Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological Variation in Response to Mass-Flowering Oilseed Rape and Surrounding Landscape Composition by Members of a Cryptic Bumblebee Complex

The Bombus sensu stricto species complex is a widespread group of cryptic bumblebee species which are important pollinators of many crops and wild plants. These cryptic species have, until now, largely been grouped together in ecological studies, and so little is known about their individual colony densities, foraging ranges or habitat requirements, which can be influenced by land use at a landscape scale. We used mass-flowering oilseed rape fields as locations to sample bees of this complex, as well as the second most common visitor to oilseed rape B. lapidarius, and molecular RFLP methods to distinguish between the cryptic species. We then used microsatellite genotyping to identify sisters and estimate colony densities, and related both proportions of cryptic species and their colony densities to the composition of the landscape surrounding the fields. We found B. lucorum was the most common member of the complex present in oilseed rape followed by B. terrestris. B. cryptarum was also present in all but one site, with higher proportions found in the east of the study area. High numbers of bumblebee colonies were estimated to be using oilseed rape fields as a forage resource, with B. terrestris colony numbers higher than previous estimates from non-mass-flowering fields. We also found that the cryptic species responded differently to surrounding landscape composition: both relative proportions of B. cryptarum in samples and colony densities of B. lucorum were negatively associated with the amount of arable land in the landscape, while proportions and colony densities of other species did not respond to landscape variables at the scale measured. This suggests that the cryptic species have different ecological requirements (which may be scale-dependent) and that oilseed rape can be an important forage resource for many colonies of bumblebees. Given this, we recommend sustainable management of this crop to benefit bumblebees.
Medicago truncatula copper transporter 1 (MtCOPT1) delivers copper for symbiotic nitrogen fixation.

Copper is an essential nutrient for symbiotic nitrogen fixation. This element is delivered by the host plant to the nodule, where membrane copper (Cu) transporter would introduce it into the cell to synthesize cupro-proteins. COPT family members in the model legume Medicago truncatula were identified and their expression determined. Yeast complementation assays, confocal microscopy and phenotypical characterization of a Tnt1 insertional mutant line were carried out in the nodule-specific M. truncatula COPT family member. Medicago truncatula genome encodes eight COPT transporters. MtCOPT1 (Medtr4g019870) is the only nodule-specific COPT gene. It is located in the plasma membrane of the differentiation, interzone and early fixation zones. Loss of MtCOPT1 function results in a Cu-mitigated reduction of biomass production when the plant obtains its nitrogen exclusively from symbiotic nitrogen fixation. Mutation of MtCOPT1 results in diminished nitrogenase activity in nodules, likely an indirect effect from the loss of a Cu-dependent function, such as cytochrome oxidase activity in copt1-1 bacteroids. These data are consistent with a model in which MtCOPT1 transports Cu from the apoplast into nodule cells to provide Cu for essential metabolic processes associated with symbiotic nitrogen fixation.
Exploiting ground plane constraints for visual-inertial navigation

In this paper, an ego-motion estimation approach is introduced that fuses visual and inertial information, using a monocular camera and an inertial measurement unit. The system maintains a set of feature points that are observed on the ground plane. Based on matched feature points between the current and previous images, a novel measurement model is introduced that imposes visual constraints on the inertial navigation system to perform 6 DoF motion estimation. Furthermore, feature points are used to impose epipolar constraints on the estimated motion between current and past images. Pose estimation is formulated implicitly in a state-space framework and is performed by a Sigma-Point Kalman filter. The presented experiments, conducted in an indoor scenario with real data, indicate the ability of the proposed method to perform accurate 6 DoF pose estimation.
Boltzmann probability of RNA structural neighbors and riboswitch detection

