Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears.

Phylogenetic relationships of the order Carnivora have been extensively studied. However, depending on the type of data, species sampling, and method of analysis used, carnivores have been placed in nearly every possible position throughout the eutherian phylogenetic tree (for a review, see Novacek 1992). The integrity of the order itself has, however, remained intact. Undisputedly monophyletic, the order Carnivora nonetheless constitutes a very adaptable and heterogeneous group (Wayne et al. 1989) whose evolution has been marked by several events of parallel or convergent evolution and rapid radiation. Consequently, phylogenetic relationships between and within many carnivore families are also still largely unresolved. For example, the families Procyonidae, Ailuridae, Mustelidae, Pinnidedia, and Ursidae are joined at a polytomy. Within Pinnipedia, the closer affinity of Otariidae to either Phocidae or Obodenidae has long been debated. Additionally, the monophyly of the family Mustelidae has been challenged, with true mustelids and mephitids thought to belong to different branches within the superfamily Musteloidea, also including Procyonidae and Ailuridae. The phylogeny of the family Ursidae is another typical example. Six species of bears, grouped under the subfamily Ursinae, are thought to have diverged at the beginning of the Pliocene through such a rapid radiation event (Thenius 1990) that the order of species divergence is difficult to determine. Hence, the speciation event that led to extant ursine bears (American black bear, Ursus americanus; brown bear, U. arctos; polar bear, U. maritimus; Asiatic black bear, U. thibetanus; sun bear, U. malayanus; and sloth bear, U. ursinus) is usually represented as a polytomy. Rapid radiations remain unresolved largely because available data contain very few informative changes essential to infer the correct phylogenetic tree. More resolving power can be reached by using longer DNA sequences to provide a sufficient number of informative characters. Moreover, it has been shown that the combination of multiple genes in a single large data set has the potential to raise a weak phylogenetic signal above the noise level (Bull et al. 1993). Combining these two advantages, complete mitochondrial (mtDNA) sequences (approximately 17 kbp and 13 protein-coding genes) offer great potential for recovering phylogenies.
Electrical Characterization and Micro X-ray Computed Tomography Analysis of Next-Generation Silicon Alloy Lithium-Ion Cells

This study analyzed a prototype of a pouch cell containing silicon alloy anodes with the potential to significantly increase the energy density, resulting in improved autonomy for electric vehicles. An electrical characterization campaign was performed, resulting in three main observations. Firstly, measurements showed a high energy density, although a high lower cutoff voltage (3.0 V) was used due to the prototypical nature of the cells. Further optimization would allow a decrease of the lower cutoff voltage, resulting in an even higher energy density. Secondly, a large open-circuit voltage hysteresis was observed, increasing the complexity for equivalent circuit models. Thirdly, ballooning of the pouch cell was observed, most likely caused by gas formation. This leads to a loss of active surface area, significantly reducing the cell’s capacity. This third observation was more thoroughly investigated by 3D computed tomography, which showed mechanical deformation of the layers. An extensive literature review revealed that the addition of fluoroethylene carbonate (FEC) to the electrolyte enhances the cycling stability of silicon alloy batteries but leads to the production of CO 2 as a side reaction. Furthermore, the usage of external pressure was proposed and validated as a methodology to reduce the production of CO 2 while improving the cells’ performance.
Microwaving Blood as a Non‐Destructive Technique for Haemoglobin Measurements on Microlitre Samples

The non‐destructive ex vivo determination of haemoglobin (Hgb) concentration offers the capability to conduct multiple red blood cell haematological measurements on a single sample, an advantage that current optical techniques are unable to offer. Here, a microwave method and device for the accurate and non‐destructive determination of Hgb concentration in microlitre blood samples are described. Using broadband microwave spectroscopy, a relationship is established between the dielectric properties of murine blood and Hgb concentration that is utilized to create a technique for the determination of Hgb concentration. Subsequently, a microwave dielectric resonator‐microfluidic system is implemented in the analysis of 52 murine samples with microlitre volumes and Hgb concentrations ranging from 0 to 17 g dL−1. Using the characterized relationship, independent and minimally invasive Hgb measurements are made on nine healthy mice as well as seven with mutations in the Adenomatous polyposis coli (APC) gene that leads to colorectal cancer and consequently anaemia.
Measuring Achilles Tendon Mechanical Properties: A Reliable, Noninvasive Method

