Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity of Phytophthora ramorum in Belgium 1

Phytophthora ramorum is thought to be an introduced pathogen in North America and in Europe based on the presence of only three clonal lineages. The North American lineages (NA1 and NA2) are responsible for infections in North American forests and nurseries, while the European lineage (EU1) is responsible for infections in Europe, mostly in nurseries. There have also been a few isolated findings of the EU1 lineage in North American nurseries. P. ramorum is heterothallic, with two opposite mating types, A1 and A2. The A1 mating type was originally only found in Europe, with the exception of three A2 isolates of the EU1 lineage collected in Belgium in 2002 and 2003. Although there is no evidence for sexual reproduction in nature, the presence of both mating types at a single site might lead to genetic recombination. To verify the hypothesis of asexual reproduction in nature, and to verify the hypothesis that P. ramorum was recently introduced in Belgium and therefore possesses only a limited amount of genetic diversity, the Belgian P. ramorum population was screened with AFLP and SSLP markers. Use of the AFLP method with five primer combinations on a selected number of isolates (80) revealed 13 polymorphic fragments. These markers identified eight isolates that differed from the main genotype by one to three polymorphisms. Use of SSLP with existing microsatellite markers revealed a limited number of polymorphisms in the EU1 population. Additional microsatellite markers were then sought. A total of 146 candidate polymorphic microsatellites were prescreened using 10 isolates belonging to different EU1 genotypes. This resulted in two new primer pairs that amplify a total of three polymorphic loci, of which one was very useful. Seven markers (four existing and three new) were used to screen all 411 Belgian isolates. In total, 30 genotypes were identified, but 68 percent of the isolates belong to the main genotype EU1MG1. Although indications of accumulated mutation events were present, the overall level of genetic diversity within these isolates of P. ramorum appears to be limited, indicating a relatively recent clonal dispersion of the pathogen. Most of the genotypes were site-specific and some of them were detected over a period of several years at a single site, sometimes discontinuously. This indicated (latent) survival of the pathogen at those sites and led to questions about the efficiency of the eradication measures. No marker recombination was observed, indicating that no sexual recombination was found in nature.
Layered Networks as a Tool for Software Development

Most software systems use simple text files to represent the current state of an evolving design. We propose that layered networks provide a much better medium to represent the design of a software system and its documentation. PIE is an experimental personal information environment which provides users with descriptive structures for documents and programs. In PIE, alternative designs for programs and documents can be examined and manipulated within the systems context structured database. This data base also facilitates cooperative design among several people.
Tyrosinase Inhibitory Effect and Antioxidative Activities of Fermented and Ethanol Extracts of Rhodiola rosea and Lonicera japonica

This is the first study to investigate the biological activities of fermented extracts of Rhodiola rosea L. (Crassulaceae) and Lonicera japonica Thunb. (Caprifoliaceae). Alcaligenes piechaudii CC-ESB2 fermented and ethanol extracts of Rhodiola rosea and Lonicera japonica were prepared and the antioxidative activities of different concentrations of samples were evaluated using in vitro antioxidative assays. Tyrosinase inhibition was determined by using the dopachrome method with L-DOPA as substrate. The results demonstrated that inhibitory effects (ED50 values) on mushroom tyrosinase of fermented Rhodiola rosea, fermented Lonicera japonica, ethanol extract of Lonicera japonica, and ethanol extract of Rhodiola rosea were 0.78, 4.07, 6.93, and >10 mg/ml, respectively. The DPPH scavenging effects of fermented Rhodiola rosea (ED50 = 0.073 mg/ml) and fermented Lonicera japonica (ED50 = 0.207 mg/ml) were stronger than effects of their respective ethanol extracts. Furthermore, the scavenging effect increases with the presence of high content of total phenol. However, the superoxide scavenging effects of fermented Rhodiola rosea was less than effects of fermented Lonicera japonica. The results indicated that fermentation of Rhodiola rosea and Lonicera japonica can be considered as an effective biochemical process for application in food, drug, and cosmetics.
Intrauterine growth restriction caused by underlying congenital cytomegalovirus infection.

