Miracle-dz/UniFAR-FTUs huggingface dataset:
Editorial: a simple faecal preparation for faecal microbiota transplantation – authors’ reply

We thank Dr C.R. Kelly for her interest and comments on our work and her balanced view on the use of faecal microbiota transplantation (FMT) for recurrent Clostridium difficile infection (rCDI). We agree with Dr Kelly’s views in general and would like to discuss some specific issues further. In our paper, we describe a simple protocol for preparing donor faeces, which facilitates some practical aspects of FMT. In faecal preparation and storage, we used 80 °C freezer, which allows quick freezing. We have not tested standard freezers for this purpose and cannot exclude the possibility that the viability of microbiota is compromised by freezing and storing at 20 °C. Considering the route of administration, we used infusion into caecum in colonoscopy, because we had previously good experience of this method in treating rCDI patients. As pointed out by Dr Kelly, FMT via sigmoidoscopy would be easier and less costly as compared with colonoscopy. However, there are only few small scale studies comparing the treatment efficacy of FMT via different routes of administration and further studies are warranted. It is still difficult to conclude what would be the optimal route of administration considering all aspects of FMT. In our study, the follow-up period was 12 months, which is longer than in most other studies. The 1-year success rate of FMT treatment for rCDI was 88% and the treatment was found to be safe. Previously, Kelly et al. have demonstrated FMT to be a safe treatment for rCDI also in immunocompromised patients. Clearly, the short-term (up to 1 year) benefits of FMT outweigh the observed harms. However, we completely agree with Dr Kelly that further studies are needed to address the long-term health implications of FMT. In clinical work, experienced physicians should make the decision on using FMT by considering and balancing both the short-term benefits and possible long-term risks.
The Efficacy of Semantic Feature Analysis for the Treatment of Aphasia: A Systematic Review

Semantic feature analysis (SFA) is a common treatment for improving naming ability in persons with aphasia (PWA). To examine the effectiveness of SFA in improving naming abilities, we conducted an evidence-based systematic review. Seven studies met the inclusion criteria, were assigned appropriate levels of evidence, and were examined for methodological quality using the Single-Case Experimental Design (SCED) scale. Inter-rater reliability was established using Cohen’s weighted kappa statistic. To determine the clinical significance of SFA, effect sizes, or percent of non-overlapping data (PND), were calculated. Results of this study indicate that SFA may be most effective for persons with fluent aphasias.
Alzheimer Disease Pathology in Subjects Without Dementia in 2 Studies of Aging: The Nun Study and the Adult Changes in Thought Study

Individuals with antemortem preservation of cognition who show autopsy evidence of at least moderate Alzheimer disease (AD) pathology suggest the possibility of brain reserve, that is, functional resistance to structural brain damage. This reserve would, however, only be relevant if the pathologic markers correlate well with dementia. Using data from the Nun Study (n = 498) and the Adult Changes in Thought (ACT) Study (n = 323), we show that Braak staging correlates strongly with dementia status. Moreover, participants with severe(Braak stage V-VI) AD pathology who remained not demented represent only 12% (Nun Study) and 8% (ACT study) of nondemented subjects. Comparison of these subjects to those who were demented revealed that the former group was often significantly memory-impaired despite not being classified as demented. Most of these nondemented participants showed only stage V neurofibrillary pathology and frontal tangle counts that were slightly lower than a comparable (Braak stage V) dementia group. In summary, these data indicate that, in individuals with AD-type pathology who do not meet criteria for dementia, neocortical neurofibrillary tangles are somewhat reduced and incipient cognitive decline is present. Our data provide a foundation for helping to define additional factors that may impair, or be protective of, cognition in older adults.
Speech synthesis using the CELP algorithm

The paper presents a phoneme/diphone based speech synthesis system for the (Brazilian) Portuguese language. The basic idea of this system is the construction of a library of phonetic units, and processing of those basic units to build an utterance. The system is complemented by a text to phoneme translator described previously. The phonate's representation in the library is based on a linear prediction model; the filter which models the vocal tract is represented by line spectrum pairs, and the excitation by code excited linear prediction (CELP) parameters. The paper is organized as follows. After a brief introduction, CELP coding is briefly presented and the relevant points to be applied in speech synthesis are presented. The main contribution of the paper is detailing the process of building the phoneme library and the interpolation techniques used.
Inferring and Applying Safety Constraints to Guide an Ensemble of Planners for Airspace Deconfliction

This paper presents a Bayesian approach to learning flexible safety constraints in a coordinated, multi-planner ensemble, along with stochastic and active experimentation approaches for assigning degrees of blame when these constraints are violated. The blame is subsequently translated and conveyed to planners, for the purpose of improved overall system performance. To illustrate the advantages of our framework, we provide and discuss examples on a real test application for Airspace Control Order (ACO) planning and deconfliction, which is a benchmark application in the DARPA Integrated
Mother and Adolescent Reports of Interparental Discord Among Parents of Adolescents With and Without Attention-Deficit/Hyperactivity Disorder