Abstract Joseph, MF, Lillie, KR, Bergeron, DJ, and Denegar, CR. Measuring Achilles tendon mechanical properties: A reliable, noninvasive method. J Strength Cond Res 26(8): 2017–2020, 2012. The purpose of this technical report is to describe a cost-effective and highly reliable methodology to measure mechanical and material properties of the Achilles tendon. Subjects are positioned on an isokinetic dynamometer time synchronized to a diagnostic ultrasound device. A tendon fascicle distal to the soleus is visualized during a ramped isometric maximal plantarflexion contraction. Excursion of the fascicle and tendon torque output yield a force-elongation curve in which mechanical characteristics and material properties are derived. Excellent intrasession and intersession reliabilities were observed for both the dynamometer (intraclass correlation coefficient [ICC] 0.99, 0.95) and excursion (ICC 0.99, 0.93) measures. Practical applications for this methodology include examination of training regimes for optimal tendon adaptation and rehabilitation in the presence of tendinopathy.
Blantyre , Malawi

Background: HIV self-testing (HIVST) has been found to be highly effective, but no cost analysis has been undertaken to guide the design of affordable and scalable implementation strategies. Methods: Consecutive HIV self-testers and facility-based testers were recruited from participants in a community clusterrandomised trial (ISRCTN02004005) investigating the impact of offering HIVST in addition to facility-based HIV testing and counselling (HTC). Primary costing studies were undertaken of the HIVST service and of health facilities providing HTC to the trial population. Costs were adjusted to 2014 US$ and INT$. Recruited participants were asked about direct non-medical and indirect costs associated with accessing either modality of HIV testing, and additionally their health-related quality of life was measured using the EuroQol EQ-5D. Results: A total of 1,241 participants underwent either HIVST (n = 775) or facility-based HTC (n = 446). The mean societal cost per participant tested through HIVST (US$9.23; 95 % CI: US$9.14-US$9.32) was lower than through facility-based HTC (US$11.84; 95 % CI: US$10.81-12.86). Although the mean health provider cost per participant tested through HIVST (US$8.78) was comparable to facility-based HTC (range: US$7.53-US$10.57), the associated mean direct non-medical and indirect cost was lower (US$2.93; 95 % CI: US$1.90-US$3.96). The mean health provider cost per HIV positive participant identified through HIVST was higher (US$97.50) than for health facilities (range: US$25.18-US$76.14), as was the mean cost per HIV positive individual assessed for anti-retroviral treatment (ART) eligibility and the mean cost per HIV positive individual initiated onto ART. In comparison to the facilitytesting group, the adjusted mean EQ-5D utility score was 0.046 (95 % CI: 0.022-0.070) higher in the HIVST group. Conclusions: HIVST reduces the economic burden on clients, but is a costlier strategy for the health provider aiming to identify HIV positive individuals for treatment. The provider cost of HIVST could be substantially lower under less restrictive distribution models, or if costs of oral fluid HIV test kits become comparable to finger-prick kits used in health facilities.
Analysis of Quickselect: An Algorithm for Order Statistics

We study QUICKSELECT a one-sided version of QUICKSORT suited for finding the order statistics of a sample. We identify procedures by which the moments of the number of comparisons can be found exactly under both assumptions that the order statistic in question is randomly chosen or fixed. The procedure is illustrated by finding the exact mean and variance for a randomly selected order statistic as well as the first few in the fixed case. The existence of an absolutely continuous infinitely divisible limit law with asymmetric left and right tails is demonstrated in the case of a randomly chosen order statistic. Some of these distributional properties carry over to the case of a very small fixed order statistic.
Expression and alteration of BKCa channels in the sphincter of Oddi's from rabbits with hypercholesterolemia

