Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results. This protocol was used to compare six different bioinformatics pipelines in the basic user context: Three common ones (mothur, QIIME and BMP) based on a clustering-first approach and three emerging ones (Kraken, CLARK and One Codex) using an assignment-first approach. This study surprisingly reveals that the effect of sequencing errors has a bigger impact on the results that choosing different amplified regions. Moreover, increasing sequencing throughput increases richness overestimation, even more so for microbiota of high complexity. Finally, the choice of the reference database has a bigger impact on richness estimation for clustering-first pipelines, and on correct taxa identification for assignment-first pipelines. Using emerging assignment-first pipelines is a valid approach for targeted metagenomics analyses, with a quality of results comparable to popular clustering-first pipelines, even with an error-prone sequencing technology like Ion Torrent. However, those pipelines are highly sensitive to the quality of databases and their annotations, which makes clustering-first pipelines still the only reliable approach for studying microbiomes that are not well described.
National Standards for Diabetes Self-Management Education

Diabetes self-management education (DSME) is a critical element of care for all people with diabetes and is necessary in order to improve patient outcomes. The National Standards for DSME are designed to define quality diabetes self-management education and to assist diabetes educators in a variety of settings to provide evidence-based education. Because of the dynamic nature of health care and diabetes-related research, these Standards are reviewed and revised approximately every 5 years by key organizations and federal agencies within the diabetes education community. A Task Force was jointly convened by the American Association of Diabetes Educators and the American Diabetes Association in the summer of 2006. Additional organizations that were represented included the American Dietetic Association, the Veteran's Health Administration, the Centers for Disease Control and Prevention, the Indian Health Service, and the American Pharmaceutical Association. Members of the Task Force included a person with diabetes; several health services researchers/behaviorists, registered nurses, and registered dietitians; and a pharmacist. The Task Force was charged with reviewing the current DSME standards for their appropriateness, relevance, and scientific basis. The Standards were then reviewed and revised based on the available evidence and expert consensus. The committee convened on 31 March 2006 and 9 September 2006, and the Standards were approved 25 March 2007. Diabetes self-management education (DSME) is the ongoing process of facilitating the knowledge, skill, and ability necessary for diabetes self-care. This process incorporates the needs, goals, and life experiences of the person with diabetes and is guided by evidence-based standards. The overall objectives of DSME are to support informed decision-making, self-care behaviors, problem-solving and active collaboration with the health care team and to improve clinical outcomes, health status, and quality of life. Before the review of the individual Standards, the Task Force identified overriding principles based on existing evidence that would …
REASSIGNMENT TECHNIQUE FOR TIME-FREQUENCY MASKING AUDIO SEPARATION

A neighborhood-based source reassignment technique is proposed for being used on time-frequency masking audio source separation methods. This technique identifies all the time-frequency clusters that form the separation masks in the Short-Time Fourier Transform (STFT) domain, and labels each time-frequency bin with a value that denotes the size of their corresponding clusters. The bins corresponding to clusters of small size are reassigned to the source which has maximum likelihood in its time-frequency neighborhood. An example is described using the DUET algorithm for underdetermined mixtures, showing that this technique improves substantially the isolation of the estimated signals.
CONSONANTS IN CONTACT: ON ASSIMILATION AND CROSS-LANGUAGE CONTRAST

The rapid technological development i n the field o f experimental phonetics makes it possible to examine closely the modification processes in connected speech. Of course, after describing the situation in individual languages (most of them concern English), the cross-language study comes to the fore. The comparative approach is very important and inspiring, because in this way one is forced to reflex on the facts which might seem to the user of the mother-tongue to b e self-evident. Also in theoretical phonetics new problems are tackled, or old on es treated anew, side by side with the a dvances in the experimental research. In this paper I will pay attention to one case of modification of articulation at the word boundary, i.e. assimilation, which regularly takes place in Dutch, but i s avoided in Czech. It is a rather complex phenomenon, and I aim to give here just a few data based on the systematicity o f the phoneme inventories of both languages. I also will try to formulate a hypothesis about t he reason for this difference. The domain where phonology overlaps with semantics then should not be overlooked. 1 The case of -s#jIn my everyday communication p ractice I do no t use my Czech mother-tongue, bu t my second language, which is Dutch. Listening to the Dutch radio I once noticed the pronunciation o f the c ombination o f consonants -s#j- at t he word bound ary, as this was strikingly different from the pronunciation of the same combination in Czech. In Dutch, [s] is palatalized in [S], thus the c ombination is realized as [-Sj-], sometimes only as [-S-], e.g. zes januari ‘January the sixth’, prinses Juliana ‘princess Juliana’. This modification is a clear case of regressive assimilation of place of articulation, as a c onsequence of the so-called coarticulation, a process which o ccurs during the production o f connected speech. The notions (and terms) coarticulation and assimilation, in the way I am using them i n this discussion, will be specified in the next section. Assimilation in Dutch in such combinations yields a c onsiderable reduction of articulatory effort: the alveolar [s] is shifted backwards along the tongue blade (closer to the palatal [j]) and the result i s the postalveolar/prepalatal [S]. The speech o rgans are thus acting n aturally, in accordance with the principle generally valid in speech production: to reach the optimal distinctiveness of the sound material by minimal articulatory effort. 1 This paper is a revised and with new information provided version of a speech in Czech held at the
Identification of network measurement challenges in OpenFlow-based service chaining

