Miracle-dz/UniFAR-FTUs huggingface dataset:
Comments on the Arjen Markus article: Design patterns and Fortran

The article by Markus [1] discusses the subject of object-oriented (OO) design patterns and describes ways in which three well-known patterns might be implemented in Fortran 90/95. It appears that the idea of object-oriented design patterns in Fortran might just be coming of age and it is a very appropriate subject for discussion in a Forum such as this.We have been developing our own implementations of design patterns in Fortran 90/95 for some time and have one paper under review [2] and another being presented at the 6th Workshop on Parallel/High-Performance Object Oriented Scientific Computing (POOSC) in Nantes, France in July 2006 [3]. Our application area is particle-in-cell simulations in plasma physics, but the results that we have obtained will, we hope, be of interest to Fortran 90/95 programmers in general.Our own starting point with design patterns in Fortran 90/95 stems from the literature on object-based programming in that language [4-10]. Several authors have observed that the obvious unit of encapsulation, the Fortran 90/95 module, can be thought of as an object-based class: it can support a type which defines the stored data together with subprograms which can operate on that data. With some discipline and ingenuity, these authors have shown how to emulate the notions of object construction and destruction, inheritance and polymorphism. These emulations were actually implemented using object composition. For example, one child module might include another parent module in order to simulate inheritance. As Markus correctly points out, most of the famous design patterns are based on object composition and the authors of [4-10] have, frequently, been using design patterns as a way of simulating OO behaviour.Because the subject of OO design patterns in Fortran 90/95 is so fresh, there is ample scope for them to be presented in different ways by different authors. Whilst appreciating the clarity and relevance of Markus' expositions, we would like to make some points of criticism which we believe are important to a further discussion of this topic. The points we make refer to the ideas expressed in the book by Gamma et al. [11] which is considered to be the fundamental exposition of the topic of OO design patterns.
Low-dosed Botulinum Toxin A in the Prophylactic Management of Unilateral Migraine: A Randomized Double-blind Placebo-Controlled Crossover Study

Botulinum toxin is a therapeutic option in chronic migraine. No dose-finding studies have been conducted so far. Some authors maintain that one injection into the corrugator muscle will do. Objective: We studied the effect of Botulinum toxin (BTX) injections in patients with strictly unilateral migraine. Methods: We treated 22 patients (ITT) in a crossover design for 4 months with 2 x 5 units Onabotulinum toxin (in the cor- rugator and occipitalis muscle ipsilaterally). Aside from patient data, we also gathered information on undesired drug ef- fects, besides IQOLA SF36, SF-MPQ SADP, OLBPDQ, VAS (pain intensity and daily living skills), PPI, frequency of at- tacks and application of medication. The statistical evaluation was guided by SPSS (V.13). Results: Assessed were 19 patients (PP) aged 45.2 ± 11.1 years, thereof 17 women. In both injection intervals there were no clinically relevant and/or statistically significant differences as to the target parameters (for example: VAS pain inten- sity p=0.702), with a notably evident placebo effect (VAS in placebo prior to the injection was 61.4, after 6 weeks 45.1; good or excellent improvement (TOQ) was quoted by 36.8% after 6 weeks in the placebo group). BTX merely proved su- perior in two aspects: Regarding the pain quality "throbbing" (SF-MPQ SADP), 11 patients initially indicated a pro- nounced intensity; after BTX only 4 of them did. As to the severity of the pain felt, (PPI) 42.2 of the subjects described "limiting" or "horrible" pain prior to the injection versus 26.3% six weeks after the injection and 21.1% 4 months later. The placebo group started out with 31.6%, that figure remaining the same (31.6%) 6 weeks later, rising to 42.2% after 4 months. 84.2% of the BTX-group and 63.2% in the placebo group requested a reinjection when the study was completed. Conclusion: The injection of low-dosed Botulinumtoxin A did not show any relevant or significant effects in patients with unilateral migraine without aura. One injection into the corrugator muscle alone must be considered as ineffective. The place-value of the two injection sites remains in the open.
The M1 Muscarinic Positive Allosteric Modulator PQCA Improves Performance on Translatable Tests of Memory and Attention in Rhesus Monkeys