ABSTRACT This study aimed to investigate the expression and function of BKCa channels in the Sphincter of Oddi (SO) in a rabbit model of hypercholesterolemia (HC). New Zealand white rabbits were randomly divided into 2 groups: the control group was fed standard chow (n = 18) whereas the high-cholesterol group was fed cholesterol-enriched chow containing 1.5% cholesterol (n = 18). The serum cholesterol level was significantly greater in the HC groups than in the control group, but there was no significant difference in body weight between the control and HC groups. Although the total protein expression of BKCa α- and β1-subunit was not significantly different between the control and HC groups, the Tyr-phosphorylation of BKCa α-subunit was significantly decreased in the HC group than in the control group. In addition, hypercholesterolemia significantly increased Acetylcholine (ACh)-induced contraction of the SO rings. Pretreatment with 30 μM NS1619, a BKCa channel agonist, significantly reduced ACh-induced contraction of the SO rings in HC rabbits. Moreover, pretreatment with 100 μM Na3OV4, a protein tyrosine phosphatase inhibitor, significantly reduced ACh-induced contraction of the SO rings in HC rabbits, whereas it significantly increased upon pretreating with 10 μM Genistein, a tyrosine kinase inhibitor. Whole-cell patch clamp recordings showed that BKCa current density was significantly lower in SOSMCs from HC group than that from control group. Our findings suggest that hypercholesterolemia-induced downregulation of BKCa channel, and Tyr-phosphorylation of BKCa α-subunit may contribute to the hyperresponsiveness of the SO ring in HC rabbits.
Analysis of content charge by ISPs

When rich content is delivered, a huge amount of traffic is transmitted over the network. For ISPs, the increase in investment cost that is required to maintain stable quality is a problem. ISPs need content providers to cover the investment cost because increase in the user fees may not be accepted by the users. However, content providers usually pay an access fee where the increase ratio diminishes as the volume of the data transmitted increases. Therefore, ISPs cannot obtain enough profit to cover the required investment costs. For this problem, content charge, in which ISPs charge content providers for each content delivery, seems effective. This work models the business relationship between ISPs and content providers, and we investigate the conditions for introducing the content charge by the ISPs. We also investigate the effects of content charge on the revenue of the ISPs by numerically comparing the content charge and the transit charge. We show that major ISPs in Japan can expect to increase their monthly income from about 100,000 USD to about one million USD when the charging ratio of content charge is set to 20%.
Objective algorithms for the aerosol problem.

Retrieval of the aerosol size distribution from optical measurements at ground level is well known to be a difficult problem. Nowadays objective techniques that can give a solution without the intervention of the researcher do not exist. We propose several objective methods that are well based in the mathematical and physical points of view. Their accuracy is evaluated and the top performance of the objective inversion techniques is presented. Moreover physical and experimental suggestions can be drawn to improve the accuracy. Inversions with experimental optical depths are also shown.
Chicken IgY Binds Its Receptor at the CH3/CH4 Interface Similarly as the Human IgA:FcαRI Interaction1

