Miracle-dz/UniFAR-FTUs huggingface dataset:
SINAPS: Prediction of microbial traits from marker gene sequences

Microbial communities are often studied by sequencing marker genes such as 16S ribosomal RNA. Marker gene sequences can be used to assess diversity and taxonomy, but do not directly measure functions arising from other genes in the community metagenome. Such functions can be predicted by algorithms that associate marker genes with experimentally determined traits in well-studied species. Typically, such methods use ancestral state reconstruction. Here I describe SINAPS, a new algorithm that predicts traits for marker gene sequences using a fast, simple word-counting algorithm that does not require alignments or trees. A measure of prediction confidence is obtained by bootstrapping. I tested SINAPS predictions from 16S V4 query sequences for traits including energy metabolism, Gram-positive staining, presence of a flagellum, V4 primer mismatches, and 16S copy number. Accuracy was >90% except for copy number, where a large majority of predictions were within +/−2 of the true value.
Understanding and improving the timing of PSR J0737−3039B

The double pulsar (PSR J0737-3039A/B) provides some of the most stringent tests of general relativity (GR) and its alternatives. The success of this system in tests of GR is largely due to the high-precision, long-term timing of its recycled-pulsar member, pulsar A. On the other hand, pulsar B is a young pulsar that exhibits significant short-term and long-term timing variations due to the electromagnetic-wind interaction with its companion and geodetic precession. Improving pulsar B's timing precision is a key step towards improving the precision in a number of GR tests with PSR J0737-3039A/B. In this paper, red noise signatures in the timing of pulsar B are investigated using roughly a four-year time span, from 2004 to 2008, beyond which time the pulsar's radio beam precessed out of view . The timing of pulsar B presented in this paper depends on the size of the pulsar's orbit, which was calculated from GR, in order to precisely account for orbital timing delays. Consequently, our timing cannot directly be used to test theories of gravity. However, our modelling of the beam shape and radial wind of pulsar B can indirectly aid future efforts to time this pulsar by constraining part of the additional red noise observed on top of the orbital delays. As such, we conclude that, in the idealised case of zero covariance between our model's parameters and those of the timing model, our model can bring about a factor 2.6 improvement on the measurement precision of the mass ratio, R = mA/mB, between the two pulsars: a theory-independent parameter, which is pivotal in tests of GR.
Analysis of the Delayed Central Nervous System Action in the Regulation of a Third-order Muscle-Tendon Model

This paper presents the analysis of a third-order linear time-invariant delay differential equation representing the regulation of a muscle-tendon system. The Central Nervous System action is modeled as a delayed proportional-derivative controller exploiting the multiplicity-induced-dominancy property. The stability analysis is illustrated via the software P3δ.
Smart kills and worthless deaths: eSports analytics for League of Legends

Abstract Vast data on eSports should be easily accessible but often is not. League of Legends (LoL) only has rudimentary statistics such as levels, items, gold, and deaths. We present a new way to capture more useful data. We track every champion’s location multiple times every second. We track every ability cast and attack made, all damages caused and avoided, vision, health, mana, and cooldowns. We track continuously, invisibly, remotely, and live. Using a combination of computer vision, dynamic client hooks, machine learning, visualization, logistic regression, large-scale cloud computing, and fast and frugal trees, we generate this new high-frequency data on millions of ranked LoL games, calibrate an in-game win probability model, develop enhanced definitions for standard metrics, introduce dozens more advanced metrics, automate player improvement analysis, and apply a new player-evaluation framework on the basic and advanced stats. How much does an individual contribute to a team’s performance? We find that individual actions conditioned on changes to estimated win probability correlate almost perfectly to team performance: regular kills and deaths do not nearly explain as much as smart kills and worthless deaths. Our approach offers applications for other eSports and traditional sports. All the code is open-sourced.
Inspection and Characterization of App File Usage in Mobile Devices