Evidence is scarce regarding the prevalence of interparental discord in families of adolescents with attention-deficit/hyperactivity disorder (ADHD). Using data collected from adolescents with childhood ADHD and comorbid oppositional defiant disorder (ODD; n = 46) or conduct disorder (CD; n = 23), with childhood ADHD only (n = 26), and without ADHD (n = 88) and their mothers, maternal and adolescent reports of interparental discord were compared. Adolescents with ADHD + CD reported witnessing more frequent and unresolved interparental conflict than adolescents without ADHD and with ADHD only. Adolescents with ADHD + CD also indicated more frequent conflict than adolescents with ADHD + ODD. However, differences in conflict resolution were nonsignificant when household income was covaried, and maternal ratings of interparental discord did not differ across groups. Findings highlight the potential utility of adolescents with ADHD as informants of interparental relationship quality.
Program fragments, linking, and modularization

Module mechanisms have received considerable theoretical attention, but the associated concepts of separate compilation and linking have not been emphasized. Anomalous module systems have emerged in functional and object-oriented programming where software components are not separately typecheckable and compilable. In this paper we provide a context where linking can be studied, and separate compilability can be formally stated and checked. We propose a framework where each module is separately compiled to a self-contained entity called a linkset; we show that separately compiled, compatible modules can be safely linked together.
Symmetric M-tree

The M-tree is a paged, dynamically balanced metric access method that responds gracefully to the insertion of new objects. To date, no algorithm has been published for the corresponding Delete operation. We believe this to be non-trivial because of the design of the M-tree's Insert algorithm. We propose a modification to Insert that overcomes this problem and give the corresponding Delete algorithm. The performance of the tree is comparable to the M-tree and offers additional benefits in terms of supported operations, which we briefly discuss.
Nested Digital Background Calibration of a 12-bit Pipelined ADC Without an Input SHA

To reduce power dissipation, the input sample-and-hold amplifier (SHA) is eliminated in a pipelined analog-to-digital converter (ADC) with nested background calibration. The nested architecture calibrates the pipelined ADC with an algorithmic ADC that is also calibrated. Without an input SHA, a timing difference between the sampling instants of the two ADCs creates an error that interferes with calibration of the pipelined ADC. This problem is overcome with digital background timing compensation. It uses a differentiator with fixed coefficients to build an adaptive interpolator. With a 58-kHz sinusoidal input, the 12-bit 20-Msample/s pipelined ADC achieves a signal-to-noise-and-distortion ratio (SNDR) of 70.2 dB, a spurious-free dynamic range (SFDR) of 80.3 dB, and an integral nonlinearity (INL) of 0.75 least significant bit (LSB). With a 9-MHz input, the SNDR is 64.2 dB, and the SFDR is 78.3 dB. About 2 million samples or 0.1 s are required for convergence. The prototype occupies 7.5 mm2 in 0.35-mum CMOS and dissipates 231 mW from 3.3 V, which is 23 mW less than in a previous prototype with the input SHA.
FastDTW: Toward Accurate Dynamic Time Warping in Linear Time and Space

The dynamic time warping (DTW) algorithm is able to find the optimal alignment between two time series. It is often used to determine time series similarity, classification, and to find corresponding regions between two time series. DTW has a quadratic time and space complexity that limits its use to only small time series data sets. In this paper we introduce FastDTW, an approximation of DTW that has a linear time and space complexity. FastDTW uses a multilevel approach that recursively projects a solution from a coarse resolution and refines the projected solution. We prove the linear time and space complexity of FastDTW both theoretically and empirically. We also analyze the accuracy of FastDTW compared to two other existing approximate DTW algorithms: Sakoe-Chuba Bands and Data Abstraction. Our results show a large improvement in accuracy over the existing methods.
Criminal intelligence surveillance and monitoring on social media: Cases of cyber-trafficking

Cyber-trafficking is the illegal transport of humans, drugs, weapons, or goods by means of Internet-enabled electronic devices. Currently, there is a lack of surveillance and understanding of the rapidly growing social concern about cyber-trafficking (CT). This paper describes the Cyber-Trafficking Surveillance System (CyTraSS) and provides preliminary findings of using the system to monitor CT social media discussions. CyTraSS supports flexible collection, analysis, and visualization of social media content, user linkage, and temporal features. The CyTraSS database contains a focused collection of over 2,318,691 social media messages posted by over 740,070 users who discussed about trafficking crimes and issues. CyTraSS supports keyword search, sentiment analysis, message statistics summarization, and influential leader identification. Emotion expressed in social media messages is extracted and aggregated quantitatively to indicate community mood. We examined three use cases about a sex trafficker identified by a flight attendant, Federal use of private prisons, and trafficking cases related to Beijing. These time-sensitive incidents are highly-relevant to CT and were identified by using clues provided by CyTraSS. The results have strong implications for understanding CT concern on social media.
A maximum likelihood decoding algorithm of Gabidulin codes in deterministic network coding

