gebhart/patrepeval huggingface dataset:
Isolation, Characterization and Anticancer Potential of Cytotoxic Triterpenes from Betula utilis Bark (2016)

Betula utilis, also known as Himalayan silver birch has been used as a traditional medicine for many health ailments like inflammatation, HIV, renal and bladder disorders as well as many cancers from ages. Here, we performed bio-guided fractionation of Betula utilis Bark (BUB), in which it was extracted in methanol and fractionated with hexane, ethyl acetate, chloroform, n-butanol and water. All six fractions were evaluated for their in-vitro anticancer activity in nine different cancer cell lines and ethyl acetate fraction was found to be one of the most potent fractions in terms of inducing cytotoxic activity against various cancer cell lines. By utilizing column chromatography, six triterpenes namely betulin, betulinic acid, lupeol, ursolic acid (UA), oleanolic acid and β-amyrin have been isolated from the ethyl acetate extract of BUB and structures of these compounds were unraveled by spectroscopic methods. β-amyrin and UA were isolated for the first time from Betula utilis. Isolated triterpenes were tested for in-vitro cytotoxic activity against six different cancer cell lines where UA was found to be selective for breast cancer cells over non-tumorigenic breast epithelial cells (MCF 10A). Tumor cell selective apoptotic action of UA was mainly attributed due to the activation of extrinsic apoptosis pathway via up regulation of DR4, DR5 and PARP cleavage in MCF-7 cells over non-tumorigenic MCF-10A cells. Moreover, UA mediated intracellular ROS generation and mitochondrial membrane potential disruption also play a key role for its anti cancer effect. UA also inhibits breast cancer migration. Altogether, we discovered novel source of UA having potent tumor cell specific cytotoxic property, indicating its therapeutic potential against breast cancer.
Characterization of a specific insulin-like growth factor-I/somatomedin-C receptor on high density, primary monolayer cultures of bovine articular chondrocytes: regulation of receptor concentration by somatomedin, insulin and growth hormone (1985)

In order to obtain a phenotypically stable cell population of chondrocytes, high density primary monolayer cultures of bovine articular chondrocytes were established. Using these cultures, a specific insulin-like growth factor-I/somatomedin-C (IGF-I/SM-C) receptor was demonstrated and characterized. At 15 degrees C steady-state binding was attained by 5 h, and averaged 25% per 2.2 X 10(6) cells. Fifty per cent displacement of 125I-labelled IGF-I/SM-C by unlabelled IGF-I/SM-C occurred at concentrations of only 2.3 ng/ml, whereas IGF-II and porcine insulin were approximately 15- and 1000-fold less potent respectively. Scatchard analysis gave a linear plot, with a calculated association constant of 2.26 X 10(9) l/mol and a receptor number of 15 400 sites per cell. Preincubation of chondrocyte monolayers with either IGF-I SM-C or porcine insulin at 37 degrees C for 20 h resulted in reduction of 125I-labelled IGF-I/SM-C binding in a dose-dependent manner, although higher concentrations were required with insulin. More than 40% down-regulation of the receptor occurred with IGF-I/SM-C at concentrations of 10 nmol/l and nearly 70% reduction at 50 nmol/l. Interestingly, after preincubation with either human (h) or bovine (b) GH, 40% down-regulation of 125I-labelled IGF-I/SM-C binding was observed at concentrations of 10 mumol/l. Local production of IGF-I/SM-C by chondrocytes in response to GH stimulation may have occurred, but, because only 120 pmol IGF-I/SM-C and less than 30 pmol IGF-I/SM-C per litre were recovered from serum-free conditioned media preincubated with bGH and hGH respectively, this was not established.(ABSTRACT TRUNCATED AT 250 WORDS)
Analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. (1986)

