gebhart/patrepeval huggingface dataset:
Growth of large-scale vertically aligned GaN nanowires and their heterostructures with high uniformity on SiOx by catalyst-free molecular beam epitaxy (2013)

The catalyst-free molecular beam epitaxial growth of GaN nanowires and their heterostructures on a SiOx template is studied in detail. It was found that by optimizing the growth temperature, highly uniform and vertically aligned GaN nanowires and InGaN/GaN heterostructures with excellent optical properties can be obtained on a SiOx template in a large-scale. This work provides an entirely new avenue for GaN nanowire based optoelectronic devices.
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform (2011)

With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
High-level expression of biologically active human alpha 1-antitrypsin in the milk of transgenic mice. (1990)

Reduced circulating levels of alpha 1-antitrypsin (alpha 1 AT) are associated with certain alpha 1 AT genotypes and increased susceptibility to emphysema. Unfortunately, the amounts of alpha 1 AT that would be required for replacement therapy are beyond the capacity of plasma fractionation and mammalian cell culture systems. Thus, we have examined the potential of transgenic animals as an alternative means of producing human alpha 1 AT. A hybrid gene constructed by using sequences from the ovine milk protein gene beta-lactoglobulin fused to an alpha 1 AT "minigene" was used to generate transgenic mice. Of 13 independent transgenic mice and mouse lines, 5 expressed the hybrid gene in the mammary gland, 5 in the salivary glands, and 2 in both these tissues. Human alpha 1 AT was secreted into the milk of each of the 7 mice and mouse lines that expressed the hybrid gene in the mammary gland. Four of these mammary-expressing transgenic mice and mouse lines produced concentrations of at least 0.5 mg of alpha 1 AT per ml in their milk; one line (AATB 35) produced 7 mg of this protein per ml. alpha 1 AT from transgenic mouse milk was similar in size to human plasma-derived alpha 1 AT and showed a similar capacity to inhibit trypsin. Expression at equivalent levels in transgenic sheep or cattle would yield sufficient alpha 1 AT for therapeutic purposes.
Reduced drug accumulation in multiply drug-resistant human KB carcinoma cell lines. (1985)

Human KB cells with increasing resistance to colchicine and other chemotherapeutic agents have been isolated in four sequential steps. This report describes the characterization of drug uptake in the parent and four mutant cell lines. Drug uptake in these cell lines occurred via a nonsaturable process. In general, drug accumulation decreased with increasing drug resistance; this relationship was seen best with colchicine, vincristine, vinblastine, and daunomycin and, to a lesser extent, with actinomycin D. The accumulation of dexamethasone, an agent to which all lines were equally sensitive, was similar for the parent and the four mutants. Drug efflux occurred rapidly, and differences among the various cell lines could be detected within the first minute. In the more resistant lines, a greater percentage of the drug was released more rapidly, although the absolute amount of drug released was less. Verapamil partially reversed the multiple drug-resistance phenotype by increasing the initial rate of uptake and accumulation of drugs in the resistant cell lines without an apparent effect on drug efflux. The results suggest that, in this human epithelial cell, the development of resistance to multiple drugs is complex, with changes in drug uptake, accumulation, and efflux.
A specific secretion system mediates PPE41 transport in pathogenic mycobacteria (2006)

Mycobacterial genomes contain two unique gene families, the so-called PE and PPE gene families, which are highly expanded in the pathogenic members of this genus. Here we report that one of the PPE proteins, i.e. PPE41, is secreted by pathogenic mycobacteria, both in culture and in infected macrophages. As PPE41 lacks a signal sequence a dedicated secretion system must be involved. A single gene was identified in Mycobacterium marinum that showed strongly reduced PPE41 secretion. This gene was located in a gene cluster whose predicted proteins encode components of an ESAT-6-like secretion system. This cluster, designated ESX-5, is conserved in various pathogenic mycobacteria, but not in the saprophytic species Mycobacterium smegmatis. Therefore, different regions of this cluster were introduced in M. smegmatis. Only introduction of the complete ESX-5 locus resulted in efficient secretion of heterologously expressed PPE41. This PPE secretion system is also involved in the virulence of pathogenic mycobacteria, as the ESX-5 mutant of M. marinum was affected in spreading to uninfected macrophages.
Identification of transcriptionally regulated genes after sciatic nerve injury (1991)

