Miracle-dz/UniFAR-FTUs huggingface dataset:
The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.
Homologous recombination between the tuf genes of Salmonella typhimurium.

The genes coding for the translation factor EF-Tu, tufA and tufB are separated by over 700 kb on the circular chromosome of Salmonella typhimurium. The coding regions of these genes have 99% identity at the nucleotide level in spite of the presumed ancient origin of the gene duplication. Sequence comparisons between S. typhimurium and Escherichia coli suggest that within each species the two tuf genes are evolving in concert. Here we show that each of the S. typhimurium tuf genes can transfer genetic information to the other. In our genetic system the transfers are seen as non-reciprocal, i.e. as gene conversion events. However, the mechanism of recombination could be reciprocal, with sister chromosome segregation and selection leading to the isolation of a particular class of recombinant. The amount of sequence information transferred in individual recombination events varies, but can be close to the entire length of the gene. The recombination is RecABCD-dependent, and is opposed by MutSHLU mismatch repair. In the wild-type, this type of recombination occurs at a rate that is two or three orders of magnitude greater than the nucleotide substitution rate. The rate of recombination differs by six orders of magnitude between a recA and a mutS strain. Mismatch repair reduces the rate of this recombination 1000-fold. The rate of recombination also differs by one order of magnitude depending on which tuf gene is donating the sequence selected for. We discuss three classes of model that could, in principle, account for the sequence transfers: (1) tuf mRNA mediated recombination; (2) non-allelic reciprocal recombination involving sister chromosomes; (3) non-allelic gene conversion involving sister chromosomes, initiated by a double-strand break close to one tuf gene. Although the mechanism remains to be determined, the effect on the bacterial cells is tuf gene sequence homogenisation. This recombination phenomenon can account for the concerted evolution of the tuf genes.
Segmentation of Brain MRI Images using Fuzzy C-Means and DWT

Medical image processing deals with enhancement, segmentation etc. of medical images like brain MRI, CT scan images of liver, pancreas etc. The segmentation of the part in image is to be done accurately. Especially in medical images, the segmentation result has to be accurate. In this proposed work, the brain MRI images segmentation using fuzzy c means clustering (FCM) and discrete wavelet transform (DWT). In this work, two algorithms are considered. One is level set segmentation using fuzzy c means by using special features (SFCM) and another one is segmentation of brain MRI images using DWT and principal component analysis (PCA) are further processed using support vector machine (SVM) for classification. The performance evaluation is done by computing mean square error, peak signal to noise ratio (PSNR), maximum difference, absolute mean error etc. Here DWT uses kmeans clustering and level set uses fuzzy cmeans clustering. The spatial constraints are named with different indexes such as the user can choose on particular region of interest and iterate the contour steps until more accurate result to be obtained.
The Elongator complex-associated protein DRL1 plays a positive role in immune responses against necrotrophic fungal pathogens in Arabidopsis.

DEFORMED ROOT AND LEAVES1 (DRL1) is an Arabidopsis homologue of the yeast TOXIN TARGET4 (TOT4)/KILLER TOXIN-INSENSITIVE12 (KTI12) protein that is physically associated with the RNA polymerase II-interacting protein complex named Elongator. Mutations in DRL1 and Elongator lead to similar morphological and molecular phenotypes, suggesting that DRL1 and Elongator may functionally overlap in Arabidopsis. We have shown previously that Elongator plays an important role in both salicylic acid (SA)- and jasmonic acid (JA)/ethylene (ET)-mediated defence responses. Here, we tested whether DRL1 also plays a similar role as Elongator in plant immune responses. Our results show that, although DRL1 partially contributes to SA-induced cytotoxicity, it does not play a significant role in SA-mediated expression of PATHOGENESIS-RELATED genes and resistance to the virulent bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. In contrast, DRL1 is required for JA/ET- and necrotrophic fungal pathogen Botrytis cinerea-induced defence gene expression and for resistance to B. cinerea and Alternaria brassicicola. Furthermore, unlike the TOT4/KTI12 gene which, when overexpressed in yeast, confers zymocin resistance, a phenotype of the tot4/kti12 mutant, overexpression of DRL1 does not change B. cinerea-induced defence gene expression and resistance to this pathogen. Finally, DRL1 contains an N-terminal P-loop and a C-terminal calmodulin (CaM)-binding domain and is a CaM-binding protein. We demonstrate that both the P-loop and the CaM-binding domain are essential for the function of DRL1 in B. cinerea-induced expression of PDF1.2 and ORA59, and in resistance to B. cinerea, suggesting that the function of DRL1 in plant immunity may be regulated by ATP/GTP and CaM binding.
Numerically efficient estimation of relaxation effects in magnetic particle imaging

