gebhart/patrepeval huggingface dataset:
Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli (2012)

We have demonstrated that simple engineering of the RNA-based Csr global regulatory system constitutes a novel approach to obtaining pathway-independent improvements within engineered hosts. Additionally, since Csr is conserved across most prokaryotic species, this approach may also be amenable to a wide variety of production hosts.
Chapter 4 (1981)

Educational levels in the population have grown enormously during the twentieth century, primarily through a process of cohort succession. Educational growth has been concentrated through the spread of grade and high school education, and not through increases in rates of progression from high school to college. Educational growth results from improvements in family socioeconomic standing, shifts in economic incentives, legislative changes facilitating school attendance, and changes in the organization of schools. School enrollment levels since World War II have been heavily influenced by the postwar baby boom and the fertility decline in the 1960s and 1970s. College enrollments will fall significantly in the next few years, but this may be mitigated by increases in the favorability of family circumstances for educational attainment. Socioeconomic differences in educational attainment have been approximately constant through the twentieth century, whereas race differentials in schooling have significantly converged. Performances on standardized aptitude and achievement tests for high school students have declined dramatically since the mid-1960s, a trend due partly to changes in schools' curricula. Elementary schools have consolidated throughout the twentieth century, while secondary schools have been approximately constant in number and institutions of higher education have proliferated.
Investigation of Lamb waves having a negative group velocity (1988)

The propagation characteristics of Lamb waves in a solid plate are typically represented by a set of dispersion curves, which describe the Lamb-wave phase velocity as a function of the product fd, where f is the acoustic frequency and d is the plate thickness. For certain modes, within a range of phase velocity and fd, it has been theoretically predicted that the associated group velocity could be negative, i.e., the energy transport is in the opposite direction to the phase velocity. In the present study, Lamb waves are generated via mode conversion from a water-borne sound beam incident onto a flat brass plate. Measurement of the phase and group velocities of the Lamb waves of the S1 mode is performed for the fd range of 2.0–2.3 MHz-mm. Comparison of the measured and computed values of phase and group velocities shows good agreement and clearly demonstrates that S1-mode Lamb waves have a negative group velocity for fd=2.08–2.24 MHz-mm.
A general and simple method for obtaining <i>R</i> <sup>2</sup> from generalized linear mixed‐effects models (2012)

Summary The use of both linear and generalized linear mixed‐effects models ( LMM s and GLMM s) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion ( AIC ), are usually presented as model comparison tools for mixed‐effects models. The presentation of ‘variance explained’ ( R 2 ) as a relevant summarizing statistic of mixed‐effects models, however, is rare, even though R 2 is routinely reported for linear models ( LM s) and also generalized linear models ( GLM s). R 2 has the extremely useful property of providing an absolute value for the goodness‐of‐fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, R 2 can also be a quantity of biological interest. One reason for the under‐appreciation of R 2 for mixed‐effects models lies in the fact that R 2 can be defined in a number of ways. Furthermore, most definitions of R 2 for mixed‐effects have theoretical problems (e.g. decreased or negative R 2 values in larger models) and/or their use is hindered by practical difficulties (e.g. implementation). Here, we make a case for the importance of reporting R 2 for mixed‐effects models. We first provide the common definitions of R 2 for LM s and GLM s and discuss the key problems associated with calculating R 2 for mixed‐effects models. We then recommend a general and simple method for calculating two types of R 2 (marginal and conditional R 2 ) for both LMM s and GLMM s, which are less susceptible to common problems. This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed‐effects models. The proposed method has the potential to facilitate the presentation of R 2 for a wide range of circumstances.
Engineering Kunitz Domain 1 (KD1) of Human Tissue Factor Pathway Inhibitor-2 to Selectively Inhibit Fibrinolysis (2010)

Tissue factor pathway inhibitor-2 (TFPI-2) inhibits factor XIa, plasma kallikrein, and factor VIIa/tissue factor; accordingly, it has been proposed for use as an anticoagulant. Full-length TFPI-2 or its isolated first Kunitz domain (KD1) also inhibits plasmin; therefore, it has been proposed for use as an antifibrinolytic agent. However, the anticoagulant properties of TFPI-2 or KD1 would diminish its antifibrinolytic function. In this study, structure-based investigations and analysis of the serine protease profiles revealed that coagulation enzymes prefer a hydrophobic residue at the P2' position in their substrates/inhibitors, whereas plasmin prefers a positively charged arginine residue at the corresponding position in its substrates/inhibitors. Based upon this observation, we changed the P2' residue Leu-17 in KD1 to Arg (KD1-L17R) and compared its inhibitory properties with wild-type KD1 (KD1-WT). Both WT and KD1-L17R were expressed in Escherichia coli, folded, and purified to homogeneity. N-terminal sequences and mass spectra confirmed proper expression of KD1-WT and KD1-L17R. Compared with KD1-WT, the KD1-L17R did not inhibit factor XIa, plasma kallikrein, or factor VIIa/tissue factor. Furthermore, KD1-L17R inhibited plasmin with ∼6-fold increased affinity and effectively prevented plasma clot fibrinolysis induced by tissue plasminogen activator. Similarly, in a mouse liver laceration bleeding model, KD1-L17R was ∼8-fold more effective than KD1-WT in preventing blood loss. Importantly, in this bleeding model, KD1-L17R was equally or more effective than aprotinin or tranexamic acid, which have been used as antifibrinolytic agents to prevent blood loss during major surgery/trauma. Furthermore, as compared with aprotinin, renal toxicity was not observed with KD1-L17R.
Inhibitory Effects of Some Natural Products on the Activation of Hyaluronidase and Their Antiallergic Actions. (1992)

The anti-allergic drugs disodium cromoglycate (DSCG) and tranilast are strong inhibitors of hyaluronidase. In the development of new anti-allergic drugs, we studied the inhibitory effects of some natural products on the activation of hyaluronidase. Among the compounds tested, liquiritigenin, isoliquiritigenin and baicalein showed dose-related inhibitory effects. Anti-allergic activities of these compounds were evident from the facts that they inhibited the histamine release from rat peritoneal exudate cells induced by antigen, compound 48/80 and calcium ionophore A-23187, and from their inhibitory effect on Shultz-Dale reaction using sensitized guinea pig ileum.
Low cost routes to high purity silicon and derivatives thereof (2023)

The present invention is directed to a method for providing an agricultural waste product having amorphous silica, carbon, and impurities; extracting from the agricultural waste product an amount of the impurities; changing the ratio of carbon to silica; and reducing the silica to a high purity silicon (e.g., to photovoltaic silicon).
Separation of strains of the yeasts Xanthophyllomyces dendrorhous and Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis (1999)

The type strains of the anamorph Phaffia rhodozyma (CBS 5905) and the teleomorph Xanthophyllomyces dendrorhous (VKM Y-2786) were analyzed by nucleotide sequence analysis and compared to the sequences found in three additional strains (ATCC 24228, ATCC 24230 and CBS 6938). The results of ribosomal DNA Internal transcribed spacer (ITS) and Intergenic spacer (IGS) region analyses indicate that P. rhodozyma, which was isolated from a beech tree, is a distinct species from the other four strains. The latter that were collected from birch trees are considered to be strains of X. dendrorhous. These individual strains of X. dendrorhous, which have geographically distinct isolation sources, can be distinguished by nucleotide substitutions and deletion/insertion gaps in sub-repeat regions of the Intergenic spacer. The conclusions demonstrate that differences in the IGS region provide molecular markers for denoting strains that may differ in their biochemical and physiological capabilities. The hypothesis is presented that strain differences in the IGS region may be useful to demonstrate geographic and host specificity.
Cross-Layer Design of the Inter-RAT Handover between UMTS and WiMAX (2011)

In future mobile networks, different radio access technologies will have to coexist. IEEE 802.21 MIH (Media-Independent Handover) provides primitive mechanisms that ease the implementation of a seamless vertical handover (inter-RAT handover) between different radio access technologies. However, it does not specify any handover execution mechanism. The first objective of this paper is to propose a novel MIHF (Media-Independent Handover Function) variant, which is renamed interworking (IW) sublayer. IW sublayer provides a seamless inter-RAT handover procedure between UMTS and WiMAX systems. It relies on a new intersystem retransmission mechanism with cross-layer interaction ability providing lossless handover while keeping acceptable delays. The second objective of this paper is to design a new TCP snoop agent (TCP Snoop), which interacts with the IW layer in order to mitigate BDP (Bandwidth Delay Product) mismatch and to solve spurious RTO (Retransmission TimeOut) problems. The cross-layer effects on the handover performance are evaluated by simulations. Our results show that cross-layer interaction between IW layer and TCP Snoop smoothes the handover procedure for TCP traffics. Additionally, this novel inter-RAT cross-layer scheme has the merit of keeping existing TCP protocol stacks unchanged.
Pharmacogenetic Associations of MMP9 and MMP12 Variants with Cardiovascular Disease in Patients with Hypertension (2011)

We observed interactions between antihypertensive drugs and MMP9 and MMP12 for CHD and composite CVD. The data suggest that these genes may provide useful clinical information with respect to treatment decisions.
Correction: Neuraminidase Subtyping of Avian Influenza Viruses with PrimerHunter-Designed Primers and Quadruplicate Primer Pools (2013)

We have previously developed a software package called PrimerHunter to design primers for PCR-based virus subtyping. In this study, 9 pairs of primers were designed with PrimerHunter and successfully used to differentiate the 9 neuraminidase (NA) genes of avian influenza viruses (AIVs) in multiple PCR-based assays. Furthermore, primer pools were designed and successfully used to decrease the number of reactions needed for NA subtyping from 9 to 4. The quadruplicate primer-pool method is cost-saving, and was shown to be suitable for the NA subtyping of both cultured AIVs and uncultured AIV swab samples. The primers selected for this study showed excellent sensitivity and specificity in NA subtyping by RT-PCR, SYBR green-based Real-time PCR and Real-time RT-PCR methods. AIV RNA of 2 to 200 copies (varied by NA subtypes) could be detected by these reactions. No unspecific amplification was displayed when detecting RNAs of other avian infectious viruses such as Infectious bronchitis virus, Infectious bursal disease virus and Newcastle disease virus. In summary, this study introduced several sensitive and specific PCR-based assays for NA subtyping of AIVs and also validated again the effectiveness of the PrimerHunter tool for the design of subtyping primers.
Surface Morphology of Annealed Polystyrene and Poly(methyl methacrylate) Thin Film Blends and Bilayers (2003)

Thin films of polystyrene (PS) and poly(methyl methacrylate) (PMMA) were spun-cast onto silicon substrates, annealed, and analyzed by atomic force microscopy (AFM), total electron yield (TEY), and partial electron yield (PEY) near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in order to resolve conflicting prior literature regarding the tendency of PS to form a wetting layer or overlayer on top of PMMA. From the comparison of the three methods of analysis and on the basis of the extraordinary surface sensitivity of PEY NEXAFS, we conclude that PS does not form an overlayer in samples with morphologies near thermodynamic equilibrium. The PS forms droplets of a large size range on top of a PMMA layer that wets the hydrophilic SiOx substrate. From our results, the maximum thickness of a continuous PS wetting layer would be about 0.25 nm. This is in contrast to recent experiments that imply an equivalent PS wetting layer of about 5−10 nm is forming during annealing.
Analysis and design of power efficient class D amplifier output stages (2000)

A Class D amplifier comprises a pulse width modulator and an output stage. In this paper we analyze the power dissipation mechanisms and derive the overall power efficiency of the output stage realized using the finger and waffle layouts. We compare the relative merits of these layouts; we propose two design methodologies to determine the aspect ratios of the transistors in the output stage for optimum power efficiency (optimum for a given fabrication process, supply voltage and load resistance): (1) optimization to a single modulation index point and (2) optimization to a range of modulation indexes. For the design of an output stage with optimum power efficiency (and small IC area), we recommend optimization to a range of modulation indexes and a layout realized by the waffle structure. The theoretical analysis and derivations are verified on the basis of computer simulations and measurements on fabricated prototype ICs.
Development of high temperature superconducting coils using Bi-2223/Ag tapes (1999)

Four double wound pancakes with inner diameters of 98 mm have been successfully fabricated with multifilamentary Bi-2223/Ag tape using the react and wind technique. Two pancakes were impregnated with wax and the other two with resin. The pancakes have been tested at 77 K producing critical current (I/sub c/) values up to 14.5 A and index of transition values (n) of up to 11.4. The field profiles produced by the pancakes have been modelled. The I/sub c/ field dependence of short samples of the component Bi-2223/Ag tape has been studied. I/sub c/ is most sensitive to field when the field is parallel to the c-axis of the tape, reducing I/sub c/ from 28 A to 13.2 A between 0 T and 30 mT. Although the bending strain of the tape in the coil is /spl sim/0.3%, the fabrication procedure for the pancakes has produced very little handling damage to the tapes. It is demonstrated that the I/sub c/ of the coils is almost entirely self field limited.
Non-linear reference model with dynamic regulator for vehicle dynamic control (2015)

The hierarchical control strategy is one of the most widely used strategies for vehicle dynamic control (VDC) implemented in electric vehicles (EVs). This paper describes the design of a novel reference model based on the structure of hierarchical VDC controller. This model can facilitate good handling performance under normal operating conditions and enhance stability under critical conditions. It consists of two parts: a non-linear basic reference model based on a 5DOF vehicle model and a dynamic regulator. Because the target response generated for stability control may be different from the handling target determined by the non-linear basic reference model, with lateral acceleration feedback a regulation coefficient is used to allow a smooth transition between them. Finally, simulation is conducted and the results confirm that tracking this reference model can reduce the driver's burden and keep the vehicle stable.
Structural Features and Healthy Properties of Polysaccharides Occurring in Mushrooms (2012)

Polysaccharides from mushrooms have attracted a great deal of attention due to the many healthy benefits they have demonstrated, such as immunomodulation, anticancer activity, prevention and treatment of cardiovascular diseases, antiviral and antimicrobial effects, among others. Isolation and purification of polysaccharides commonly involve several steps, and different techniques are actually available in order to increase extraction yield and purity. Studies have demonstrated that the molecular structure and arrangement significantly influence the biological activity; therefore, there is a wide range of analytical techniques for the elucidation of chemical structures. Different polysaccharides have been isolated from mushrooms, most of them consisting of β-linked glucans, such as lentinan from Lentinus edodes, pleuran from Pleurotus species, schizophyllan from Schizophyllum commune, calocyban from Calocybe indica, or ganoderan and ganopoly from Ganoderma lucidum. This article reviews the main methods of polysaccharide isolation and structural characterization, as well as some of the most important polysaccharides isolated from mushrooms and the healthy benefits they provide.
Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells (2005)

The hematopoietic stem cell (HSC) compartment is composed of long-term reconstituting (LTR) and short-term reconstituting (STR) stem cells. LTR HSC can reconstitute the hematopoietic system for life, whereas STR HSC can sustain hematopoiesis for only a few weeks in the mouse. Several excellent gene expression profiles have been obtained of the total hematopoietic stem cell population. We have used five-color FACS sorting to isolate separate populations of LTR and STR stem cell subsets. The LTR HSC has the phenotype defined as Lin- Sca+ Kit+ 38+ 34-; two subsets of STR HSC were obtained with phenotypes of Lin- Sca+ Kit+ 38+ 34+ and Lin- Sca+ Kit+ 38- 34+. The microarray profiling study reported here was able to identify genes specific for LTR functions. In the interrogated genes (approximately 12,000 probe sets corresponding to 8,000 genes), 210 genes are differentially expressed, and 72 genes are associated with LTR activity, including membrane proteins, signal transduction molecules, and transcription factors. Hierarchical clustering of the 210 differentially expressed genes suggested that they are not bone marrow-specific but rather appear to be stem cell-specific. Transcription factor-binding site analysis suggested that GATA3 might play an important role in the biology of LTR HSC.
CHAPTER 7. Poly(phenylenevinylene)s (2013)