BACKGROUND Human cytomegalovirus (HCMV) is the major viral etiology of congenital infection and birth defects. Fetal transmission is high (30%-40%) in primary maternal infection, and symptomatic babies have permanent neurological, hearing, and vision defects. Recurrent infection is infrequently transmitted (2%) and largely asymptomatic. Congenital infection is also associated with intrauterine growth restriction (IUGR). METHODS To investigate possible underlying HCMV infection in cases of idiopathic IUGR, we studied maternal and cord sera and placentas from 19 pregnancies. Anti-HCMV antibodies, hypoxia-related factors, and cmvIL-10 were measured in sera. Placental biopsy specimens were examined for viral DNA, expression of infected cell proteins, and pathology. RESULTS Among 7 IUGR cases, we identified 2 primary and 3 recurrent HCMV infections. Virus replicated in glandular epithelium and lymphatic endothelium in the decidua, cytotrophoblasts, and smooth muscle cells in blood vessels of floating villi and the chorion. Large fibrinoids with avascular villi, edema, and inflammation were significantly increased. Detection of viral proteins in the amniotic epithelium indicated transmission in 2 cases of IUGR with primary infection and 3 asymptomatic recurrent infections. CONCLUSIONS Congenital HCMV infection impairs placental development and functions and should be considered as an underlying cause of IUGR, regardless of virus transmission to the fetus.
General solution for asynchronous sensors bias estimation

In multisensor systems, the measurements reported by local sensors are usually not time aligned or synchronous due to different data rates. A novel algorithm, based on Kalman filter combined with pseudomeasurement and equivalent bias, is proposed to solve a general bias estimate problem in asynchronous sensors systems. The pseudomeasurement equation of sensor biases is obtained by linearizing the last measurements provided by asynchronous sensors to remove the target state. The equivalent bias equation in each sampling interval of fusion center is derived from the bias dynamic equation of asynchronous sensors with different rates. Monte Carlo simulation results show that the Cramer-Rao lower bound (CRLB) is achievable, i.e., the new algorithm is statistically efficient.
LTBI: latent tuberculosis infection or lasting immune responses to M. tuberculosis? A TBNET consensus statement

Tuberculosis control relies on the identification and preventive treatment of individuals who are latently infected with Mycobacterium tuberculosis. However, direct identification of latent tuberculosis infection is not possible. The diagnostic tests used to identify individuals latently infected with M. tuberculosis, the in vivo tuberculin skin test and the ex vivo interferon-γ release assays (IGRAs), are designed to identify an adaptive immune response against, but not necessarily a latent infection with, M. tuberculosis. The proportion of individuals who truly remain infected with M. tuberculosis after tuberculin skin test or IGRA conversion is unknown. It is also uncertain how long adaptive immune responses towards mycobacterial antigens persist in the absence of live mycobacteria. Clinical management and public healthcare policies for preventive chemotherapy against tuberculosis could be improved, if we were to gain a better understanding on M. tuberculosis latency and reactivation. This statement by the TBNET summarises knowledge and limitations of the currently available tests used in adults and children for the diagnosis of latent tuberculosis infection. In summary, the main issue regarding testing is to restrict it to those who are known to be at higher risk of developing tuberculosis and who are willing to accept preventive chemotherapy.
Assessment of nonuniformity of transmural myocardial velocities by color-coded tissue Doppler imaging: characterization of normal, ischemic, and stunned myocardium.

