gebhart/patrepeval huggingface dataset:
Editor's Note (2008)

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Tumor-derived exosomes are enriched in ΔNp73, which promotes oncogenic potential in acceptor cells and correlates with patient survival (2013)

Tumor-derived exosomes are emerging as local and systemic cell-to-cell mediators of oncogenic information through the horizontal transfer of mRNAs, microRNAs and proteins during tumorigenesis. The exosomal content has been described as biologically active when taken up by the recipient cell. Identifying the specific molecular cargo of exosomes will help to determine their function in specific steps of the tumorigenic process. Here we evaluate whether ΔNp73 is selectively packaged in tumor-derived exosomes, its function in the acceptor cells in vitro and in vivo and its prognosis potential in cancer. ΔNp73 messenger is enriched in tumor-derived exosomes, suggesting its active sorting in these microvesicles. We observed the transmission of this exosome cargo to different cell types and how it confers proliferation potential and chemoresistance to the acceptor cells in vitro and in animal models. Finally, our data support the potential prognostic value of exosomal ΔNp73 in colon cancer patients.
Least-squares reverse-time migration for reflectivity imaging (2015)

A least-squares reverse-time migration scheme is presented for reflectivity imaging. Based on an accurate reflection modeling formula, this scheme produces amplitude-preserved stacked reflectivity images with zero phase. Spatial preconditioning, weighting and the Barzilai-Borwein method are applied to speed up the convergence of the least-squares inversion. In addition, this scheme compensates the effect of ghost waves to broaden the bandwidth of the reflectivity images. Furthermore, roughness penalty constraint is used to regularize the inversion, which in turn stabilizes inversion and removes high-wavenumber artifacts and mitigates spatial aliasing. The examples of synthetic and field datasets demonstrate the scheme can generate zerophase reflectivity images with broader bandwidth, higher resolution, fewer artifacts and more reliable amplitudes than conventional reverse-time migration.
Betaine-Palmitate Reduces Acetylsalicylic Acid-induced Gastric Damage in Rats (2001)

Betaine-palmitate affords a significant protective effect against ASA-induced injury, without influencing the ATP synthesis, and this suggests that the defence is due to its ability to prevent secondary damage.
A NEW SYNTHESIS OF WATASENIA PRELUCIFERIN BY CYCLIZATION OF 2-AMINO-3-BENZYL-5-(p-HYDROXYPHENYL)PYRAZINE WITH p-HYDROXYPHENYLPYRUVIC ACID (1980)

Abstract The reaction of 2-amino-3-benzyl-5-(p-hydroxyphenyl)pyrazine with p-hydroxyphenylpyruvic acid gave directly Watasenia preluciferin in a satisfactory yield without any reductive treatment.
Principles and Practice of Radiation Oncology (1999)

Principles and practice of radiation oncology , Principles and practice of radiation oncology , کتابخانه دیجیتال جندی شاپور اهواز
Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis (2017)

Dactylicapnos scandens (D. Don) Hutch (Papaveraceae) is a well-known traditional Chinese herb used for treatment of hypertension, inflammation, bleeding and pain for centuries. Although the major bioactive components in this herb are considered as isoquinoline alkaloids (IQAs), little is known about molecular basis of their biosynthesis. Here, we carried out transcriptomic analysis of roots, leaves and stems of D. scandens, and obtained a total of 96,741 unigenes. Based on gene expression and phylogenetic relationship, we proposed the biosynthetic pathways of isocorydine, corydine, glaucine and sinomenine, and identified 67 unigenes encoding enzymes potentially involved in biosynthesis of IQAs in D. scandens. High performance liquid chromatography analysis demonstrated that while isocorydine is the most abundant IQA in D. scandens, the last O-methylation biosynthesis step remains unclear. Further enzyme activity assay, for the first time, characterized a gene encoding O- methyltransferase (DsOMT), which catalyzes O-methylation at C7 of (S)-corytuberine to form isocorydine. We also identified candidate transcription factor genes belonging to WRKY and bHLH families that may be involved in the regulation of IQAs biosynthesis. Taken together, we first provided valuable genetic information for D. scandens, shedding light on candidate genes involved in IQA biosynthesis, which will be critical for further gene functional characterization.
Controlled synthesis of fluorescent silica nanoparticles inside microfluidic droplets (2012)

