gebhart/patrepeval huggingface dataset:
Efferent Projections to the Host Brain from Intrastriatal Striatal Mouse‐to‐rat Grafts: Time Course and Tissue‐type Specificity as Revealed by a Mouse Specific Neuronal Marker (1991)

The developmental time-course and growth characteristics of efferent graft-to-host projections were studied from mouse fetal striatal grafts (E13 - 14) implanted as a cell suspension into the ibotenate-lesioned striatum of immunosuppressed adult rats. A cell surface monoclonal antibody specific for mouse neurons (M6) was used to identify the donor cells and their projections into the host brain. At 3 - 5 days after implantation, sparse fascicles of M6-positive graft-derived fibres extended for approximately 0.3 - 0.4 mm across the graft - host border into the surrounding host striatum. From the beginning they were selectively orientated in one direction, i.e. caudally along the myelinated fibre bundles of the internal capsule. At 8 days, the graft-derived fibres were more numerous and more densely labelled. They ran in dense fascicles inside the myelinated bundles of the host internal capsule and reached the rostral host globus pallidus, a distance of approximately 1.2 mm from the caudal tip of the graft. Two weeks after grafting, the M6-positive fibre fascicles were clearly seen to branch within the globus pallidus to form terminal-like networks. From this time onwards, the immunoreactivity of the outgrowing fibre fascicles gradually diminished, although small but dense terminal-like networks could be found in the host globus pallidus in most, but not all, of the rats at longer survival times (3 - 15 weeks). This is consistent with previous work showing that outgrowing axons lose their M6 immunoreactivity as they mature and become myelinated. Control grafts of fetal neocortical and fetal cerebellar tissue were used to assess the tissue-type specificity of the efferent fibre growth. The neocortical implants projected densely up to about 3 mm into the host brain, along the internal capsule and the corpus callosum and into the overlying cortex. By contrast, although the cerebellar grafts survived well, they showed very little efferent fibre growth. Double immunostaining for DARPP-32 and M6 revealed that all M6-positive fibre fascicles extending from the striatal (but not neocortical) grafts also showed DARPP-32 positivity, and thus that it was the DARPP-32-positive regions of the striatal grafts that projected to the host brain. It is concluded that graft-to-host projections, running along and inside host myelinated bundles, are formed from intrastriatal striatal grafts within 1 - 2 weeks of implantation. Grafts of neocortical tissue grew well along the same trajectory, whereas neurons of a type not normally projecting along the internal capsule, i.e. cerebellum, failed to extend axons over any significant distance along this trajectory.
Room Temperature Ionic Liquids for Mercury Capture from Flue Gas (2008)

Six room temperature ionic liquids (RTILs) were synthesized and tested as coatings for adsorbents for mercury capture from nitrogen at 160 °C. All six RTILs were thermally stable to temperatures above 160 °C. These RTILs were coated on mesoporous silica gel, and the fixed-bed mercury capture characteristics of these adsorbents were observed at 160 °C. Hg0 capture appears to result from the formation of a complex involving Hg0 and ions in the RTIL complex, and not from oxidation by the RTIL. The high observed oxidized mercury capacity for Cl−-based RTILs is believed to be due to greater dissociation of HgCl2 in the RTILs that incorporate chloride anion. The higher hydrogen-bond basicity and dipolarity of these RTILs might underlie improved HgCl2 dissociation. [bmim]Cl was identified as a promising RTIL for the simultaneous capture of elemental and oxidized mercury from the gas phase. A nanostructured chelating adsorbent with a coating of 25 wt % [bmim]Cl has an elemental mercury capacity of 10 mg/g and an oxidized mercury capacity of at least 38 mg/g.
Control independence in trace processors (1999)

