Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Ustilago hordei Causing Covered Smut of Barley

Barley covered smut (CS) pathogen Ustilago hordei genome was mined for microsatellite distribution and their application in defining population structure and genetic variation. To dissect the molecular variation and genetic structure of U. hordei, 59 fungal isolates representing two distinct agro-ecological zones of India were analyzed by employing simple sequence repeats (SSRs). Using bioinformatic approaches, a total of 100,239 and 137,442 microsatellites were identified from 20.13 and 26.94 Mb of assembled genomic sequences of Uh364 and Uh4857-4 isolates of U. hordei, respectively. Penta-nucleotides (31.29 and 29.75%) followed by tri-nucleotide (28.27 and 29.88%) were most prevalent in both the genomes. Out of them, 15 polymorphic microsatellites showing conservancies in both the genomes were selected for exploring population genetic structure of U. hordei. An average of two alleles per microsatellite marker was generated with band size ranging from 180 to 850 bp. Polymorphic information content (PIC) varied between 0.095 and 0.37. Fifty-nine isolates were distributed in two distinct groups with about 65% genetic similarity according to UPGMA clustering and population structure analysis (K = 2). Gene flow analysis (Nm = 1.009) reflected moderate gene flow among the analyzed population. An analysis of molecular variance (AMOVA) displayed high level of genetic variation within population (87%) and low variation among populations (13%). Linkage disequilibrium (LD) analysis indicated positively significant but relatively low standardized index of association (SIA) value in both the population sets (SIA = 0.181), advocating a state of LD with epidemic population structure. In conclusion, the newly developed neutral SSR markers are highly polymorphic within U. hordei and will be useful for revealing evolutionary history and providing deep insight into the population dynamics of U. hordei in India as well as facilitating developing management strategies for CS of barley.
Social Stress-Related Epigenetic Changes Associated With Increased Heart Rate Variability in Infants

Early life stress can result in persistent alterations of an individual’s stress regulation through epigenetic modifications. Epigenetic alteration of the NR3C1 gene is associated with changes in the stress response system during infancy as measured by cortisol reactivity. Although autonomic nervous system (ANS) reactivity is a key component of the stress response, we have a limited understanding of the effects of NR3C1 DNA methylation on ANS reactivity. To examine this relation, ANS stress responses of term, 4–5-month-old healthy infants were elicited using the face-to-face still-face paradigm, which involved five, 2-min episodes. Two of these episodes were the “still-face” in which the mother was non-responsive to her infant. EKG was acquired continuously and analyzed in 30 s-intervals. Cheek swabs were collected, and DNA was extracted from buccal cells. Respiratory sinus arrhythmia (RSA) was measured as heart rate variability (HRV). Mean HRV was calculated for each 30-s “face to face” episode. DNA methylation of NR3C1 was calculated using bisulfite pyrosequencing. Percent DNA methylation was computed for each of the 13 NR3C1 CpG sites. The relations between mean HRV for each “face to face” episode and percent DNA methylation was examined averaged over CpG sites 1–6 and 7–13 and at each individual CpG site. Higher HRV at baseline, first reunion, and second still-face was related to greater methylation of NR3C1 CpG sites 1–6. Higher HRV at the second reunion was related to greater methylation of NR3C1 CpG sites 12 and 13. These data provide evidence that increased methylation of NR3C1 at CpG sites 12 and 13 are associated with increased activation of parasympathetic pathways as represented by increased HRV.
Patching and Suppression in Amblyopia: One Mechanism or Two?

Purpose To determine if benefits from occlusion therapy are due to decreased suppression from the fellow eye in children with amblyopia. Methods Ten newly diagnosed amblyopes (7.2 ± 1.4 years old), two with strabismus and eight with anisometropia, participated. Patients were first given a 2-month period of refractive adaptation, followed by occlusion therapy (i.e., patching their fellow eye with an opaque patch for 4 h/day). Visual acuity of the amblyopic eye and interocular suppression were measured before and after 0.5, 1, 2, 4, and 6 months of occlusion therapy. We quantified interocular suppression with a binocular phase combination task. Results Visual acuity (in logMAR) improved from 0.50 ± 0.22 (mean ± SD) to 0.33 ± 0.20 for patients who finished a short-term (2 months) occlusion (A1–A10), from 0.53 ± 0.20 to 0.32 ± 0.22 for patients who finished a medium-term (4 months) occlusion (A1–A9), and from 0.48 ± 0.19 to 0.22 ± 0.10 for patients who finished a long-term (6 months) occlusion (A1–A8). Although their visual acuity significantly improved, their degree of suppression, which was abnormal in all cases, did not change consistently. This was true in all durations of occlusion therapy. Conclusion Reduced suppression from the fixing eye might not be result from occlusion therapy.
ACHIEVING SOFT REAL-TIME GUARANTEES