BACKGROUND Transmural myocardial contractile performance is nonuniform across the different layers of the left ventricular wall. We evaluated the accuracy of color M-mode tissue Doppler imaging (TDI) to assess the transmural distribution of myocardial velocities and to quantify the severity of dysfunction induced by acute ischemia and reperfusion in the inner and outer myocardial layers. METHODS AND RESULTS Thirteen open-chest dogs underwent 15 minutes of left anterior descending coronary artery occlusion followed by 120 minutes of reperfusion. M-mode TDI was obtained from an epicardial short-axis view. Systolic velocities were calculated within endocardium and epicardium of the anterior and posterior walls. Regional myocardial blood flow was assessed by radioactive microspheres. Segment shortening was measured by sonomicrometry in endocardium and epicardium of both the anterior and posterior walls. At baseline, endocardial velocities were higher than epicardial velocities, resulting in an inner/outer myocardial velocity gradient. Ischemia caused a significant and comparable reduction in endocardial and epicardial systolic velocities in the anterior wall with the disappearance of the velocity gradient. Systolic velocities significantly correlated with segment shortening in both endocardium and epicardium during ischemia and reperfusion. In the first minutes after reflow, endocardial velocities showed a greater improvement than epicardial velocities, and the velocity gradient resumed although to a limited extent, indicative of stunning. CONCLUSIONS TDI is an accurate method to assess the nonuniformity of transmural velocities and may be a promising new tool for quantifying ischemia-induced regional myocardial dysfunction.
Auditory-Visual Speech Perception and Aging

Objective This experiment was designed to assess the integration of auditory and visual information for speech perception in older adults. The integration of place and voicing information was assessed across modalities using the McGurk effect. The following questions were addressed: 1) Are older adults as successful as younger adults at integrating auditory and visual information for speech perception? 2) Is successful integration of this information related to lipreading performance? Design The performance of three groups of participants was compared: young adults with normal hearing and vision, older adults with normal to near-normal hearing and vision, and young controls, whose hearing thresholds were shifted with noise to match the older adults. Each participant completed a lipreading test and auditory and auditory-plus-visual identification of syllables with conflicting auditory and visual cues. Results The results show that on average older adults are as successful as young adults at integrating auditory and visual information for speech perception at the syllable level. The number of fused responses did not differ for the CV tokens across the ages tested. Although there were no significant differences between groups for integration at the syllable level, there were differences in the response alternatives chosen. Young adults with normal peripheral sensitivity often chose an auditory alternative whereas, older adults and control participants leaned toward visual alternatives. In additions, older adults demonstrated poorer lipreading performance than their younger counterparts. This was not related to successful integration of information at the syllable level. Conclusions Based on the findings of this study, when auditory and visual integration of speech information fails to occur, producing a nonfused response, participants select an alternative response from the modality with the least ambiguous signal.
Knowledge Driven Query Sharding

We present the idea of an approach to database query sharding that makes use of knowledge about data structure and purpose. It is based on a case study for a database system that contains information about documents. By making use of knowledge about the data structure and the specific top-k queries to be processed we demonstrate a method for avoiding costly and unnecessary steps in query answering. We also demonstrate how the knowledge of data structure may be used to perform sharding and how such sharding may improve performance. We propose generalization of our findings that could lead to self-optimization and self-tuning in RDBMS engines, especially for column-based solutions.
Steering a virtual blowfly: simulation of visual pursuit

The behavioural repertoire of male flies includes visually guided chasing after moving targets. The visuomotor control system for these pursuits belongs to the fastest found in the animal kingdom. We simulated a virtual fly, to test whether or not experimentally established hypotheses on the underlying control system are sufficient to explain chasing behaviour. Two operating instructions for steering the chasing virtual fly were derived from behavioural experiments: (i) the retinal size of the target controls the fly's forward speed and, thus, indirectly its distance to the target; and (ii) a smooth pursuit system uses the retinal position of the target to regulate the fly's flight direction. Low–pass filters implement neuronal processing time. Treating the virtual fly as a point mass, its kinematics are modelled in consideration of the effects of translatory inertia and air friction. Despite its simplicity, the model shows behaviour similar to that of real flies. Depending on its starting position and orientation as well as on target size and speed, the virtual fly either catches the target or follows it indefinitely without capture. These two behavioural modes of the virtual fly emerge from the control system for flight steering without implementation of an explicit decision maker.
Analysis and Construction of Full-Diversity Joint Network-LDPC Codes for Cooperative Communications

