gebhart/patrepeval huggingface dataset:
Reconstruction of <i>de novo</i> pathway for synthesis of UDP‐glucuronic acid and UDP‐xylose from intrinsic UDP‐glucose in <i>Saccharomyces cerevisiae</i> (2006)

UDP-D-glucuronic acid and UDP-D-xylose are required for the biosynthesis of glycosaminoglycan in mammals and of cell wall polysaccharides in plants. Given the importance of these glycans to some organisms, the development of a system for production of UDP-D-glucuronic acid and UDP-D-xylose from a common precursor could prove useful for a number of applications. The budding yeast Saccharomyces cerevisiae lacks an endogenous ability to synthesize or consume UDP-D-glucuronic acid and UDP-D-xylose. However, yeast have a large cytoplasmic pool of UDP-D-glucose that could be used to synthesize cell wall beta-glucan, as a precursor of UDP-D-glucuronic acid and UDP-D-xylose. Thus, if a mechanism for converting the precursors into the end-products can be identified, yeast may be harnessed as a system for production of glycans. Here we report a novel S. cerevisiae strain that coexpresses the Arabidopsis thaliana genes UGD1 and UXS3, which encode a UDP-glucose dehydrogenase (AtUGD1) and a UDP-glucuronic acid decarboxylase (AtUXS3), respectively, which are required for the conversion of UDP-D-glucose to UDP-D-xylose in plants. The recombinant yeast strain was capable of converting UDP-D-glucose to UDP-D-glucuronic acid, and UDP-D-glucuronic acid to UDP-D-xylose, in the cytoplasm, demonstrating the usefulness of this yeast system for the synthesis of glycans. Furthermore, we observed that overexpression of AtUGD1 caused a reduction in the UDP-D-glucose pool, whereas coexpression of AtUXS3 and AtUGD1 did not result in reduction of the UDP-D-glucose pool. Enzymatic analysis of the purified hexamer His-AtUGD1 revealed that AtUGD1 activity is strongly inhibited by UDP-D-xylose, suggesting that AtUGD1 maintains intracellular levels of UDP-D-glucose in cooperation with AtUXS3 via the inhibition of AtUGD1 by UDP-D-xylose.
Study of the Influence of Osmotic Dehydration and Freezing on the Volatile Profile of Strawberries (2002)

ABSTRACT: The effect of osmotic process conditions on the volatile fraction of strawberries was studied, as well as the effect of freezing and frozen storage. Osmotic treatments were carried out on strawberries in sucrose solutions up to 20 °Brix, at atmospheric pressure (OD), and by applying a vacuum pulse (PVOD). Volatile compounds of fresh, dehydrated, and frozen‐stored (at –18 °C for 1 mo) samples were obtained by simultaneous distillation‐extraction. Osmotic treatments caused an increase in ester concentration and, in some cases, in furaneol less marked in PVOD. Freezing implied losses in all components, although in pre‐dehydrated samples the concentration of some esters (and furaneol) remained greater than in the fresh samples.
Analysis of<i>DPP6</i>and<i>FGGY</i>as candidate genes for amyotrophic lateral sclerosis (2009)

DPP6 and FGGY genes have been recently associated with an increased susceptibility for sporadic amyotrophic lateral sclerosis. Here, we evaluated the role of these genes in ALS pathogenesis by undertaking a sequence analysis of a cohort of 190 ALS patients from France and Quebec. We did not observe any evidence that mutations in DPP6 and FGGY genes are involved in ALS. Our data indicate that mutations in these genes are unlikely to be a common cause of ALS in the French and French Canadian populations.
Architecture of a Fungal Fatty Acid Synthase at 5 A Resolution (2006)

All steps of fatty acid synthesis in fungi are catalyzed by the fatty acid synthase, which forms a 2.6-megadalton alpha6beta6 complex. We have determined the molecular architecture of this multienzyme by fitting the structures of homologous enzymes that catalyze the individual steps of the reaction pathway into a 5 angstrom x-ray crystallographic electron density map. The huge assembly contains two separated reaction chambers, each equipped with three sets of active sites separated by distances up to approximately 130 angstroms, across which acyl carrier protein shuttles substrates during the reaction cycle. Regions of the electron density arising from well-defined structural features outside the catalytic domains separate the two reaction chambers and serve as a matrix in which domains carrying the various active sites are embedded. The structure rationalizes the compartmentalization of fatty acid synthesis, and the spatial arrangement of the active sites has specific implications for our understanding of the reaction cycle mechanism and of the architecture of multienzymes in general.
Quantum limit of magnetic recording density (2001)

