speech separation employing directional statistics in an Expectation Maximization framework (2010)

In this paper we propose to employ directional statistics in a complex vector space to approach the problem of blind speech separation in the presence of spatially correlated noise. We interpret the values of the short time Fourier transform of the microphone signals to be draws from a mixture of complexWatson distributions, a probabilistic model which naturally accounts for spatial aliasing. The parameters of the density are related to the a priori source probabilities, the power of the sources and the transfer function ratios from sources to sensors. Estimation formulas are derived for these parameters by employing the Expectation Maximization (EM) algorithm. The E-step corresponds to the estimation of the source presence probabilities for each time-frequency bin, while the M-step leads to a maximum signal-to-noise ratio (MaxSNR) beamformer in the presence of uncertainty about the source activity. Experimental results are reported for an implementation in a generalized sidelobe canceller (GSC) like spatial beamforming configuration for 3 speech sources with significant coherent noise in reverberant environments, demonstrating the usefulness of the novel modeling framework.
Supplementary Ultraviolet Radiation B Together with Blue Light at Night Increased Quercetin Content and Flavonol Synthase Gene Expression in Leaf Lettuce (Lactuca sativa L.) (2008)

Establishment of an effective supplementary lighting procedure is necessary to increase the value of leaf lettuce grown using a hydroponic method involving a low production cost. In leaf lettuce extracts, quercetin, one of the flavonoids, was isolated and identified. It was investigated that quercetin has important functions that can be used as a dietary supplement. Flavonol synthase (FLS) is a key enzyme involved in quercetin biosynthesis, catalyzes the conversion of dihydroquercetin to quercetin. Therefore, we determined the sequence of the flavonol synthase gene (FLS) in red leaf lettuce. We harvested leaf lettuce grown using supplementary light sources, such as ultraviolet radiation B (UV-B), ultraviolet radiation A, blue, and red lamps during the night. It is noteworthy that FLS expression and the quercetin content were particularly increased to a greater extent in young leaves than in mature leaves when UV-B and blue light were used simultaneously at night. We suggest that UV-B with blue light is used simultaneously at night for producing leaf lettuce with high quercetin content.
Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5‘ of an ATG initiation codon (1983)

The nine base pairs immediately 5' of the initiation codon for the bovine growth hormone (BGH) structural gene have been mutagenized. The mutagenesis method employs the ligation of an ambiguously synthesized oligonucleotide duplex into a previously engineered gap in an expression plasmid for BGH. The mutation method, coupled with hybridization screening, is efficient at isolating 1 and 2 base pair changes within the targeted region. The E. coli cultures harboring the mutant plasmids were assayed for relative levels of BGH expression. The most notable result is the varied effect of substitution of G into the mRNA at various positions in this region.
Intestinal Microbiota in Bone Marrow Transplantation (2012)

Abstract Abstract SCI-51 Regulators of the intestinal flora include diet, antibiotics, and importantly, intestinal inflammation. As a result, the cause-effect relationships between intestinal inflammation and changes in microbiota have been difficult to define. The success of allogeneic bone marrow transplantation (allo BMT), a standard therapy for conditions including hematopoietic malignancies and inherited hematopoietic disorders, is limited by graft-versus-host disease (GVHD) morbidity and mortality. With GVHD, vigorous activation of donor immune cells, most importantly T cells, leads to damage of the skin, liver, hematopoietic system, and gut. The major sources of immune activation are histocompatibility complex differences between donor and recipient. Combinations of chemotherapy and radiation also contribute, as damage to the intestinal epithelium results in systemic exposure to microbial products normally sequestered in the intestinal lumen. We have demonstrated in murine and human recipients of allo BMT that intestinal inflammation secondary to GVHD is associated with major shifts in the composition of the intestinal microbiota. The microbiota, in turn, can modulate the severity of intestinal inflammation. In mouse models of GVHD we observed loss of overall diversity and expansion of Lactobacillales and loss of Clostridiales. Eliminating Lactobacillales from the flora of mice prior to BMT aggravated GVHD, while reintroducing the predominant species of Lactobacillus mediated significant protection against GVHD. We then characterized the gut flora of patients during onset of intestinal inflammation due to GVHD and found patterns mirroring those in mice. We also identified increased microbial chaos soon after allo BMT as a potential risk factor for subsequent GVHD. Together, these data demonstrate regulation of flora by intestinal inflammation, and suggest that flora manipulation may reduce intestinal inflammation and improve outcomes for allo BMT recipients. Disclosures: No relevant conflicts of interest to declare.
T cell-specific gamma genes in C57BL/10 mice. Sequence and expression of new constant and variable region genes. (1986)