Chicken IgY, the ancestral form of mammalian IgE and IgG, is recognized by the high-affinity FcY receptor CHIR-AB1, a member of the leukocyte receptor family. In this study, we have characterized the receptor ligand interaction site by consecutive truncations of the Fcυ IgY domains and mutational analyses of selected residues. Using several fusion proteins that linked the human Cγ2 and Cγ3 domains with the Fcυ IgY domains, a binding assay revealed that both the Fcυ3 and Fcυ4 domains were essential for the IgY CHIR-AB1 interaction. Sequence comparisons of chicken IgY with human IgA demonstrated that 11 of the 19 contact residues important for the IgA FcαRI interaction have been conserved in chicken IgY, although the overall amino acid identity is only 34%. Among the 19 amino acids at respective positions in IgY, the mutation of two residues in the Fcυ3 and two in the Fcυ4 domain completely abolished the IgY to CHIR-AB1 binding revealed by two independent assays. Three further mutations substantially altered the interaction. Molecular modeling on the Cυ3 to Cυ4 crystal structure revealed that all critical residues, although on two domains, are in close proximity. The importance of N-linked carbohydrates was demonstrated by the failure of the CHIR-AB1 interaction after mutation of the glycosylation site. The identification of the IgY Cυ3/Cυ4 interdomain region as critical for binding to CHIR-AB1 significantly enhances our understanding of the IgY receptor interaction and allows further conclusions regarding the FcR phylogeny.
The effect of multi-walled carbon nanotubes/hydroxyapatite nanocomposites on biocompatibility

In the present study, multi-walled carbon nanotubes/hydroxyapatite (MWCNTs/HA) nanocomposites with various MWCNT contents were manufactured by sol-gel processing. The MWCNTs/HA powder was characterized using field-emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Raman analysis. The results show that the MWCNTs were fully covered with HA nanoparticles and help forming the crystallized hydroxyapatite. In addition, in vitro tests highlighted the excellent biocompatibility of the MWCNTs/HA composite.
Distributed power allocation and user assignment in OFDMA cellular networks

We consider a wireless OFDMA cellular network and address the problem of jointly allocating power to frequencies (subbands) and assigning users to cells, for a variety of elastic and inelastic services. The goal is to maximize the sum of the users' throughput utility functions subject to various constraints, such as minimum throughput requirements. The problem naturally fits into a Network Utility Maximization (NUM) framework with a mixture of concave (e.g., data rates) and nonconcave (e.g., voice/video streaming) utilities. The hardness of this nonconvex, mixed integer program prohibits the use of standard convex optimization algorithms, or efficient combinatorial approximation techniques. We devise a randomized algorithm for the said NUM problem, whose proof of asymptotic optimality is derived from the classical framework of interacting particle systems, via a judiciously selected neighborhood structure. The proposed algorithm is highly distributed, asynchronous, requires limited computational effort per node/iteration, and yields provable convergence in the limit. Several numerical experiments are presented to illustrate the convergence speed and performance of the proposed method.
How Do Banks Adjust Their Capital Ratios? Evidence from Germany

We analyze the dynamics of banks' regulatory capital ratios. Using monthly data of regulatory capital ratios for a subset of large German banks, we estimate the target level and the adjustment speed of the capital ratio for each bank separately. We find evidence that, first, there exists a target level for a substantial percentage of banks; second, that private banks and banks with liquid assets are more likely to adjust their capital ratio tightly; and third, that banks compensate for low target capital ratios with low asset volatilities and high adjustment speeds. Fourth, banks with a target capital ratio seem to use an internal lower limit for their current ratios that is just above the regulatory minimum of 8%.
Granger Causality for Multivariate Time Series Classification

Multivariate time series, which is a set of ordered observations for multiple variables, is pervasively generated in air condition, traffic, entertainment, etc. Echo State Network has shown promising performance for processing multivariate time series due to its ability to approximate sequential dynamics. However, the intrinsic relationships among time series have not been generally analyzed in the previous Echo State Network based methods. These relationships may help reveal the intrinsic characteristics of multivariate time series and benefit the classification performance. In this paper, we propose a novel method for approximating the sequential dynamics and learning the relationship among multiple variables explicitly in a unified framework. We learn a model for each multivariate time series and evaluate the distance of the original multivariate time series by the distance of their models. The relationship among variables in a multivariate time series is learnt according to Granger causality. We further constrain the sparsity of the learnt time series models to find the Focal series which help explain all the series. Experiments on benchmark datasets demonstrate superior classification performance of the proposed method.
Mastering strategies in a board game of imperfect information for different search techniques

