gebhart/patrepeval huggingface dataset:
Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management (2019)

Small intestinal bacterial overgrowth (SIBO) is a common, yet underrecognized, problem. Its prevalence is unknown because SIBO requires diagnostic testing. Although abdominal bloating, gas, distension, and diarrhea are common symptoms, they do not predict positive diagnosis. Predisposing factors include proton-pump inhibitors, opioids, gastric bypass, colectomy, and dysmotility. Small bowel aspirate/culture with growth of 10-10 cfu/mL is generally accepted as the "best diagnostic method," but it is invasive. Glucose or lactulose breath testing is noninvasive but an indirect method that requires further standardization and validation for SIBO. Treatment, usually with antibiotics, aims to provide symptom relief through eradication of bacteria in the small intestine. Limited numbers of controlled studies have shown systemic antibiotics (norfloxacin and metronidazole) to be efficacious. However, 15 studies have shown rifaximin, a nonsystemic antibiotic, to be effective against SIBO and well tolerated. Through improved awareness and scientific rigor, the SIBO landscape is poised for transformation.
Advances in AP2/ERF super-family transcription factors in plant (2020)

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.
Loop and data transformations for sparse matrix code (2015)

This paper introduces three new compiler transformations for representing and transforming sparse matrix computations and their data representations. In cooperation with run-time inspection, our compiler derives transformed matrix representations and associated transformed code to implement a variety of representations targeting different architecture platforms. This systematic approach to combining code and data transformations on sparse computations, which extends a polyhedral transformation and code generation framework, permits the compiler to compose these transformations with other transformations to generate code that is on average within 5% and often exceeds manually-tuned, high-performance sparse matrix libraries CUSP and OSKI. Additionally, the compiler-generated inspector codes are on average 1.5 faster than OSKI and perform comparably to CUSP, respectively.
Functional role of an islet transcription factor, INSM1/IA‐1, on pancreatic acinar cell trans‐differentiation (2011)

In this study, the functional role of INSM1 is examined with an AR42J acinar cell model for trans-differentiation into insulin-positive cells. Islet transcription factors (ITFs: INSM1, Pdx-1, and NeuroD1) are over-expressed in AR42J cells using adenoviral vectors. Addition of Ad-INSM1 alone or the combination of three ITFs to the AR42J cells triggers cellular trans-differentiation. Ectopic expression of INSM1 directly induces insulin, Pax6, and Nkx6.1 expression, whereas Pdx-1 and NeuroD1 were slightly suppressed by INSM1. Addition of Pdx-1 and NeuroD1 with INSM1 further enhances endocrine trans-differentiation by increasing both the numbers and intensity of the insulin-positive cells with simultaneous activation of ITFs, Ngn3 and MafA. INSM1 expression alone partially inhibits dexamethasone-induced exocrine amylase expression. The combination of the three ITFs completely inhibits amylase expression and concomitantly induces greater acinar cell trans-differentiation into endocrine cells. Also, addition of the three ITFs promotes EGF and TGFβ receptors expression. Stimulation by the three ITFs along with the EGF/TGFβ growth factors strongly promotes insulin gene expression. The combination of the three ITFs and EGF/TGFβ growth factors with the primary cultured pancreatic acini also facilitates exocrine to endocrine cell differentiation. Taken together, both the AR42J cell line and the primary cultured mouse acinar cells support INSM1 induced acini trans-differentiation model.
Preparation and Characterization of Chitosan-Insulin-Tripolyphosphate Membrane for Controlled Drug Release: Effect of Cross Linking Agent (2014)

The term Diabetes Mellitus (DM) comprises a group of metabolic disorders characterized by chronic hyperglycemia resulting from defects in the secretion and/or action of insulin. The Insulin therapy constitutes the preferred treatment for DM, consisting of daily subcutaneous insulin injections to control blood glucose levels. The chitosan studied for Biomedicine is a biomaterial that can be used for controlled release of drugs whose release rate can be controlled by Sodium Tripolyphosphate (TPP), which is an ionic cross linker of the chitosan. Present study, therefore, was aimed to develop and evaluate membranes of chitosan and chitosan cross linked by TPP for use in controlled release of insulin system, with the purpose of obtaining an alternative to the injectable administration of this drug. The developed membranes were characterized by the techniques of Fourier Transform Infrared spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDX), High Performance Liquid Chromatography (HPLC) and Evaluation of Cell Viability of Macrophages (MTT). With the FTIR technique the interaction between chitosan, tripolyphosphate and insulin was identified. Chemical elements present in chitosan, insulin and sodium tripolyphosphate membranes were detected by EDX technique. By SEM technique, the changes in the morphology of the membrane containing insulin, with the presence of granular particles of varying sizes, could be observed when compared to pure chitosan. With HPLC assay insulin was identified and it was shown that it gets separated from chitosan membrane even when the membrane was cross linked by the TPP, though at a reduced rate. The crosslinking agent was effective to control the rate of insulin release. The biocompatibility of the prepared membranes was confirmed by cell viability of macrophages using the MTT assay. The developed membranes, therefore, have potential for use as a biomaterial in controlled release systems for insulin.
A zero-skew clock routing scheme for VLSI circuits (1992)