The use of 802.11-based multi-hop wireless mesh networks fo r Internet access is extensive and growing. The primary advantages of this approac h are ease of deployment and lower cost. However, these networks are designed for web and e-mail applications. Highly interactive applications, such as multiplayer onli ne games and VoIP, with their requirements for low delay, present significant challenges to these networks. In particular, the interaction between real-time traffic and TCP traffic ten ds to result in either a failure of the real-time traffic getting its needed QoS or the TCP traf fic unnecessarily experiencing very poor throughput. To solve this problem we place real -time and TCP traffic into separate queues. We then rate-limit TCP traffic based on the a verage queue size of the local or remote real-time queues. Thus, TCP traffic is permit ted to use excess bandwidth as long as it does not interfere with real-time traffic guaran tees. We therefore call our scheme Real-time Queue-based Rate and Admission Control, R Q-RAC. Extensive simulations using the network simulator, ns-2, demonstrate th at our approach is effective in providing soft real-time support, while allowing efficient use of the remaining bandwidth for TCP traffic.
Can syntax influence morphological complexity? Evidence from the gender congruency effect

When speakers have the option of using either a morphologically complex form or a synonymous simpler base form, which factors influence their choice? In this project we ask whether syntactic context is one such factor. We compare the production of Dutch noun phrases with diminutive and non-diminutive heads. Previous literature (Janssen and Caramazza, 2003) showed that naming latencies in the production of diminutive nouns are affected by syntactic information—specifically, grammatical gender and the presence of a agreeing determiner. Here, we ask whether this information affects whether the diminutive is used at all.
Inositol enhances lipid production by Schizochytrium limacinum SR21 using defatted silkworm pupae hydrolysate

In the present study, the inositol was evaluated for its effect on lipid and docosahexaenoic acid (DHA) accumulation in Schizochytrium limacinum SR21. To investigate effects of inositol on lipid and DHA yield during the whole fermentation process, the time courses (120 h) of lipid and DHA yields by S. limacinum SR21. It was found that lipid content and DHA yield of S. limacinum SR21 increased by 13.64% and 20.82%, respectively, with 120 mg/L of inositol being added to the medium at 48 h. However, the content of total polyunsaturated fatty acids in the cells increased with the addition of inositol, especially the content of DHA contents were majorly induced. To understand the biochemistry behind these improvements, lipogenic enzyme assays were used and revealed that enzyme activity were increased with inositol addition. Thus, inositol can be used as a new enhancer to improve accumulation of lipid and DHA yield.
Paper 19:text

ROM grade variability is one of the most important factors influencing plant product recovery. Therefore, it is critical to reduce the head grade variability feeding the processing plant. Blending piles play an important role on this task, as they substantially reduce the inherent variability of the deposit, even when mining follows a schedule defined along a stationary mining route. A typical chevron type blending system basically spreads and piles up successive horizontal layers of the ore. These layers form a triangular base prism which lies in the blending area and is reclaimed by vertical slices comprised of multiple layers (Figure 1). Traditionally, kriging (Matheron, 1963)1 or any other estimation method is applied, aimed at measuring variability in a fine scale. In these situations, the uncertainty associated with the interpolated value cannot be properly incorporated (Costa et al., 2007)2. As a result of the socalled smoothing effect, the variance of the estimated values is smaller than that of the original data. There are also limitations associated with the use of the kriging variance as a measure of uncertainty (Isaaks and Srivastava, 1989)3. The methodology suggested in this study quantifies the variability of the homogenization system by using multiple equally probable realizations derived from a geostatistical simulation of the grade block model. Geostatistical simulation methods aim primarily at reproducing in situ variability, provided that the spatial continuity of the input data-set is respected. Conditional simulation honours values at the sampled points while reproducing the same dispersion characteristics of the original data-set, the mean, variance and semi-variogram functions. The equally probable realizations will generate a group of possible values for the blocks that form each homogenization pile. Finally, it is possible to predict the in situ grade variability, given the real grades. The methodology is illustrated using a data-set from a large phosphate mine in central Brazil.
Science Journals — AAAS

Optoelectronics Group, Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue,CambridgeCB30HE,U.K. DepartmentofChemistry andCenter forNanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377München, Germany. Department ofMaterials ScienceandEngineering,MonashUniversity, Clayton Campus,Wellington Road, Clayton, Victoria 3800, Australia. Department ofMaterials Science andMetallurgy, University of Cambridge, 27Charles BabbageRoad, CambridgeCB3 0FS, U.K. Department of Physics and Astronomy, University of Missouri, 223 Physics Building, Columbia, MO 65211–7010, USA. School of Electrical and Electronic Engineering, Newcastle University, Merz Court, Newcastle upon Tyne NE1 7RU, U.K. †These authors contributed equally to the work. *Corresponding author. Email: sps54@cam.ac. uk (S.P.S.); hs220@cam.ac. uk (H.S.)
Biochemical evaluation and hypoglycemic activity of ethanolic extract of Xanthium strumarium L. on normoglycemic and alloxan-induced diabetic mice

