Miracle-dz/UniFAR-FTUs huggingface dataset:
Monitoring the Bacterial Population Dynamics in Sourdough Fermentation Processes by Using PCR-Denaturing Gradient Gel Electrophoresis

ABSTRACT Four sourdoughs (A to D) were produced under practical conditions by using a starter mixture of three commercially available sourdough starters and a baker's yeast constitutively containing various species of lactic acid bacteria (LAB). The sourdoughs were continuously propagated until the composition of the LAB flora remained stable. Two LAB-specific PCR-denaturing gradient gel electrophoresis (DGGE) systems were established and used to monitor the development of the microflora. Depending on the prevailing ecological conditions in the different sourdough fermentations, only a few Lactobacillus species were found to be competitive and became dominant. In sourdough A (traditional process with rye flour), Lactobacillus sanfranciscensis and a new species, L. mindensis, were detected. In rye flour sourdoughs B and C, which differed in the process temperature, exclusively L. crispatus and L. pontis became the predominant species in sourdough B and L. crispatus, L. panis, and L. frumenti became the predominant species in sourdough C. On the other hand, in sourdough D (corresponding to sourdough C but produced with rye bran), L. johnsonii and L. reuteri were found. The results of PCR-DGGE were consistent with those obtained by culturing, except for sourdough B, in which L. fermentum was also detected. Isolates of the species L. sanfranciscensis and L. fermentum were shown by randomly amplified polymorphic DNA-PCR analysis to originate from the commercial starters and the baker's yeast, respectively.
Embedding System Dynamics in Agent Based Models for Complex Adaptive Systems

Complex adaptive systems (CAS) are composed of interacting agents, exhibit nonlinear properties such as positive and negative feedback, and tend to produce emergent behavior that cannot be wholly explained by deconstructing the system into its constituent parts. Both system dynamics (equation-based) approaches and agent-based approaches have been used to model such systems, and each has its benefits and drawbacks. In this paper, we introduce a class of agent-based models with an embedded system dynamics model, and detail the semantics of a simulation framework for these models. This model definition, along with the simulation framework, combines agent-based and system dynamics approaches in a way that retains the strengths of both paradigms. We show the applicability of our model by instantiating it for two example complex adaptive systems in the field of Computational Sustainability, drawn from ecology and epidemiology. We then present a more detailed application in epidemiology, in which we compare a previously unstudied intervention strategy to established ones. Our experimental results, unattainable using previous methods, yield insight into the effectiveness of these intervention strategies.
Scrubbing-based SEU mitigation approach for Systems-on-Programmable-Chips

The extensive use of Systems-on-Programmable-Chips (SoPCs) in many application domains emphasizes the importance of analysing the vulnerability of the designs to single-event upsets (SEUs) and proposing efficient low-cost mitigation approaches. Most SEU mitigation approaches proposed so far in the literature for SoPCs are based on the use of popular hardware redundant techniques combined with memory scrubbing to avoid fault accumulation. However, all these approaches do not exploit the fact that a large portion of the configuration bits for a particular mapped design are non-sensitive, i.e. do not affect the circuit behaviour in the presence of upsets. In this paper, we first analyse the sensitivity of the configuration bits of a SoPC mapped in a Xilinx Virtex-5 device relying on the vendor implementation tools. The sensitivity analysis showed that the configuration memory scrubbing “wastes” time scanning a large number of frames containing a disproportionately small number of configuration bits due to their high dispersion. To resolve this, we propose a constraint-driven re-placement method to reduce the number of sensitive configuration frames and consequently the scrubbing time. Finally, we present a low-cost SEU mitigation approach for SoPCs which uses configuration memory scan and scrubbing as fault detection and fault repair mechanisms combined with checkpointing and rollback for fault recovery. We demonstrate the efficiency of the proposed mitigation approach in a Leon3-based SoPC implemented in a Xilinx Virtex-5 device.
Folate content in different strawberry genotypes and folate status in healthy subjects after strawberry consumption