The Schizosaccharomyces pombe centromere-linked genes, LYS1 and CYH1 on chromosome I and TPS13 and RAN1 on chromosome II, have been isolated. The genetic order of these markers with respect to their centromeres was determined to establish relative directionality on the genetic and physical maps. Chromosome walking toward the centromeres reveals a group of repetitive sequences that occur only in the centromere regions of chromosomes I and II and at one other specific location in the S. pombe genome, presumably the centromere of chromosome III. The major class of large repeated sequence elements is 6.4 kilobases (kb) long (repeat K), portions of which occur at least twice on chromosome II and in several tandemly arranged intact copies at another centromeric location. Repeat K in turn contains groups of smaller repeats. Genetic recombination is strongly suppressed in the centromere II region, which contains at least 30 kb of repeated sequences. Centromeric DNA organization is much more complex in fission yeast than has been described in budding yeast (Saccharomyces cerevisiae), possibly because of the larger more condensed nature of the S. pombe chromosomes.
Effect of phenolic acids of microbial origin on production of reactive oxygen species in mitochondria and neutrophils (2012)

The most potent activators of ROS production in mitochondria are phenolic acids whose effect is mediated via the interaction with thiol groups. Among these are benzoic and cinnamic acids. Some phenolic acids, in particular phenyllactate and p-hydroxyphenyllactate, which decrease ROS production in mitochondria and neutrophils, can play a role of natural antioxidants. The results indicate that low-molecular weight phenolic acids of microbial origin participate in the regulation of the ROS production in both the circulation and tissues, thereby affecting the level of oxidative stress in sepsis.
A high quality subband speech coder with backward adaptive predictor and optimal time-frequency bit assignment (1986)

In this paper we propose a hybrid speech coder which utilizes properties of APC, ATC, and subband coding. Subband splitting is used to reduce the dynamic range of a full-band APC. As a result, the prediction or power gain is reduced and the instability problem associated with the APC coder is alleviated to a large extent. The optimal bit allocations used in ATC is extended in the new coder where the available coding bits are optimally allocated, both in the time and frequency domains. Frame boundary artifacts (such as those found in ATC) are not present due to the time-domain processing nature of SBC. In order to improve the efficiency in quantizing the side information (time and frequency domain signal power and the corresponding bit allocations), vector quantization is used. Adaptive backward predictors are used to further reduce the number of bits allocated to side information, leaving more bits to encode the prediction residual signals. At 16 kbps the coder achieves better than 20 dB segmental signal-to-noise ratio and sounds transparent for most speakers.
Side-By-Side Comparison of Areas with and without Cellulite Depressions Using Magnetic Resonance Imaging (2009)

Results of the MRI analysis showed that cellulite depressions on the buttocks were significantly associated with the presence of underlying fibrous septa.
Elemental Diet Induces Histologic Response in Adult Eosinophilic Esophagitis (2013)

While symptoms did not improve and dietary compliance was problematic, there was substantial histologic improvement after 4 weeks on the elemental diet. EoE in adults is substantially triggered by foods.
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities (2015)

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.
MicroRNA-214 Promotes Myogenic Differentiation by Facilitating Exit from Mitosis via Down-regulation of Proto-oncogene N-ras (2010)

Vertebrate muscle differentiation is coordinated by an intricate network of transcription factors requiring proliferating myogenic precursors to withdraw irreversibly from the cell cycle. Recent studies have implicated a large number of microRNAs exerting another layer of control in many aspects of muscle differentiation. By annealing to short recognition sequences in the 3'-untranslated region, microRNAs attenuate target gene expression through translation repression or mRNA degradation. Here, we show that miR-214 promotes myogenic differentiation in mouse C2C12 myoblasts at a step preceding the induction of p21 and myogenin. Blocking miR-214 function with a 2'-O-methylated double-stranded inhibitor maintained C2C12 cells in the active cell cycle, thereby inhibiting the myogenic differentiation. By global gene expression profiling, we identified the proto-oncogene N-ras as one of miR-214 targets. Furthermore, manipulating the N-Ras level with small interfering RNA or adenovirus-mediated forced expression either augmented or attenuated the effect of miR-214, respectively. Thus, our data uncovered a novel microRNA-mediated mechanism that controls myogenic differentiation.
The Role of Mononuclear Phagocytes in HTLV-III/LAV Infection (1986)