Mammalian peripheral nerve fibres can regenerate after injury. In an attempt toward a better understanding of the underlying molecular events, we have isolated novel and known rat cDNA sequences, the expression of which are regulated during sciatic nerve regeneration. For this purpose, cDNA libraries were constructed from either the nerve segment distal to the crush site or the corresponding contralateral uninjured nerve of the same animals. These libraries were screened by differential hybridization and several transcriptionally repressed and induced sequences were isolated. Out of 2,000 cDNA clones screened from the distal library, 11 sequences were found to be induced in the distal nerve segment. This set of induced cDNAs included the rat homolog of vimentin, 28 S and 18 S ribosomal RNA species, and two novel sequences. Of 5,000 screened colonies of the contralateral library, 30 colonies contained sequences that were repressed in the distal segment after nerve crush. They were identified as myelin basic protein, myelin P0, alpha-globin, cytochrome oxidase subunit 1, creatine kinase (muscle type, M) and collagen type I. In addition, five novel sequences were found that were dramatically repressed after sciatic nerve crush. Representative clones were tested by northern blot analysis to study their time course of transcriptional regulation during nerve regeneration. The observed patterns suggest that the regeneration phenomenon shows complex gene regulation in which the nonneuronal cells of the distal segment play an important role. Further characterization of the isolated regulated known and unknown sequences will increase our understanding of the molecular events associated with neuronal regeneration.
Myeloid leukemias have increased activity of the nonhomologous end-joining pathway and concomitant DNA misrepair that is dependent on the Ku70/86 heterodimer. (2002)

Human myeloid leukemias are characterized by chromosomal abnormalities, including translocations, deletions, and allelic loss. These alterations are known to disrupt the function of genes that contribute to tumor initiation and progression. The mechanism underlying the appearance of these chromosomal alterations is poorly understood. Recent evidence suggests that altered nonhomologous end joining (NHEJ) is associated with the incidence of chromosome abnormalities in mutant rodent cells. This pathway is thought to provide a major mechanism for the repair of double-strand breaks (DSB) in higher eukaryotes. Here, we show that in an in vitro assay for DSB end ligation, nuclear extracts prepared from cultured and primary myeloid leukemia cells show a 2-7-fold increase in end-ligation efficiency as compared with mobilized peripheral CD34+ blood progenitor cells (CD34+) and interleukin-2-stimulated peripheral blood lymphocytes from normal healthy donors (P < 0.001). Furthermore, using an in vitro plasmid LacZ gene reactivation assay to determine DSB repair fidelity, nuclear extracts prepared from myeloid leukemia cells showed an increased frequency of misrepair compared with normal control cells (P < 0.001). Most importantly, this misrepair in myeloid leukemia cells is associated with large deletions (30-400 bp) within the test plasmids used in our assay. These deletions were not observed using normal hematopoietic cells (<28 bp). Strikingly, we show that the NHEJ proteins, Ku70 and 86, are required for the deletions in myeloid leukemias because preincubating nuclear extracts from leukemic cells with antisera against Ku86 and Ku70 inhibits plasmid reactivation and restores the frequency and size of deletions to control levels. Our findings suggest that an overactive NHEJ system and, specifically, aberrant Ku70/86 activity is a candidate mechanism for chromosomal instability in myeloid leukemias.
The antimitogenic action of tumor necrosis factor is associated with increased AP-1/c-jun proto-oncogene transcription (1989)

Tumor necrosis factor alpha (TNF) mediates its in vivo antineoplastic effect primarily through its action on the endothelial surfaces of tumor vessels. Among other changes, endothelial cells increase the expression of surface procoagulant molecules which allow for the genesis of microthrombi and the eventual anoxic killing of the tumor tissue. TNF is also a potent antimitotic factor for endothelial cells. We investigated the molecular basis for these diverse actions of TNF by differential screening of a cDNA library prepared from TNF and cycloheximide-treated human umbilical vein endothelial (HUVE) cells. One of the cDNA clones identified encodes the transcription factor and proto-oncogene AP-1/c-jun. The expression of AP-1/c-jun following TNF treatment is mediated largely at the transcriptional level. Neither c-myc nor c-fos transcripts were induced by TNF. Since AP-1/c-jun has been previously identified as one of the earliest transcripts expressed in quiescent cells that have been stimulated by growth factors, our results suggest that mitogenic and antimitogenic stimuli evoke distinct yet overlapping sets of molecular responses and that the coordinate expression of AP-1/c-jun and c-fos is not mandatory. AP-1/c-jun transcript induction is thus one of the initial events mediated by TNF treatment of HUVE cells.
Homology between the glycoproteins of vesicular stomatitis virus and rabies virus (1982)

We compared the predicted amino acid sequences of the vesicular stomatitis virus and rabies virus glycoproteins by using a computer program which provides an optimal alignment and a statistical significance for the match. Highly significant homology between these two proteins was detected, including identical positioning of one glycosylation site. A significant homology between the predicted amino acid sequences of vesicular stomatitis virus and influenza virus matrix proteins was also found.
Precision Shock Tuning on the National Ignition Facility (2012)