The T cell-specific gamma genes in C57BL/10 (B10) mice have been analyzed. Based on the cDNA sequences of these genes from antigen-specific MHC-restricted cytotoxic T cells, we found that the repertoire of these genes is not as limited as previously postulated (8). T cells from the B10 mice express an identical copy of V gamma J gamma C gamma (V gamma 10.8A-JC gamma 10.5) transcript previously found in T cells of BALB/c mice. In addition, a potentially functional mRNA using V gamma 10.8B and newly identified J gamma and C gamma gene segments were found. The new J gamma C gamma (JC gamma 10.8) is located 5' to the inverted V gamma 10.8B in the germline DNA of both B10 and BALB/c mice. This new C gamma is only 77 and 66% homologous to the C gamma 10.5 at the nucleotide and deduced protein sequences, respectively, thus making it a potential isotype of the C gamma genes reported previously. The V gamma 5.7, J gamma 2.3 gene segments and pseudogene C gamma 7.5 found in the germline DNA of BALB/c mice are absent in B10 mice. The loss of this gamma chain pseudogene in the B10 mouse strain, and the retention of all potentially functional V gamma, J gamma, and C gamma genes with highly conserved coding sequences supports the importance of these genes.
Receptor-binding domain as a target for developing SARS vaccines. (2013)

A decade ago, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) caused a global pandemic with a mortality rate of 10%. Reports of recent outbreaks of a SARS-like disease caused by Middle East respiratory syndrome coronavirus (MERS-CoV) have raised serious concerns of a possible reemergence of SARS-CoV, either by laboratory escape or the presence of a natural reservoir. Therefore, the development of effective and safe SARS vaccines is still needed. Based on our previous studies, we believe that the receptor-binding domain (RBD) in the S1 subunit of the SARS-CoV spike (S) protein is the most important target for developing a SARS vaccine. In particular, RBD of S protein contains the critical neutralizing domain (CND), which is able to induce highly potent neutralizing antibody response and cross-protection against divergent SARS-CoV strains. Furthermore, a RBD-based subunit vaccine is expected to be safer than other vaccines that may induce Th2-type immunopathology. This review will discuss key advances in the development of RBD-based SARS vaccines and the possibility of using a similar strategy to develop vaccines against MERS-CoV.
Introduction to Fracture Mechanics (1996)

Abstract : This text is based on a series of lectures conducted on fracture mechanics. As an introductory course, the test is focused on the essential concepts and analytical methods of fracture mechanics, aiming at painting a broad picture of the theoretical background to fracture mechanics. While a brief review of some important issues in the theory of elasticity is provided in the first chapter, the main focus of the test is centered on stress analysis and energetic approaches to cracked components, local plastic deformation at crack tips, fracture criteria and fatigue life prediction.
Carbonylation of vinyl halides with carbonylcobalt (1989)

The reactions of both (E)-β-bromostyrene (E)-(1a) and its Z-isomer (Z)-(1a) with octacarbonyldicobalt in the presence of methyl iodide and calcium hydroxide at 20 °C in dioxane-water under carbon monoxide (1 atm) gave (E)-cinnamic acid (E)-(2a) exclusively. In contrast, with (E)-1-bromo-2-phenylpropene (E)-(1b), the thermodynamically less stable (Z)-3-phenylbut-2-enoic acid (Z)-(2b) was obtained as the major product together with the (E)-isomer (E)-(2b). The carbonylation of 3-chloroprop-2-enols (7a–f) gave the corresponding furan-2(5H)-ones (8a–f) in good yield.
Two mouse genes encoding potential transcription factors with identical DNA-binding domains are activated by growth factors in cultured cells. (1988)

