Miracle-dz/UniFAR-FTUs huggingface dataset:
The post-translational amino acid epimerase BotH defines a new group of atypical alpha/beta-hydrolase-fold enzymes

D -amino acids endow peptides with diverse, desirable properties, but the post-translational and site-specific epimerization of L -amino acids into their D -counterparts is rare and very challenging. Bottromycins are ribosomally synthesized and post-translationally modified peptides that have overcome this challenge and feature a D -aspartate ( D -Asp), which was previously proposed to arise spontaneously during biosynthesis. We have identified the highly unusual alpha/beta-hydrolase (ABH) fold enzyme BotH as a novel peptide epimerase responsible for the post-translational epimerization of L -Asp to D -Asp during bottromycin biosynthesis. To understand the mechanism of this reaction, we determined the structures of BotH and the BotH-substrate complex. We also found BotH to bind the natural product itself, which has implications for the regulation of bottromycin biosynthesis. Bioinformatic analyses of BotH homologs show that similar ABH enzymes are found in diverse biosynthetic gene clusters.
The ex vivo purge of cancer cells using oncolytic viruses: recent advances and clinical implications

: Hematological malignancies are treated with intensive high-dose chemotherapy, with or without radiation. This is followed by hematopoietic stem cell (HSC) transplantation (HSCT) to rescue or reconstitute hematopoiesis damaged by the anticancer therapy. Autologous HSC grafts may contain cancer cells and purging could further improve treatment outcomes. Similarly, allogeneic HSCT may be improved by selectively purging alloreactive effector cells from the graft rather than wholesale immune cell depletion. Viral agents that selectively replicate in specific cell populations are being studied in experimental models of cancer and immunological diseases and have potential applications in the context of HSC graft engineering. This review describes preclinical studies involving oncolytic virus strains of adenovirus, herpes simplex virus type 1, myxoma virus, and reovirus as ex vivo purging agents for HSC grafts, as well as in vitro and in vivo experimental studies using oncolytic coxsackievirus, measles virus, parvovirus, vaccinia virus, and vesicular stomatitis virus to eradicate hematopoietic malignancies. Alternative ex vivo oncolytic virus strategies are also outlined that aim to reduce the risk of relapse following autologous HSCT and mitigate morbidity and mortality due to graft-versus-host disease in allogeneic HSCT.
Full Band Incorporation in Ab-initio Simulations of Two-dimensional Semiconductor Based Devices

—Quantum transport simulations based on the Non-Equilibrium Green’s Function formalism require accurate integration of the charges in the system. We demonstrate our implementation of a full-band integration scheme, which automatically incorporates electronic screening effects and is predicted to incorporate interface charges more correctly than the simpler excess charge approach. We show that for single doping type purely semiconducting devices, the two approaches are equivalent. We also highlight the inﬂuence of using the full-band approach for devices containing metals
Speech Recognition Based on Statistical Features

The requisition of intelligent devices that might classify a vocalized utterance have been skippering utterance research. The challenging task with utterance recognition models given for the language nature whereby there’re nope apparent limits among words, an acoustic start with ending are impacted through the neighboring words, also, with various talkers utterance: female/male, senior/young, low/loud utterance, read/spontaneous, fast/slow vocalizing proportion and the utterance sign could be influenced by ambient noise. Accordingly, utterance recognition was exceeding abound of such challenges. To avert particular problems, information steered statistical curriculum built on considerable amounts of vocalized data has been utilized. With this itemize, the aim is to reconnoiter creativity that has making these implements plausible. Utterance recognition and language comprehension have been two important reconnoitering antes thereupon has normally been logged nearer as matters with indicatively and audio vocal, whereby the domain for audio vocal data have stayed introduced as robust impact to the matter thru drib accomplishment. Hence, we amid about determinate methods to utterances and language manipulating, whereby a data around a talking sign and a language that it converses, adjoining thru valuable utilized of information, is established come from inherent recognition of utterance data thru an understandable math-statistical formality.
Bertholletia excelsa: Key Species for Sustainable Livelihoods and Forest Conservation