MOTIVATION We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure S of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure. RESULTS A secondary structure T of s is called a delta-neighbor of S if T and S differ by exactly delta base pairs. RNAbor computes the number (N(delta)), the Boltzmann partition function (Z(delta)) and the minimum free energy (MFE(delta)) and corresponding structure over the collection of all delta-neighbors of S. This computation is done simultaneously for all delta < or = m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction. AVAILABILITY http://bioinformatics.bc. edu/clotelab/RNAbor/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
New fabrication methods of bioactive and biodegradable scaffolds for bone tissue engineering

Bioceramic and polymers have been used as matrices for bone tissue engineering, and successful bone regeneration depends on cellular interaction with these matrices. The aim of this study was to fabricate polymer/ceramics composites with a novel sintering method. Also, we prepared homogenous porous poly(lactide-co-glycolide (PLGA) scaffolds in the supercritical CO2. These scaffolds had homogenous porous structure and high tensile and compressive mechanical properties compared to the scaffold prepared by conventional solvent casting method. This study revealed that generating bioactive and porous polymer scaffolds with novel sintering method or supercritical fluid technique could be useful for bone tissue engineering.
Genetic Structure of Wild Bonobo Populations: Diversity of Mitochondrial DNA and Geographical Distribution

Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species’ range. In 136 effective samples from different individuals (range: 7–37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.
Cost-effectiveness Analysis in R Using a Multi-state Modeling Survival Analysis Framework: A Tutorial

This tutorial provides a step-by-step guide to performing cost-effectiveness analysis using a multi-state modeling approach. Alongside the tutorial, we provide easy-to-use functions in the statistics package R. We argue that this multi-state modeling approach using a package such as R has advantages over approaches where models are built in a spreadsheet package. In particular, using a syntax-based approach means there is a written record of what was done and the calculations are transparent. Reproducing the analysis is straightforward as the syntax just needs to be run again. The approach can be thought of as an alternative way to build a Markov decision-analytic model, which also has the option to use a state-arrival extended approach. In the state-arrival extended multi-state model, a covariate that represents patients’ history is included, allowing the Markov property to be tested. We illustrate the building of multi-state survival models, making predictions from the models and assessing fits. We then proceed to perform a cost-effectiveness analysis, including deterministic and probabilistic sensitivity analyses. Finally, we show how to create 2 common methods of visualizing the results—namely, cost-effectiveness planes and cost-effectiveness acceptability curves. The analysis is implemented entirely within R. It is based on adaptions to functions in the existing R package mstate to accommodate parametric multi-state modeling that facilitates extrapolation of survival curves.
Purification of a Novel Bacteriocin-Like Inhibitory Substance Produced by Enterococcus faecium ICIS 8 and Characterization of Its Mode of Action.

OBJECTIVE The aim of this work was to purify and characterize a bacteriocin-like antimicrobial substance produced by an antagonistic active strain of Enterococcus faecium. METHODS AND RESULTS A novel bacteriocin-like inhibitory substance (BLIS) produced by the E. faecium ICIS 8 strain was purified and characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and N-terminal amino acid sequencing revealed the following partial sequence: NH2-APKEKCFPKYCV. The proteinaceous nature of purified BLIS was assessed by treatment with proteolytic enzyme. Studies of the action of BLIS using bacteriological and bioluminescence assays revealed a dose-dependent inhibition of Listeria monocytogenes 88BK and Escherichia coli K12 TG1 lac::lux viability. The interaction of the BLIS with the bacterial surface led to the compensation of a negative charge value, as shown by zeta-potential measurements. Assessments of membrane integrity using fluorescent probes and atomic force microscopy revealed the permeabilization of the cellular barrier structures in both L. monocytogenes and E. coli. CONCLUSION The novel BLIS from E. faecium ICIS 8 was characterized by a unique primary peptide sequence and exerted bactericidal activity against L. monocytogenes and E. coli by disrupting membrane integrity.
The Three Pillars of Machine-Based Programming