Abstract Current simulations of the signal in magnetic particle imaging (MPI) are either based on the Langevin function or on directly measuring the system function. The former completely ignores the influence of finite relaxation times of magnetic particles, and the latter requires time-consuming reference scans with an existing MPI scanner. Therefore, the resulting system function only applies for a given tracer type and the properties of the applied scanning trajectory. It requires separate reference scans for different trajectories and does not allow simulating theoretical magnetic particle suspensions. The most accessible and accurate way for including relaxation effects in the signal simulation would be using the Langevin equation. However, this is a very time-consuming approach because it calculates the stochastic dynamics of the individual particles and averages over large particle ensembles. In the current article, a numerically efficient way for approximating the averaged Langevin equation is proposed, which is much faster than the approach based on the Langevin equation because it is directly calculating the averaged time evolution of the magnetization. The proposed simulation yields promising results. Except for the case of small orthogonal offset fields, a high agreement with the full but significantly slower simulation could be shown.
Inverted Voronoi-Based kNN Query Processing with MapReduce

In mobile cloud computing environments distributed k Nearest Neighbor (kNN) query is an important issue. We consider the problem of processing kNN query over large data sets where the index is jointly maintained by a set of machines in a computing cluster. The kNN query is a primitive operator that is widely used in many fields ranging from knowledge discovery, data mining and spatial databases etc. A scalable and distributed spatial data index plays an important role in conducting kNN query effectively. We can use different ways to conduct distributed indexes and kNN query processing by using MapReduce, i.e. R-tree and Grid-based index, etc. Nevertheless, R-tree is not compatible with parallelization, and Grid is a many-to-many index, which could potentially lead to content redundancy. In the paper, a distributed method of kNN queries applying MapReduce program model will be introduced. In the very beginning, I propose distributed methods which set up a novel distributed spatial data index: Inverted Voronoi Index that combines both inverted index and Voronoi diagram. Next, I propose a kNN queries processing algorithm, it is very efficient because it is based on Voronoi and uses MapReduce. Last but not least, I present the outcomes of extensive experiment that are gained by both real and simulated data sets which indicate efficiency and scalability of the proposed approach.
Oviductal fluid modulates the dynamics of tyrosine phosphorylation in cryopreserved boar spermatozoa during capacitation

Following insemination, spermatozoa are retained in the utero‐tubal junction and isthmic region of the oviduct, where essential steps of capacitation are coordinated. Although a majority of the spermatozoa is exposed to similar conditions in the oviduct, the speed of the response varies depending on the individual male and the state of the spermatozoa. The present study evaluated individual boar variations in terms of the ability of spermatozoa to undergo tyrosine phosphorylation in response to isthmic oviductal fluid (ODF). Cryopreserved spermatozoa from four boars were incubated with pre‐ and post‐ovulatory ODF for 6 hr. Sperm kinematics, global protein tyrosine phosphorylation, and dynamics of different phosphorylation patterns were analyzed at hourly interval. The percentage of phosphorylated spermatozoa in the pre‐ovulatory ODF‐treated group was significantly (P < 0.001) higher than in the other treatment groups. Motility, velocity, and protein tyrosine phosphorylation in spermatozoa in response to ODF and control media also showed differences between boars. Spermatozoa from all four boars showed strong expression of a 19‐kDa phosphoprotein while spermatozoa from two boars showed additionally strong expression of a 32‐kDa phosphoprotein when incubated with pre‐ovulatory ODF. While phosphorylation of proteins in the acrosome and the equatorial segment of the sperm were noticed at an early stage during incubation with ODF, tail phosphorylation appeared at a later stage of capacitation. The results indicate individual variation between boars in terms of sperm proteins, including different phosphorylation patterns, in response to ODF, which might be related to fertility.Mol. Reprod. Dev. 79: 525‐540, 2012. © 2012 Wiley Periodicals, Inc.
Surgical Treatment of Cor Triatriatum Sinister in a Cat Under Cardiopulmonary Bypass.

OBJECTIVE To report the surgical repair of cor triatriatum sinister (CTS) incorporating heart-beating cardiopulmonary bypass (CPB) in a cat. STUDY DESIGN Clinical case report. ANIMAL Fourteen-month-old, 5.9-kg male castrated Maine Coon cat. MATERIALS AND METHODS The cat had a 3 month history of inappetance, weight loss, and recurrent pulmonary edema. CTS with severe systolic pulmonary arterial (SPA) hypertension (124 mm Hg) was diagnosed by 2D echocardiography, color flow and continuous wave Doppler modes, and left atrial and pulmonary angiography. Surgery was performed through a left intercostal thoracotomy. CPB was initiated and the heart was kept beating. The left atrial appendage was opened and the intra-atrial membrane was excised. RESULTS After 48 hours, the cat was doing well. Reduced SPA pressure (52 mm Hg) with decreased right heart enlargement was observed on ultrasound examination and the cat was discharged 6 days after surgery with oral antibiotics for 10 days, aspirin, and furosemide. Four months after surgery, the cat presented with increased activity and weight gain and was completely asymptomatic. Transthoracic echocardiography showed a marked improvement of all echo-Doppler variables with disappearance of SPA hypertension (24 mm Hg). Four years after surgery, the cat was still doing well with no recurrence of clinical signs despite the lack of medical treatment. CONCLUSION CTS in the cat may be successfully treated by surgery facilitated by use of CPB leading to early and long-term substantial improvement in clinical status and cardiac function. CTS can safely be repaired under CPB in cats.
Reflections on Gulf War illness