Transmit diversity is necessary in harsh environments to reduce the required transmit power for achieving a given error performance at a certain transmission rate. In networks, cooperative communication is a well-known technique to yield transmit diversity and network coding can increase the spectral efficiency. These two techniques can be combined to achieve a double diversity order for a maximum coding rate on the Multiple-Access Relay Channel (MARC), where two sources share a common relay in their transmission to the destination. However, codes have to be carefully designed to obtain the intrinsic diversity offered by the MARC. This paper presents the principles to design a family of full-diversity LDPC codes with maximum rate. Simulation of the word error rate performance of the new proposed family of LDPC codes for the MARC confirms the full diversity.
Sotagliflozin, a Dual SGLT1 and SGLT2 Inhibitor, as Adjunct Therapy to Insulin in Type 1 Diabetes

OBJECTIVE To assess the safety and efficacy of dual sodium–glucose cotransporter (SGLT) 1 and SGLT2 inhibition with sotagliflozin as adjunct therapy to insulin in type 1 diabetes. RESEARCH DESIGN AND METHODS We treated 33 patients with sotagliflozin, an oral dual SGLT1 and SGLT2 inhibitor, or placebo in a randomized, double-blind trial assessing safety, insulin dose, glycemic control, and other metabolic parameters over 29 days of treatment. RESULTS In the sotagliflozin-treated group, the percent reduction from baseline in the primary end point of bolus insulin dose was 32.1% (P = 0.007), accompanied by lower mean daily glucose measured by continuous glucose monitoring (CGM) of 148.8 mg/dL (8.3 mmol/L) (P = 0.010) and a reduction of 0.55% (5.9 mmol/mol) (P = 0.002) in HbA1c compared with the placebo group that showed 6.4% reduction in bolus insulin dose, a mean daily glucose of 170.3 mg/dL (9.5 mmol/L), and a decrease of 0.06% (0.65 mmol/mol) in HbA1c. The percentage of time in target glucose range 70–180 mg/dL (3.9–10.0 mmol/L) increased from baseline with sotagliflozin compared with placebo, to 68.2% vs. 54.0% (P = 0.003), while the percentage of time in hyperglycemic range >180 mg/dL (10.0 mmol/L) decreased from baseline, to 25.0% vs. 40.2% (P = 0.002), for sotagliflozin and placebo, respectively. Body weight decreased (1.7 kg) with sotagliflozin compared with a 0.5 kg gain (P = 0.005) in the placebo group. CONCLUSIONS As adjunct to insulin, dual SGLT1 and SGLT2 inhibition with sotagliflozin improved glycemic control and the CGM profile with bolus insulin dose reduction, weight loss, and no increased hypoglycemia in type 1 diabetes.
ULisboa: Identification and Classification of Medical Concepts

This paper describes our participation on Task 7 of SemEval 2014, which focused on the recognition and disambiguation of medical concepts. We used an adapted version of the Stanford NER system to train CRF models to recognize textual spans denoting diseases and disorders, within clinical notes. We considered an encoding that accounts with noncontinuous entities, together with a rich set of features (i) based on domain specific lexicons like SNOMED CT, or (ii) leveraging Brown clusters inferred from a large collection of clinical texts. Together with this recognition mechanism, we used a heuristic similarity search method, to assign an unambiguous identifier to each concept recognized in the text. Our best run on Task A (i.e., in the recognition of medical concepts in the text) achieved an F-measure of 0.705 in the strict evaluation mode, and a promising F-measure of 0.862 in the relaxed mode, with a precision of 0.914. For Task B (i.e., the disambiguation of the recognized concepts), we achieved less promising results, with an accuracy of 0.405 in the strict mode, and of 0.615 in the relaxed mode.
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes*

We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensional protein structure and does not require any knowledge about a potential ligand molecule. We validated this algorithm using two systematically collected data sets of ligand binding pockets from complexed (bound) and uncomplexed (apo) structures from the Protein Data Bank, 5616 and 11,510, respectively. As many as 96.8% of experimental binding sites were predicted at better than 50% overlap level. Furthermore 95.0% of the asserted sites from the apo receptors were predicted at the same level. We demonstrate that conformational differences between the apo and bound pockets do not dramatically affect the prediction results. The algorithm can be used to predict ligand binding pockets of uncharacterized protein structures, suggest new allosteric pockets, evaluate feasibility of protein-protein interaction inhibition, and prioritize molecular targets. Finally the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified. The pocketome can be used for rapid evaluation of possible binding partners of a given chemical compound.
Combining overall and local class accuracies in an oracle-based method for dynamic ensemble selection

This paper presents a k-nearest oracle-based dynamic ensemble selection method in which overall local accuracy (OLA) and local class accuracy (LCA) are combined into a twostep selection scheme. The OLA and LCA are computed on the neighborhood of the test pattern in a validation set to filter out the classifiers selected by the k-nearest oracles. The complementary information of OLA and LCA has shown to be an interesting alternative to approximate the classification performance to that estimated for the oracle of the initial pool of classifiers. The results were compared with the recognition rates of the majority voting of all classifiers in the initial pool, and also with the recognition rates of related classifier and ensemble selection methods which have inspired the proposed method and its variants. The proposed method achieved the best results on 5 out of 8 experiments using small and large datasets of different applications.
Modeling of nano- and micro-spheres for sensing applications

The design of both active and passive micro/nano-sphere systems is performed by optimizing their sizes, spatial distribution and the other physical and geometrical parameters. In particular, rare earth doped spherical particles are designed in order to obtain distributed and highly efficient light sources for active sensors. The lasing characteristics of active silica glass microsphere are numerically simulated in the third band of optical fibre communication by means of a home made computer code. Finally, passive and active spherical nanoparticles, covered by a thin metallic shell, surrounded by different dielectric materials and arranged in different lattices are optimized for sensing applications.
Ageing and the use of the internet – current engagement and future needs:state-of-the-art report

Foreword Over the past five years the number of people online, aged 65 and over, has remained relatively static, with between 25% and 35% using the internet (Oxford Internet Institute Survey 2011). As new online services become available and more benefits of being digitally connected are highlighted, this figure presents a real challenge to those working with this demographic group as there seems to be little impact aggregated to a national scale. Yet the over-65 population describes a diverse group. There can be up to 40 years' life experience between those in early old age and those in late old age; it can describe people in good health and poor health; those who are physically or socially isolated or those living with, or supported by families. As such, a diverse range of approaches need to be put in place if we are to support them to benefit from using the internet. Similarly, when the online/offline figure is broken down into smaller age groups or correlated with other socioeconomic characteristics (such as housing status, educational attainment, income levels etc) a clearer picture of internet use and the mechanisms of support for novice and advanced users becomes apparent. This publication sets out the latest research into how the internet is, and can be, used to support those over 65 as well as highlighting the mechanisms, themes and social situations that best enable this group to benefit from the internet. By doing so, it sets out a number of ways in which we can look to develop new approaches to supporting people over the age of 65 to get online in a sustained and meaningful way. Foreword Ageing and the use of the Internet – current engagement and future needs 3 > About the series About the series Nominet Trust State of the Art Reviews are undertaken by leading academics to collate and analyse the latest research at the intersection of the internet and society. Drawing on national and international work, these reviews aim to share the latest research to inform the work of the Trust, those applying to the Trust for support and our wider partner organisations. We value your comments and suggestions for how to act on the recommendations in these Reviews, and how we can build the series, so that it is more useful to us all as we work towards a safer, more accessible internet, used for social good. …