While the computing power of mobile devices has been quickly evolving in recent years, the growth of mobile storage capacity is, however, relatively slower. A common problem shared by budget-phone users is that they frequently run out of storage space. This article conducts a deep inspection of file usage of mobile applications and their potential implications on user experience. Our major findings are as follows: First, mobile applications could rapidly consume storage space by creating temporary cache files, but these cache files quickly become obsolete after being re-used for a short period of time. Second, file access patterns of large files, especially executable files, appear highly sparse and random, and therefore large portions of file space are never visited. Third, file prefetching brings an excessive amount of file data into page cache but only a few prefetched data are actually used. The unnecessary memory pressure causes premature memory reclamation and prolongs application launching time. Through the feasibility study of two preliminary optimizations, we demonstrated a high potential to eliminate unnecessary storage and memory space consumption with a minimal impact on user experience.
Nuclei graph local features for basal cell carcinoma classification in whole slide images

Evidence based medicine aims to provide a quantifiable framework to support cancer optimal treatment selection. Pathological examination is the main evidence used in medical management, yet the level of quantification is low and highly dependent on the examiner expertise. This paper presents and evaluates a method to extract graph based topological features from skin tissue images to identify cancerous regions associated to basal cell carcinoma. The graph features constitute a quantitative measure of the architectural tissue organization. Results show that graph topological features extracted from a nuclei based distance graph, particularly those related to local density, have a high predictive value in the automated detection of basal cell carcinoma. The method was evaluated using a leave-one-out validation scheme in a set of 9 skin Whole Slide Images obtaining a 0.76 F-score in distinguishing basal cell carcinoma regions in skin tissue whole slide images.
HPLC analysis of vitamin B1, B2, B3, B6, B9, B12 and vitamin C in various food matrices

Various methods had been described for the analysis of vitamins in food matrices, with more and more of these including the use of HPLC to measure the levels of these micronutrients in foodstuffs. The renewed interest in rapid and accurate quantification of micronutrients in foodstuffs is due to more stringent requirements by food regulatory agencies around the world. Legislation now demands that the nutrition information displayed on food labels be backed up by reliable results obtained using validated analyses. Three challenges are common in terms of quantifying vitamins in food matrices: 1) extraction techniques that are sufficiently effective to liberate the various forms of the vitamin from each unique matrix, 2) ensuring that labile forms of the vitamin are protected against degeneration by light and/or air (oxygen) for a sufficiently long period to afford accurate quantification and 3) obtaining an analytical method with sufficient sensitivity, selectivity, accuracy and precision, with cost and time also being considerations . The chapter dealt with these aspects concerning vitamin B1, B2, B3, B6, B9, B12 and vitamin C. Extraction procedures were described, as well as typical HPLC methods and recent improvements in this field.
Fabrication of nanoparticles using Annona squamosa leaf and assessment of its effect on liver (Hep G2) cancer cell line

Annona squamosa is a fruit bearing plant possesses potent bioactive compounds in all its part. In this present investigation iron oxide nanoparticle was synthesized from hydroethanol extract of Annona squamosa leaves at 60°C temperature. Production of iron oxide nanoparticles in extraction is detected by UV–V spectrophotometer, Scanning electron microscopy was employed to analyse the structure of nanoparticles. Fourier transform infrared spectroscopy (FT-IR) analysis were performed, in order to determine the functional groups on Annona squamosa leaves extract. The synthesized Fe3O4 NPs shows potential cytotoxicity against liver carcinoma cell line (HepG2), and there is no toxicity on the normal liver cell line. Our reports confirmed that the Annona squamosa leaf is a very good eco-friendly and nontoxic bioreductant for the synthesis of Iron oxide nanoparticle and opens up further opportunities for fabrication of drugs towards cancer therapy.
Research on 4D Simulation Technology of Reconstruction Engineering Construction Organization Based on BIM

This research is based on BIM technology to achieve 4D simulation of highway construction organization. By correlating BIM model and construction process, it can identify potential process errors or conflicts in advance, optimize construction organization process, and reduce unnecessary capital investment. Relying on the research results, the collaborative management of the quality, schedule and cost of complex projects in the construction process is realized.
Different changes in dry and humid heat waves over China