We study the droplet-based synthesis of fluorescent silica nanoparticles (50-350 nm size) in a microfluidic chip. Fluorescein-isothiocyanate (FITC) dye is first chemically linked to aminopropyl triethoxysilane (APTES) in ethanol and this reaction product is subsequently mixed with tetraethyl orthosilicate (TEOS) to yield a fluorescent silicon alkoxide precursor solution. The latter reacts with an aqueous ethanol-ammonia hydrolysing mixture inside droplets, forming fluorescent silica nanoparticles. The droplets are obtained by pinching-off side-by-side flowing streams of alkoxide solution/hydrolysing mixture on a microfluidic chip using a Fluorinert oil continuous phase flow. Synthesis in droplets leads to a faster reaction and allows drastically improved nanoparticle size uniformity (down to 3% relative standard deviation for 350 nm size particles) when compared to conventional bulk synthesis methods, thanks to the precise control of reagent concentrations and reaction times offered by the microfluidic format. Incorporating FITC inside silica nanoparticles using our method leads to reduced dye leakage and increases the dye's stability, as evidenced by a reduced photochemical bleaching compared to a pure FITC solution.
Anti-CD19-Targeted Liposomal Doxorubicin Improves the Therapeutic Efficacy in Murine B-Cell Lymphoma and Ameliorates the Toxicity of Liposomes with Varying Drug Release Rates (2005)

Some formulations of liposomal doxorubicin with intermediate rates of drug release have shown increased levels of toxicity in mice. Because antibody-mediated targeting of liposomal drugs influences the pharmacokinetics, mechanism of uptake, and selectivity of the associated drugs, we hypothesized that anti-CD19-mediated targeting of liposomal doxorubicin might moderate the toxicity of the problem formulations. Phosphatidylcholine/cholesterol liposomal formulations of doxorubicin having faster, intermediate, and slower drug release rates were prepared by altering the fatty acyl chain length or degree of saturation of the phosphatidylcholine component. Pharmacokinetic and biodistribution studies and in vivo drug release rates were determined in mice using liposomes dual labeled with [3H]cholesteryl hexadecylether and [14C]doxorubicin. Therapeutic studies were done in xenograft models of human B lymphoma (Namalwa cells). The rate of clearance of the liposomal lipid was similar for all formulations (average t1/2, 18 hours), but the rate of clearance of doxorubicin was dependent on the release rate of the formulation (t1/2, 2-315 hours). Liposomes with the slowest drug release rates showed no toxicity and exhibited therapeutic activity that was superior to the other formulations when targeted with anti-CD19; liposomes with the most rapid drug release rates also showed no toxicity but showed little therapeutic effect even when targeted. Liposomes with intermediate drug release rates exhibited varying degrees of toxicity. The toxicities could be reduced and even overcome by targeting with anti-CD19 antibodies. For these formulations, therapeutic effects were intermediate between those found for liposomes with the fastest and slowest drug release rates.
Frequency-resolved optical gating measurement of ultrashort pulses passing through a high numerical aperture objective (1999)

We investigate using collinear type II second harmonic generation frequency-resolved optical gating (SHG FROG) to measure the pulse intensity and phase at the focus of high numerical aperture (NA) oil objectives. Because of the strong focusing for such objectives, it is not clear theoretically that such a measurement should work. Such objectives can produce severe distortions of the pulse as a function of radius in the objective. In addition, the standard SHG FROG algorithms are based on the assumption that the fundamental and second harmonic fields are plane waves that can be described by the paraxial approximation, and for high NA objectives, such assumptions are suspect. We show that such measurements work remarkably well. The tight focus, while a theoretical difficulty, eliminates many of the problems traditionally associated with SHG FROG including the difficulty of phase matching and walkoff of different polarizations in the crystal. Specifically, we use collinear type II SHG FROG to measure the intensity and phase at the focus of a Zeiss CP-Achromat 100x, 1.25 NA, infinity-corrected oil objective, and accurately retrieve 20 fs pulses.
Electron backscattering on single-wall carbon nanotubes observed by scanning tunneling microscopy (1999)