Branch mispredictions are a major obstacle to exploiting instruction-level parallelism, at least in part because all instructions after a mispredicted branch are squashed. However, instructions that are control independent of the branch must be fetched regardless of the branch outcome, and do not necessarily have to be squashed and re-executed. Control independence exists when the two paths following a branch re-converge. A trace processor microarchitecture is developed to exploit control independence and thereby reduce branch misprediction penalties. There are three major contributions: 1) Trace-level re-convergence is not guaranteed despite re-convergence at the instruction-level. Novel trace selection techniques are developed to expose control independence at the trace-level. 2) Control independence's potential complexity stems from insertion and removal of instructions from the middle of the instruction window. Trace processors manage control flow hierarchically (traces are the fundamental unit of control flow) and this results in an efficient implementation. 3) Control independent instructions must be inspected for incorrect data dependences caused by mispredicted control flow. Existing data speculation support is easily leveraged to selectively re-execute incorrect-data dependent, control independent instructions. For five of the SPEC95 integer benchmarks, control independence improves trace processor performance from 5% to 25%, and 17% on average.
In-silico analysis for RNA-interference mechanism of α-synuclein to treat Parkinson's disease (2013)

Parkinson's Disease (PD) causing mutations in α-synuclein gene are ALA30PRO, GLU46LYS and ALA53THR. The conformational changes in proteins with respect to all the three mutations were analysed. These were used to predict the structures of Short Interfering RNA (siRNA) antisense strand and siRNA region. The siRNA binds with the argonaute protein forming RNA Induced Silencing Complex (RISC). Then, siRNA antisense-strand was attached to RISC. The structure of dicer (RNase-III-enzyme) cleaves double-stranded RNA (dsRNA) into two siRNA-strands. Incorporation of single siRNA-strand into RISC guides to pair with the complementary α-synuclein target-messenger RNA (mRNA) thereby enabling it to cleave the target.
Alcohols, Aliphatic (2013)

Abstract The article contains sections titled: 1. Introduction 2. Saturated Alcohols 2.1. Physical Properties 2.2. Chemical Properties 2.3. Production 2.3.1. Synthesis from Carbon Monoxide and Hydrogen 2.3.2. Oxo Synthesis 2.3.3. Hydrogenation of Aldehydes, Carboxylic Acids, and Esters 2.3.4. Aldol Condensation of Lower Aldehydes and Hydrogenation of the Alkenals 2.3.5. Oxidation of Trialkylaluminum Compounds 2.3.6. Oxidation of Saturated Hydrocarbons 2.3.7. Hydration of Olefins 2.3.8. Homologation of Alcohols 2.3.9. Reppe Process 2.3.10. Hydrocarboxymethylation 2.3.11. Fermentation 2.3.12. Guerbet Alcohols 2.3.13. Other Processes 2.4. Individual Alcohols 2.4.1. C 6 Alcohols 2.4.2. C 7 Alcohols 2.4.3. C 8 Alcohols 2.4.4. C 9 Alcohols 2.4.5. C 10 Alcohols 2.4.6. Mixtures of Linear C 12 ‐C 18 Alcohols (Detergent Alcohols) 2.4.7. C 13 ‐C 18 Isoalcohols 2.5. Economic Aspects 2.6. Quality Specifications 2.7. Storage and Transportation 3. Unsaturated Alcohols 4. Alkoxides 4.1. Properties 4.2. Preparation 4.3. Uses 5. Toxicology
Global signatures of protein and mRNA expression levels (2009)

Cellular states are determined by differential expression of the cell's proteins. The relationship between protein and mRNA expression levels informs about the combined outcomes of translation and protein degradation which are, in addition to transcription and mRNA stability, essential contributors to gene expression regulation. This review summarizes the state of knowledge about large-scale measurements of absolute protein and mRNA expression levels, and the degree of correlation between the two parameters. We summarize the information that can be derived from comparison of protein and mRNA expression levels and discuss how corresponding sequence characteristics suggest modes of regulation.
Polyesters and Poly(ester-urethane)s from Biobased Difuranic Polyols (2016)