Cells with properties characteristic of mononuclear phagocytes were evaluated for infectivity with five different isolates of the AIDS virus, HTLV-III/LAV. Mononuclear phagocytes cultured from brain and lung tissues of AIDS patients harbored the virus. In vitro-infected macrophages from the peripheral blood, bone marrow, or cord blood of healthy donors produced large quantities of virus. Virus production persisted for at least 40 days and was not dependent on host cell proliferation. Giant multinucleated cells were frequently observed in the macrophage cultures and numerous virus particles, often located within vacuole-like structures, were present in infected cells. The different virus isolates were compared for their ability to infect macrophages and T cells. Isolates from lung- and brain-derived macrophages had a significantly higher ability to infect macrophages than T cells. In contrast, the prototype HTLV-III beta showed a 10,000-fold lower ability to infect macrophages than T cells and virus production was one-tenth that in macrophage cultures infected with other isolates, indicating that a particular variant of HTLV-III/LAV may have a preferential tropism for macrophages or T cells. These results suggest that mononuclear phagocytes may serve as primary targets for infection and agents for virus dissemination and that these virus-infected cells may play a role in the pathogenesis of the disease.
CC Chemokine Ligand 20 and Its Cognate Receptor CCR6 in Mucosal T Cell Immunology and Inflammatory Bowel Disease: Odd Couple or Axis of Evil? (2013)

Chemokines and their cognate receptors have been identified as major factors initiating and governing cell movement and interaction. These ligands and their receptors are expressed on a wide variety of cells and act during steady-state migration as well as inflammatory recruitment. CCR6 is a non-promiscuous chemokine receptor that has only one known chemokine ligand, CCL20, and is present on B and T cells as well as dendritic cells (DCs). Two CD4(+) T cell populations with opposing functions present in the intestines and the mesenteric lymph nodes express CCR6: the pro-inflammatory TH17 and regulatory Treg cells. CCL20 is also present in the intestine and is strongly up-regulated after an inflammatory stimulus. Interestingly, this ligand is also expressed by TH17 cells, which opens up the possibility of autocrine/paracrine signaling and, consequently, a self-perpetuating cycle of recruitment, thereby promoting inflammation. Recently, CCR6 has been implicated in inflammatory bowel disease (IBD) by genome wide association studies which showed an association between SNPs in the genomic region of the CCR6 gene and the inflammation. Furthermore, recent research targeting the biological function of CCR6 indicates a significant role for this chemokine receptor in the development of chronic IBD. It is therefore possible that IBD is facilitated by a disordered regulation of TH17 and Treg cells due to a disruption in the CCL20-CCR6 axis and consequently disturbed mucosal homeostasis. This review will summarize the literature on CCL20-CCR6 in mucosal immunology and will analyze the role this receptor-ligand axis has in chronic IBD.
Complete nucleotide sequence of type 6 M protein of the group A Streptococcus. Repetitive structure and membrane anchor. (1986)

The DNA sequence of the gene for type 6 M protein of Streptococcus pyogenes contains two extended tandem repeat regions and one nontandem repeat region. We suggest that the duplication and deletion of these repeats generates the observed diversity in size and sequence among the family of M proteins in the group A streptococci. In addition, the DNA sequence reveals the presence of a 42-amino-acid signal peptide, a region rich in proline that is thought to be located in the cell wall, and a membrane anchor sequence at the carboxyl-terminal end of the protein. Signals similar to the consensus sequences recognized for the initiation of transcription and translation in Gram-positive bacteria have been identified in the DNA sequence. Codon usage is similar to that of other Gram-positive bacteria and significantly different from that of Escherichia coli.
Surface-enhanced Raman spectroscopy of DOPA-containing peptides related to adhesive protein of marine mussel,Mytilus edulis (2000)