In this position paper, we describe our vision of the future of machine-based programming through a categorical examination of three pillars of research. Those pillars are: (i) intention, (ii) invention, and(iii) adaptation. Intention emphasizes advancements in the human-to-computer and computer-to-machine-learning interfaces. Invention emphasizes the creation or refinement of algorithms or core hardware and software building blocks through machine learning (ML). Adaptation emphasizes advances in the use of ML-based constructs to autonomously evolve software.
SEISMIC SOIL-PILE INTERACTION — INFLUENCE OF SOIL INELASTICITY

The main purpose of this study is to investigate the influence of soil p-y nonlinearity in soil–pile–structure kinematic and inertia interaction. Within this context, a beam on nonlinear Winkler foundation model is adopted based on the Boundary Element Method (BEM), accounting for the effects induced by geometrical nonlinearity, rotary inertia and shear deformation, employing the concept of shear deformation coefficients. The soil nonlinearity is taken into consideration by means of a hybrid spring configuration consisting of a nonlinear (p-y) spring connected in series to an elastic spring–damper model. The nonlinear spring   ,   ,       ,, , ,       ,,
Information Caching Strategy for Cyber Social Computing Based Wireless Networks

Cyber social computing has brought great changes and potential intelligent technologies for wireless networks. Among these technologies, information caching strategies are promising approaches to achieving lower delay, higher throughput and energy efficiency (EE) of user equipment (UE) in 5G wireless networks, by deploying intelligent caching and computing at the mobile edge. However, the static information caching strategies ignore the relevance of traffic fluctuation among different base stations (BSs) and the variance of users’ interests. Thus in this paper, an information caching strategy for cyber social computing based wireless network is proposed, taking advantages of two layer social cyberspaces in both traffic correlation between BSs and the social relationship between UEs. In the first layer, a base station social network (BSSN) is constructed based on the social relationship between BSs, which is defined as social-tie factor (STF). In the second layer, the Indian Buffet Model (IBM) is used to describe the social influence of one UE to another. To reduce base station’s traffic load, users with similar social interest can share the contents they cached with each other. Therefore, device-to-device (D2D) communication is taken as the underlay to cellular networks in our proposed information caching strategy. By utilizing the social characteristic of BSSN, the very important BSs (VIBSs) with higher averages STF are selected. Then the normal small cells (NSCs) within the VIBS’s coverage are linked to the VIBSs only and the other unique small cells (USCs) will be routed back into the core network (CN) directly. Limited cache and backhaul capacity in the whole network are only shared by VIBSs and USCs. UEs will communicate with each other via D2D links only if they have i) similar interests, ii) enough encounter duration between users and iii) are adjacent with each other. Otherwise, the UE shall obtain the required contents via cellular networks. With the tool of stochastic geometry process, key performance indicators, e.g., coverage probability, network throughput power consumption, EE, delay and offloaded traffic are studied. Both the theoretical and numerical results show that the proposed information caching strategy for cyber social computing can achieve high coverage probability, throughput, EE and delay by optimizing STF threshold, VIBS coverage and D2D communication radius.
New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research

Background A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Objective Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. Methods We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. Results We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Conclusions Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health.
Mathematical Modeling of Heat Transfer for Steel Continuous Casting Process

Heat transfer mechanisms and the solidification process are simulated for a continuous casting machine and the geometric shape of the liquid pool is predicted considering different conditions. A heat transfer and solidification model is described for the continuous casting of steel slabs. The model has been established on the basis of the technical conditions of the slab caster in the continuous casting unit of Mobarakeh Steel Company. This model involves a two-dimensional (2-D) transient energy equation. The governing equation was solved using the finite-volume procedure. The boundary conditions of the mold, water spray cooling, and air cooling regions have been defined. The mathematical model is able to predict the shell thickness, temperature distribution in the mold and shell, and the interfacial gap between shell and mold. The modeling results were verified by the measured slab surface temperatures and a reasonable agreement was achieved.
High-resolution radio study of SNR IC 443 at low radio frequencies