Brazil nut (Bertholletia excelsa Bonpl.) is vital for livelihoods in the Amazon region as a source of income and food, and since it is collected mainly from old-growth forests, it is also a cornerstone for forest conservation. This chapter presents socioeconomic and cultural characteristics of Brazil nut collectors, depicting their production systems and identifying individual perceptions about the effects of this activity on their livelihoods and on forest conservation. We interviewed 119 collectors, organized in associations, cooperatives, or autonomous informal organizations. Collectors live from agriculture, fishing, and forest extractivism, and reported the of use more than 30 forest products, highlighting their refined knowledge on forests. On the other hand, they have little access to formal education and information technology. The collection of Brazil nuts proved to positively impacts livelihoods’ capitals, being a key species for forest conservation and maintenance of Amazonian livelihoods. Forests are plentiful in Brazil nut trees and collectors are much more likely to remain in forests, incentivizing their conservation. Moreover, the organization into associations or cooperatives is especially positive to broaden sales options and achieve better market prices, breaking historical cycles where middlemen played a preponderant role in Brazil nut commercialization processes across the Amazon region.
Word Embedding for French Natural Language in Healthcare: A Comparative Study

Structuring raw medical documents with ontology mapping is now the next step for medical intelligence. Deep learning models take as input mathematically embedded information, such as encoded texts. To do so, word embedding methods can represent every word from a text as a fixed-length vector. A formal evaluation of three word embedding methods has been performed on raw medical documents. The data corresponds to more than 12M diverse documents produced in the Rouen hospital (drug prescriptions, discharge and surgery summaries, inter-services letters, etc.). Automatic and manual validation demonstrates that Word2Vec based on the skip-gram architecture had the best rate on three out of four accuracy tests. This model will now be used as the first layer of an AI-based semantic annotator.
Variability of water masses through the Mernoo Saddle, South Island, New Zealand

Abstract The Mernoo Saddle is situated c. 100 km east of Banks Peninsula, Canterbury, New Zealand at 44°S 174°E. The Saddle separates the South Island of New Zealand from an underwater ridge known as the Chatham Rise. The Rise acts as a partial barrier to the flow of the subantarctic surface water mass (SAW) and the subtropical surface water mass (STW), which are part of the global Subtropical Front extending around the Southern Ocean. This study examined the variability of the water masses flowing through the Mernoo Saddle using a 3‐year data set of Advanced Very High Resolution Radiometer (AVHRR) Sea Surface Temperature (SST) imagery. This investigation revealed that SAW extended north through the western edge of the Mernoo Saddle for most of the year, however in winter and early spring a southward extension of STW was observed.
A Time-Dependent Metaheuristic Algorithm for Post Enrolment-based Course Timetabling

A metaheuristic-based algorithm is presented for the post enrolment-based course timetabling problem used in track-2 of the Second International Timetabling Competition (ITC2007). The featured algorithm operates in three distinct stages – a constructive phase followed by two separate phases of simulated annealing – and is time dependent, due to the fact that various run-time parameters are calculated automatically according to the amount of computation time available. Overall, the method produces results in line with the oﬃcial ﬁnalists to the timetabling competition, though experiments show that this algorithm also seems to ﬁnd certain instances more diﬃcult to solve than others. A number of reasons for this latter feature are discussed.
Kidney Manifestation of Systemic Lupus Erythematosus

Kidney disease secondary to SLE can affects up to 50% of patients with SLE and largely mediated by deposition of immune complex in the kidneys (1) (2). The clinical diagnosis of lupus nephritis is usually made following a diagnostic kidney biopsy in the presence of proteinuria and/or hematouria,positive serology,and extrarenal manifestation of SLE. The presence of kidney disease is the most important predictor of morbidity and mortality in the patients with SLE. Several demographic,serologic,and genetic risk factors are associated with an increased risk for developing kidney disease. Patient with lupus nephritis are more likely than SLE patients without kidney involvement to have a family history of SLE,anemia,high antidsDNA antibody titer,and hypocomplementemia. Children with SLE develop nephritis more frequently than adults and so do males.
Post-fire seeding with ryegrass: implications for understorey plant communities and overall effectiveness