Of Britain's recent wars, the Falklands campaign of 1982 was anomalous in many respects, fought to defend a colony with a small but a loyal population, 8000 miles away, but it was also relatively straightforward. It involved high-level diplomacy and consultations at the United Nations, but it was
Relationship Between Processes of Care and Coronary Bypass Operative Mortality and Morbidity

BackgroundInformation is limited regarding the effects of processes of care on cardiac surgical outcomes. Correspondingly, many recommended cardiac surgical processes of care are derived from animal experiments or clinical judgment. This report from the VA Cooperative Study in Health Services, “Processes, Structures, and Outcomes of Cardiac Surgery,” focuses on the relationships between 3 process groups (preoperative evaluation, intraoperative care, and supervision by senior physicians) and a composite outcome, perioperative mortality and morbidity. MethodsData on 734 risk, process, and structure variables were collected prospectively on 3988 patients who underwent coronary artery bypass grafting at 14 VA medical centers between 1992 and 1996. Data reduction was accomplished by examining data completeness and variation across sites and surgeon, using previously published data and clinical judgment. We then applied multivariable logistic regression to the 39 remaining processes of care to determine which were related to the composite outcome after adjusting for 17 patient-related risk factors and controlling for intraoperative complications. ResultsOur first analysis showed several measures of operative duration, the use of inotropic agents, transesophageal echo, lowest systemic temperature, and hemoconcentration/ultrafiltration, to be powerful predictors of the composite outcome. Because the use of inotropic agents and operative duration may be related to an intermediate outcome (eg, intraoperative complications), we performed a second analysis omitting these processes. The use of intraoperative transesophageal echo and hemoconcentration/ultrafiltration remained significantly associated with an increased risk of an event (odds ratios 1.60 and 1.36, respectively). ConclusionsOur results viewed in the context of past studies suggest the possibility that inotropic use, TEE, and hemoconcentration/ultrafiltration may have adverse effects on operative outcome. Further evaluation of these processes of care using observational data, as well as randomized trials when feasible, would be of interest.
Alexithymia in Schizophrenia: An Exploratory Study

This study assessed a relationship between alexithymia and schizophrenia suggested by reports based on small samples of patients. Here, 50 outpatients with a diagnosis of paranoid schizophrenia were compared with 50 pair-matched healthy subjects. Alexithymia was measured by the Polish version of the Toronto Alexithymia Scale–20. The mean total score was significantly higher in the schizophrenia group (M = 52.3, SD = 13.47) than in the healthy controls (M = 45.8, SD = 11.39, p < .02). This replicates earlier findings showing that a group of patients with paranoid schizophrenia have higher scores on alexithymia scales than healthy controls. There seems a need for a comprehensive examination of relations between alexithymia and other concepts denoting pathology of affect in schizophrenia.
Important role of temporal cues in speaker identification for simulated cochlear implants

Speaker identification is still challenging issue for cochlear implant (CI) users due to the poor spectral cue provided by the CI device. To optimize CI systems for the users, it is important to understand the role of temporal modulation cues in speaker identification, as the CI device provides temporal modulation cues as primary cues. This study investigates the relative contributions of spectral and temporal cue on speaker identification by using noise-vocoded speech (NVS) as a CI simulation. In the experiment, speaker identification was conducted in normalhearing listeners as a function of the number of channels (4, 8, and 16) and upper limitation of envelope frequency (0, 0.5, 1, 2, 4, 8, 16, 32, and 64 Hz) in NVS. The number of channels and upper limitation of envelope frequency present the spectral and temporal resolution of NVS separately. Results showed that the performance of speaker identification was not affected by spectral resolution significantly, at least in the limited set of stimuli in the present study. In addition, the results also showed that the performance was more sensitive to temporal resolution. It is suggested that temporal modulation cues contribute to speaker identification and have the potential to improve speaker identification if enhanced.
Performance Optimization of Multi-Tenant Software Systems

