scholarly journals AutoParallel: Automatic parallelisation and distributed execution of affine loop nests in Python

2020 ◽  
Vol 34 (6) ◽  
pp. 659-675
Author(s):  
Cristian Ramon-Cortes ◽  
Ramon Amela ◽  
Jorge Ejarque ◽  
Philippe Clauss ◽  
Rosa M. Badia
Keyword(s):  
Programming Languages ◽  
Scale Up ◽  
Distributed Applications ◽  
Loop Nests ◽  
Sequential Programming ◽  
Distributed Execution ◽  
One Step ◽  
The One ◽  
Blocked Algorithms ◽  
Distributed And Parallel Computing

The last improvements in programming languages and models have focused on simplicity and abstraction; leading Python to the top of the list of the programming languages. However, there is still room for improvement when preventing users from dealing directly with distributed and parallel computing issues. This paper proposes and evaluates AutoParallel, a Python module to automatically find an appropriate task-based parallelisation of affine loop nests and execute them in parallel in a distributed computing infrastructure. It is based on sequential programming and contains one single annotation (in the form of a Python decorator) so that anyone with intermediate-level programming skills can scale up an application to hundreds of cores. The evaluation demonstrates that AutoParallel goes one step further in easing the development of distributed applications. On the one hand, the programmability evaluation highlights the benefits of using a single Python decorator instead of manually annotating each task and its parameters or, even worse, having to develop the parallel code explicitly (e.g., using OpenMP, MPI). On the other hand, the performance evaluation demonstrates that AutoParallel is capable of automatically generating task-based workflows from sequential Python code while achieving the same performances than manually taskified versions of established state-of-the-art algorithms (i.e., Cholesky, LU, and QR decompositions). Finally, AutoParallel is also capable of automatically building data blocks to increase the tasks’ granularity; freeing the user from creating the data chunks, and re-designing the algorithm. For advanced users, we believe that this feature can be useful as a baseline to design blocked algorithms.

scholarly journals An Abstract Contract Theory for Programs with Procedures

2021 ◽  
pp. 152-171
Author(s):  
Christian Lidström ◽  
Dilian Gurov
Keyword(s):  
Programming Languages ◽  
Contract Theory ◽  
Denotational Semantics ◽  
The Other ◽  
Hoare Logic ◽  
Basic Building Block ◽  
Sequential Programming ◽  
Modular Verification ◽  
The One ◽  
Meta Theory

AbstractWhen developing complex software and systems, contracts provide a means for controlling the complexity by dividing the responsibilities among the components of the system in a hierarchical fashion. In specific application areas, dedicated contract theories formalise the notion of contract and the operations on contracts in a manner that supports best the development of systems in that area. At the other end, contract meta-theories attempt to provide a systematic view on the various contract theories by axiomatising their desired properties. However, there exists a noticeable gap between the most well-known contract meta-theory of Benveniste et al. [5], which focuses on the design of embedded and cyber-physical systems, and the established way of using contracts when developing general software, following Meyer’s design-by-contract methodology [18]. At the core of this gap appears to be the notion of procedure: while it is a central unit of composition in software development, the meta-theory does not suggest an obvious way of treating procedures as components.In this paper, we provide a first step towards a contract theory that takes procedures as the basic building block, and is at the same time an instantiation of the meta-theory. To this end, we propose an abstract contract theory for sequential programming languages with procedures, based on denotational semantics. We show that, on the one hand, the specification of contracts of procedures in Hoare logic, and their procedure-modular verification, can be cast naturally in the framework of our abstract contract theory. On the other hand, we also show our contract theory to fulfil the axioms of the meta-theory. In this way, we give further evidence for the utility of the meta-theory, and prepare the ground for combining our instantiation with other, already existing instantiations.

scholarly journals Scale-Up Synthesis and In Vivo Anti-Tumor Activity of Curcumin Diethyl Disuccinate, an Ester Prodrug of Curcumin, in HepG2-Xenograft Mice

Pharmaceutics ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 373 ◽  
Author(s):  
Chawanphat Muangnoi ◽  
Pahweenvaj Ratnatilaka Na Bhuket ◽  
Ponsiree Jithavech ◽  
Wisut Wichitnithad ◽  
Onsiri Srikun ◽  
...  
Keyword(s):  
Scale Up ◽  
Chemical Reactor ◽  
One Pot ◽  
One Step ◽  
Xenograft Mice ◽  
The One ◽  
Key Steps ◽  
Ester Prodrug ◽  
Anti Tumor Activity