Improved treatment of Alzheimer disease (AD) is a significant unmet medical need that is becoming even more critical given the rise in the number of patients and the substantial economic burden. The current standards of care, acetylcholinesterase inhibitors (AChEIs), are hindered by gastrointestinal side effects owing to their nonselective activation of muscarinic and nicotinic receptors. Recently, the highly selective M1 positive allosteric modulator PQCA (1-((4-cyano-4-(pyridine-2-yl)piperidin-1-yl)methyl-4-oxo-4 H-quinolizine-3-carboxylic acid) has been demonstrated to improve cognition in a variety of rodent and nonhuman primate cognition models without producing significant gastrointestinal side effects. Here we describe the effect of PQCA and the AChEI donepezil on two clinically relevant and highly translatable touchscreen cognition tasks in nonhuman primates: paired-associates learning (PAL) and the continuous-performance task (CPT). Blockade of muscarinic signaling by scopolamine produced significant impairments in both PAL and CPT. PQCA and donepezil attenuated the scopolamine deficits in both tasks, and the action of these two compounds was similar in magnitude. In addition, the combination of subeffective doses of PQCA and donepezil enhanced PAL performance. These results further suggest that M1-positive allosteric modulators, either as monotherapy or as an add-on to current standards of care, have potential to reduce the cognitive deficits associated with AD.
TOWARDS AN IMPROVED ENVIRONMENTAL REPORTING STRUCTURE FOR COMPANIES IN FOOD AND AGRIBUSINESS CHAINS

The present paper focuses on the perceived quality of information exchange between government and business (G2B) in the field of environmental reporting in the Dutch agrifood industry. It seems most important for environmental performance enhancement (a concept that includes the quality of information given to stakeholders in our view) that companies are entangled in a network of intermediary institutions (branch organizations, covenants, existence of chain leaders etc.). It seems that that these mediating institutions are very instrumental in translating the governmental message to the companies. The companies choose the (related to the development of internal care) improvement of electronic reporting as the most promising innovation for the G2B communication. This shows that the companies still have a long way to go towards chain oriented care systems.
Simulation through explicit state description and its application to semiconductor fab operation

A nonstandard methodology in simulator construction is introduced along with its application to on-line simulation of semiconductor fabs. The simulation proceeds by sequentially rewriting state description, written in a language. A text in the state description language consists of a collection of titled two-column tables. The description is stored in an in-core database equipped with a splay tree algorithm. The initial state representing the fab's present state is downloaded from the fab's database. The simulation is for lotwise trace prediction needed for day-today fab operation rather than to estimate steady state performance indices. Its use at production sites involves frequent model modification. A one-month simulation of a clean room operation involving 1,300 lots and 200 machines is processed in five to ten minutes on a workst at ion, using 30 megabytes of internal memory. The execution time is 0(/ogN), where N is the number of lots and machines; memory usage is proportional to N. The simulator enjoys an extremely small source code: 1,200 lines in C. 1 INTRODUCTION This paper proposes to look at discrete event simulation as a form of language processing. The word " language " here means a system of symbols used to describe the state of the object to simulate rather than a simulation language such as SIMULA or GPSS. Consider the case of simulating a semiconductor fab. The contents of a state description would be like this: " Lot L consists of W wafers of product type P. Lot L is presently being processed by machine kf, scheduled to finish at time t.Machine M is processing lot L and will go through maintenance after time s. Etc. " The system of symbols used to describe this is called a state description language. The language may resemble a natural language as above, or may be more succinctly coded. Simulation proceeds by rewriting such a description step by step according to a set of rules. This process parallels interpretive execution of a computer language. The language is to be used by a team involved in building a model for negotiating an agreement among themselves and to communicate with computers for discovering mistakes, delegating execution, and receiving the result reports. We design a common language for people and machines, taking them as equals with different characteristics and abilities. Consequently west art with what computers are rather than what they should be. This is in contrast with modern computer …
Preventing Memory Errors in Networked Vehicle Services Through Diversification

Car-to-X communication stands for the communication of di↵erent vehicles (vehicle-to-vehicle) as well as for the communication of vehicles and infrastructure (vehicle-to-infrastructure). The development of these technologies promotes the emergence of new car infotainment and telematic services of added value for users. The side e↵ect is the exposure of vehicles to a number of new threats, such as memory errors. Among other consequences, the exploitation of memory errors may lead to code-reuse attacks, where intruders reuse existing non-malicious code with malicious purposes, such as gaining complete car control. Since memory error exploits usually rely on highly specific processor characteristics, the same exploit rarely works on di↵erent hardware architectures. This paper proposes a strategy to thwart memory error exploitation by combining the diversification of HWthrough processor emulation with the creation of Service variants using o↵-the-shelf cross-compilation suites.
Optimal Environmental Tax-Subsidy Regime in the Presence of Increasing Returns