Poly(phenylenevinylene) PPV is a class of conjugated polymer with great functional group diversity. This has resulted from the wide range of synthetic methods available. The choice of synthetic methods depends on the material requirements for application, particularly in the area of organic electronics. A comprehensive review of the preparation methods is provided along with example experimental procedures for the most popular synthetic routes.
Essential oil eugenol: sources, extraction techniques and nutraceutical perspectives (2017)

Graphical representation regarding sources, extraction techniques and nutraceutical perspectives of eugenol.
EGFR and K‐ras Mutation Analysis in Non‐Small Cell Lung Cancer: Comparison of Paraffin Embedded versus Frozen Specimens (2007)

Our results indicate that RNA extracted from frozen tissue is the preferred source for EGFR and K-ras mutation testing. When analyzing FPE samples, reducing the size of the amplified fragments would increase PCR success rate, and care should be taken to control for false-positive results.
SCG3 Transcript in Peripheral Blood Is a Prognostic Biomarker for REST-Deficient Small Cell Lung Cancer (2008)

SCG3 mRNA, a component of the REST-dependent neurosecretory transcriptional profile, provides a sensitive prognostic biomarker for noninvasive monitoring of neuroendocrine lung cancer.
Redesigning the old 555 [timer circuit] (1997)

It is rare that an integrated circuit stays on the market for 25 years. And it is surprising that, except for a CMOS derivative, the 555 timer has never been updated. It has been shrunk somewhat, but the original schematic and layout have remained intact. For a long time this situation could be explained by the versatility of the 555, whose speed, current draw and voltage range sit right in the middle of a vast field of applications. But in the last few years, supply voltages have moved downward, well below the 4.5 V at which the 555 cuts off, and the unit's 5-10 mA current requirement now seems wasteful. A better design is clearly needed. The author describes the features of the original timer before discussing the redesign. The voltage versus current design and output stage are discussed.
Assessing out-of-band flare effects at the wafer level for EUV lithography (2010)

To accurately estimate the flare contribution from the out-of-band (OOB), the integration of a DUV source into the SEMATECH Berkeley 0.3-NA Micro-field Exposure tool is proposed, enabling precisely controlled exposures along with the EUV patterning of resists in vacuum. First measurements evaluating the impact of bandwidth selected exposures with a table-top set-up and subsequent EUV patterning show significant impact on line-edge roughness and process performance. We outline a simulation-based method for computing the effective flare from resist sensitive wavelengths as a function of mask pattern types and sizes. This simulation method is benchmarked against measured OOB flare measurements and the results obtained are in agreement.
Simulations of Multi-Phase Particle Deposition on Endwall Film-Cooling Holes in Transverse Trenches (2011)

Integrated gasification combined cycle (IGCC) power plants allow for increased efficiency and reduced emissions as compared to pulverized coal plants. A concern with IGCCs is that impurities in the fuel from the gasification of coal can deposit on turbine components reducing the performance of sophisticated film-cooling geometries. Studies have shown that recessing a row of film-cooling holes in a transverse trench can improve cooling performance; however, the question remains as to whether or not these improvements exist in severe environments such as when particle deposition occurs. Dynamic simulations of deposition were completed using wax injection in a large-scale vane cascade with endwall film-cooling. Endwall cooling effectiveness was quantified in two specific endwall locations using trenches with depths of 0.4D, 0.8D, and 1.2D, where D is the diameter of a film-cooling hole. The effects of trench depth, momentum flux ratio, and particle phase on adiabatic effectiveness were quantified using infrared thermography. Results showed that the 0.8D trench outperformed other geometries with and without deposition on the surface. Deposition of particles reduced the cooling effectiveness by as much as 15% at I = 0.23 with the trenched holes as compared to 30% for holes that were not placed in a transverse trench.