Seeding following high-severity wildfires is motivated by the goals of increasing vegetative cover and decreasing bare soil in order to minimise soil erosion and exotic plant invasions. We compared the ground cover and vegetation response of seeded versus non-seeded areas located in the Warm Fire in northern Arizona, where post-fire seeding treatments with Italian ryegrass (Lolium perenne spp. multiflorum (L.)) were conducted in 4000 ha of high-severity burned areas. Over the course of the study, we observed no significant difference between seeded and non-seeded plots in percentage of bare soil, total vegetative cover or exotic plant cover. However, there were significant differences in plant community composition as revealed by PERMANOVA and Indicator Species Analysis. Two years post-fire there were significantly fewer ponderosa pine seedlings, and the cover of annual and biennial forbs was significantly lower in plots that were seeded with Italian ryegrass. In the third year, the cover of native bunch grasses was significantly lower in seeded plots. The differences we observed may be due to differences in pre-existing vegetation composition because of the geographic separation of the plots across the landscape. Our results illustrate the ineffectiveness of post-fire seeding in achieving the goals of increasing vegetative cover and decreasing the invasion of non-native plants, and we suggest that alternative post-fire remediation should be considered in the future.
A method to evaluate the usability issues experienced when using Tor browser

With the internet being a global phenomenon of information exchange for users worldwide, people can easily communicate with each other, view information and also execute transactions. However, with increasing online surveillance, the identity of users is compromised, making anonymity a concern. Thus, it led to several anonymity services implementations, and Tor is one among them. The strength of the Tor network relies on the number of volunteers contributing as relays, i.e., the more the number of users connected, the greater is the level of anonymity achieved. Hence, user experience and usability become critically important as the more usable a system is, the better the experience users can get. However, it is found that the Tor browser has many usability issues. Therefore, this thesis aims to find the cause of its usability issues. This thesis evaluates the usability issues Tor users face by conducting experiments. First, a method to detect the presence of usability issues such as Broken content, Websites blocking Tor connection, Broken elements and Login Failure is developed. Second, the outcomes of experiments are evaluated by comparing the findings. It shows that Broken content, Broken elements, and Login failure occur due to Tor’s security restrictions that disable JavaScript on the websites. In addition, websites become unresponsive when they detect traffic coming from the Tor network based on the IPs blacklisted by the websites. A method to evaluate the usability issues experienced when using Tor browser i
Protocol to evaluate the effectiveness and cost-effectiveness of an environmental nutrition and physical activity intervention in nurseries (Nutrition and Physical Activity Self Assessment for Child Care - NAP SACC UK): a multicentre cluster randomised controlled trial