Fil: Castelletti, Gabriela Marta. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Astronomia y Fisica del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomia y Fisica del Espacio; Argentina
QoE-Oriented Resource Allocation for 360-degree Video Transmission over Heterogeneous Networks

Immersive media streaming, especially virtual reality (VR)/360-degree video streaming which is very bandwidth demanding, has become more and more popular due to the rapid growth of the multimedia and networking deployments. To better explore the usage of resource and achieve better quality of experience (QoE) perceived by users, this paper develops an application-layer scheme to jointly exploit the available bandwidth from the LTE and Wi-Fi networks in 360-degree video streaming. This newly proposed scheme and the corresponding solution algorithms utilize the saliency of video, prediction of users' view and the status information of users to obtain an optimal association of the users with different Wi-Fi access points (APs) for maximizing the system's utility. Besides, a novel buffer strategy is proposed to mitigate the influence of short-time prediction problem for transmitting 360-degree videos in time-varying networks. The promising performance and low complexity of the proposed scheme and algorithms are validated in simulations with various 360-degree videos.
Fabrication and characterization of polycarbonate microstructured polymer optical fibers for high-temperature-resistant fiber Bragg grating strain sensors

Here we present the fabrication of a solid-core microstructured polymer optical fiber (mPOF) made of polycarbonate (PC), and report the first experimental demonstration of a fiber Bragg grating (FBG) written in a PC optical fiber. The PC used in this work has a glass transition temperature of 145°C. We also characterize the mPOF optically and mechanically, and further test the sensitivity of the PC FBG to strain and temperature. We demonstrate that the PC FBG can bear temperatures as high as 125°C without malfunctioning. In contrast, polymethyl methacrylate-based FBG technology is generally limited to temperatures below 90°C.
Modeling Random Deployment in Wireless Sensor Networks for Infrastructure-less Cyber Physical Systems

Random deployment enables rapid installation of a large number of sensors in locations of difficult access, which is important for many infrastructure-less cyber physical systems (CPS), e.g., for disaster response, battle field and extraterrestrial operations. However, random deployment results in heterogeneous sensor postures with varying antenna orientations, a source of network performance degradation. Although much is known about the effect of antenna orientations in 802.15-based wireless sensor networks (WSNs), most works assume no physical disturbance to antennas. However, heterogeneous sensor postures (e.g., overturned sensors) may cause significant disruption to the functionalities of antennas in addition to the reported variation of received signal strength (RSSI). In this paper, we provide empirical characterization of node-to-node communication in random deployment and present the first radio model that effectively captures the distinctive characteristics. Through simulations using our model, we provide a quantitative analysis of the aggregate effect of random antenna orientations of a large number of sensors with heterogeneous postures. Furthermore, we introduce a prototype sensor package that can be used to reduce the impact of random deployment.
Taking Costs and Diagnostic Test Accuracy into Account When Designing Prevalence Studies: An Application to Childhood Tuberculosis Prevalence

Background. When planning a study to estimate disease prevalence to a pre-specified precision, it is of interest to minimize total testing cost. This is particularly challenging in the absence of a perfect reference test for the disease because different combinations of imperfect tests need to be considered. We illustrate the problem and a solution by designing a study to estimate the prevalence of childhood tuberculosis in a hospital setting. Methods. All possible combinations of 3 commonly used tuberculosis tests, including chest X-ray, tuberculin skin test, and a sputum-based test, either culture or Xpert, are considered. For each of the 11 possible test combinations, 3 Bayesian sample size criteria, including average coverage criterion, average length criterion and modified worst outcome criterion, are used to determine the required sample size and total testing cost, taking into consideration prior knowledge about the accuracy of the tests. Results. In some cases, the required sample sizes and total testing costs were both reduced when more tests were used, whereas, in other examples, lower costs are achieved with fewer tests. Conclusion. Total testing cost should be formally considered when designing a prevalence study.