Previously, we synthesized curcumin and a succinate ester prodrug of curcumin namely curcumin diethyl disuccinate (CurDD) in the lab scale, which yielded hundred milligrams to few grams of the compounds. CurDD was found to be more stable in a phosphate buffer pH 7.4 and exhibited better cytotoxicity against Caco-2 cells than curcumin. Here, the one-pot syntheses of curcumin and CurDD were scaled up to afford multigram quantities of both compounds for preclinical studies using a 10-L chemical reactor. The key steps for the synthesis of curcumin were the formation of boron-acetylacetone complex and the decomplexation of boron-curcumin complex. The synthesis of CurDD could be achieved via a one-step esterification between curcumin and succinic acid monoethyl ester chloride using 4-(N,N-dimethylamino)pyridine as a catalyst. The synthesized curcumin and CurDD were then investigated and compared for an anti-tumor activity in HepG2-xenograft mice. CurDD could reduce the tumor growth in HepG2-xenograft mice better than curcumin. CurDD also exerted the stronger inhibition on VEGF secretion, COX-2 and Bcl-2 expression and induced higher Bax expression in comparison with curcumin. The results suggest that CurDD is a promising prodrug of curcumin and has a potential to be further developed as a therapeutic agent or an adjuvant for the treatment of hepatocellular carcinoma.

A Study on the Rearrangement of Dialkyl 1-Aryl-1-hydroxymethylphosphonates to Benzyl Phosphates

2020 ◽  
Vol 24 (4) ◽  
pp. 465-471 ◽  
Author(s):  
Zita Rádai ◽  
Réka Szabó ◽  
Áron Szigetvári ◽  
Nóra Zsuzsa Kiss ◽  
Zoltán Mucsi ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Room Temperature ◽  
Phase Transfer ◽  
One Pot ◽  
Substrate Dependence ◽  
Triethylbenzylammonium Chloride ◽  
One Step ◽  
The Pudovik Reaction ◽  
The One ◽  
Solid Liquid

The phospha-Brook rearrangement of dialkyl 1-aryl-1-hydroxymethylphosphonates (HPs) to the corresponding benzyl phosphates (BPs) has been elaborated under solid-liquid phase transfer catalytic conditions. The best procedure involved the use of triethylbenzylammonium chloride as the catalyst and Cs2CO3 as the base in acetonitrile as the solvent at room temperature. The substrate dependence of the rearrangement has been studied, and the mechanism of the transformation under discussion was explored by quantum chemical calculations. The key intermediate is an oxaphosphirane. The one-pot version starting with the Pudovik reaction has also been developed. The conditions of this tandem transformation were the same, as those for the one-step HP→BP conversion.

scholarly journals One-Year Clinical Evaluation of the Bonding Effectiveness of a One-Step, Self-Etch Adhesive in Noncarious Cervical Lesion Therapy

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Babacar Faye ◽  
Mouhamed Sarr ◽  
Khaly Bane ◽  
Adjaratou Wakha Aidara ◽  
Seydina Ousmane Niang ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Retention Rate ◽  
Recall Rate ◽  
Acid Etching ◽  
Significant Difference ◽  
Usphs Criteria ◽  
One Step ◽  
One Year ◽  
The One ◽  
Self Etch

This study evaluated the one-year clinical performance of a one-step, self-etch adhesive (Optibond All-in-One, Kerr, CA, USA) combined with a composite (Herculite XRV Ultra, Kerr Hawe, CA, USA) to restore NCCLs with or without prior acid etching. Restorations performed by the same practitioner were evaluated at baseline and after 3, 6, and 12 months using modified USPHS criteria. At 6 months, the recall rate was 100%. The retention rate was 84.2% for restorations with prior acid etching, but statistically significant differences were observed between baseline and 6 months. Without acid etching, the retention rate was 77%, and no statistically significant difference was noted between 3 and 6 months. Marginal integrity (93.7% with and 87.7% without acid etching) and discoloration (95.3% with and 92.9% without acid etching) were scored as Alpha or Bravo, with better results after acid etching. After one year, the recall rate was 58.06%. Loss of pulp vitality, postoperative sensitivity, or secondary caries were not observed. After one year retention rate was of 90.6% and 76.9% with and without acid conditioning. Optibond All-in-One performs at a satisfactory clinical performance level for restoration of NCCLs after 12 months especially after acid etching.

scholarly journals Building up cyclodextrins from scratch – templated enzymatic synthesis of cyclodextrins directly from maltose

2021 ◽  
Author(s):  
Dennis Larsen ◽  
Sophie R. Beeren
Keyword(s):  
Enzymatic Synthesis ◽  
Combinatorial Libraries ◽  
One Step ◽  
The One ◽  
Kinetic Trapping

Template-induced kinetic trapping of specific cyclodextrins in enzyme-mediated dynamic combinatorial libraries of linear and cyclic α-glucans enables the one-step synthesis of cyclodextrins from maltose in water.

scholarly journals Efficient Cryopreservation of Populus tremula by In Vitro-Grown Axillary Buds and Genetic Stability of Recovered Plants

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 77
Author(s):  
Elena O. Vidyagina ◽  
Nikolay N. Kharchenko ◽  
Konstantin A. Shestibratov
Keyword(s):  
Survival Rate ◽  
Axillary Buds ◽  
Long Term Storage ◽  
Average Survival ◽  
Transgenic Lines ◽  
Ssr Loci ◽  
One Step ◽  
The One