To the best authors' knowledge this work is the first to develop a full computer implementation of The Great Turtle Race (GTR), a complex board game characterized by several uncertainties that uses computational techniques to evaluate board positions and select the best move. In the game, a novel combination of popular propagation-based optimization techniques and four playing strategies is implemented. One of the main goals of this study is to determine how to generate opponents that are quick and safe to play against, rather than being necessarily superior. The paper starts by a brief overview of the game and its rules, followed by some analytical results that emerge from its characteristics. It then moves to provide relevant reinforcement learning methods by which Monte Carlo tree search, minimax and alpha-beta pruning were implemented. The validity of the concept is finalized by a series of experiments, in which these algorithms and strategies were successfully verified against each other.
Recent changes in drug poisoning mortality in the United States by urban–rural status and by drug type

This study was conducted to determine how the recently reported increase in drug poisoning mortality rates in the United States varied by degree of urbanization. Although drug poisoning is traditionally seen as an urban problem, evidence suggested that at least one component of the recent increase, deaths involving opioid analgesics, was increasing more rapidly in rural areas.
SPLAY: Distributed Systems Evaluation Made Simple (or How to Turn Ideas into Live Systems in a Breeze)

This paper presents SPLAY, an integrated system that facilitates the design, deployment and testing of large-scale distributed applications. Unlike existing systems, SPLAY covers all aspects of the development and evaluation chain. It allows developers to express algorithms in a concise, simple language that highly resembles pseudocode found in research papers. The execution environment has low overheads and footprint, and provides a comprehensive set of libraries for common distributed systems operations. SPLAY applications are run by a set of daemons distributed on one or several testbeds. They execute in a sandboxed environment that shields the host system and enables SPLAY to also be used on nondedicated platforms, in addition to classical testbeds like PlanetLab or ModelNet. A controller manages applications, offering multi-criterion resource selection, deployment control, and churn management by reproducing the system's dynamics from traces or synthetic descriptions. SPLAY's features, usefulness, performance and scalability are evaluated using deployment of representative experiments on PlanetLab and ModelNet clusters
On-chip enucleation of an oocyte by untethered microrobots

We propose a novel on-chip enucleation of an oocyte with zona pellucida by using a combination of untethered microrobots. To achieve enucleation within the closed space of a microfluidic chip, two microrobots, a microknife and a microgripper were integrated into the microfluidic chip. These microrobots were actuated by an external magnetic force produced by permanent magnets placed on the robotic stage. The tip of the microknife was designed by considering the biological geometric feature of an oocyte, i.e. the oocyte has a polar body in maturation stage II. Moreover, the microknife was fabricated by using grayscale lithography, which allows fabrication of three-dimensional microstructures. The microgripper has a gripping function that is independent of the driving mechanism. On-chip enucleation was demonstrated, and the enucleated oocytes are spherical, indicating that the cell membrane of the oocytes remained intact. To confirm successful enucleation using this method, we investigated the viability of oocytes after enucleation. The results show that the production rate, i.e. the ratio between the number of oocytes that reach the blastocyst stage and the number of bovine oocytes after nucleus transfer, is 100%. The technique will contribute to complex cell manipulation such as cell surgery in lab-on-a-chip devices.
One-step Consensus with Zero-Degradation

In the asynchronous distributed system model, consensus is obtained in one communication step if all processes propose the same value. Assuming f<n/3, this is regardless of the failure detector output. A zero-degrading protocol reaches consensus in two communication steps in every stable run, i.e., when the failure detector makes no mistakes and its output does not change. We show that no leader-based consensus protocol can be simultaneously one-step and zero-degrading. We propose two approaches to circumvent the impossibility result and present corresponding consensus protocols. Further, we present an atomic broadcast protocol that has a latency of 3delta in every stable run and a latency of 2delta in case of no collisions. Finally, we evaluate its performance in a cluster of workstations