A new clock routing scheme that guarantees zeroskew routing result is proposed. It is shown that the time complexity for the algorithm can be reduced to O(n210gn) by using the modified Voronoi diagram to structure the algorithm. L-shaped pairing and Hflapping operations are introduced to further reduce the clock wire length. Eztensions are made to the algorithm for use in Building-block Layout and zero skew is also achieved. Significant reduction in total clock wire lengths is observed.
Simple calculation of a computer-generated hologram for lensless holographic 3D projection using a nonuniform sampled wavefront recording plane (2016)

In this paper, we present a method for calculation of a computer-generated hologram (CGH) from a 3D object. A virtual wavefront recording plane (WRP) which is close to the 3D object is established. This WRP is nonuniformly sampled according to the depth map of the 3D object. The generation of CGH only involves two nonuniform fast Fourier transform (NUFFT) and two fast Fourier transform (FFT) operations, the whole computational procedure is greatly simplified by diffraction calculation from a 2D planar image instead of 3D object voxels. Numerical simulations and optical experiments are carried out to confirm the feasibility of our proposed method. The CGH calculated with our method is capable to project zoomable 3D objects without lens.
Probing Higgs boson couplings in H + γ production at the LHC (2017)

In this paper, we examine the potential of Higgs boson production associated with a photon at the LHC to probe the new physics effects in the framework of the standard model effective field theory. It is shown that the differential kinematic distributions such as photon transverse momentum and invariant mass of Higgs+γ in Higgs associated production are powerful variables to explore the coefficients of dimension six operators. The analysis is performed in the decay channel of Higgs boson into a bb¯ pair including the main sources of background processes and a realistic simulation of the detector effects. We provide constraints at 95% confidence level on the Wilson coefficients of dimension-six operators affecting Higgs boson plus a photon production. We show to what extent these limits could be improved at the high luminosity LHC. The effect of these constraints on a well-motivated beyond standard model scenario is presented.
Intramolecular activation of aliphatic carbon-hydrogen bonds at tantalum(V) metal centers: a comparison of activation by methyl and methylidene functional groups (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular activation of aliphatic carbon-hydrogen bonds at tantalum(V) metal centers: a comparison of activation by methyl and methylidene functional groupsLinda R. Chamberlain, Ian P. Rothwell, and John C. HuffmanCite this: J. Am. Chem. Soc. 1986, 108, 7, 1502–1509Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://doi.org/10.1021/ja00267a020RIGHTS & PERMISSIONSArticle Views293Altmetric-Citations90LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (969 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The first half-century of nuclear transplantation (2003)

Fifty years after Briggs and King first succeeded in obtaining normal tadpoles from transplanted embryo nuclei in vertebrates, two general principles have emerged from work in amphibia and mammals. One is the conservation of the genome during cell differentiation. A small percentage of adult or differentiated cells have totipotent nuclei, and a much higher percentage of cells committed to one pathway of cell differentiation have multipotent nuclei. The other is the remarkable reprogramming capacity of cell, and especially egg, cytoplasm. The eventual identification of reprogramming molecules and mechanisms could facilitate a route toward cell replacement therapy in humans.
Overexpression of FGF-2 modulates fiber cell differentiation and survival in the mouse lens (1997)