Axillary buds of in vitro microshoots were successfully frozen at –196 °C by the one-step freezing method using the protective vitrification solution 2 (PVS2). Microshoots were taken from 11 transgenic lines and three wild type lines. Influence of different explant pretreatments were analyzed from the point of their influence towards recovery after cryopreservation. It was found out that the use of axillary buds as explants after removal of the apical one increases recovery on average by 8%. The cultivation on growth medium of higher density insignificantly raises the regenerants survival rate. Pretreatment of the osmotic fluid (OF) shows the greatest influence on the survival rate. It leads to the increase in survival rate by 20%. The cryopreservation technology providing regenerants average survival rate of 83% was developed. It was based on the experimental results obtained with explant pretreatment. Incubation time in liquid nitrogen did not affect the explants survival rate after thawing. After six months cryostorage of samples their genetic variability was analyzed. Six variable simple sequence repeat (SSR) loci were used to analyze genotype variability after the freezing-thawing procedure. The microsatellite analysis showed the genetic status identity of plants after cryopreservation and of the original genotypes. The presence of the recombinant gene in the transgenic lines after cryostorage were confirmed so as the interclonal variation in the growth rate under greenhouse conditions. The developed technique is recommended for long-term storage of various breeding and genetically modified lines of aspen plants, as it provides a high percentage of explants survival with no changes in genotype.

scholarly journals Understanding mathematics of Grover’s algorithm

2021 ◽  
Vol 20 (5) ◽  
Author(s):  
Paweł J. Szabłowski
Keyword(s):  
Phase Change ◽  
Unitary Operator ◽  
Mathematical Structure ◽  
Complex Numbers ◽  
Unitary Operators ◽  
Grover’S Algorithm ◽  
Great Probability ◽  
Grover's Algorithm ◽  
One Step ◽  
The One

AbstractWe analyze the mathematical structure of the classical Grover’s algorithm and put it within the framework of linear algebra over the complex numbers. We also generalize it in the sense, that we are seeking not the one ‘chosen’ element (sometimes called a ‘solution’) of the dataset, but a set of m such ‘chosen’ elements (out of $$n>m)$$ n > m ) . Besides, we do not assume that the so-called initial superposition is uniform. We assume also that we have at our disposal an oracle that ‘marks,’ by a suitable phase change $$\varphi $$ φ , all these ‘chosen’ elements. In the first part of the paper, we construct a unique unitary operator that selects all ‘chosen’ elements in one step. The constructed operator is uniquely defined by the numbers $$\varphi $$ φ and $$\alpha $$ α which is a certain function of the coefficients of the initial superposition. Moreover, it is in the form of a composition of two so-called reflections. The result is purely theoretical since the phase change required to reach this heavily depends on $$\alpha $$ α . In the second part, we construct unitary operators having a form of composition of two or more reflections (generalizing the constructed operator) given the set of orthogonal versors. We find properties of these operations, in particular, their compositions. Further, by considering a fixed, ‘convenient’ phase change $$\varphi ,$$ φ , and by sequentially applying the so-constructed operator, we find the number of steps to find these ‘chosen’ elements with great probability. We apply this knowledge to study the generalizations of Grover’s algorithm ($$m=1,\phi =\pi $$ m = 1 , ϕ = π ), which are of the form, the found previously, unitary operators.

KSeCN as an Efficient Cyanide Source for the One-Step Synthesis of Imino-1-oxoisoindolines via Copper-Promoted C−H Activation

2021 ◽  
pp. 153062
Author(s):  
Yue Zhang ◽  
Xinpeng Liu ◽  
Yanan Wang ◽  
Yinan Zhang ◽  
Junwei Wang ◽  
...  
Keyword(s):  
One Step ◽  
The One

scholarly journals Complete biosynthesis of a sulfated chondroitin in Escherichia coli

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Abinaya Badri ◽  
Asher Williams ◽  
Adeola Awofiranye ◽  
Payel Datta ◽  
Ke Xia ◽  
...  
Keyword(s):  
Chondroitin Sulfate ◽  
Scale Up ◽  
Production Methods ◽  
E Coli ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Microbial Product ◽  
Dry Cell Weight ◽  
One Step ◽  
Dry Cell

AbstractSulfated glycosaminoglycans (GAGs) are a class of important biologics that are currently manufactured by extraction from animal tissues. Although such methods are unsustainable and prone to contamination, animal-free production methods have not emerged as competitive alternatives due to complexities in scale-up, requirement for multiple stages and cost of co-factors and purification. Here, we demonstrate the development of single microbial cell factories capable of complete, one-step biosynthesis of chondroitin sulfate (CS), a type of GAG. We engineer E. coli to produce all three required components for CS production–chondroitin, sulfate donor and sulfotransferase. In this way, we achieve intracellular CS production of ~27 μg/g dry-cell-weight with about 96% of the disaccharides sulfated. We further explore four different factors that can affect the sulfation levels of this microbial product. Overall, this is a demonstration of simple, one-step microbial production of a sulfated GAG and marks an important step in the animal-free production of these molecules.

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