This contribution investigates the impact of rigid and flexible difuranic polyols on the resulting polyester (PE) and poly(ester-urethane) (PEU) properties. Three biobased difuranic polyol monomers, 5,5′-bihydroxymethyl furil (BHMF), 5,5′-dihydroxymethyl furoin (DHMF), and bis[5-(hydroxymethyl)furan-2-yl)methyl]adipate (BHFA), all derived from the biomass platform chemical 5-hydroxymethylfurfural (HMF), were employed for the synthesis of a series of new linear and cross-linked PEs as well as amorphous and semicrystalline PEUs. The polycondensations of diols (rigid BHMF and flexible BHFA) with various diacyl chlorides afford linear PEs, whereas the rigid triol (DHMF) reacts with diacyl chlorides to form cross-linked PEs. Among these difuranic PEs, the most intriguing PE is the one containing C═C double bonds, derived from BHFA and fumaryl chloride, which exhibits the unique self-curing ability via the Diels–Alder reaction. Furthermore, the catalyzed polyaddition of BHFA with various diiscyanates produces novel PEUs, the most interesting of which is the one derived from BHFA and hexamethylene diisocyanate, a semicrystalline material displaying a high melting-transition temperature of 135.8 °C.
Upgrading in Mechanical Properties of High Performance Aluminum Alloys by Compressive Torsion Process (2014)

Abstract The originally developed severe plastic deformation process, the compressive torsion process (CTP) was applied to Al-Fe series alloys to improve their ductility and waste 7050 alloy chips to reprise their solid phase recycling. In the Al alloys containing Fe element, the large precipitates with length of 500∼1000 μm were refined under 20 μm and dispersed uniformly in the matrix alloy. Then the ductility was significantly improved to over 30% elongation from 5% or below before the CTP. In the solid phase recycling of waste 7050 alloy chips, the chips can be consolidated into high density bulk alloy with good strength and ductility even at lower temperature by the CTP. The consolidation at elevated temperature is suitable for the subsequent heat treatment like annealing or solid solution treatment.
The second-largest subunit of the poxvirus RNA polymerase is similar to the corresponding subunits of procaryotic and eucaryotic RNA polymerases (1989)

We have characterized the poxvirus gene encoding the second-largest subunit of the viral DNA-dependent RNA polymerase. This gene, designated rpo132, is located in the HindIII A fragment of the DNA of the Brighton Red strain of cowpox virus. A similar gene is located in the corresponding position in the HindIII A fragment of the DNA of the Western Reserve strain of vaccinia virus. The rpo132 gene is transcribed throughout the viral multiplication cycle. It has two transcriptional start sites; one is operative at late times only, and the other (80 base pairs downstream) is operative both at early times and at late times. Neither early nor late transcripts originating from the latter RNA start site contain long 5'-terminal poly(A) sequences. The rpo132 gene has the capacity to encode primary gene products of two types. The RNA transcripts whose 5' ends correspond to the early RNA start site can encode a 133-kilodalton (kDa) protein. The RNA transcripts whose 5' ends correspond to the early RNA start site can encode a 132-kDa protein. Transcripts of the latter type are more abundant, suggesting that the 132-kDa protein is the major primary product of this gene. The predicted amino acid sequences of both gene products share extensive similarities with the amino acid sequences of the second-largest subunits of the following enzymes: the RNA polymerase of Escherichia coli, the RNA polymerase II of Saccharomyces cerevisiae, and the RNA polymerase II of Drosophila melanogaster. This result provides further evidence of relatedness between multisubunit DNA-dependent RNA polymerases.
Regulation and mechanisms of gene amplification (1995)

Amplification in rodent cells usually involves bridge-breakage-fusion (BBF) cycles initiated either by end-to-end fusion of sister chromatids, or by chromosome breakage. In contrast, in human cells, resistance to the antimetabolite N-(phosphonacetyl)-L-aspartate (PALA) can be mediated by several different mechanisms that lead to overexpression of the target enzyme carbamyl-P synthetase, aspartate transcarbamylase, dihydro-orotase (CAD). Mechanisms involving BBF cycles account for only a minority of CAD amplification events in the human fibrosarcoma cell line HT 1080. Here, formation of a 2p isochromosome and overexpression of CAD by other types of amplification events (and even without amplification) are much more prevalent. Broken DNA is recognized by mammalian cells with intact damage-recognition pathways, as a signal to arrest or to die. Loss of these pathways by, for example, loss of p53 or pRb tumour suppressor function, or by increased expression of ras and myc oncogenes, causes non-permissive rat and human cells to become permissive both for amplification and for other manifestations of DNA damage. In cells that are already permissive, amplification can be stimulated by overexpressing oncogenes such as c-myc or ras, or by damaging DNA in a variety of ways. To supplement genetic analysis of amplification in mammalian cells, an amplification selection has been established in Schizosaccharomyces pombe. Selection with LiCl yields cells with amplified sod2 genes in structures related to those observed in mammalian cells. The effect on amplification in S. pombe can now be tested for any mutation in a gene involved in repair of damaged DNA or in normal cellular responses to DNA damage.
Flexible Operating System Internals: The Design and Implementation of the Anykernel and Rump Kernels (2012)

The monolithic kernel architecture is significant in the real world due to the large amount of working and proven code. However, the architecture is not without problems: testing and development is difficult, virtualizing kernel services can be done only by duplicating the entire kernel, and security is weak due to a single domain where all code has direct access to everything. Alternate kernel architectures such as the microkernel and exokernel have been proposed to rectify these problems with monolithic kernels. However, alternate system structures do not address the common desire of using a monolithic kernel when the abovementioned problems do not apply.\nWe propose a flexible anykernel architecture which enables running kernel drivers in a variety of configurations, examples of which include microkernel-style servers and application libraries. A monolithic kernel is shown to be convertible into an anykernel with a reasonable amount of effort and without introducing performance-hindering indirection layers. The original monolithic mode of operation is preserved after the anykernel adjustments, and alternate modes of operation for drivers are available as a runtime choice. For non-monolithic modes of operation, the rump kernel is introduced as a lightweight container for drivers. A rump kernel runs on top of a hypervisor which offers high-level primitives such as thread scheduling and virtual memory. A production quality implementation for the NetBSD open source OS has been done. The anykernel architecture and rump kernels are evaluated both against four years of real-world experience from daily NetBSD development as well as against synthetic benchmarks.
Isolation of two novel <i>myb</i>‐like genes from <i>Arabidopsis</i> and studies on the DNA‐binding properties of their products (1995)

Two novel myb-like genes (atmyb6 and atmyb7) were isolated from an Arabidopsis thaliana cDNA library. The entire proteins or the Myb domains encoded by the genes were expressed as fusion proteins in Escherichia coli. The DNA-binding domain of the murine c-Myb was also expressed in the same way for use in comparative studies. The fusion proteins were examined for their DNA-binding activity using the animal c-Myb DNA-binding site (MBS) and the binding site of the maize P gene product (PBS). The Myb domain of Atmyb6 bound to PBS more efficiently than to MBS. Complete Atmyb6 and Atmyb7 proteins preferentially bound to PBS but not MBS. This suggests that the in vitro binding consensus sequences for both Atmyb6 and Atmyb7 are similar to PBS. The binding of the Myb domain of Atmyb6 to both PBS and MBS raises the possibility that the protein recognizes multiple sequences in vivo. The third alpha-helix and three adjacent amino acids in the third repeat (R3) of c-Myb was replaced with the analogous sequence of Atmyb6 to create a chimeric Myb protein. This chimeric protein bound to PBS with a low affinity but failed to bind to MBS. Thus the binding pattern of the chimeric Myb protein is similar to that of the Atmyb6. This result suggests that the last 20 amino acids in the R3 repeat of Atmyb6 play a major role in DNA-binding.
Principles of collisional activation in analytical mass spectrometry (1992)

Collisional activation has played an essential role in the development of mass spectrometry/mass spectrometry (MS/MS). It was the first activation method to be employed and continues to be by far the most widely used. As instrumentation for MS/MS has evolved it has been found that collisional activation can be effected under a remarkably wide range of conditions for a wide range of ions. It is fair to conclude from the growth of MS/MS over the past fifteen years that collisional activation has been spectacularly successful. However, it has limitations. As a community, we have learned much over the years regarding these limitations both from empirical and fundamental points of view. This overview provides background on the development of collisional activation and discusses the importance of the interaction potential and timing on mechanisms for energy transfer. Parts of the discussion is devoted to changing reference frames from the laboratory to the center of mass to simplify visualizing what is possible and what is probable in collisional activation.
Observers for multivariable systems (1966)