Background One in seven UK children have obesity when starting school, with higher prevalence associated with deprivation. Most pre-school children do not meet UK recommendations for physical activity and nutrition. Formal childcare settings provide opportunities to deliver interventions to improve nutritional quality and physical activity to the majority of 3–4-year-olds. The nutrition and physical activity self-assessment for childcare (NAP SACC) intervention has demonstrated effectiveness in the USA with high acceptability in the UK. The study aims to evaluate the effectiveness and cost-effectiveness of the NAP SACC UK intervention to increase physical activity, reduce sedentary time and improve nutritional intake. Methods Multi-centre cluster RCT with process and economic evaluation. Participants are children aged 2 years or over, attending UK early years settings (nurseries) for ≥ 12 hours/week or ≥ 15 hours/week during term time and their parents, and staff at participating nurseries. The 12-month intervention involves nursery managers working with a Partner (public health practitioner) to self-assess policies and practices relating to physical activity and nutrition; nursery staff attending one physical activity and one nutrition training workshop and setting goals to be achieved within six months. The Partner provides support and reviews progress. Nursery staff receive a further workshop and new goals are set, with Partner support for a further six months. The comparator is usual practice. Up to 56 nurseries will be stratified by area and randomly allocated to intervention or comparator arm with minimisation of differences in level of deprivation. Primary outcomes: accelerometer-assessed mean total activity time on nursery days and average total energy (kcal) intake per eating occasion of lunch and morning/afternoon snacks consumed within nurseries. Secondary outcomes: accelerometer-assessed mean daily minutes of moderate-to-vigorous physical activity and sedentary time per nursery day, total physical activity on nursery days compared to non-nursery days, average serving size of lunch and morning/afternoon snacks in nursery per day, average percentage of core and non-core food in lunch and morning/afternoon snacks, zBMI, proportion of children who are overweight/obese and child quality-of-life. A process evaluation will examine fidelity, acceptability, sustainability and context. An economic evaluation will compare costs and consequences from the perspective of the local government, nursery and parents. Trial registration: ISRCTN33134697
Mapping of Social Functions in a Smart City When Considering Sparse Knowledge

In recent years, technological advances, specifically new sensing and communication technologies, have brought new opportunities for a less expensive, dynamic, and more accurate mapping of social land use in cities. However, most research has featured complex methodologies that integrate several data resources or require much prior knowledge about the examined city. We offer a methodology that requires little prior knowledge and mainly relies on call detail records, which is an inexpensive available data resource of mobile phone signals. We introduce the Semi-supervised Self-labeled K-nearest neighbor (SSK) algorithm that combines distance-weighted k-nearest neighbors (DKNN) with a self-labeled iterative technique designed for training classifiers with only a small number of labeled samples. In each iteration, the samples (small land units) that we are most confident of their classification by DKNN are added to the training set of the next iteration. We perform neighbor smoothing to the land-use classification by considering feature-space neighbors as in the regular KNN but also geographical space neighbors, and thereby leverage the tendency of approximate land areas to share similar social land use. Based only on a few labeled examples, the SSK algorithm achieves a high accuracy rate, between 74% without neighbor smoothing, and 80% with it.
Impact of ECCO Ocean-State Estimates on the Initialization of Seasonal Climate Forecasts

Abstract The impact of ocean-state estimates generated by the consortium for Estimating the Circulation and Climate of the Ocean (ECCO) on the initialization of a coupled general circulation model (CGCM) for seasonal climate forecasts is examined. The CGCM consists of the University of California, Los Angeles, Atmospheric GCM (UCLA AGCM) and an ECCO ocean configuration of the Massachusetts Institute of Technology GCM (MITgcm). The forecasts correspond to ensemble seasonal hindcasts for the period 1993–2001. For the forecasts, the ocean component of the CGCM is initialized in either early March or in early June using ocean states provided either by an unconstrained forward ocean integration of the MITgcm (the “baseline” hindcasts) or by data-constrained ECCO results (the “ECCO” hindcasts). Forecast skill for both the baseline and the ECCO hindcasts is significantly higher than persistence and compares well with the skill of other state-of-the art CGCM forecast systems. For March initial conditions, the sta.
Notes on a collection of bats and observations on other vertebrates from the Macquarie Marshes, New South Wales

From 25 to 31 March, 1989, the Mammal Section of the Royal Zoological Society of NSW conducted a fauna survey of part of the Mac- quarie Marshes Nature Reserve. The primary purpose of our survey was to add to the knowledge of the mammalian fauna of the Marshes since the avifauna and herpetofauna have been well surveyed (Brooker and Wombey 1986; Cooper 1954). This note presents a summary of bat captures and inci- dental observations of other vertebrates made during the recent Mammal Section survey. Macquarie Marshes Nature Reserve is situated approximately 100 km north of Warren in central western New South Wales (Fig. 1). The reserve is covered by large areas of wetland vegetation, and significant areas of eucalypt woodland dominated by River Red Gum Euculyptus cam1duleusi.s. There are also extensive areas of dead standing and fallen timber in former woodland apparently killed by changes in water regime associated with the construction of irrigation works. A more detailed descri~tion can be found in Paiimans (1981) and
An Investigation of the Weak Form of the Efficient Markets Hypothesis for the Kuwait Stock Exchange