This paper develops a set of three models to study the optimal tax-subsidy regime in an economy characterised by two deviations from the perfect competition model – negative externality from pollution by the "dirty" industry, and increasing returns in the "clean" industry. Its main conclusions are: (1) the optimal single pollution tax is higher than the Pigouvian level; (2) a combination of pollution tax and quantity subsidy increases consumer welfare at a lower level of pollution tax; (3) the optimal pollution tax can be further lowered and consumer welfare further increased if the quantity subsidy is supplemented by a lump-sum subsidy.
CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um. edu.my/.
Robustness of minimal biochemical oscillators

Robustness-the insensitivity to perturbations-is a hallmark of biological systems and it could provide a key to understanding design principles of complex cellular networks. However, current methods for the characterization of parametric robustness in (dynamic models of) biological systems are insufficient because of their local nature and the high dimensionality of the corresponding parameter spaces. Here, we propose first methods for a quantitative characterization of geometries in parameter space that are related to qualitative systems behavior. Using minimal biochemical oscillators as examples, we show that such approaches can provide detailed insight into relations between network structures, behavior, and robustness properties, which is not possible with traditional sampling-based methods. We expect that scaling and resolution of the algorithms could be vastly improved by using more advanced concepts from computational geometry.
An efficient algorithm for depth image rendering

As depth sensing devices become popular and affordable, end-users can have the freedom to choose a different point of view in a multicamera transmission. In this paper, we propose an image-based rendering (IBR) algorithm to generate perceptually accurate virtual views of a scene in real-time. The proposed algorithm is implemented and tests with publicly available datasets are presented. From these results one can evaluate the efficiency and quality of the algorithm.
Contrast-induced Hyperemia as an Alternative to Drug-induced Hyperemia in the Evaluation of the Fractional Flow Reserve in Coronary Lesions

Objective Measuring the fractional flow reserve (FFR) requires the induction of coronary hyperemia, usually with adenosine, adenosine triphosphate (ATP), or papaverine. However, adenosine can induce rhythmic complications, and intracoronary boluses of papaverine that prolong the QT interval can cause ventricular tachycardia. Injection of contrast media, which is routinely performed to validate the FFR guidewire placement, also induces hyperemia and may be an alternative method of measuring the FFR. We evaluated the diagnostic accuracy of the FFR after contrast hyperemia (FFRcont) compared to FFR evaluated after intracoronary papaverine (FFRpp). Methods This study included 109 lesions in 93 patients (mean age 70.4±8.7 years) with stable coronary disease. The FFR was measured as follows: 1) baseline pressure value; 2) FFRcont after intracoronary contrast injection (iopamidol, 8 mL for left coronary artery [LCA] or 6 mL for right coronary artery [RCA]); 3) FFRpp after intracoronary injection of papaverine (12 mg for LCA or 8 mg for RCA). Results FFRcont values were strongly correlated with FFRpp (R=0.940, p<0.0001; FFRpp = FFRcont ×1.007-0.032). The best cut-off point in the receiver operator curve analysis for predicting a FFRpp <0.80 was 0.82 (area under the curve =0.980; sensitivity 95.1%, specificity 91.2%, positive predictive value 86.7%, negative predictive value 96.9%). Conclusion FFRcont is highly accurate for predicting FFRpp. An FFRcont threshold value of 0.82 provides excellent sensitivity and a negative predictive value. FFRcont is an alternative method of inducing hyperemia.
Preliminaries to linguistic phonetics

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A first AFLP-Based Genetic Linkage Map for Brine Shrimp Artemia franciscana and Its Application in Mapping the Sex Locus

We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ–ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species.
On the Restore Operation in MTJ-Based Nonvolatile SRAM Cells

This brief investigates the Restore mechanism of a nonvolatile static random access memory (NVSRAM) cell that utilizes two magnetic tunneling junctions (MTJs) as nonvolatile resistive elements and a 6T SRAM core. Two cells are proposed by employing different mechanisms for the Restore operation once the power is reestablished. The proposed cells use the bitline and supply as mechanisms to initiate the Restore operation, so connecting the two MTJs to different nodes of the NVSRAM circuitry. The cells are extensively analyzed in terms of their operations with respect to different figures of merit, such as operational delays (for the Write, Read, and Restore operations), the static noise margin, power consumption, critical charge, and process variations (in both the MOSFETs and the resistive elements). Simulation results show that the cell with the MTJs connected to the supply offers the best performance in terms of power for the Read/Restore operations; it also achieves the best Read delay, but the worst Restore delay.
The tumor suppressive miR-200b subfamily is an ERG target gene in human prostate tumors

The TMPRSS2-ERG fusion occurs in approximately 50% of prostate cancer (PCa), resulting in expression of the oncogenic ERG in the prostate. Because ERG is a transcriptional activator, we hypothesized that ERG-regulated genes contribute to PCa development. Since microRNA (miRNA) has crucial functions in cancer, we searched for miRNAs regulated by ERG in PCas. We mined published datasets based on the MSKCC Prostate Oncogene Project, in which a comprehensive analysis defined the miRNA transcriptomes in 113 PCas. We retrieved the miRNA expression datasets, and identified miRNAs differentially expressed between ERG-positive and ERG-negative samples. Out of 369 miRNAs, miR-200a, −200b, −429 and −205 are the only miRNAs significantly increased in ERG-positive tumors. Strikingly, miR-200a, −200b and −429 are transcribed as a single polycistronic transcript, suggesting they are regulated at the transcriptional level. With ChIP-qPCR and in vitro binding assay, we identified two functional ETS motifs in the miR-200b/a/429 gene promoter. Knockdown of ERG in PCa cells reduced expression of these three miRNAs. In agreement with the well-established tumor suppressor function, overexpression of the miR-200b/a/429 gene inhibited PCa cell growth and invasion. In summary, our study reveals that miR-200b/a/429 is an ERG target gene, which implicates an important role in TMPRSS2/ERG-dependent PCa development. Although induction of the tumor suppressive miR-200b subfamily by oncogenic ERG appears to be counterintuitive, it is consistent with the observation that the vast majority of primary prostate cancers are slow-growing and indolent.
Predicting endemic cholera: the role of climate variability and disease dynamics

ABSTRACT: Retrospective studies of cholera time series in Bangladesh have established a role of theEl Nino Southern Oscillation (ENSO), but also of the non-linear dynamics of the disease itself,through changes in the population levels of immunity in this endemic region. The prediction abilityof a semi-mechanistic time series model that incorporates both these elements is examined. Resultsshow that ENSO is a key covariate and confirm the importance of its interplay with immunity levels,now from the perspective of prediction. They support the feasibility of using the model as a forecast-ing tool: the lack of extreme events between 2001 and 2005 would have been anticipated with 75%confidence half a year ahead with a model fitted to data up to 2000. Long-term change in the trans-mission rate, the non-mechanistic part of the model, sets limits to the forecasting horizon because ofa breakdown in its relationship with river discharge towards the end of the 1990s. We discuss this andother limitations of the approach as well as future directions related to the development of an earlywarning system for cholera in this region.KEY WORDS: Cholera prediction · ENSO · Climate forcing · Population immunity · Early-warningsystems · Time series model · TSIRS · Nonlinear disease dynamics
Information Retrieval and Information Extraction in Web 2.0 environment

With the rise of Web 2.0 paradigm new trends in information retrieval (IR) and information extraction (IE) can be observed. Significance of IR and IE as fundamental method of acquiring new and up-to-date information is crucial for efficient decision making. Social aspects of modern information retrieval are gaining on its importance over technical aspects. The main reason for this trend is that IR and IE services are becoming more and more widely available to end users that are not information professionals but regular users. Also new methods that rely primarily on user interaction and communication show similar success in IR and IE tasks. Web 2.0 has overall positive impact on IR and IE as it is based on a more structured data platform than the earlier web. Moreover, new tools are being developed for online IE services that make IE more accessible even to users without technical knowledge and background. The goal of this paper is to review these trends and put them into context of what improvements and potential IR and IE have to offer to knowledge engineers, information workers, but also typical Internet users.