Folate is a micronutrient essential in a variety of biological processes, and an adequate dietary folate intake seems to play a crucial role in health promotion and disease prevention. The importance of strawberry as a natural food source of folate has been recognised only recently, and few pilot studies have investigated the impact of strawberry intake on human folate status. In this study, firstly, we evaluated the folate content of different commercial varieties (Alba, Irma, Patty, Adria, Sveva) and advanced selections (AN99.78.51; AN94.414.52; AN00.239.55) of strawberry. Significant differences were observed among genotypes, confirming the breeding approach as a reliable tool to increase folate content in strawberry. Secondly, the variety Sveva was selected for a medium‐term strawberry consumption study, in order to check if a 2‐weeks strawberry intake could have any effects on folate status and plasma homocysteine levels, in healthy subjects. An average 3.4% increase in serum folate was observed, however without any statistical significance, as shown by reference change value of each analyte in each subject. This study should be considered as a first pilot investigation, and further investigations are strongly hoped to evaluate the potential impact of strawberry consumption on human folate status, particularly in the case of a previously diagnosed deficiency.
Power control and scheduling for joint detection cooperative cellular systems

Cooperative joint detection in the uplink of cellular systems is a promising means to combat inter-cell interference. In fact, interference from other users in the same cooperation cluster is turned into useful signal energy in such systems. While cooperation is generally beneficial, the system behavior largely depends on the power control and scheduling strategies employed, as demonstrated in this paper. We investigate different combinations of these two mechanisms and provide insights into the system behavior considering spectral efficiency, fairness and energy efficiency.
Extracting Knowledge from Stream Behavioural Patterns

The increasing number of small, cheap devices full of sensing capabilities lead to an untapped source of information that can be explored to improve and optimize several systems. Yet, as this number grows it becomes increasingly difficult to manage and organize all this new information. The lack of a standard context representation scheme is one of the main difficulties in this research area (Antunes et al., 2016b). With this in mind we propose a stream characterization model which aims to provide the foundations of a new stream similarity metric. Complementing previous work on context organization, we aim to provide an automatic organizational model without enforcing specific representations.
Differences of Functional Connectivity Brain Network in Emotional Judgment

Using combined emotional stimuli, combining photos of faces and recording of voices, we investigated the neural dynamics of emotional judgment using scalp EEG recordings. Stimuli could be either combioned in a congruent, or a non-congruent way. As many evidences show the major role of alpha in emotional processing, the alpha band was subjected to be analyzed. Analysis was performed by computing the synchronization of the EEGs and the conditions congruent vs. non-congruent were compared using statistical tools. The obtained results demonstrate that scalp EEG ccould be used as a tool to investigate the neural dynamics of emotional valence and discriminate various emotions (angry, happy and neutral stimuli).
Water region and multiple ship detection for port surveillance

In this paper, we present a robust and accurate multiple ship detection system for port surveillance. First, water region is detected using a region-based technique. Second, ships are located by a cabin detector for the same port surveillance sequences. Third, a verification process is performed to remove the false detections of ships using the detected water region as contextual cues. We have analyzed our water region detection algorithm by experimenting on 5 sequences and we have found that it achieves an average pixel classification precision of 96.9% and a recall of 91.8%. The multiple ship detection system is tested on 3 different surveillance sequences. We successfully detect 133 ships out of 150 ships with a precision of 87.5% and a recall of 88.7%.
NOISE REDUCTION IN TERAHERTZ THIN FILM MEASUREMENTS USING A DOUBLE MODULATED DIFFERENTIAL TECHNIQUE

Differential terahertz (THz) time-domain spectroscopy (TDS) is a technique for decreasing noise levels in THz thin film characterization experiments. Characterizing thin films in the GHz to THz range is critical for the development of fast integrated circuits and photonic systems, and is potentially applicable to biosensors and proteomics. This paper shows how the differential technique, combined with double modulation, enables the study of thin films with noise reduction over normal TDS that improves at the film gets thinner. Double modulated differential THz-TDS has enabled the characterization of films with less than 1-μm thickness.
Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispecies

Hepatitis C virus (HCV) is a major cause of liver disease worldwide. Understanding the mechanisms responsible for the establishment of chronic HCV infection is critical to the development of efficient therapeutics and vaccines. The mechanism of intra-host HCV evolution assumed by most models is based on immune escape via random mutations. However, continuous immune escape does not explain our observation of a consistent increase in negative selection during chronic infection, which suggests extensive intra-host HCV adaptation. Using a model of cross-immunoreactivity, we show that the level of HCV intra-host adaptation correlates with the rate of cross-immunoreactivity among HCV quasispecies. We present a mathematical model describing the immunological interaction among quasispecies that involves, in addition to neutralization, a non-neutralizing cross-immunoreactivity. The model describes how HCV variants escape immune responses and persist, owing to their capability to stimulate non-neutralizing immune responses developed earlier against preceding variants without eliciting specific responses against the variant itself.
Opening the fuzzy front end: A synthesis of two theories

Companies must innovate, today and tomorrow. The ability to provide new products and solutions to the markets is critical for maintaining a continuous revenue stream, especially in this age of fundamental changes. Product development processes have been studied since 80s and nearing 90s academic attention turned to early phases of development, i.e. fuzzy front-end. Activities at the fuzzy front end of product development process are often chaotic and experimental with rather unpredictable or uncertain commercialization future. Opportunities are raising, but a firm still cannot do all needed development actions in-house. The theory of open innovation has tackled some of emerged dilemmas. It proposes that one should open knowledge and technology borders of the company for idea exchange, because there might be better business model for the technology that apparently is not valuable for you. In our paper OI and FFE theories are merged to introduce a framework for parallel business plan and technology development, leading to new discoveries in the relation between FFE and external technology exploitation. The framework is evaluated by how it can help organizations to improve their product development profitability by coping with in- and outflows of technology.
Identifying Concepts Across Languages: A First Step towards a Corpus-based Approach to Automatic Ontology Alignment

The growing importance of multilingual information retrieval and machine translation has made multilingual ontologies an extremely valuable resource. Since the construction of an ontology from scratch is a very expensive and time consuming undertaking, it is attractive to consider ways of automatically aligning monolingual ontologies, which already exist for many of the world's major languages.
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis

Background: Recent improvements in DNA microarray techniques have made a large variety of gene expression data available in public databases. This data can be used to evaluate the strength of gene coexpression by calculating the correlation of expression patterns among different genes between many experiments. However, gene expression levels differ significantly across various tissues in higher organisms, as well as in different cellular location in eukaryotes in different cell state. Thus the usual correlation measure can only evaluate the difference of tissues or cellular localizations, and cannot adequately elucidate the functional relationship from the coexpression of genes. Method: We propose a new measure of coexpression by expanding the generally used correlation into a multidimensional one. We used principal component analyses to identify the major factors of gene expression correlation, and then re-calculate the correlation by subtracting the major components in order to remove biases cased by a few experiments. The repeated subtractions of the major components yielded a set of correlation values for each pair of genes. We observed the correlation changes when the first ten principal components were subtracted step-by-step in large-scale Arabidopsis expression data. Results: We found two extreme patterns of correlation changes, corresponding to stable and fragile coexpression. Our new indexes provided a good means to determine the functional relationships of the genes, by examining a few examples, and higher performance of Gene Ontology term prediction by using the support vector machine and the multidimensional correlation. Availability: The results are available from the expression detail pages in ATTED-II (http://atted.jp). Contact: kinosita@hgc.jp Supplementary information: Supplementary data are available at Bioinformatics online.
Harmonically tuned 100 W broadband GaN HEMT power amplifier with more than 60 % PAE

This paper presents a GaN HEMT based harmonically tuned broadband power amplifier. The amplifier uses the CGH40120F GaN device from Cree Inc. and delivers 100 W output power across the bandwidth 1.55–2.25 GHz. The minimum power added efficiency (PAE) over the bandwidth is higher than 60 % with maximum values up to 70 %, respectively. Measurements using digital modulated signals were performed, too. At 38.5 dBm average output power more than 40 dBc ACLR has been achieved for an UMTS signal applying memory DPD. The PA covers the frequency range of modern wireless standards like DCS1800/LTE, PCS1900/LTE and WCDMA/LTE and is well suited for multi-band, mult-standard applications.
Robust Transceiver Design Based on Joint Signal and Interference Alignment for MIMO Interference Channels With Imperfect Channel Knowledge

In this letter, we propose a new transceiver design based on joint signal and interference alignment, which provides the robustness against imperfect channel knowledge in multiple-input multiple-output (MIMO) interference channels. Under the assumption of norm-bounded channel uncertainties, the proposed robust transceiver design minimizes the interference signals that leak outside the interference subspace and makes the desired signal fall into the orthogonal complement of the interference subspace. From simulation results, we demonstrate that our proposed robust transceiver design offers not only better sum rate performance but also higher robustness against imperfect channel knowledge than the conventional scheme.
Childhood diabetic neuropathy: functional impairment and non‐invasive screening assessment

Aim Sensory diabetic neuropathy, determined by nerve conduction studies, is common in children with Type 1 diabetes. Diabetic neuropathy diagnoses are rarely made in paediatric daily care because they are asymptomatic, vibration detection is mostly normal and nerve‐conduction testing is impractical. The present study aims to: (1) describe somatosensory dysfunction in children with diabetes, (2) test whether diabetes duration and HbA1c are related to somatosensory dysfunction and (3) identify the best screening test for large‐fibre dysfunction, as indicated by nerve conduction studies.
P2U: A Privacy Policy Specification Language for Secondary Data Sharing and Usage

Within the last decade, there are growing economic social incentives and opportunities for secondary use of data in many sectors, and strong market forces currently drive the active development of systems that aggregate user data gathered by many sources. This secondary use of data poses privacy threats due to unwanted use of data for the wrong purposes such as discriminating the user for employment, loan and insurance. Traditional privacy policy languages such as the Platform for Privacy Preferences (P3P) are inadequate since they were designed long before many of these technologies were invented and basically focus on enabling user-awareness and control during primary data collection (e.g. by a website). However, with the advent of Web 2.0 and Social Networking Sites, the landscape of privacy is shifting from limiting collection of data by websites to ensuring ethical use of the data after initial collection. To meet the current challenges of privacy protection in secondary context, we propose a privacy policy language, Purpose-to-Use (P2U), aimed at enforcing privacy while enabling secondary user information sharing across applications, devices, and services on the Web.
Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.
Speed is as powerful as clairvoyance

We introduce resource augmentation as a method for analyzing online scheduling problems. In resource augmentation analysis the on-line scheduler is given more resources, say faster processors or more processors, than the adversary. We apply this analysis to two well-known on-line scheduling problems, the classic uniprocessor CPU scheduling problem 1 |<italic>r<subscrpt>i</subscrpt>, pmtn|&Sgr; F<subscrpt>i</subscrpt>,</italic> and the best-effort firm real-time scheduling problem 1|<italic>r<subscrpt>i</subscrpt>, pmtn</italic>| &Sgr; <italic>w<subscrpt>i</subscrpt></italic>( 1- <italic>U<subscrpt>i</subscrpt></italic>). It is known that there are no constant competitive nonclairvoyant on-line algorithms for these problems. We show that there are simple on-line scheduling algorithms for these problems that are constant competitive if the online scheduler is equipped with a slightly faster processor than the adversary. Thus, a moderate increase in processor speed effectively gives the on-line scheduler the power of clairvoyance. Furthermore, the on-line scheduler can be constant competitive on all inputs that are not closely correlated with processor speed. We also show that the performance of an on-line scheduler is best-effort real time scheduling can be significantly improved if the system is designed in such a way that the laxity of every job is proportional to its length.
A neural tissue interfacing chip for in-vitro applications with 32k recording / stimulation channels on an active area of 2.6 mm2

A neural tissue interfacing chip for in-vitro applications is presented based on an extended 0.5 μm, 5 V, standard CMOS process. The chip provides 256 × 128 bidirectional recording / stimulation sites on a total active area of 2.28 mm × 1.14 mm, and a fully digital interface. Full frame recording rate is 2.4 kHz. Selection of a subset of sites is possible and translates into higher bandwidth per site accordingly. Electrical and biological results are presented which reveal proper functionality.
From program verification to program synthesis

This paper describes a novel technique for the synthesis of imperative programs. Automated program synthesis has the potential to make programming and the design of systems easier by allowing programs to be specified at a higher-level than executable code. In our approach, which we call proof-theoretic synthesis, the user provides an input-output functional specification, a description of the atomic operations in the programming language, and a specification of the synthesized program's looping structure, allowed stack space, and bound on usage of certain operations. Our technique synthesizes a program, if there exists one, that meets the input-output specification and uses only the given resources. The insight behind our approach is to interpret program synthesis as generalized program verification, which allows us to bring verification tools and techniques to program synthesis. Our synthesis algorithm works by creating a program with unknown statements, guards, inductive invariants, and ranking functions. It then generates constraints that relate the unknowns and enforces three kinds of requirements: partial correctness, loop termination, and well-formedness conditions on program guards. We formalize the requirements that program verification tools must meet to solve these constraint and use tools from prior work as our synthesizers. We demonstrate the feasibility of the proposed approach by synthesizing programs in three different domains: arithmetic, sorting, and dynamic programming. Using verification tools that we previously built in the VS3 project we are able to synthesize programs for complicated arithmetic algorithms including Strassen's matrix multiplication and Bresenham's line drawing; several sorting algorithms; and several dynamic programming algorithms. For these programs, the median time for synthesis is 14 seconds, and the ratio of synthesis to verification time ranges between 1x to 92x (with an median of 7x), illustrating the potential of the approach.