Single-wall carbon nanotubes, seamless cylindrical molecules formed from a graphene sheet, are either conducting or semiconducting, depending on the particular "wrapping vector" that defines the waist of the tube. Scanning tunneling microscopy experiments have tested this idea by simultaneously measuring a tube's lattice structure and electronic properties. Here we present a series of STM images of single-wall carbon nanotubes with a strikingly rich set of superstructures. The observed patterns can be understood as due to interference between propagating electron waves that are reflected from defects on the tube walls and ends, or as intrinsic to states propagating on semiconducting tubes. The measured broken symmetries can be used to directly probe electronic backscattering on the tube and provide a key element in the understanding of low-energy electron transport on these structures.
Oxidative Stress and Platelet Activation in Homozygous Homocystinuria (2001)

The results of the present study suggest that enhanced peroxidation of arachidonic acid to form bioactive F(2)-isoprostanes may represent an important mechanism linking hyperhomocysteinemia and platelet activation in CbetaSD patients. Moreover, they provide a rationale for dose-finding studies of vitamin E supplementation in this setting.
Platelet-derived growth factor (PDGF) and PDGF receptor are induced in mesangial proliferative nephritis in the rat. (1991)

We investigated whether platelet-derived growth factor (PDGF), or its receptor (PDGF-R), was upregulated in a rat model of mesangial proliferative glomerulonephritis. A marked increase in both PDGF A- and B-chain mRNA could be demonstrated in glomerular RNA by Northern blot analysis 3 and 5 days after disease induction, corresponding to the time of mesangial cell proliferation. PDGF-R beta-subunit mRNA and protein were also increased in glomeruli in mesangial proliferative nephritis, being maximal at day 5. The principal cells expressing PDGF B-chain appeared by immunostaining to be a subpopulation of mesangial cells; in contrast, the majority of the mesangial cells expressed the PDGF-R beta-subunit protein. Both complement depletion and platelet depletion significantly reduced cell proliferation and expression of both PDGF and PDGF-R. Thus, in mesangial proliferative nephritis there is a platelet- and complement-mediated induction of PDGF A and B chain and PDGF-R beta-subunit gene transcription and protein synthesis. The finding that the majority of PDGF is produced by the mesangial cell supports the role of PDGF as an autocrine growth factor in glomerulonephritis.
HLA-DQ alpha allele and genotype frequencies in various human populations, determined by using enzymatic amplification and oligonucleotide probes. (1990)

Allele and genotype frequencies at the HLA-DQ alpha locus have been determined by the use of polymerase chain reaction (PCR) amplification and nonradioactive oligonucleotide probes. The probes define six alleles and 21 genotypes in a dot-blot format. A total of over 1,400 individuals from 11 populations has been typed by two different laboratories using this method. In contrast to some variable-number-of-tandem-repeat markers that have been used for identity determination, DQ alpha genotype frequencies do not deviate significantly from Hardy-Weinberg equilibrium in all populations studied. The distribution of alleles varies significantly between most of these populations. In Caucasians, the allele frequencies range from 4.3% to 28.5%. In this population, the power of discrimination is .94, and, for paternity determination, the power of exclusion is .642. These population data will allow the use of the HLA-DQ alpha marker in paternity determination, the analysis of individual identity in forensic samples, and anthropological studies.
Unremodeled and Remodeled Cardiolipin Are Functionally Indistinguishable in Yeast (2013)