Macroscopic quantum tunneling imposes an upper limit on the areal density of magnetic disk drives. We derive a general expression for this limit, and apply it to Co-alloy-based longitudinally recorded media, as well as to potential future media based on the high anisotropy material FePt. We estimate the temperature at which the switching rate due to quantum tunneling becomes comparable to the thermally activated switching rate. This is the lowest temperature to which a magnetic storage device can be cooled with the expectation of increasing the areal density by enhancing stability against spontaneous switching.
Adaptation of Energy Metabolism in Breast Cancer Brain Metastases (2007)

Brain metastases are among the most feared complications in breast cancer, as no therapy exists that prevents or eliminates breast cancer spreading to the brain. New therapeutic strategies depend on specific knowledge of tumor cell properties that allow breast cancer cell growth within the brain tissue. To provide information in this direction, we established a human breast cancer cell model for brain metastasis based on circulating tumor cells from a breast cancer patient and variants of these cells derived from bone or brain lesions in immunodeficient mice. The brain-derived cells showed an increased potential for brain metastasis in vivo and exhibited a unique protein expression profile identified by large-scale proteomic analysis. This protein profile is consistent with either a selection of predisposed cells or bioenergetic adaptation of the tumor cells to the unique energy metabolism of the brain. Increased expression of enzymes involved in glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation pathways suggests that the brain metastatic cells derive energy from glucose oxidation. The cells further showed enhanced activation of the pentose phosphate pathway and the glutathione system, which can minimize production of reactive oxygen species resulting from an enhanced oxidative metabolism. These changes promoted resistance of brain metastatic cells to drugs that affect the cellular redox balance. Importantly, the metabolic alterations are associated with strongly enhanced tumor cell survival and proliferation in the brain microenvironment. Thus, our data support the hypothesis that predisposition or adaptation of the tumor cell energy metabolism is a key element in breast cancer brain metastasis, and raise the possibility of targeting the functional differentiation in breast cancer brain lesions as a novel therapeutic strategy.
30 GHz Zeno-based Graphene Electro-optic Modulator (2015)

Graphene has generated exceptional interest as an optoelectronic material because its high carrier mobility and broadband absorption promise to make extremely fast and broadband electro-optic devices possible. Electro-optic graphene modulators reported to date, however, have been limited in bandwidth to a few GHz because of the large capacitance required to achieve reasonable voltage swings. Here we demonstrate a graphene electro-optic modulator based on the classical Zeno effect that shows drastically increased speed and efficiency. Our device operates with a 30 GHz bandwidth, over an order of magnitude faster than prior work, and a state-of-the-art modulation efficiency of 1.5 dB/V. We also show the first high-speed large-signal operation in a graphene modulator, paving the way for fast digital communications using this platform. The modulator uniquely uses silicon nitride waveguides, an otherwise completely passive material platform, with promising applications for ultra-low-loss broadband structures and nonlinear optics.
High frequency ultrasound signal statistics from mouse mammary tissue during involution (2005)

We investigate the use of signal envelope statistics to monitor the tissue restructuring process during mouse mammary tissue involution. Using an f/3 transducer operating at a centre frequency of 20 MHz, ultrasound backscatter data were collected from mouse mammary tissue following removal of the litter. The signal envelope statistics were examined by fitting the Rayleigh and generalized gamma distributions. The goodness of fit of the distributions was evaluated by the Kolmogorov-Smirnov test. The goodness of fit of the Rayleigh distribution increased to a maximum at day 3 of involution, roughly corresponding to the peak of apoptosis in the tissue. Similarly, the fit parameters of the generalized gamma distribution indicate that at day 3 the distribution is most Rayleigh like. It is believed that the condensation of the nucleus and reorganization of the tissue structure produced these changes in the statistics of the signal envelope. The results demonstrate that high frequency ultrasound signal envelope statistics can be applied to monitor changes to tissue structure in vivo.
Molecular Identification of AMY, an Alzheimer Disease Amyloid-Associated Protein (2003)

One of the neuropathological lesions characteristic of Alzheimer disease (AD) is the cerebral accumulation of the amyloid beta-peptide (A beta). Although numerous studies have demonstrated that A beta spontaneously forms amyloid in vitro, the molecular events underlying A beta amyloid formation in vivo are less well understood. Immunohistochemical studies have shown that other proteins colocalize with A beta in amyloid deposits in brain. The identity of one of these proteins, AMY, has so far remained elusive; therefore we attempted to purify AMY. The AMY protein was found to co-purify with A beta in insoluble fractions from human AD brain, and was absent in brains from control subjects. AMY immunoreactivity was primarily restricted to a 50-kDa and 100-kDa protein species. Interestingly, the chromatographic and immunological profile of AMY resembled the recently identified amyloid-associated protein CLAC, derived from a transmembrane collagen-like precursor, CLAC-P. Antibodies against AMY recognized CLAC-P expressed in mammalian cells. In addition, side-by-side comparisons of AD brain sections and extracts, using antibodies against both AMY and CLAC, respectively, resulted in almost identical staining patterns. Therefore, we conclude that the AMY immunoreactivity seen in association with amyloid in AD brain is due to the presence of the CLAC protein.
Surface and bulk characteristics of a polyether urethane for artificial hearts (1975)

A segmented polyether urethane was used as the blood contacting surface in a series of 10 heart assist devices implanted in calves for periods up to 35 weeks. At termination, each was examined to correlate blood compatibility and device performance with surface properties, chemical purity, physical stability and affinity for lipid absorption.
Black Words and the Flinders University Librarian Trainee (2008)

The first Indigenous Librarian Trainee at Flinders University presents an account of BlackWords, a leading online database of Indigenous Australian writing and storytelling. The Black Words (http://www.austlit.edu.au/specialistDatasets/BlackWords), is a team of five Indigenous women committed to Indigenous literature in all its forms.
Triplet radical pairs of 3‐carboxyproxyl encapsulated in a dendritic box (1995)

The encapsulation of small molecules inside a dendrimeric “box” has recently been reported. Here, the encapsulation and mobility of triplet radical moieties is described. For “boxes” (e.g. see Figure) containing two or more radicals the intermolecular ferromagnetic alignment of the encapsulated radicals to triplet state radical pairs is observed. magnified image
Design and implementation of WIMAX LDPC code decoder based on FPGA (2012)

A partial parallel low density parity-check(LDPC) code decoder architecture based on turbo decoding message passing(TDMP)-normalized minimun sum(NMS) algorithm is proposed,which can not only achieve a convergence speed as high as TDMP algorithm,but also possess the easy-to-implement advantage of NMS algorithm while keeping a good bit error rate(BER) performance.The decoder supports the decoding of LDPC code of any code rate and code length defined in WIMAX standard.A barrel shifter-based shuffle network is designed which enables the decoder to support all the 19 code lengths.A dynamic iteration stopping criterion suitable for TDMP algorithm and its simplified version is employed with which the decoder can adjust the iteration number according to the decoding state adaptively.Experimental results show that the schemes proposed reduce the hardware cost as well as improve the throughput of the decoder effectively.
Enhanced Nitrogen Removal and Distribution Distributions ofMicrobial Genes Associated with Nitrogen Cycling in AVertical-flow Biofilter Treating Domestic Wastewater (2018)