During mammalian embryogenesis, the ocular lens forms through a temporally and spatially regulated pattern of differentiation which is thought to be coordinated at least in part by the FGF-1 and FGF-2 members of the fibroblast growth factor (FGF) family. Previous transgenic experiments in which FGF-1 or dominant negative FGF receptors were overexpressed in the lens indicated that FGF-1 could induce differentiation while differentiated lens cells rely upon FGF signaling for their survival. In this study, we asked if the 17.5 kDa FGF-2 protein was capable of inducing differentiation of lens cells in transgenic mice. Unexpectedly, differentiation was inhibited by lens-specific expression of a transgene encoding a secreted form of the 17.5 kDa bovine FGF-2 protein under the transcriptional control of the murine alphaA-crystallin promoter (alphaAIgFGF-2 transgenic mice). To address the possibility that FGF-2 functions as a modulator of fiber cell survival, alphaAIgFGF-2 transgenic mice were crossed to transgenic mice exhibiting extensive apoptosis in the lens due to the functional inactivation of the retinoblastoma protein (alphaAE7 transgenic mice). The level of apoptosis in the lenses of double transgenic mice was substantially reduced as compared to the level in lenses from alphaAE7 only mice. These studies indicate that FGF-2 can act as a modulator of the later stages of differentiation including fiber cell survival. Additionally, they imply that control of lens development by FGFs is a complex process in which FGF-1 and FGF-2 play distinct roles.
Sources et bibliographie (2012)

Archives publiques manuscrites Archives nationales Sous-série F 17 – Instruction publique (7 bobines de microfilms) Mémoires des instituteurs des sept départements de l’académie de Rennes, rédigés à l’occasion du concours ministériel de 1860 (en gras, les 60 mémoires ou extraits de mémoires des instituteurs, figurant dans l’ouvrage). AN F17/10792/1, mémoires des instituteurs d’Ille-et-Vilaine (29 manuscrits)Louis-Marie Berger (Chartres), Victor Berhaut (Saint-Hilaire-des-Landes), Isidore Bois...
The Bulk of Autotaxin Activity Is Dispensable for Adult Mouse Life (2015)

Autotaxin (ATX, Enpp2) is a secreted lysophospholipase D catalysing the production of lysophosphatidic acid, a pleiotropic growth factor-like lysophospholipid. Increased ATX expression has been detected in a number of chronic inflammatory diseases and different types of cancer, while genetic interventions have proven a role for ATX in disease pathogenesis. Therefore, ATX has emerged as a potential drug target and a large number of ATX inhibitors have been developed exhibiting promising therapeutic potential. However, the embryonic lethality of ATX null mice and the ubiquitous expression of ATX and LPA receptors in adult life question the suitability of ATX as a drug target. Here we show that inducible, ubiquitous genetic deletion of ATX in adult mice, as well as long-term potent pharmacologic inhibition, are well tolerated, alleviating potential toxicity concerns of ATX therapeutic targeting.
Cross Talk between Hydrogen Peroxide and Nitric Oxide in the Unicellular Green Algae Cell Cycle: How Does It Work? (2022)

The regulatory role of some reactive oxygen species (ROS) and reactive nitrogen species (RNS), such as hydrogen peroxide or nitric oxide, has been demonstrated in some higher plants and algae. Their involvement in regulation of the organism, tissue and single cell development can also be seen in many animals. In green cells, the redox potential is an important photosynthesis regulatory factor that may lead to an increase or decrease in growth rate. ROS and RNS are important signals involved in the regulation of photoautotrophic growth that, in turn, allow the cell to attain the commitment competence. Both hydrogen peroxide and nitric oxide are directly involved in algal cell development as the signals that regulate expression of proteins required for completing the cell cycle, such as cyclins and cyclin-dependent kinases, or histone proteins and E2F complex proteins. Such regulation seems to relate to the direct interaction of these signaling molecules with the redox-sensitive transcription factors, but also with regulation of signaling pathways including MAPK, G-protein and calmodulin-dependent pathways. In this paper, we aim to elucidate the involvement of hydrogen peroxide and nitric oxide in algal cell cycle regulation, considering the role of these molecules in higher plants. We also evaluate the commercial applicability of this knowledge. The creation of a simple tool, such as a precisely established modification of hydrogen peroxide and/or nitric oxide at the cellular level, leading to changes in the ROS-RNS cross-talk network, can be used for the optimization of the efficiency of algal cell growth and may be especially important in the context of increasing the role of algal biomass in science and industry. It could be a part of an important scientific challenge that biotechnology is currently focused on.
Charles Hamm. Putting Popular Music in Its Place. Cambridge: Cambridge University Press, 1995. xii, 390 pp. ISBN 0-521-47198-2 (hardcover) (1998)

Charles Hamm. Putting Popular Music in Its Place. Cambridge: Cambridge University Press, 1995. xii, 390 pp. ISBN 0-521-47198-2 (hardcover). Un article de la revue Canadian University Music Review / Revue de musique des universités canadiennes (Volume 18, numéro 2, 1998, p. 1-134) diffusée par la plateforme Érudit.
Tofu Production from Soybeans or Full‐Fat Soyflakes Using Direct and Indirect Heating Processes (1999)