Recently, studies of linear network coding have attracted attention. This paper considers a probabilistic error model for the deterministic linear network coding. In the previous studies of error-correcting codes, Kaneko et al. proposed a decod­ing algorithms for probabilistic error model. This is a maximum likelihood decoding algorithm that uses the optimization method called branch and bound method. This paper constructs a new model of deterministic linear network coding and proposes a maximum likelihood decoding algorithm that uses the branch and bound method.
Distributed under Creative Commons Cc-by 4.0 in Vitro Effect of Direct Current Electrical Stimulation on Rat Mesenchymal Stem Cells

Background. Electrical stimulation (ES) has been successfully used to treat bone defects clinically. Recently, both cellular and molecular approaches have demonstrated that ES can change cell behavior such as migration, proliferation and differentiation. Methods. In the present study we exposed rat bone marrow-(BM-) and adipose tissue-(AT-) derived mesenchymal stem cells (MSCs) to direct current electrical stimulation (DC ES) and assessed temporal changes in osteogenic differentiation. We applied 100 mV/mm of DC ES for 1 h per day for three, seven and 14 days to cells cultivated in osteogenic differentiation medium and assessed viability and calcium deposition at the different time points. In addition, expression of osteogenic genes, Runx2, Osteopontin, and Col1A2 was assessed in BM-and AT-derived MSCs at the different time points. Results. Results showed that ES changed osteogenic gene expression patterns in both BM-and AT-MSCs, and these changes differed between the two groups. In BM-MSCs, ES caused a significant increase in mRNA levels of Runx2, Osteopontin and Col1A2 at day 7, while in AT-MSCs, the increase in Runx2 and Osteopontin expression were observed after 14 days of ES. Discussion. This study shows that rat bone marrow-and adipose tissue-derived stem cells react differently to electrical stimuli, an observation that could be important for application of electrical stimulation in tissue engineering.
A Conceptual Language for the Description and Manipulation of Complex Information Models

Conceptual data modelling techniques aim at the representation of data (structures) at a high level of abstraction. This implies that conceptual data modelling techniques should not only be capable of representing complex structures in a natural way, but also the rules (constraints) that must hold for these structures. Contemporary data modelling techniques, however, do not provide a language which, on the one hand, has a formal semantics and, on the other hand, leads to natural looking expressions. In this paper, an informal introduction to such a language (LISA-D) for the data modelling technique (PSM), is presented. PSM is a generalisation of object-role models (such as ER, NIAM and FORM).
Fault modeling using the program dependence graph

We present a fault classification scheme and a fault seeding method that is based on the manifestation of faults in the program dependence graph (PDG). We enhance the domain/computation fault classification scheme to further characterize faults as structural and statement level, depending on the differences between the PDG for the original program and the PDG for the faulty program. Structural faults correspond to differences in the control dependence or data dependence information in the PDGs, whereas statement level faults correspond to differences in the information within PDG nodes. We perform transformations on the PDG to produce the different types of faults described in our PDG-based fault classification scheme. To demonstrate the usefulness of our technique, we implemented a fault seeder to embed faults into C programs. We are using our fault seeder to experiment with the effectiveness of unit testing techniques, and are investigating the application of our fault seeder for formulating a fault based testing method. <<ETX>>
Recognition of Professional Activities with Displaceable Sensors

The applications of activity recognition have increased in the last years. Among its uses are promoting healthy life styles or monitoring professional users (like first responders) during life-threatening operations; which caused the need for new research lines. However systems using common devices (like smart phones) equipped with the necessary sensors (e.g. inertial sensors) are not fully developed. Our work develops and activity recognition system, with a focus on professional users, that uses a displaceable sensor. The activity set is comprised of the most common activities (static, walking, running, etc.) but also crawling and 3D motions like stairs walking. A detector of upright dynamic activities has been developed and implemented to cope with the changing sensor position. The system is evaluated using 10-fold cross validation with the inference network, and recall with the detector. The final system proves to perform well with respect to the initial requirements.
A Dividing Rectangles Algorithm for Stochastic Simulation Optimization