The common blue marine mussel adheres to underwater surfaces using an adhesive protein (Mefp-1) extruded from its foot. This highly hydroxylated protein contains a number of unusual amino acids, including 3,4-dihydroxyphenylalanine (DOPA), which is thought to contribute to the crosslinking of the extruded threads and adhesion to the substratum. Mefp-1 adheres to a wide variety of surfaces and is ultimately biodegradable. In this study we use surface-enhanced Raman spectroscopy (SERS) to characterize the adsorption of DOPA-containing peptides on colloidal gold. The peptides are simplified fragments of the Mefp-1 consensus decapeptide repeat, Ala-Lys-Pro-Ser-Tyr-DHP-Hyp-Thr-DOPA-Lys. Our results show that the peptides TDeltaKA, PTDeltaKA, and PPTDeltaKA (where Delta represents DOPA) coordinate to the gold surface through the catechol oxygens of the DOPA residue and through primary amine groups. The diproline sequence introduces conformational constraints that influence the conformations of the adsorbed peptides. These findings lay the groundwork for developing synthetic adhesives for underwater and medical applications.
Evaluation of a Junction Termination Extension Avalanche Photodiode for X-Ray Detection (2007)

An avalanche photodiode (APD) with a ring structure around the active area was built. The junction termination extension (JTE) APD has three diffused rings around the main junction to reduce the electric field at the surface. This design has the advantage that it does not need a sharp bevel edge or grooves to avoid early breakdown at the surface. The JTE rings can be obtained by a well-controlled ion-implantation through a single mask. The process uses standard planar technology for silicon devices. Several APDs with 2-mm diameter active area have been built by implantation of boron with a dose of 2, 3, 4, and 5 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , followed by deep diffusion to 14 mum. The dark current is strongly dependent on the implantation charge, decreasing with decreasing charge. For the APDs with an implanted dose of 5 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , a gain of 8 is obtained at 1120 V, indicating that the devices have premature breakdown. The energy resolution from a 109Cd X-ray source (22.16 keV) was measured to be 4.7-keV full-width at half-maximum, which corresponds to 560 rms electrons noise. We have also performed simulations of the gain and breakdown voltage that correlate well with the results up to a gain of 5.
Fetal growth promoting effect of hydroxyethylrutoside in pregnant women (2014)

Abstract
A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. (1994)

The homeobox gene knotted1 (kn1) was first isolated by transposon tagging a dominant leaf mutant in maize. Related maize genes, isolated by virtue of sequence conservation within the homeobox, fall into two classes based on sequence similarity and expression patterns. Here, we report the characterization of two genes, KNAT1 and KNAT2 (for knotted-like from Arabidopsis thaliana) that were cloned from Arabidopsis using the kn1 homeobox as a heterologous probe. The homeodomains of KNAT1 and KNAT2 are very similar to the homeodomains of proteins encoded by class 1 maize genes, ranging from 78 to 95% amino acid identity. Overall, the deduced KNAT1 and KNAT2 proteins share amino acid identities of 53 and 40%, respectively, with the KN1 protein. Intron positions are also fairly well conserved among KNAT1, KNAT2, and kn1. Based on in situ hybridization analysis, the expression pattern of KNAT1 during vegetative development is similar to that of class 1 maize genes. In the shoot apex, KNAT1 transcript is localized primarily to the shoot apical meristem; down-regulation of expression occurs as leaf primordia are initiated. In contrast to the expression of class 1 maize genes in floral and inflorescence meristems, the expression of KNAT1 in the shoot meristem decreases during the floral transition and is restricted to the cortex of the inflorescence stem. Transgenic Arabidopsis plants carrying the KNAT1 cDNA and the kn1 cDNA fused to the cauliflower mosaic virus 35S promoter were generated. Misexpression of KNAT1 and kn1 resulted in highly abnormal leaf morphology that included severely lobed leaves. The expression pattern of KNAT1 in the shoot meristem combined with the results of transgenic overexpression experiments supports the hypothesis that class 1 kn1-like genes play a role in morphogenesis.
Poor sleep quality and fatigue but no excessive daytime sleepiness in myotonic dystrophy type 2 (2010)