After biosynthesis, an evolutionarily conserved acyl chain remodeling process generates a final highly homogeneous and yet tissue-specific molecular form of the mitochondrial lipid cardiolipin. Hence, cardiolipin molecules in different organisms, and even different tissues within the same organism, contain a distinct collection of attached acyl chains. This observation is the basis for the widely accepted paradigm that the acyl chain composition of cardiolipin is matched to the unique mitochondrial demands of a tissue. For this hypothesis to be correct, cardiolipin molecules with different acyl chain compositions should have distinct functional capacities, and cardiolipin that has been remodeled should promote cardiolipin-dependent mitochondrial processes better than its unremodeled form. However, functional disparities between different molecular forms of cardiolipin have never been established. Here, we interrogate this simple but crucial prediction utilizing the best available model to do so, Saccharomyces cerevisiae. Specifically, we compare the ability of unremodeled and remodeled cardiolipin, which differ markedly in their acyl chain composition, to support mitochondrial activities known to require cardiolipin. Surprisingly, defined changes in the acyl chain composition of cardiolipin do not alter either mitochondrial morphology or oxidative phosphorylation. Importantly, preventing cardiolipin remodeling initiation in yeast lacking TAZ1, an ortholog of the causative gene in Barth syndrome, ameliorates mitochondrial dysfunction. Thus, our data do not support the prevailing hypothesis that unremodeled cardiolipin is functionally distinct from remodeled cardiolipin, at least for the functions examined, suggesting alternative physiological roles for this conserved pathway.
MBONE: the multicast backbone (1994)

article Free Access Share on MBONE: the multicast backbone Author: Hans Eriksson Swedish Institute of Computer Science (SICS), Kista, Sweden Swedish Institute of Computer Science (SICS), Kista, SwedenView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 8Aug. 1994pp 54–60https://doi.org/10.1145/179606.179627Published:01 August 1994Publication History 455citation1,645DownloadsMetricsTotal Citations455Total Downloads1,645Last 12 Months34Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Highly Efficient Nickel-Catalyzed Cross-Coupling of Succinic and Glutaric Anhydrides with Organozinc Reagents (2004)

A nickel-catalyzed alkylation of succinic and glutaric anhydrides with alkyl- and arylzinc reagents has been developed. A dramatic olefin effect has been investigated resulting in the identification of several styrene-based promoters which show pronounced enhancements in reaction rate. The substrate scope with respect to electrophilic and nucleophilic coupling partners has been examined and found to be remarkably broad, allowing for rapid introduction of molecular complexity through the use of functionalized coupling partners. Regioselective alkylation of an unsymmetrical succinic anhydride and a profound effect of pendent coordinating olefins on reaction rate suggest a mechanism involving discrete oxidative addition of the nickel complex into the cyclic anhydride followed by a transmetalation event.
Parvalbumin and calbindin D‐28k in the human motor system and in motor neuron disease (1993)

Calbindin D-28k and parvalbumin are neuronal calcium binding proteins of interest in relation to neurodegenerative diseases. Expression of calbindin and parvalbumin may be one of the determinants of selective vulnerability in these disorders. The distribution of these proteins was surveyed in the normal human motor system and in motor neuron disease (MND) using immunocytochemistry in formalin fixed post-mortem tissues. CNS tissues from 14 MND patients (mean age 61.2 years, mean post-mortem delay 24.6 h) and seven controls (mean age 62.6 years, mean post-mortem delay 25.3 h) were studied. Preliminary studies on the effects of fixation were performed. In normal cases upper and lower motor neurons showed absent expression of both proteins. Several neuronal groups characteristically spared in MND showed varying patterns of immunoreactivity: oculomotor neurons showed parvalbumin staining of the perikaryon; the thoracic preganglionic sympathetic neurons showed calbindin staining in perikarya. Onuf's nucleus showed calbindin staining in the neuropil only. In motor neuron disease a loss of ventral horn interneurons and calbindin immunoreactive processes was observed with no other disease related changes in the spinal cord, brain-stem, or motor cortex. These findings are consistent with the hypothesis that the distribution of these proteins is one determinant of selective vulnerability to the neurodegenerative processes in MND acting via disturbance of neuronal calcium homeostasis.
Long-term preservation of canine pancreas by a new simple cold storage method using perfluorochemical--the two-layer cold storage method (Euro-Collins' solution/perfluorochemical). (1992)