This article investigates the weak form of the efficient market hypothesis (EMH) for the Kuwait Stock Exchange (KSE). In particular, it tests whether share returns on the KSE exhibit patterns which may be used to predict future share price changes. Ten filter rules are tested on weekly data for 42 firms over the period 1998–2011. The results suggest that the KSE was not weak-form efficient because patterns and trends were present in security prices. In addition, the results are consistent with the substantive literature which has argued that emerging stock markets are informationally inefficient, such as Fifield, Power and Sinclair (2005, 2008) and Xu (2010) and particularly those early studies of Al-Shamali (1989) and Al-Loughani and Moosa (1999) that looked at trading rules for the KSE.
The First Offer of Alcohol from the Adult Person and Cannabis Use

This chapter is based on the data from the national survey on tobacco, alcohol, and drugs among primary and secondary school students aged 15–19 implemented in eight regions of Slovakia during Spring 2018. An unexpected shift was observed in the relationship between the age young people were offered alcohol by an adult and the age when they first experienced its effect. In previous surveys, the mean age of the first offer predated the felt effect of alcohol (“tipsiness”) by about 1 year on average. Our data revealed that following the initial offer of alcohol by an adult, approximately 3⁄4 of participants felt the effect of alcohol later or during the same year (groups 1 and 2); however, in the remaining cases, the effect was felt before alcohol was offered by an adult (group 3). Thus, it appears that one-fifth to one-quarter of participants did not go through the usual ritual of initiation by adults. The analysis showed that this group of participants used cannabis more often than the rest of the sample. Furthermore, there were differences observed among the three groups in reported school attendance, legal and illegal drug use, and bullying. Possible implications of these findings are discussed.
Analysis of the inverse problem for transient unsaturated flow

The inverse problem of determining unsaturated soil hydraulic properties from one-dimensional, transient infiltration and redistribution events is analyzed. Hydraulic properties are assumed to be described by an extension of van Genuchten's (1980) model which allows for hysteresis in the retention function and air entrapment. Unknown parameters in the model are estimated from observed water contents and heads during transient flow by numerical inversion of the unsaturated flow equation. The inverse problem is formulated as a weighted least squares problem and solved using an efficient Levenberg-Marquardt algorithm. The flow event consists of ponded infiltration followed by gravity drainage with evaporation at the soil surface. Sensitivity analyses indicate that observations during ponded infiltration should be made near the position of the wetting front. The location of observation points during the drying stage is less critical than during the infiltration stage, but for the relatively high imposed evaporative flux sensitivity of pressure head is highest near the soil surface. Large differences in sensitivity are observed among the various model parameters. Unknown evaporative fluxes are approximated in the inverse solution as an equivalent first-type boundary condition requiring only periodic measurements of surface water content during the drying stage. Little error is incurred provided accurate measurements are possible. Corruption of input data with random error is shown to have a larger effect on the predicted conductivity function than on the retention function and more effect on the wetting branch of the hysteretic retention function than on the drying. When measurements are subject to error and the assumed parametric model for water retention and conductivity relations is not exact, it may no longer be possible to detect hysteresis in the retention function.
Characteristics of lakes in the eastern United States. Volume 1. Population descriptions and physico-chemical relationships

A water sample was collected from each of 1612 lakes. This subset of lakes was selected from within three regions of the eastern U.S. (the Northeast, Upper Midwest, and Southeast) expected to exhibit low buffering capacity. Each region was divided in subregions. Subregions were further stratified by alkalinity map class. A suite of chemical variables and physical attributes thought to influence or be influenced by surface-water acidification was measured for each lake. The results of these measurements and data analyses are described in the report.