Many important real-world optimization problems are stochastic, non-linear, nondifferentiable, and non-convex. To solve these difficult problems, practitioners often rely on black-box optimization methods which make no or few assumptions of internal problem structure. The Dividing Rectangles (DIRECT) algorithm has proven popular for deterministic, low-dimensional black-box problems. The algorithm does not require calculation of a gradient, is relatively simple (having only one tuning parameter), and is widely applicable, requiring only that the function be Lipschitz continuous. We describe a new DIRECT algorithm to support stochastic simulation optimization that retains the global convergence properties of the original. Our algorithm iterates between searching for new solutions and reducing the variance of existing solutions using Bayesian sample information. The algorithm intelligently allocates available computational resources using the Optimal Computing Budget Allocation (OCBA) methodology, and includes several heuristic mechanisms which in practice increase the likelihood of quickly obtaining desirable solutions. In computational experiments, we find this new algorithm can provide better performance than the only other known modification of DIRECT for stochastic problems. We provide the results of a realistic application where we use the algorithm to design a wireless mesh network supporting uncertain traffic demands.
Expecting the Unexpected: Understanding Mismatched Privacy Expectations Online

Online privacy notices are supposed to act as the primary mechanism to inform users about the data practices of online services. In practice, users ignore notices as they are too long and complex to read. Instead, users rely on formed expectations to determine with which site they feel comfortable interacting. Mismatches between actual practices and a user’s expectations may result in users exposing themselves to unanticipated privacy risks – even if the practices were disclosed in a privacy notice. One approach for mitigating these risks is to highlight elements of privacy notices that users do not likely expect. We present an approach for identifying such mismatches and analyze the results of a study based on this approach. Our findings suggest that focusing on mismatches could help design privacy notice interfaces that significantly reduce user burden. Author
Coding for the variably coherent channel

This talk introduces the concept of coding for variable channel coherence. The need for this type of coding arises naturally in the multiuser broadcast channel since the more mobile a terminal, the harder it is to maintain coherence. The talk shows that noncoherent users can be accommodated without loss to the overall capacity, as long as there are not too many of them. This derivation leads naturally to an efficient (capacity lossless) method of using codes designed for memoryless channels on channels with memory.
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives in transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model and newly discovered organisms because it does not require a predefined measuring platform (like e.g. microarrays). However, these novel technologies pose new challenges: the raw data need to be rigorously quality checked and filtered prior to analysis, and proper statistical methods have to be applied to extract biologically relevant information. Given the sheer volume of data, this is no trivial task and requires a combination of considerable technical resources along with bioinformatics expertise. To aid the individual researcher, we have developed RobiNA as an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis. Installer packages for Mac OS X, Windows and Linux are available under the LGPL licence from http://mapman.gabipd. org/web/guest/robin.
In Vivo Development of Outer Retinal Synapses in the Absence of Glial Contact

Astroglia secrete factors that promote synapse formation and maintenance. In culture, glial contact has also been shown to facilitate synaptogenesis. Here, we examined whether glial contact is important for establishing circuits in vivo by simultaneously monitoring differentiation of glial cells and local synaptogenesis over time. Photoreceptor circuits of the vertebrate retina are particularly suitable for this study because of the relatively simple, laminar organization of their connectivity with their target neurons, horizontal cells and bipolar cells. Also, individual photoreceptor terminals are ensheathed within the outer plexiform layer (OPL) by the processes of one type of glia, Müller glia cells (MGs). We conducted in vivo time-lapse multiphoton imaging of the rapidly developing and relatively transparent zebrafish retina to ascertain the time course of MG development relative to OPL synaptogenesis. The emergence of synaptic triads, indicative of functional photoreceptor circuits, and structural association with glial processes were also examined across ages by electron microscopy. We first show that MG processes form territories that tile within the inner and outer synaptic layers. We then demonstrate that cone photoreceptor synapses are assembled before the elaboration of MG processes in the OPL. Using a targeted cell ablation approach, we also determined whether the maintenance of photoreceptor synapses is perturbed when local MGs are absent. We found that removal of MGs had no appreciable effect on the stability of newly formed cone synapses. Thus, in contrast to other CNS circuits, contact from glia is not necessary for the formation or immediate stabilization of outer retinal synapses.
Designing personal tele-embodiment

At the intersection of telerobotics, computer networking and human social interaction we have chosen to explore an area we identify as personal tele-embodiment. At the core of this research is an emphasis on the individual person rather than the intricate complexities of the machine. While the mechanical elements of our system are essential to its over-all functionality, our research is driven solely by the study and understanding of the social and psychological aspects of extended human-human interactions rather than the latest techno-gadgetry. In this paper we emphasize the importance of the human component and describe the development of one such simple, inexpensive, Internet-controlled, untethered telerobot or PRoP (personal roving presence) that provides several fundamental elements of personal tele-embodiment.