Long term preservation of canine pancreas by a new simple cold storage method using perfluorochemical (PFC), two-layer (Euro-Collins' solution (EC)/PFC) cold storage method, was tested in the canine model of segmental pancreas autotransplantation. The functional recovery of the graft preserved by this method (group 1) was determined by daily fasting blood glucose concentration and intravenous glucose tolerance test at two weeks after autotransplantation and compared with simple cold storage with EC (group 2), cold storage in EC with simple bubbling of oxygen (group 3), and control (no preservation) (group 4). Maintenance of normoglycemia at least 5 days after transplantation was considered a success of preservation. The functional success rates after 24 hour preservation were 4/4 (100%), 4/4 (100%) and 4/5 (80%) for groups 1, 2 and 3 respectively, and the functional success rates of groups 1, 2 and 3 after 48 hour preservation were 5/6 (86%), 1/5 (20%) and 1/5 (20%) respectively. In addition the functional success rates after 72 hour preservation were 6/6 (100%), 0/6 (0%) and 0/5 (0%) for groups 1, 2, and 3 respectively. It was clear that the two-layer cold storage method had made it possible to preserve the canine pancreas for up to 72 hours although the upper limit of reliable preservation time of groups 2 and 3 was 24 hours. The mean K value of group 1 after 72 hour preservation was 1.78 +/- 0.42 compared with 2.05 +/- 0.32 of group 4 at two weeks after transplantation. Biopsies of grafts of group 2 and 3 after 72 hours preservation showed remarkable autolytic changes in exocrine and endocrine tissues. In contrast, biopsies of grafts of group 1 after 72 hour preservation showed almost normal architecture in both tissues. In addition, biopsies of 72 hour preserved grafts of group 1 at 4 weeks after autotransplantation showed almost normal pancreatic architecture with minimal fibrotic changes in the exocrine tissue. This study demonstrated the possibility of long-term preservation of the pancreas for transplantation.
A Nonribosomal System of Peptide Biosynthesis (1996)

This review covers peptide structures originating from the concerted action of enzyme systems without the direct participation of nucleic acids. Biosynthesis proceeds by formation of linear peptidyl intermediates which may be enzymatically modified as well as transformed into specific cyclic structures. The respective enzyme systems are constructed of biosynthetic modules integrated into multienzyme structures. Genetic and DNA-sequence analysis of biosynthetic gene clusters have revealed extensive similarities between prokaryotic and eukaryotic systems, conserved principles of organisation, and a unique mechanism of transport of intermediates during elongation and modification steps involving 4'-phospho-pantetheine. These similarities permit the identification of peptide synthetases and related aminoacyl-ligases and acyl-ligases from sequence data. Similarities to other biosynthetic systems involved in the assembly of polyketide metabolites are discussed.
Abnormalp53Expression in Human Lung Cancer is Associated with Histologic Subtypes and Patient Smoking History (1994)

Among the most common mutations in human lung cancer are those affecting the p53 gene. The expression of p53 in the nucleus is considered an immunohistochemical reflection of the nuclear accumulation of mutant p53 protein, which is coded by the p53 gene with missense mutation and has a prolonged half-life. In the present study, p53 expression detected by means of immunohistochemistry occurred frequently in human lung cancer and was associated with histologic subtypes. The alteration in the p53 gene was found to be a relatively early genetic event in the development and progression of lung cancer and to be maintained in the process of metastasis: abnormal p53 expression was found in both the early and late clinical stages, and identical p53 expression was detected consistently among primary and metastatic lesions from the same patients. Furthermore, an observed association between abnormal p53 expression and the patients' smoking history suggests that the p53 gene could be a common target of tobacco-associated carcinogenesis in lung cancer.
Read count approach for DNA copy number variants detection (2011)

Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform.