gebhart/patrepeval huggingface dataset:
Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains (2015)

Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.
CEREBRAL THROMBOANGIITIS OBLITERANS (1957)

Assistant Clinical Professor of Neurology, Harvard Medical School and Neurologist, Massachusetts General Hospital, Boston
Improved retarding field optics via image outside field (1995)

The advantages of a retarding field immersion lens for focusing low energy electrons and ions have been well chronicled. One recent development is a retarding field lens in which the sample is outside the retarding field (i.e., a nonimmersion lens). Thus, any sample roughness will not distort the focusing field. We describe here a simple model and analysis that indicates that the performance of such a lens can be almost as good as that of a retarding field immersion lens. For example, it should be possible to focus 1 keV electrons with an energy spread of 1 eV into a beam diameter of 4 nm using realistic values of maximum voltage and retarding field strength; the effective resolution under these conditions is estimated to be 1.4 nm.
Invloed van mastitis op melkproduksie, somatiese seltelling, natrium-, kalium-en laktosekonsentrasies in beesmelk (1990)

Influence of mastitis on milk production, somatic cell count, and concentrations of sodium, potassium and lactose in bovine milk . Milk production, somatic cell count, and concentrations of sodium, potassium and lactose of 32 pairs of normal equivalent quarters as well as 54 pairs of equivalent quarters, in the case of which one quarter was affected with subclinical mastitis, were investigated. Affected quarters showed a definite decrease in milk production, lactose and potassium content. The mastitis quarters showed an increase in the somatic cell count and sodium content. Melkproduksie, somatiese seltelling, natrium-, kalium- en laktose-inhoud van 32 pare normaal-ooreenstemmende kwarte asook 54 pare ooreenstemmende kwarte, waarvan een kwart met subkliniese mastitis aangetas was, is ondersoek. Besmette kwarte het 'n afname in melkproduksie, laktose- en kaliuminhoud getoon. Die mastitiskwarte het 'n toename in somatiese seltelling en natriuminhoud getoon. Keywords : Lactose, mastitis, milk production, potassium, sodium, somatic cell count.
A Facile and Efficient Synthesis of 3,3-Dimethyl Isopropylidene Proline From (+)-3-Carene (2010)

A highly efficient and practical route to 3,4-isopropylidene proline I, starting from (+)-3-carene, was developed. The three continuous stereocenters were constructed using the inherent chirality of the starting natural product 2. The overall yield for the 12-step synthesis is 34%. The optimized sequence leading to 1 has been successfully applied on a multigram scale, thereby establishing the practicality of this route.
miRBase: annotating high confidence microRNAs using deep sequencing data (2013)

We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.
Real-time emulation for power equipmentdevelopment.Part 2: The virtual machine (1998)

Power electronic control of electromechanical systems has become common. These systems employ electronic components which switch at high frequency and have very complex interactions. The load which they supply is often intricate in itself and difficult (or often impossible) to create in an experimental environment. It would be advantageous to replace the electromechanics with a solid-state equivalent which can be flexibly programmed to emulate the real system. The paper is concerned with describing this idea, illustrating the concept by emulating an electric motor and its associated mechanical load. The phrase ‘virtual machine’ has been coined to describe the system. It gives/takes power from the electronic converter to match as closely as possible the real electrical machine and load. The virtual machine is effectively a dynamically controllable source/sink which is capable of providing a bidirectional power level interface to a power electronic converter. Using the virtual machine, a power electronic converter can be tested in diverse applications and under a wide variety of loading conditions without the need for any electromechanics. Test results show that close agreement between the virtual and real systems is possible. The limits imposed by practical implementation of the concept are also examined.
Conclusion (1991)

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Ionization-Induced Electron Trapping in Ultrarelativistic Plasma Wakes (2007)

The onset of trapping of electrons born inside a highly relativistic, 3D beam-driven plasma wake is investigated. Trapping occurs in the transition regions of a Li plasma confined by He gas. Li plasma electrons support the wake, and higher ionization potential He atoms are ionized as the beam is focused by Li ions and can be trapped. As the wake amplitude is increased, the onset of trapping is observed. Some electrons gain up to 7.6 GeV in a 30.5 cm plasma. The experimentally inferred trapping threshold is at a wake amplitude of 36 GV/m, in good agreement with an analytical model and PIC simulations.
Psychological Effects of Cyclosporin A (2003)

One of the most widely used immunosuppressive drugs is cyclosporin A. This fungal metabolite extracted from Tolypocladium inflatum Gams was introduced in early 1970s and has been used in organ transplantation. Recently, neural transplantation became a potential treatment for neurodegenerative disorders such as Parkinson’s disease, Alzheimer’ s disease and Huntington’s disease. Because these diseases are associated with cognitive disorder, examination of possible effects of cyclosporin A upon cognitive ability is an important topic. There is no direct evidence demonstrating that cyclosporin A passes the blood—brain barrier, but several experimental data suggest CNS effects after systemic injection of cyclosporin A (e.g., 1, 2). Even though psychological effects of cyclosporin A may be principally mediated by peripheral mechanisms, it is also essential to identify the brain processes accompanying such effects. Elucidation of neural mechanisms underlying cyclosporin A will allow not only a better understanding of central action of the drug in producing psychological effects, but also draw attention to the potential use of cyclosporin A as a therapeutic agent for brain dysfunctions.
Basic block distribution analysis to find periodic behavior and simulation points in applications (2002)

Modern architecture research relies heavily on detailed pipeline simulation. Simulating the full execution of an industry standard benchmark can take weeks to months to complete. To overcome this problem researchers choose a very small portion of a program's execution to evaluate their results, rather than simulating the entire program. In this paper we propose Basic Block Distribution Analysis as an automated approach for finding these small portions of the program to simulate that are representative of the entire program's execution. This approach is based upon using profiles of a program's code structure (basic blocks) to uniquely identify different phases of execution in the program. We show that the periodicity of the basic block frequency profile reflects the periodicity of detailed simulation across several different architectural metrics (e.g., IPC, branch miss rate, cache miss rate, value misprediction, address misprediction, and reorder buffer occupancy). Since basic block frequencies can be collected using very fast profiling tools, our approach provides a practical technique for finding the periodicity and simulation points in applications.
Molecular Mechanism of Anti-Prostate Cancer Activity of<i>Scutellaria Baicalensis</i>Extract (2007)

Scutellaria baicalensis is a widely used Chinese herbal medicine historically used in antiinflammatory and anticancer therapy. The goals of the study were to 1) determine its in vitro and in vivo anti-prostate cancer activity, 2) investigate its molecular mechanism directed at cell proliferation control including cyclooxygenase-2(COX-2) prostaglandin E2 (PGE2) and cyclins/cdks pathways, and 3) compare it with those of PC-SPES (PC stands for prostate cancer and spes is Latin for hope), a former herbal mixture for prostate cancer treatment of which S. baicalensis is a major constituent. Two human prostate cancer cell lines (LNCaP, androgen dependent, and PC-3, androgen independent) were assessed for growth inhibition. S. baicalensis exerted dose- and time-dependent increased growth inhibition in both cell lines. However, the PC-3 cells IC50 (50% growth inhibition concentration) were slightly more sensitive than LNCaP cells (IC50=0.15 mg/ml), although the former is androgen independent. S. baicalensis was more effective in inhibition of cell growth compared with PC-SPES (IC50=0.38 mg/ml for PC-3 cells). Significant reduction of PGE2 synthesis in both cells after treatment with S. baicalensis resulted from direct inhibition of COX-2 activity rather than COX-2 protein suppression. S. baicalensis also inhibited prostate-specific antigen production in LNCaP cells. Finally, S. baicalensis suppressed expression of cyclin D1 in LNCaP cells, resulting in a G1 phase arrest, while inhibiting cdk1 expression and kinase activity in PC-3 cells, ultimately leading to a G2/M cell cycle arrest. Animal studies showed a 50% reduction in tumor volume after a 7-wk treatment period. This study demonstrated that S. baicalensis may be a novel anticancer agent for the treatment of prostate cancer.
Buffered clock tree for high quality IC design (2004)

In ultra-deep submicron VLSI designs, clock network layout plays an increasingly important role on determining circuit quality indicated by timing, power consumption, cost, power supply noise and tolerance to process variations. In this paper, a clock tree routing algorithm is proposed to achieve any prescribed non-zero skews which are useful in reducing clock cycle time, suppressing power supply noise and improving tolerance to process variations. The interactions among skew targets, sink location proximities and capacitive load balance are analyzed. Based on this analysis, a maximum delay-target ordering merging scheme is suggested to minimize wire and buffer area which imply cost, power consumption and vulnerability to process variations. During the clock routing, buffers are inserted simultaneously to facilitate a proper skew rate level and reduce wire snaking. The proposed algorithm is simple and fast for practical applications. Experimental results on benchmark circuits show that the proposed algorithm can reduce the total wire and buffer capacitance by 60% over an extension of existing zero skew routing method.
Natural Honey Lowers Plasma Glucose, C-Reactive Protein, Homocysteine, and Blood Lipids in Healthy, Diabetic, and Hyperlipidemic Subjects: Comparison with Dextrose and Sucrose (2004)

This study included the following experiments: (1) effects of dextrose solution (250 mL of water containing 75 g of dextrose) or honey solution (250 mL of water containing 75 g of natural honey) on plasma glucose level (PGL), plasma insulin, and plasma C-peptide (eight subjects); (2) effects of dextrose, honey, or artificial honey (250 mL of water containing 35 g of dextrose and 40 g of fructose) on cholesterol and triglycerides (TG) (nine subjects); (3) effects of honey solution, administered for 15 days, on PGL, blood lipids, C-reactive protein (CRP), and homocysteine (eight subjects); (4) effects of honey or artificial honey on cholesterol and TG in six patients with hypercholesterolemia and five patients with hypertriglyceridemia; (5) effects of honey for 15 days on blood lipid and CRP in five patients with elevated cholesterol and CRP; (6) effects of 70 g of dextrose or 90 g of honey on PGL in seven patients with type 2 diabetes mellitus; and (7) effects of 30 g of sucrose or 30 g of honey on PGL, plasma insulin, and plasma C-peptide in five diabetic patients. In healthy subjects, dextrose elevated PGL at 1 (53%) and 2 (3%) hours, and decreased PGL after 3 hours (20%). Honey elevated PGL after 1 hour (14%) and decreased it after 3 hours (10%). Elevation of insulin and C-peptide was significantly higher after dextrose than after honey. Dextrose slightly reduced cholesterol and low-density lipoprotein-cholesterol (LDL-C) after 1 hour and significantly after 2 hours, and increased TG after 1, 2, and 3 hours. Artificial honey slightly decreased cholesterol and LDL-C and elevated TG. Honey reduced cholesterol, LDL-C, and TG and slightly elevated high-density lipoprotein-cholesterol (HDL-C). Honey consumed for 15 days decreased cholesterol (7%), LDL-C (1%), TG (2%), CRP (7%), homocysteine (6%), and PGL (6%), and increased HDL-C (2%). In patients with hypertriglyceridemia, artificial honey increased TG, while honey decreased TG. In patients with hyperlipidemia, artificial honey increased LDL-C, while honey decreased LDL-C. Honey decreased cholesterol (8%), LDL-C (11%), and CRP (75%) after 15 days. In diabetic patients, honey compared with dextrose caused a significantly lower rise of PGL. Elevation of PGL was greater after honey than after sucrose at 30 minutes, and was lower after honey than it was after sucrose at 60, 120, and 180 minutes. Honey caused greater elevation of insulin than sucrose did after 30, 120, and 180 minutes. Honey reduces blood lipids, homocysteine, and CRP in normal and hyperlipidemic subjects. Honey compared with dextrose and sucrose caused lower elevation of PGL in diabetics.
A trace-based binary compilation framework for energy-aware computing (2004)

Energy-aware compilers are becoming increasingly important for embedded systems due to the need to meet conflicting constraints on time, code size and power consumption. We introduce a trace-based, offline compiler framework on binaries and demonstrate its benefits in supporting energy optimisations. The key innovation lies in identifying frequently executed paths in a binary program and duplicating them as single-entry traces. Separating frequently from infrequently executed paths enables the compiler to focus both performance and energy optimisations on the hot traces.Traces constructed at the level of binaries are inherently inter-procedural, spanning both application and library code. Such a framework allows an embedded application developer to exploit optimisation opportunities made possible due to the information that is available only at link time.We describe the implementation of our trace-based framework in alto, a link-time optimiser for the Alpha architecture. We present a new algorithm for constructing the hot traces from binaries. This algorithm is both effective (since the execution cycles are mostly spent on traces) and practical (due to small code size increases caused). We have developed and implemented a new optimisation to reduce the functional unit leakage energy. We show how the traces facilitate the development of such an optimisation, which results in significant leakage energy savings for benchmark programs at the cost of small performance penalties.
Experimental Design for Estimating Electro-Thermophysical Properties of a Thermopile Thermal Radiation Detector (1998)