Vertical-flow biofilters have been investigated as a sustainable technology for nitrogen (N) and chemical oxygen demand (COD) removal from domestic wastewater. However, the distribution contributions of microbial genes responsible for removing N remain largely unexplored, particularly along the depth gradient in vertical-flow biofilters. Here, a three-stage vertical-flow bio-filter (three stages: P1, P2, and P3) achieved large removal efficiencies for total nitrogen (TN; 87.00% and 33.69 g/m2·d), NH4 +-N (95.90% and 24.17 g/m2·d) and COD (92.00% and 558.15 g/ m2·d). The removal contributions of NH4+-N and TN in P1, P2, and P3 can be ranked as follows: P1 (45.9% and 38.4%, respectively) >P2 (39.6% and 28.2%, respectively) >P3 (10.6% and 20.5% respectively). The results revealed that amoA/bacteria, (nirK + nirS + nosZ)/bacteria, amoA/anammox and anammox/bacteria were the predominant gene groups responsible for NH4+-N and TN removal in P1, P2 and P3 and the contributions of these gene groups along the depth gradient of the bio-filter. Specifically, the NO3--N removal rate in P3 was notably enhanced and collectively governed by the (napA + narG) and nxrA gene groups. Integrated analyses confirmed that the coupling of nitrification and denitrification governed the enhanced removal of NH4+-N and TN in P1. Combining anammox and nitrification contributed to the removal of NH4+-N and TN in P2. Enhanced anammox and denitrification accounted for the robust TN reduction in P3. This study indicated that biofilters have great potential applicability for treating domestic wastewater without a sequential chain of treatments and extra aerations.
Arbitrary Viewpoint Rendering from Multiple Omnidirectional Images for Interactive Walkthroughs (2002)

Fig.1 Arbitrary novel viewpoint and multiple positions of omnidirectional camera. Recently, the interactive walkthrough which enables us to look around a virtualized real world has been widely investigated. The walkthrough system can be applied to simulation, telepresence, and so on. This paper describes a method of interactive walkthrough which takes a real scene and enables us to look around in the virtualized scene. Our method is based on acquiring omnidirectional images at multiple points in the real world by using an omnidirectional camera. The method generates an omni-directional image at an arbitrary location from captured omnidirectional images, and presents a user a converted view-dependent perspective image. In the experiment, we realized the interactive walkthrough using indoor omnidi-rectional images and confirmed the feasibility of the method.
Average cost temporal-difference learning (2002)

We describe a variant of temporal-difference learning that approximates average and differential costs of an irreducible aperiodic Markov chain. Approximations are comprised of linear combinations of fixed basis functions whose weights are incrementally updated during a single endless trajectory of the Markov chain. We present results concerning convergence and the limit of convergence. We also provide a bound on the resulting approximation error that exhibits an interesting dependence on the "mixing time" of the Markov chain. The results parallel previous work by the authors (1997), involving approximations of discounted cost-to-go.
Determining the Nucleation Rate Curve for Lithium Disilicate Glass by Differential Thermal Analysis (1990)

The crystallization of lithium disilicate (Li 2 O·2SiO 2 ) glass nucleated at various temperatures was studied by differential thermal analysis (DTA). A plot of the DTA crystallization peak height versus nucleation temperature closely resembles the classical nucleation rate curve for lithium disilicate glass whose maximum is at 453°C. The glass becomes saturated with internal nuclei when heated at 453°C for 10 h. The DTA technique is a rapid, alternative method for determining the temperature for maximum nucleation. The activation energy for crystallization, E , and the heat of crystallization, H , are independent of the concentration of nuclei and are 249±10 and 67±3 kJ/mol, respectively. The Avrami exponent, n , depends strongly on the concentration of nuclei in the glass.
Impact of highly active anti-retroviral therapy (HAART) on cytokine production and monocyte subsets in HIV-infected patients (2000)

HIV infection is associated with cytokine production by monocytes and expansion of a monocyte subset that expresses high levels of CD16. Our study was designed to investigate the effects of anti-retroviral therapies on these immune parameters. Four groups of HIV+ patients were included in the study. The first group comprised drug-naive patients (n = 20); the second included patients who received two inhibitors of HIV reverse transcriptase (n = 45); the third group received a therapy combining these two inhibitors and one inhibitor of HIV protease (HAART) (n = 35); the fourth consisted of patients who had stopped their treatment (n = 20). The release of inflammatory cytokines (tumour necrosis factor, IL-1beta, IL-6) and immunoregulatory cytokines such as IL-10 by monocytes was determined by ELISA. The monocyte subsets expressing low or high levels of CD16 were studied by flow cytometry. Monocytes from patients naive of treatment released higher amounts of inflammatory cytokines and IL-10 than HIV- individuals. Each anti-retroviral therapy restored a normal pattern of cytokine secretion. Nevertheless, the release of cytokines increased again after the arrest of the treatment. The expansion of the monocyte subset that expresses high levels of CD16 was significantly decreased by HAART but not by the treatment including two inhibitors of reverse transcriptase. These results suggest that only HAART controls monocyte activation in the treatment of HIV infection.
New Advances in the Field of Calcium Channel Antagonists: Cardiovascular Effects and Structure-Activity Relationships (2003)