Software-defined networking and Network Function Virtualization (NFV) have simplified the coordination efforts for “service chaining. ” Consequently, network services such as firewall, load balancing, etc. may be service chained in the forwarding (data) plane for specific applications and/or traffic. A specific case is for the firewall rules that depend on deep packet inspection for application identification. If a particular application is identified and is “safe,” would it be worthwhile to program the data plane to bypass the FW for the duration of the application session? For such a traffic-steering case, we report measurement challenges on various setups and the related cost analysis based on the network delay. Measurements of the network and processing delay have been performed with virtualized resources, on GENI testbed, and with isolated hardware units. Experiences are also reported on how a commercial firewall virtual appliance has been deployed on the GENI testbed for experimentation. The results illustrate the measurement uncertainties and challenges for DPI-based traffic steering in virtualized environments. In addition, we show that such a service chaining may increase throughput and relieve DPI-based processing overhead on firewall units.
Development of interpretive breakpoints for antifungal susceptibility testing: conceptual framework and analysis of in vitro-in vivo correlation data for fluconazole, itraconazole, and candida infections. Subcommittee on Antifungal Susceptibility Testing of the National Committee for Clinical Labora

The availability of reproducible antifungal susceptibility testing methods now permits analysis of data correlating susceptibility in vitro with outcome in vivo in order to define interpretive breakpoints. In this paper, we have examined the conceptual framework underlying interpretation of antimicrobial susceptibility testing results and then used these ideas to drive analysis of data packages developed by the respective manufacturers that correlate fluconazole and itraconazole MICs with outcome of candidal infections. Tentative fluconazole interpretive breakpoints for MICs determined by the National Committee for Clinical Laboratory Standards' M27-T broth macrodilution methodology are proposed: isolates for which MICs are < or = 8 microg/mL are susceptible to fluconazole, whereas those for which MICs are > or = 64 microg/mL appear resistant. Isolates for which the MIC of fluconazole is 16-32 microg/mL are considered susceptible dependent upon dose (S-DD), on the basis of data indicating clinical response when > 100 mg of fluconazole per day is given. These breakpoints do not, however, apply to Candida krusei, as it is considered inherently resistant to fluconazole. Tentative interpretive MIC breakpoints for itraconazole apply only to mucosal candidal infections and are as follows: susceptible, < or = 0.125 microg/mL; S-DD, 0.25-0.5 microg/mL; and resistant, > or = 1.0 microg/mL. These tentative breakpoints are now open for public commentary.
Picocell positioning in an LTE network

—As a way to increase the capacity of the mobile communications network, the service provider usually chooses to place more macrocells in the areas in which there is a big intensity of data trafﬁc. This approach has, as a disadvantage, an elevated cost of implementation. In the LTE (Long Term Evolution) project it is proposed the placement of smaller cells with smaller coverage and a lower implementation cost, called picocells. The work here presented aims to study the way in which the picocells are placed in the system in order to optimize the results of its introduction. The various scenarios of picocell placement simulated were analysed through the measuring of the SINR (Signal to Noise and Interference Ratio) value and the values of the throughputs of the network users. It is shown that the result of the introduction of picocells in the network greatly depends on the positions in which these are placed, but by following some rules there can be a positive outcome.
The 32 Days of Christmas: Understanding Temporal Intent in Image Search Queries

Temporal terms, such as 'winter', 'Christmas', or 'January' are often used in search queries for personal images. But how do people's memories and perceptions of time match with the actual dates when their images were captured? We compared the temporal terms that 74 Flickr users used to search their own photo collections, and compared them to the date captured data in the target image. We also conducted a larger study across several billion images, comparing user-applied tags for holidays and seasons to the dates the images were captured. We demonstrate that various query terms and tags can be in conflict with the actual dates photos were taken for specific types of temporal terms up to 40% of the time. We will conclude by highlighting implications for search systems where users are querying for personal content by date.
Fair bandwidth allocation for multicasting in networks with discrete feasible set