Ignition implosions on the National Ignition Facility [J. D. Lindl et al., Phys. Plasmas 11, 339 (2004)] are underway with the goal of compressing deuterium-tritium fuel to a sufficiently high areal density (ρR) to sustain a self-propagating burn wave required for fusion power gain greater than unity. These implosions are driven with a very carefully tailored sequence of four shock waves that must be timed to very high precision to keep the fuel entropy and adiabat low and ρR high. The first series of precision tuning experiments on the National Ignition Facility, which use optical diagnostics to directly measure the strength and timing of all four shocks inside a hohlraum-driven, cryogenic liquid-deuterium-filled capsule interior have now been performed. The results of these experiments are presented demonstrating a significant decrease in adiabat over previously untuned implosions. The impact of the improved shock timing is confirmed in related deuterium-tritium layered capsule implosions, which show the highest fuel compression (ρR~1.0 g/cm(2)) measured to date, exceeding the previous record [V. Goncharov et al., Phys. Rev. Lett. 104, 165001 (2010)] by more than a factor of 3. The experiments also clearly reveal an issue with the 4th shock velocity, which is observed to be 20% slower than predictions from numerical simulation.
Synthesis of di‐ and tetraalkyl‐3‐piperazinoisoquinolines and related compounds as potential antidepressant agents (1987)

Abstract A series of di‐ and tetraalkyl‐3‐piperazinoisoquinolines and related compounds was synthesized via di‐ and tetraalkylated 1‐indanones as intermediates.
Elasticity of weakly aggregating polystyrene latex dispersions (1994)

The elastic behavior of a weakly aggregating polystyrene latex dispersion was investigated using a homemade controlled stress rheometer and commercially available dynamic rheometers. Both the creep measurements and the oscillatory experiments show the absence of a yield stress. The low-shear-limiting viscosity obtained with the controlled stress apparatus shows a power-law dependence upon volume fraction with a power of 5.3\ifmmode\pm\else\textpm\fi{}0.3. Combining the data of the different rheometers, the storage shear modulus G' at high frequencies was found to depend upon volume fraction with a power of 4.6\ifmmode\pm\else\textpm\fi{}0.3, being in line with earlier data mentioned in the literature. Using an additional exponent, i.e., one describing the critical strain above which the material deforms nonlinearly, the fractal dimension ${\mathit{d}}_{\mathit{f}}$ and the upper and lower bounds of the structural parameter \ensuremath{\varepsilon} were obtained. The latter is a measure for the degree of anisotropy of the network skeleton. The values ${\mathit{d}}_{\mathit{f}}$=2.0\ifmmode\pm\else\textpm\fi{}0.2 and 0.5\ensuremath{\le}\ensuremath{\varepsilon}\ensuremath{\le}1 are consistent with a model based on noncentral or bond-bending interactions. It was shown that the structural parameters and hence the microstructure change significantly when going from rest to high shear rates. Thus, in general, one cannot use the results obtained with one type of experiment in another type of experiment.
A colour atlas of the brain & spinal cord (1990)

A colour atlas of the brain & spinal cord , A colour atlas of the brain & spinal cord , کتابخانه دیجیتالی دانشگاه علوم پزشکی و خدمات درمانی شهید بهشتی
CNS Regenerative Medicine and Stem Cells (2016)

Stem cells research has passed a long and exciting way from discovery to clinical applications. Every year more and more scientific reports and solid research breakthroughs are published in this fascinating field making it difficult to follow new discoveries and cover the history. In the current review we overviewed the history of stem cells research starting from the discovery and ending with the current state-of-art. We discussed the obstacles and future perspectives of the cell-based therapy, with a special focus made on the protection and regeneration of the lost functions after injury/degeneration of adult central nervous system.
Automatic spelling correction in scientific and scholarly text (1984)

An automatic spelling correcting algorithm corrects most of the 50,000 misspellings culled from 25,000,000 words of text from seven scientific and scholarly databases. It uses a similarity key to identify words in a large dictionary that are most similar to a particular misspelling, and'then an error-reversal test to select from these the most plausible correction(s).
Side effects of anti-TNF therapy: current knowledge. (2003)

The development of the anti-TNF therapies is a milestone in the therapy of rheumatic diseases. As in all new treatment opportunities it is of concern whether all potential undesired side effects have been evaluated within the clinical trials which have lead to approval of the drugs. Postmarketing experience and pharmacovigilance programs are necessary to determine the overall safety profile of the new agents. From the clinical trials and the practical experience of the first years we know that side effects have occurred in patients treated with anti-TNF agents. Sufficient knowledge about these partly specific side effects is critical for rheumatologists who treat their patients with these very effective biologic drugs.
Infection and Activation of Monocytes by Marburg and Ebola Viruses (2001)