ABSTRACT We compared processing yield, composition, and quality of tofu from soybeans and from full‐fat soyflakes. Tofu was made using a steam‐jacketed kettle and a commercial steam‐injected cooker. Hydration time was 10 min for flakes and 12h for whole beans. Regardless of cultivar, a higher tofu yield was obtained from the steam‐injected cooker system than from the steam‐jacketed kettle system. Utilization of flakes required 62‐‐65% less water during soymilk production. Independent of cultivar, tofu produced from full‐fat soyflakes was lower in fat (26% d.b.) than whole soybean tofu (40% d.b.).
Exact Approaches for Single Machine Total Weighted Tardiness Batch Scheduling (2022)

This paper addresses a single machine total weighted tardiness (TWT) batch-scheduling problem in which jobs have release dates, nonidentical sizes, and are compatible between each other. We propose two integer linear programming models: the first one is a time-indexed formulation (TIF), and the second is an innovative time-size-indexed formulation (TSIF). Although TIF clearly outperforms the existing formulation for the problem, TSIF is capable of producing much stronger bounds in practice. The latter also enables us to develop an efficient column-generation (CG) algorithm. The pricing subproblem corresponds to a resource-constrained shortest path problem that is solved using a bucket graph–based labeling algorithm. The solutions of such a subproblem may contain cycles (reprocessing of jobs), and thus, a memory mechanism called dynamic arc-based ng-sets is employed in the labeling with a view toward avoiding some of them. Moreover, we also implement a preprocessing scheme based on Lagrangian relaxation to perform variable fixing. Extensive computational experiments were carried out in 810 benchmark instances. The proposed CG algorithm is capable of solving instances with up to 100 jobs to optimality. In addition, we believe that this is the first exact approach for a TWT batch-scheduling variant capable of systematically solving instances with up to 50 jobs. High-quality results are also reported for three special cases of the problem—more precisely, when (i) the penalty weights are unitary, (ii) there are no release dates, and (iii) all due dates are set to zero and, hence, the objective becomes equivalent to minimizing the weighted completion time. Summary of Contribution: This paper provides the first exact algorithm for a standard variant of a batch-scheduling total weighted tardiness problem that can solve instances with up to 100 jobs to optimality, a considerable leap with respect to previous works. In particular, we propose a time-indexed formulation that has the advantage of being relatively simple to implement, and yet we show that it is not theoretically dominated by the other innovative formulation proposed in the paper referred to as the time-size-indexed formulation (TSIF). Moreover, we present a Lagrangian approach to quickly fix variables and an iterative column-generation (CG) procedure over a Dantzig–Wolfe decomposition of TSIF that combines an efficient pricing algorithm with a dynamic scheme to adjust the subproblem constraints. The proposed CG approach is capable of producing very strong bounds for the problem as well as for some of its special cases.
Design and application of NMR‐compatible bioreactor circuits for extended perfusion of high‐density mammalian cell cultures (1993)

MR spectroscopy of cultured cells allows non-invasive analyses of the metabolism of cells with specific phenotypes under defined conditions. This technique can be used to investigate the intracellular metabolism of cells or extended to critically evaluate phenomena observed by in vivo MRS. In this paper, a cell maintenance system is described which allows MR analyses with unparalleled spectral resolution, S/N and stability. This system consists of a 25 mm diameter hollow fiber bioreactor and a supporting circuit. The hollow fiber reactor was chosen because it yields a large filling factor which can be perfused through defined volumes. The fibers were 300 microns diameter microporous (0.2 micron) cellulose acetate/cellulose nitrate membranes with high porosity, which allow bulk convective flow throughout the extracapillary space. This flow (Starling flow) is necessary to disrupt steady-state gradients in substrates and waste products. In many respects, the design of the supporting circuit is more important than the bioreactor itself, since it provides the reactor with the proper chemical and physical environment. Hence, this circuit can be applied to a variety of bioreactor configurations. The circuit consists of a hollow fiber oxygenator and a bleed-and-feed system housed in a temperature-controlled cabinet. Culture of mammalian cells in this reactor yields 31P spectra which have excellent spectral and temporal resolution. At confluence, endogenous 31P line widths were typically < 10 Hz (at 162 MHz) and well resolved spectra were obtained in < 30 s.