We study fairness in allocating bandwidth for loss-tolerant real-time multicast applications. We assume that the traffic is encoded in several layers so that the network can adapt to the available bandwidth and receiver processing capabilities by varying the number of layers delivered. We consider the case where receivers cannot subscribe to fractional layers. Therefore, the network can allocate only a discrete set of bandwidth to a receiver, whereas a continuous set of rates can be allocated when receivers can subscribe to fractional layers. Fairness issues differ vastly in these two different cases. Computation of lexicographic optimal rate allocation becomes NP-hard in this case, while lexicographic optimal rate allocation is polynomial complexity computable when fractional layers can be allocated. Furthermore, maxmin fair rate vector may not exist in this case. We introduce a new notion of fairness, maximal fairness. Even though maximal fairness is a weaker notion of fairness, it has many intuitively appealing fairness properties. For example, it coincides with lexicographic optimally and maxmin fairness, when maxmin fair rate allocation exists. We propose a polynomial complexity algorithm for computation of maximally fair rates allocated to various source-destination pairs, which incidentally computes the maxmin fair rate allocation, when the latter exists.
Assessing the protective value of protective behavioral strategies.

OBJECTIVE Many students report using strategies believed to reduce risk of harm from consumption of alcohol. The effectiveness of these strategies was tested in this study. METHOD A sample of 442 undergraduate students (50.5% female) was asked to report how many alcoholic drinks they consumed on a recent drinking occasion, which protective strategies were used, and which harms were experienced. RESULTS Although reported use of more protective strategies was associated with less consumption, it appeared to be unrelated to harmful consequences. More detailed analyses suggested that only a small subset of strategies (primarily those concerning the manner of drinking) was consistently associated with reduced consumption and/or harms. CONCLUSIONS The findings cast doubt on the efficacy of protective strategies or at least the validity of the self-report instruments used to assess these strategies.
Sperm DNA fragmentation: paternal effect on early post-implantation embryo development in ART.

BACKGROUND The relationship between early embryo post-implantation development in couples undergoing assisted reproductive techniques (ARTs) and sperm chromatin alterations has not been satisfactorily explained. The aim of this study was to assess the relationship between sperm DNA fragmentation in IVF/ICSI patients, sperm parameters (concentration, motility and morphology) and ART outcome, especially with regard to clinical pregnancy and pregnancy loss (spontaneous miscarriage or biochemical pregnancy). METHODS DNA fragmentation was evaluated by TUNEL assay, performed on sperm suspensions after density gradient separation, in 132 men undergoing an ART cycle (82 IVF and 50 ICSI) and correlated with sperm parameters and ART outcome. RESULTS A highly significant negative correlation was found between DNA fragmentation and sperm parameters. There was a close relationship between DNA fragmentation and post-implantation development in ICSI patients: the clinical pregnancy and pregnancy loss rates significantly differed between patients with high and low sperm DNA fragmentation (P = 0.007 and P = 0.009, respectively). CONCLUSIONS Sperm DNA fragmentation seems to affect embryo post-implantation development in ICSI procedures: high sperm DNA fragmentation can compromise 'embryo viability', resulting in pregnancy loss.
Using continuous renal replacement therapy to manage patients of shock and acute renal failure

Background: The incidence of acute renal failure (ARF) in the hospital setting is increasing. It portends excessive morbidity and mortality and a considerable burden on hospital resources. Extracorporeal therapies show promise in the management of patients with shock and ARF. It is said that the potential of such therapy goes beyond just providing renal support. The aim of our study was to analyze the clinical setting and outcomes of critically ill ARF patients managed with continuous renal replacement therapy (CRRT). Patients and Methods: Ours was a retrospective study of 50 patients treated between January 2004 and November 2005. These 50 patients were in clinical shock and had concomitant ARF. All of these patients underwent CVVHDF (continuous veno-venous hemodiafiltration) in the intensive care unit. For the purpose of this study, shock was defined as systolic BP < 100 mm Hg in spite of administration of one or more inotropic agents. SOFA (Sequential Organ Failure Assessment) score before initiation of dialysis support was recorded in all cases. CVVHDF was performed using the Diapact® (Braun) CRRT machine. The vascular access used was as follows: femoral in 32, internal jugular in 8, arteriovenous fistula (AVF) in 4, and subclavian in 6 patients. We used 0.9% or 0.45% (half-normal) saline as a prefilter replacement, with addition of 10% calcium gluconate, magnesium sulphate, sodium bicarbonate, and potassium chloride in separate units, while maintaining careful monitoring of electrolytes. Anticoagulation of the extracorporeal circuit was achieved with systemic heparin in 26 patients; frequent saline flushes were used in the other 24 patients. Results: Of the 50 patients studied, 29 were males and 21 females (1.4:1). The average age was 52.88 years (range: 20–75 years). Causes of ARF included sepsis in 24 (48%), hemodynamically mediated renal failure (HMRF) in 18 (36%), and acute over chronic kidney disease in 8 (16%) patients. The overall mortality was 74%. The average SOFA score was 14.31. The variables influencing mortality on multivariate analysis were: age [odds ratio (OR):1.65; 95% CI: 1.35 to 1.92; P = 0.04], serum creatinine (OR:1.68; 95% CI: 1.44 to 1.86; P = 0.03), and serum bicarbonate (OR: 0.76; 95% CI: 0.55 to 0.94; P = 0.01). On univariate analysis the SOFA score was found to be a useful predictor of mortality. Conclusions: Despite advances in treating critically ill patients with newer extracorporeal therapies, mortality is dismally high. Multiorgan dysfunction adversely affects outcome of CRRT. Older age, level of azotemia, and severity of metabolic acidosis are important predictors of adverse outcome.
Video DSP architecture for MPEG2 codec