We previously reported the identification of a mouse gene, Krox-20, encoding a protein with three "zinc fingers" (DNA-binding domains with coordinated zinc ions) whose expression is regulated during G0/G1 transition (cell-cycle reentry). We now have isolated cDNAs corresponding to a related gene, Krox-24. Krox-24 encodes a protein with zinc fingers nearly identical to those encoded by Krox-20 and similar to those of transcription factor Sp1. Similarity between Krox-20 and Krox-24 proteins also extends to several blocks of amino acid sequence located upstream of the finger region. Like Krox-20, Krox-24 is transiently activated in quiescent cells after treatment with fetal bovine serum or purified growth factors. The kinetics of activation are similar to those of the protooncogene c-fos. The induction does not require de novo protein synthesis, and cycloheximide treatment of the cells leads to superinduction due, at least in part, to mRNA stabilization. In the mouse, the two genes are expressed in a tissue-specific manner, with slightly different patterns. These properties suggest that Krox-20 and Krox-24 may encode transcription factors with identical DNA target sequences and that these factors may be involved in the modulation of cell proliferation and differentiation.
Very low frequencies of human normal CD34+ haematopoietic progenitor cells express the Wilms' tumour gene WT1 at levels similar to those in leukaemia cells (2002)

The Wilms' tumour gene, WT1, is expressed at high levels in leukaemia cells and plays an important role in leukaemogenesis. WT1 is also expressed in human normal CD34+ bone marrow (BM) cells at about 100 times lower levels than in leukaemia cells. To identify and characterize WT1-expressing cells in CD34+ BM cells, they were sorted into single cells and analysed for WT1 expression using two kinds of single-cell reverse transcriptase polymerase chain reaction (RT-PCR) methods. Using the semiquantitative single-cell polyA-PCR + sequence-specific (SS)-PCR method, WT1 expression was detected in four (1.3%) out of 319 CD34+ BM single cells. To confirm the above results, a single-cell nested sequence-specific (NSS)-RT-PCR method that was less quantitative but more sensitive than the polyA-PCR + SS-PCR method was also performed, and WT1 expression was detected in 15 (1.1%) out of 1315 CD34+ BM single cells. In total, WT1 expression was found in 19 (1.2%) out of 1634 CD34+ BM single cells. No significant differences in the frequencies of WT1-expressing cells were found between CD34+CD38- and CD34+CD38+ BM single cells. Furthermore, WT1-expressing CD34+ BM single cells expressed WT1 at levels similar to those in K562 leukaemia single cells. Analysis of lineage-specific and cell cycle gene expression in WT1-expressing CD34+ BM single cells showed that the WT1 gene could be expressed in both uncommitted, dormant CD34+CD38- and lineage-committed, proliferating CD34+CD38+ BM cells. Our results could indicate that these WT1-expressing CD34+ BM cells were normal counterparts of leukaemia cells.
T 2 -Weighted Contrast for NMR Characterization of Human Atherosclerosis (1995)

We sought to determine whether 1H NMR images without chemical-shift selection can adequately characterize the components of human atheromatous arteries. NMR, as a nondestructive, biochemical imaging tool, has the potential to identify lipids in atherosclerotic plaques but has not yet produced detailed images of atheroma components. Using 1H NMR spectroscopy at 9.4 T, we examined microdissected components of diseased and normal arteries to determine water relaxation constants (T1 and T2) as well as the relative content of mobile lipid. Relaxation times were also measured at 1.5 and 4.7 T. Sections of arteries with atherosclerotic lesions of graded severity were imaged at 1.5 and 9.4 T. The contrast-to-noise ratio (CNR) was used to assess lesion conspicuity. In the atheromatous core, the water NMR signal predominates over that of lipid (lipid-to-water ratio, 0.11). At 9.4 T, T2 is 20.2 ms for the atheromatous core, 30.1 ms for the collagenous cap, and 29.5 ms for normal media. This results in a high CNR on T2-weighted (T2w) images for atheromatous core compared with the collagenous cap and normal media. A similar contrast was measured at lower field strength. Calcifications do not generate appreciable signal due to their low water content but can be detected on T1-weighted (T1w) images. The water T2 contrast allows discrimination of the atheromatous lipid core from collagenous regions. The combination of T1w and T2w sequences permits in vitro identification of the atheromatous core, collagenous cap, calcifications, media, adventitia, and perivascular fat. The discrimination of collagen fibers that overlie lipid deposits permits study of plaque protection and stability at all field strengths and may provide the basis for in vivo microscopy of human atherosclerosis.
The CRISPR/Cas9 system for plant genome editing and beyond (2014)

Targeted genome editing using artificial nucleases has the potential to accelerate basic research as well as plant breeding by providing the means to modify genomes rapidly in a precise and predictable manner. Here we describe the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a recently developed tool for the introduction of site-specific double-stranded DNA breaks. We highlight the strengths and weaknesses of this technology compared with two well-established genome editing platforms: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). We summarize recent results obtained in plants using CRISPR/Cas9 technology, discuss possible applications in plant breeding and consider potential future developments.