These results provide new insight into the phenotype of DM2 and have consequences for clinical treatment. In addition, the absence of EDS in DM2 is a new discriminative feature with adult onset DM1.
Improving accuracy of Gaussian mixture model classifiers with additional discriminative training (2016)

Gaussian mixture models (GMM) remain popular in pattern classification applications due to their well understood Bayesian framework and the availability of good training algorithms such as the expectation maximization (EM) algorithm. EM is a non-discriminative training algorithm. The performance of a GMM trained with the EM algorithm can often fall short of other discriminative pattern classification techniques such as support vector machines (SVM) and artificial neural network (ANN) architectures such as deep networks and extreme learning machines (ELM). In this paper a discriminative training method based on the Moore-Penrose pseudo-inverse, often used in the ELM, is applied to the GMM classifier first trained with the EM algorithm. It is shown that on a number of benchmark pattern classification problems the proposed method improves accuracy of the GMM classifier significantly and produces results that are comparable to the SVM or ELM. The advantages of the proposed method are that there are no tunable parameters and the training is straightforward and fast.
Frontiers in Optical Imaging of Cerebral Blood Flow and Metabolism (2012)

In vivo optical imaging of cerebral blood flow (CBF) and metabolism did not exist 50 years ago. While point optical fluorescence and absorption measurements of cellular metabolism and hemoglobin concentrations had already been introduced by then, point blood flow measurements appeared only 40 years ago. The advent of digital cameras has significantly advanced two-dimensional optical imaging of neuronal, metabolic, vascular, and hemodynamic signals. More recently, advanced laser sources have enabled a variety of novel three-dimensional high-spatial-resolution imaging approaches. Combined, as we discuss here, these methods are permitting a multifaceted investigation of the local regulation of CBF and metabolism with unprecedented spatial and temporal resolution. Through multimodal combination of these optical techniques with genetic methods of encoding optical reporter and actuator proteins, the future is bright for solving the mysteries of neurometabolic and neurovascular coupling and translating them to clinical utility.
High-speed two-dimensional gas chromatography using microfabricated GC columns combined with nanoelectromechanical mass sensors (2009)

We report here for the first time the combination of microfabricated gas chromatography (GC) columns with pneumatic modulation to achieve high-speed comprehensive two-dimensional gas chromatography (GCxGC) using microfabricated components. The GCxGC system is in turn combined with nanoelectromechanical (NEMS) resonator mass sensors that have been coated with a chemically-selective polymer to enhance detection of phosphonate compounds that are useful surrogates for chemical warfare agents (CWA). GC elution peak widths on the order of 20 msec have been achieved. Retention times on the order of 2-4 seconds have been demonstrated for polar compounds, indicating that this microfabricated GCxGC system can be applied for rapid analyses.
Board-to-board free-space optical interconnections passing through boards for a bookshelf-assembled terabit-per-second-class ATM switch (1998)

We propose free-space optical interconnections for a bookshelf-assembled terabit-per-second-class ATM switch. Thousands of arrayed optical beams, each having a rate of a few gigabits per second, propagate vertically to printed circuit boards, passing through some boards, and are connected to arbitrary transmitters and receivers on boards by polarization controllers and prism arrays. We describe a preliminary experiment using a 1-mm-pitch 2 x 2 beam-collimator array that uses vertical-cavity surface-emitting laser diodes. These optical interconnections can be made quite stable in terms of mechanical shock and temperature fluctuation by the attachment of reinforcing frames to the boards and use of an autoalignment system.