We developed a DSP named VDSP2 (Video Digital Signal Processor version 2) for MPEG2 video coding and decoding. In order to obtain the necessary performance, we employed a 2-level parallel processing scheme consisting of a pipeline processing at the macro block level and a parallel vector processing using a SIMD configuration at the block level. In the VDSP2, we included a DSP core which execute 4 parallel vector operations and scalar operations, a DRAM controller, a DCT/IDCT circuit, a VLC/VLD circuit including a programmable controller and a data communication circuit. As a result, the real-time encoder specified in MPEG2 can be realized with two VDSP2 chips, and the decoder can be realized with one VDSP2 chip. <<ETX>>
ARGOS-Venice Boat Classification

Detection, classification, and tracking of people and vehicles are fundamental processes in intelligent surveillance systems. The use of publicly available data set is the appropriate way to compare the relative merits of existing methods and to develop and assess new robust solutions. In this paper, we focus on the maritime domain and we describe the generation of boat classification data sets, containing images of boats automatically extracted by the ARGOS system, operating 24/7 in Venice, Italy. The data sets are unique in their nature, since they come from an incomparable environment like Venice, but they present very interesting challenges to vehicle classification, due to changes in the environmental conditions, boat wakes, waves, reflections, etc. We thus believe that robust techniques, validated through the ARGOS Boat Classification data sets, will improve the development and deployment of solutions in similar applications related to vehicle detection and classification.
Undocumented water column sink for cadmium in open ocean oxygen-deficient zones

Significance Cadmium (Cd), a trace nutrient for marine algae, has a marine distribution that closely matches the macronutrients nitrate and phosphate. Sedimentary microfossil records of Cd provide reconstructions of past ocean nutrient distributions that facilitate understanding the role of the oceans in the carbon cycle and climate change. However, incomplete knowledge of processes that control the addition and removal of Cd in the ocean, and Cd’s variability relative to major nutrients, limit use of the paleoceanographic proxy. We present coupled data of Cd concentration and isotopic composition in seawater and suspended marine particles, indicating direct removal of Cd via coprecipitation with sulfide in oxygen-deficient waters. Thus, the marine Cd cycle may be highly sensitive to the extent of global oceanic oxygen depletion. Cadmium (Cd) is a micronutrient and a tracer of biological productivity and circulation in the ocean. The correlation between dissolved Cd and the major algal nutrients in seawater has led to the use of Cd preserved in microfossils to constrain past ocean nutrient distributions. However, linking Cd to marine biological processes requires constraints on marine sources and sinks of Cd. Here, we show a decoupling between Cd and major nutrients within oxygen-deficient zones (ODZs) in both the Northeast Pacific and North Atlantic Oceans, which we attribute to Cd sulfide (CdS) precipitation in euxinic microenvironments around sinking biological particles. We find that dissolved Cd correlates well with dissolved phosphate in oxygenated waters, but is depleted compared with phosphate in ODZs. Additionally, suspended particles from the North Atlantic show high Cd content and light Cd stable isotope ratios within the ODZ, indicative of CdS precipitation. Globally, we calculate that CdS precipitation in ODZs is an important, and to our knowledge a previously undocumented marine sink of Cd. Our results suggest that water column oxygen depletion has a substantial impact on Cd biogeochemical cycling, impacting the global relationship between Cd and major nutrients and suggesting that Cd may be a previously unidentified tracer for water column oxygen deficiency on geological timescales. Similar depletions of copper and zinc in the Northeast Pacific indicate that sulfide precipitation in ODZs may also have an influence on the global distribution of other trace metals.