In this study we investigated the effects of Marburg virus and Ebola virus (species Zaire and Reston) infections on freshly isolated suspended monocytes in comparison to adherent macrophages under culture conditions. Our data showed that monocytes are permissive for both filoviruses. As is the case in macrophages, infection resulted in the activation of monocytes which was largely independent of virus replication. The activation was triggered similarly by Marburg and Ebola viruses, species Zaire and Reston, as indicated by the release of the proinflammatory cytokines interleukin-1beta (IL-1beta), tumor necrosis factor alpha, and IL-6 as well as the chemokines IL-8 and gro-alpha. Our data suggest that infected monocytes may play an important role in the spread of filoviruses and in the pathogenesis of filoviral hemorrhagic disease.
Using collaborative plans to model the intentional structure of discourse (1995)

An agent&amp;apos;s ability to understand an utterance depends upon its ability to relate that utterance to the preceding discourse. The agent must determine whether the utterance begins a new segment of the discourse, completes the current segment, or contributes to it. The intentional structure of the discourse, comprised of discourse segment purposes and their interrelationships, plays a central role in this process (Grosz and Sidner, 1986). In this thesis, we provide a computational model for recognizing intentional structure and utilizing it in discourse processing. The model specifies how an agent&amp;apos;s beliefs about the intentions underlying a discourse affects and are affected by its subsequent discourse. We characterize this process for both interpretation and generation and then provide specific algorithms for modeling the interpretation process. The collaborative planning framework of SharedPlans (Lochbaum, Grosz, and Sidner, 1990; Grosz and Kraus, 1993) provides the basis for our model ...
Unifying Packet and Circuit Switched Networks (2009)

There have been many attempts to unify the control and management of circuit and packet switched networks, but none have taken hold. In this paper we propose a simple way to unify both types of network using OpenFlow. The basic idea is that a simple flow abstraction fits well with both types of network, provides a common paradigm for control, and makes it easy to insert new functionality into the network. OpenFlow provides a common API to the underlying hardware, and allows all of the routing, control and management to be defined in software outside the datapath.
Abstract interpretation (1977)

A program denotes computations in some universe of objects. Abstract interpretation of programs consists in using that denotation to describe computations in another universe of abstract objects, so that the results of abstract execution give some information on the actual computations. An intuitive example (which we borrow from Sintzoff [72]) is the rule of signs. The text -1515 * 17 may be understood to denote computations on the abstract universe {(+), (-), (±)} where the semantics of arithmetic operators is defined by the rule of signs. The abstract execution -1515 * 17 → -(+) * (+) → (-) * (+) → (-), proves that -1515 * 17 is a negative number. Abstract interpretation is concerned by a particular underlying structure of the usual universe of computations (the sign, in our example). It gives a summary of some facets of the actual executions of a program. In general this summary is simple to obtain but inaccurate (e.g. -1515 + 17 → -(+) + (+) → (-) + (+) → (±)). Despite its fundamentally incomplete results abstract interpretation allows the programmer or the compiler to answer questions which do not need full knowledge of program executions or which tolerate an imprecise answer, (e.g. partial correctness proofs of programs ignoring the termination problems, type checking, program optimizations which are not carried in the absence of certainty about their feasibility, …).
Highly Enantioselective Construction of 3‐Hydroxy Oxindoles through a Decarboxylative Aldol Addition of Trifluoromethyl α‐Fluorinated gem‐Diols to N‐Benzyl Isatins (2013)

An organocatalytic asymmetric direct aldol addition reaction that involves cleavage of a carbon–carbon bond through the release of trifluoroacetate was developed. The protocol is wide in scope, generating the desired oxindoles of biological interest in nearly quantitative yields (up to 99 %) with excellent enantioselectivities (up to 98 % ee) and diastereoselectivities (up to 99:1 d.r.).
Genomic imbalances including amplification of the tyrosine kinase gene JAK2 in CD30+ Hodgkin cells. (2000)

Comparative genomic hybridization was applied for a comprehensive screening of frequently occurring net gains and losses of chromosomal subregions in small populations of CD30+ Hodgkin cells and their morphological variants. In 12 Hodgkin's lymphomas, recurrent gains were detected on chromosomal arms 2p, 9p, and 12q (in six, four, and five tumors, respectively) and distinct high-level amplifications were identified on chromosomal bands 4p16, 4q23-q24, and 9p23-p24. In Hodgkin cells with 9p23-p24 amplification, fluorescence in situ hybridization revealed an increased copy number of chromosomal sequences spanning the tyrosine kinase gene JAK2. Several of the imbalances described, in particular a gain in chromosomal arm 9p that includes JAK2 amplification, are similar to the genomic changes detected in primary mediastinal B-cell lymphoma.
Cryptography and data security (1982)

out of print, but ACM has made available as a 19 MB .pdf