In the last 15 years, calcium channel blockers have been widely used for treating cardiovascular diseases. These agents are a heterogeneous group of drugs with differing cardiovascular effects, and are effective in the treatment of angina and hypertension. These synthetic compounds bind separately with receptor sites located in or near the calcium channel, at molecular sites still to be fully identified. Verapamil, nifedipine and diltiazem are the most representative calcium channel blockers and used as prototypes for the design and development of new anticalcium molecules with potential efficacy and reduced toxic effects. There are three different types of voltage-operated calcium channels (VOCs): L-type, T-type and N-type, which are considered extra-cellular, but some anti-calcium agents as bepridil possess potential intracellular calcium activity. Many synthetic compounds containing heterocyclic ring in their structures have attracted considerable interest since current studies revealed their mechanisms and sites of action. This article reviews the new advances in the calcium channel antagonist group, showing new structures with longer-acting and higher vascular selectivity.
Pathophysiology of NAFLD and NASH in Experimental Models: The Role of Food Intake Regulating Peptides (2020)

Obesity, diabetes, insulin resistance, sedentary lifestyle, and Western diet are the key factors underlying non-alcoholic fatty liver disease (NAFLD), one of the most common liver diseases in developed countries. In many cases, NAFLD further progresses to non-alcoholic steatohepatitis (NASH), fibrosis, cirrhosis, and to hepatocellular carcinoma. The hepatic lipotoxicity and non-liver factors, such as adipose tissue inflammation and gastrointestinal imbalances were linked to evolution of NAFLD. Nowadays, the degree of adipose tissue inflammation was shown to directly correlate with the severity of NAFLD. Consumption of higher caloric intake is increasingly emerging as a fuel of metabolic inflammation not only in obesity-related disorders but also NAFLD. However, multiple causes of NAFLD are the reason why the mechanisms of NAFLD progression to NASH are still not well understood. In this review, we explore the role of food intake regulating peptides in NAFLD and NASH mouse models. Leptin, an anorexigenic peptide, is involved in hepatic metabolism, and has an effect on NAFLD experimental models. Glucagon-like peptide-1 (GLP-1), another anorexigenic peptide, and GLP-1 receptor agonists (GLP-1R), represent potential therapeutic agents to prevent NAFLD progression to NASH. On the other hand, the deletion of ghrelin, an orexigenic peptide, prevents age-associated hepatic steatosis in mice. Because of the increasing incidence of NAFLD and NASH worldwide, the selection of appropriate animal models is important to clarify aspects of pathogenesis and progression in this field.
Capture division packet access: a new cellular access architecture for future PCNs (1996)

The authors describe a new cellular access architecture, known as capture-division packet access, which is a packet-oriented architecture able to support the constant bit rate traffic and variable bandwidth on demand necessary for multimedia traffic. The approach integrates the multiple access and channel reuse issues to achieve a high degree of spectral efficiency, and presents general advantages even if used for delay-constrained circuit-oriented traffic. Unlike CDMA and TDMA, wherein the effective data rate of each connection is typically a small fraction of the total radio channel allocated for PCN, the CDPA approach allows each user to access the entire channel, if necessary, for brief periods of time (packet access). Spectrum sharing is accomplished by exploiting the different path losses suffered by the various signals as they appear at the base stations (the capture effect), with co-channel interference abated through time diversity (colliding users do not successively retry in the same time interval). Results suggest that abating co-channel interference by random retransmission may be more effective than spatial isolation at cells using the same channel, as is usual in FDMA-TDMA systems.