As the Earth's atmosphere evolves due to human activity, today's modern industrial society relies significantly on the scientific community to foresee possible atmospheric complications such as the celebrated greenhouse effect. Scientists, in turn, rely on accurate measurements of the Earth Radiation Budget (ERB) in order to quantify changes in the atmosphere. The Thermal Radiation Group (TRG), a laboratory in the Department of Mechanical Engineering at Virginia Polytechnic Institute and State University, has been at the edge of technology designing and modeling ERB instruments. \nTRG is currently developing a new generation of thermoelectric detectors for ERB applications. These detectors consist of an array of thermocouple junction pairs that are based on a new thermopile technology using materials whose electro-thermophysical properties are not completely characterized. \nThe objective of this investigation is to design experiments aimed at determining the electro-thermophysical properties of the detector materials. These properties are the thermal conductivity and diffusivity of the materials and the Seebeck coefficient of the thermocouple junctions. Knowledge of these properties will provide fundamental information needed for the development of optimally designed detectors that rigorously meet required design specifications.
μGC × μGC: Comprehensive Two-Dimensional Gas Chromatographic Separations with Microfabricated Components (2014)

The development and characterization of a microanalytical subsystem comprising silicon-micromachined first- and second-dimension separation columns and a silicon-micromachined thermal modulator (μTM) for comprehensive two-dimensional (i.e., μGC × μGC) separations are described. The first dimension consists of two series-coupled 3.1 cm × 3.1 cm μcolumn chips with etched channels 3 m long and 250 μm × 140 μm in cross section, wall-coated with a poly(dimethylsiloxane) (PDMS) stationary phase. The second dimension consists of a 1.2 cm × 1.2 cm μcolumn chip with an etched channel 0.5 m long and 46 μm × 150 μm in cross section wall-coated with either a trigonal tricationic room-temperature ionic liquid (RTIL) or a commercial poly(trifluoropropylmethyl siloxane) (OV-215) stationary phase. The two-stage, cryogen-free μTM consists of a Si chip containing two series-coupled, square spiral channels 4.2 cm and 2.8 cm long and 250 μm × 140 μm in cross section wall-coated with PDMS. Conventional injection methods and flame ionization detection were used. Temperature-ramped separations of a simple alkane mixture using the RTIL-coated second-dimension ((2)D) μcolumn produced reasonably good peak shapes and modulation numbers; however, strong retention of polar compounds on the RTIL-coated (2)D μcolumn led to excessively broad peaks with low (2)D resolution. Substituting OV-215 as the (2)D μcolumn stationary phase markedly improved the performance, and a structured 22 min chromatogram of a 36-component mixture spanning a vapor pressure range of 0.027 to 13 kPa was generated with modulated peak fwhm (full width at half-maximum) values ranging from 90 to 643 ms and modulation numbers of 1-6.
PMD-insensitive DOP-based OSNR monitoring by spectral SOP measurements (2005)

We present a DOP (degree of polarization) based OSNR (optical signal-to-noise ratio) monitoring method with spectral SOP (state of polarization) measurement to perform OSNR measurements insensitive to PMD (polarization-mode dispersion). Measurements at OSNR = 25 dB and DGD (differential group delay) = 32% of bitslot are performed with a standard deviation of 0.67 dB.
Alternatives to in-feed antibiotics in pigs: Evaluation of probiotics, zinc or organic acids as protective agents for the intestinal mucosa. A comparison of in vitro and in vivo results (2005)

Weaned pigs are susceptible to frequent infectious diseases. Antibiotics have been used over decades to reduce pathogen infections, but many microorganisms are becoming resistant to antibiotics. Thus, there is an urgent need to find alternatives to in-feed antibiotics. Up to now, various compounds have been used as alternatives, giving promising but sometimes contrasting results. In recent years, the in vitro models of cell culture have been proposed for the screening of various compounds and understanding their mechanisms of action. The intestine is a complex system with a continuous cross-talk among epithelial cells, the local immune system and microflora. Alternatives to in-feed antibiotics may interact with any of these constituents. This review presents data on the protective effects of probiotics, zinc salts and organic acids, used as alternatives to in-feed antibiotics, against pathogen induced damage and inflammatory processes in the intestinal cells and the underlying mechanisms, with an attempt to compare in vitro and in vivo results. All the alternatives tested resulted in effective protection against pathogens by a series of interactions with intestinal cells and pathogens, including the inhibition of adhesion and invasion of pathogens, interference in signalling pathways induced by pathogenic bacteria, maintenance of the epithelial cell cytoskeleton and junctional structure and modulation of the host immune response.
EXTENSION OF ISCHEMIC TOLERANCE OF PORCINE LIVERS BY COLD PRESERVATION INCLUDING POSTCONDITIONING WITH GASEOUS OXYGEN1 (2001)

Venous systemic oxygen persufflation in combination with antioxidative medication is a promising new method of resuscitating ischemically altered livers from nonheartbeating donors for successful transplantation.