Heat waves (HWs) are expected to increase in many parts of the world under climate warming. However, most existing studies examined the changes in HWs that are derived from air temperature only, possible different changes in humid HWs that consider the combined effects of relative humidity (RH) are much less understood. This study investigates the spatial and temporal changes in two different HW types, namely, dry and humid HWs, in China from 1961 to 2014. Analysis results show that, on average, humid HWs in China occur 20% more frequently than dry HWs. Dry HWs are more commonly located in northern China, while humid events mainly appear in monsoonal southern and eastern regions. It is also found that all measures of both dry and humid HWs across China have been increasing during the past decades, and humid HWs exhibit a more prominent intensifying trend than dry ones. In particular, the national mean frequency, participating days, magnitude, and duration of dry (humid) HWs increased by 0.061 (0.069) events decade−1, 0.32 (0.39) days decade−1, 0.53 (0.62) °C decade−1, and 0.19 (0.21) days decade−1, respectively. These trends vary in different parts of China. The largest increment of dry HW frequency appears in the arid region of northwest China, while the fastest increase of the humid HW frequency is observed in southeastern China. Given the additional stress induced by high humidity to extreme high temperature, we suggest that future climate change mitigation and adaption should consider the change and impacts of humid heat events.
Analysis of the Drivers of Occupational Health and Safety Performance Disclosures by Romanian Companies

The paper addresses the issue of the disclosure of occupational health and safety (OHS) performances by the Romanian companies. Although under-researched in the literature, the topic received a great deal of attention after the Directive 2014/95/EU on non-financial reporting came into force. The study is aimed both at examining the extent to which OHS issues are disclosed within CSR/sustainability reports and at establishing whether the quality of the disclosure is affected by a group of determinants such as: the size of the reporting company, its profitability, the ownership structure, the financial position and the company’s age.
Effects of economic globalization and trade on forest transitions: Evidence from 76 developing countries

Current forest recovery efforts in developing countries are different from previous efforts in developed countries, especially since the rise of economic globalization in the 1980s. Therefore, forest transition theory should now consider factors relating to industrialization, urbanization, and globalization. While previous studies have mainly focused on the variable trade of primary sector products, this study applies a more holistic research perspective and discusses, more widely, the links between trade, adjustment of trade structure, FDI, and forest transition. The results suggest that the total export value has a significant negative effect on forest area and volume, while the percentage of non-primary products has a significant positive impact on forest volume and density in the 76 developing countries studied. These results indicate that a country or region may improve the forest resource conditions by upgrading the export structure through the development of export-oriented manufacturing and servic.
Precise on-Fiber Plasmonic Spectroscopy Using a Gradient-Index Microlens

Plasmonic spectroscopy has emerged as a powerful technique for interrogation of light in the subwavelength regime. Realization of active plasmonic elements on optical fibers can simplify the optical design, allow for performing remote tasks and thus extend the scope of plasmonic utilization. However, the optimization of fiber optics for improving the plasmonic excitation condition has been overlooked. Here we present a plasmonic spectroscopy platform that combines a gradient-index microlens and a single-mode optical fiber. This design ensures large-area and uniform illumination in normal incidence for the excitation of surface plasmon resonance. We demonstrate precise plasmonic spectroscopy with a fiber-optic platform by patterning a nanohole array onto the facet of a gradient-index microlens with our template transfer technique. The experimental spectra are almost identical to the simulated results under ideal conditions, with accurate resonance wavelength (<10 nm deviation), high sensitivity (5 nm/RIU deviation), narrow linewidth (about 5 nm deviation), and diverse shifting patterns. This platform provides a fiber-optic avenue of precise plasmonic spectroscopy for remote interrogation.
Community-Based Crime Reduction in Tulsa: An Application of Petersilia’s Multi-Stakeholder Collaborative Approach to Improve Policy Relevance and Reduce Crime Risk

Abstract The most fitting way to celebrate Joan Petersilia’s numerous advancements within the field of criminal justice is to deliberately practice the two most important lessons that perhaps best define her legacy. First, embedded research should drive collaborative partnerships to foster real-world change based on science. Second, such real-world change should reduce the consequences of crime as well as the social costs of heavy-handed criminal justice sanctions within distressed communities to transform criminal justice policy and practice. In this paper, we outline future directions for policing practice and research as a result of the embedded, collaborative partnerships that led to the Tulsa Community-Based Crime Reduction (CBCR) initiative. The Tulsa CBCR initiative and subsequent evaluation shows that police-driven, collaborative stakeholder partnerships (including business owners, resident steering committees, local government, police, and researchers) significantly reduced crime within targeted areas, allayed many citizens’ perceptions of risk, and improved residents’ attitudes about the Tulsa Police Department.
Disentangling multi‐scale environmental effects on stream microbial communities