Multi-tenant software systems are Software-as-a-Service systems in which customers (or tenants) share the same resources. The key characteristics of multi-tenancy are hardware resource sharing, a high degree of configurability and a shared application and database instance. We can deduct from these characteristics that they lead to challenges compared to traditional software schemes. To better understand these challenges, we have come up with a reengineering pattern for transforming an existing single-tenant application into a multi-tenant one. We have done a case study in which we transform a single-tenant research prototype into a multi-tenant version. This case study showed that in a layered application, this transformation could be done in less than 100 lines of code. With a better understanding of the challenges inflicted by multi-tenancy, we have focused on one of these challenges in this thesis, namely performance. Because tenants share resources in multi-tenant applications, it is necessary to optimize these applications on two levels: (1) at the hardware level and (2) at the software level. In this thesis, we present and evaluate methods to analyze and optimize the performance of multi-tenant software on those two levels.
A French monitoring programme for determining ochratoxin A occurrence in pig kidneys.

Ochratoxin A is a carcinogen and nephrotoxin which can enter the food chain resulting in human exposure. As pig herds are exposed to ochratoxin A through their feed, their kidneys, livers and pork meat are considered as a possible route of exposure for humans. France, an important producer of pork and pork products, set up a national monitoring programme which included the training of six routine public laboratories in the analysis of ochratoxin A using an immunoaffinity step followed by a HPLC-fluorimetric detection. The programme randomly sampled 300 healthy and 100 nephropathic pig kidneys in 1997 and 710 healthy pig kidneys in 1998. Less than 10% of samples were significantly contaminated by ochratoxin A : in the 1997 survey, 1% of samples contained 0.40-1.40 microg kg(-1) of ochratoxin A and in the 1998 survey 7.6 % exhibited ochratoxin A levels in the range 0.5-5 microg kg(-1). In the case of nephropathic kidneys, only traces of ochratoxin A (0.16 to 0.48 microg kg(-1)) were detected in six samples out of 100. Even if not a major route of exposure for humans, pigs are clearly exposed to this mycotoxin and monitoring of pork products and of feed for swine is necessary.
Native Ant Responses to Solenopsis invicta Buren Reduction Using Broadcast Baits

Abstract A pilot study was conducted to investigate the impact of Solenopsis invicta management with an insect growth regulator bait (s-methoprene) on native ant species and to determine the responses of these species to S. invicta reduction. This invasive species alters the diversity and structure of different trophic levels of arthropod assemblages. Despite advances in S. invicta management using biological control agents, poison baits remain as the primary tool for effective fire ant management. However, the effect of these products on native ants is relatively unknown. Understanding these effects is critical to the development of S. invicta management strategies that include conservation of native ants. Native ants compete with S. invicta to some degree and can bolster efforts to release and establish exotic biological control agents to more effectively manage S. invicta. The study was carried out in Mumford, TX. Two treatments were used: a bait treatment that reduced S. invicta densities and a control. The treatments were randomly assigned to 1.33-ha blocks, replicated four times, and periodically inspected using complementary sampling techniques (pitfall traps, baited vials, manual collections, and nest surveys). Sixteen ant species were found among the two treatments. After S. invicta reduction, significant increases in densities of several other ant species were observed. Species within the assemblage shifted from the dominance by S. invicta to the dominance of the native pyramid ant, Dorymyrmex flavus McCook, which showed the most significant increase in bait treated blocks and was found to persist at densities significantly higher than the control for >2 yr after the last bait treatment. A temporary change in diversity was observed, indicating that use of a poison bait for S. invicta management benefited numerous resident species in the ant assemblage.
From DevOps to BizOps

Virtualization of resources in cloud computing has enabled developers to commission and recommission resources at will and on demand. This virtualization is a coin with two sides. On one hand, the flexibility in managing virtual resources has enabled developers to efficiently manage their costs; they can easily remove unnecessary resources or add resources temporarily when the demand increases. On the other hand, the volatility of such environment and the velocity with which changes can occur may have a greater impact on the economic position of a stakeholder and the business balance of the overall ecosystem. In this work, we recognise the business ecosystem of cloud computing as an economy of scale and explore the effect of this fact on decisions concerning scaling the infrastructure of web applications to account for fluctuations in demand. The goal is to reveal and formalize opportunities for economically optimal scaling that takes into account not only the cost of infrastructure but also the revenue from service delivery and eventually the profit of the service provider. The end product is a scaling mechanism that makes decisions based on both performance and economic criteria and takes adaptive actions to optimize both performance and profitability for the system.
Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India

ABSTRACT The draft genome sequence of a novel strain, Pseudomonas sp. MR 02, a pyomelanin-producing bacterium isolated from the Mahananda River at Siliguri, West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb, with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean gene length, 923 bp), among which 5,503 are protein-coding genes, including the genes required for the catabolism of tyrosine or phenylalanine for the characteristic production of homogentisic acid (HGA). Excess HGA, on excretion, auto-oxidizes and polymerizes to form pyomelanin.