Often in control design it is necessary to construct estimates of state variables which are not available by direct measurement. If a system is linear, its state vector can be approximately reconstructed by building an observer which is itself a linear system driven by the available outputs and inputs of the original system. The state vector of an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> th order system with <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> independent outputs can be reconstructed with an observer of order <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n-m</tex> . In this paper it is shown that the design of an observer for a system with <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</tex> outputs can be reduced to the design of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> separate observers for single-output subsystems. This result is a consequence of a special canonical form developed in the paper for multiple-output systems. In the special case of reconstruction of a single linear functional of the unknown state vector, it is shown that a great reduction in observer complexity is often possible. Finally, the application of observers to control design is investigated. It is shown that an observer's estimate of the system state vector can be used in place of the actual state vector in linear or nonlinear feedback designs without loss of stability.
Dynamic calibration of tipping-bucket raingauges and rainfall intensity data processing (2006)

Two tipping-bucket raingauges and one siphon raingauge with different collecting areas are used at TESTCOM for the measurement of rainfall intensities. These raingauges were dynamically calibrated by flowmeters in June 2006. The used method of dynamic calibration of raingauges and our experience obtained is described. Data obtained from three dynamically calibrated raingauges was statistically processed over three one-month periods and whole 1-year period. The methods of rainfall intensity data processing are described. The cumulative distributions of average 1-minute rainfall intensities obtained from three raingauges, with and without dynamic calibration involved, are presented. The results obtained are compared and discussed.
Molecular systematics and phylogeography of the <i>Gibberella fujikuroi</i> species complex (1998)

Phylogenetic relationships of the phyto-pathogenic Gibberella fujikuroi species complex were investigated by maximum parsimony analysis of DNA sequences from multiple loci. Gene trees inferred from the β-tubulin gene exons and introns, mitochondrial small subunit (mtSSU) rDNA, and 5′ portion of the nuclear 28S rDNA were largely concordant, and in a combined analysis, provide strong statistical support for a phylogeny consistent with species radiations in South America, Africa, and Asia. These analyses place the American clade as a mono-phyletic sister-group of an African-Asian clade. Africa is the most phylogenetically diverse area examined with 16 species, followed by America (12 species) and Asia (8 species). The biogeographic hypothesis proposed from the phylogenetic evidence is based primarily on the formation of natural barriers associated with the fragmentation of the ancient super-continent Gondwana. Discordance of the nuclear ribosomal internal transcribed spacer (ITS) based tree with gene trees from the other loci sequenced is due to nonorthologous ITS2 sequences. The molecular evidence suggests the divergent ITS2 types were combined by an ancient interspecific hybridization (xenologous origin) or gene duplication (paralogous origin) that predates the evolutionary radiation of the G. fujikuroi complex. Two highly divergent nonorthologous ITS2 types designated type I and type II were identified and characterized with conserved ITS and ITS2 type-specific polymerase chain reaction (PCR) primers and DNA sequence analysis. Only the major ITS2 type is discernible when conserved ITS primers are used; however, a minor ITS2 type was amplified from every strain tested with type-specific PCR primers. The evolutionary pattern exhibited by the major ITS2 type is homoplastic when mapped onto the species lineages inferred from the combined nuclear 28S rDNA, mtSSU rDNA, and β-tubulin gene sequences. Remarkably, the data indicate the major ITS2 type has switched between a type I and type II sequence at least three times during the evolution of the G. fujikuroi complex, but neither type has been fixed in any of the 45 species examined. Twenty-six of the 45 species included in this study represent either new species (23 species), new combinations (F. bulbicola and F. phyllophilum), or a rediscovered species (F. lactis). The results further indicate that traditional sectional and species-level taxonomic schemes for this lineage are artificial and a more natural classification is proposed.