Climate change and anthropogenic environmental deterioration strongly affect aquatic microbial communities. Although microbes have irreplaceable roles in various ecosystems, the spatial variation in microbial communities has received less attention in comparison to macro‐organisms. Studies aiming to disentangle the effects of local environmental, catchment and climatic variables on microbial communities are also rare. Here, we disentangled the effects of local, catchment, spatial and climatic variables on boreal stream diatom and bacterial communities.
Inclusion of the microbial additive Vitafert in the in vitro ruminal fermentation of a goat diet

For determining the effect of Vitafert on the kinetics and fermentation indicators of a goat diet (80:20 forage: concentrate ratio), the in vitro gas production technique was applied. One gram of the diet was incubated alone (0 level) or with three Vitafert levels (110 ? L, 150 ? L and 210 ? L), equivalent to 4.5, 6.0 and 8.5 mL Vitafert kg-1. For each treatment specific blanks were established. Gas production was measured until 120 h and its kinetics was estimated by the Gompertz model. At 120 h, DM and NFD degradability were determined. Production and efficiency of the microbial biomass synthesis were calculated. A completely randomized design was used. MANOVA did not show treatment x hours of incubation interaction regarding gas production. On applying a linear model, there were no differences in accumulated gas production, although the specific blanks showed increase in gas production, as the Vitafert level increased. Differences between timings were only at two hours of incubation as regard the remaining hours (P < 0.001), Vitafert inclusion did not influence on the kinetic parameters. The time at which the maximum speed was attained ranged between 20 and 21 h. The 4.5 level increased DM and NFD degradability (P < 0.05), and the 8.5 level increased the production and efficiency of microbial biomass synthesis (P < 0.01). It is concluded that Vitafert did not affect gas production or the kinetic parameters of the diet fermentation. The 4.5 level increased DM and NFD degradability and the 8.5 level, the production and efficiency of the microbial biomass synthesis. Key words: Vitafert, goats, gas production, kinetic parameters, microbial biomass
The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.
BODIPY bearing alkylthienyl side chains: a new building block to design conjugated polymers with near infrared absorption for organic photovoltaics

To effectively harvest sunlight, polymer donors with near infrared (NIR) absorption properties are important for high-performance polymer solar cells (PSCs), especially semitransparent PSCs. However, building blocks to design this kind of polymer donor are rare. In this manuscript, we report 3,11-dibromo-5,9-bis(5-(2-decyltetradecyl)thiophen-2-yl)-7,7-difluoro-7H-6λ4,7λ4-[1,3,2]diazaborinino[4,3-a:6,1-a′]diisoindole (BOPT) as a new building block to design polymer donors with NIR absorption. In BOPT, the 4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) core unit is fused with two benzene rings for a reduced bandgap and is attached with two alkylthienyl groups as conjugated side chains. We synthesized two polymers consisting of alternating BOPT units and thiophene or bithiophene units, respectively. The two polymers displayed near-infrared (NIR) light absorption with the maximum absorption peaks at wavelengths exceeding 800 nm and small bandgaps of ca. 1.3 eV. They showed high highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels of about −5.0 eV/−3.5 eV and high hole mobilities of ca. 3 × 10−3 cm2 V−1 s−1. PSC devices using the two polymers as electron donors exhibited power conversion efficiencies of 2.6%. These results indicate that BOPT is a promising building block in designing polymer donors with near-infrared absorption for organic photovoltaics.
High occurrence of extra-pair partnerships and homosexuality in a captive Cape Vulture Gyps coprotheres colony§

The Cape Vulture Gyps coprotheres is an Endangered colonial cliff-nesting species that is typically cited as monogamous. Observations of wild Cape Vulture colonies note extra-pair breeding activities but homosexual activity has never been confirmed. Observations of breeding behaviours within a captive colony were conducted at VulPro’s breeding facilities in South Africa The captive breeding programme included 10 breeding pairs and a total of 41 non-releasable, individually recognisable, and genetically sexed subadults or adults. Observations were conducted over the 2014 breeding season as part of a study investigating the social and rearing conditions of chicks intended for release in a population supplementation programme. A high percentage of total colony copulation attempts (22%) were extra-pair copulations but only 23 interactions resulted in cloacal contact or possible sperm transfer. Four paired males formed extra-pair relationships, two of which were homosexual.