The aim of present study was to evaluate the hypoglycemic activity of some fractions of ethanolic extracts in normal and diabetic rats as a step toward activity directed isolation of the hypoglycemic component. Spectral analysis were used for structural determination of isolated compound (II). Oral administration of ethanolic extract and isolated compound-II (300 and 500 mg/kg bw) for 14 days resulted in a significant reduction in blood sugar level. The effect was compared with 10mg/kg (i.p.) Glibenclamide. Alloxan-induced hyperglycemic rats were used for the evaluation of antidiabetic activity. The effect of ethanolic extracts and compound-II on normal and alloxan-induced hyperglycemic rats were compared. The results shows Antihyperglycemic activity of ethanolic extract and compound-II were in dose dependent manner. The activity was more for 500mg/kg bw dose in comparision with 300mg/kg bw for both and compound-II showed better reduction of blood glucose level compared to ethanolic extracts.
Surface reconstruction for complex surfaces metrology

Freeform surfaces have seen enlarged applications since their complex shapes closely express a product’s functional specifications and their machining is obtained with higher accuracy. In particular, optical surfaces exhibit enhanced performance especially when they take aspheric or more complex forms. This study is mainly focused on the reconstruction of freeform optical surfaces. The computer graphics community has proposed various algorithms for constructing a mesh based on the cloud of sample points. A comparative study carried out on these methods will be presented. We stress the importance of the pre-processing phase and the significance of initial conditions. When initial conditions on the point set are not met, meshing tends to fail. In this context, we propose a different approach to reconstruction, and present a new BSpline geometric convection algorithm for curves. RÉSUMÉ. Les surfaces gauches ont vu un essor dans le cadre d’applications en mécanique et en optique. Leurs formes complexes permettent de répondre à des exigences fonctionnelles très poussées. En particulier, les surfaces asphériques et/ou free-form présentent des performances inégalées par rapport à des formes plus simples. Cette étude est focalisée sur la reconstruction de surfaces complexes à partir de grands flots de données. L’état de l’art des algorithmes de reconstruction ainsi que leur comparaison sont évoqués. Les méthodes proposées sont basées sur de fortes conditions d’utilisations et présentent ainsi des contraintes. Sachant que ces conditions sont rarement respectées lors d’une mesure, ces algorithmes sont très conditionnés et donc pas robustes. Une approche par convection géométrique de BSpline qui ne requiert aucune condition sur les données est alors proposée et présentée en 2D.
Dotty Phantom Types

Phantom types are a well-known type-level, design pattern which is commonly used to express constraints encoded in types. We observe that in modern, multi-paradigm programming languages, these encodings are too restrictive or do not provide the guarantees that phantom types try to enforce. Furthermore, in some cases they introduce unwanted runtime overhead. We propose a new design for phantom types as a language feature that: (a) solves the aforementioned issues and (b) makes the rst step towards new programming paradigms such as proof-carrying code and static capabilities. This paper presents the design of phantom types for Scala, as implemented in the Dotty compiler.
Fire weather and prototype fire danger ratings for the Gell River fire, Tasmania

Rainfall in the weeks leading to the fire ignition had been sporadic. While December rainfall had been close to average, the three months leading up to the start of January had generally seen below average rainfall in the vicinity of the ignition area (Fig. 3a, b). Rainfall of 10-15 mm had occurred in the 24 hours to 0900 EDST (Eastern Daylight Savings Time) 22 December but there was subsequent no rainfall. Fuel availability calculations indicated that moorland fuels were available to burn when ignition occurred on 27 December. While sufficient antecedent rainfall had occurred to prevent the fire from spreading freely into many wet forest areas at that time, some rainforest areas, particularly about forest margins, were drier than others and available to burn.
HDC-IM: Hyperdimensional Computing In-Memory Architecture based on RRAM

Brain-inspired Hyperdimensional Computing (HDC) is a fast and robust classification algorithm, which works by mapping low-dimensional features to high-dimensional vectors and comparing distance in a high dimensional space. However, in traditional Von Neumann architecture, HDC causes high energy consumption because of large data movements between processor and memory. In this paper, we propose HDC-IM, a Hyperdimensional Computing-In-Memory architecture based on Resistive Random-Access Memory (RRAM), to boost the energy efficiency of HDC. HDC-IM puts computations in or near memory, which eliminates most of the data movements, providing a solution to reduce the energy consumption. In addition, to improve the computing parallelism, we use in-crossbar RRAM-based logic design to process encoding operation in HDC. The experimental results show that HDC-IM provides more than 100× speedup and higher energy efficiency compared with HDC on CPU. Moreover, in comparison with existing RRAM-based Neural Network accelerators, HDC-IM is more fault-tolerant taking into account RRAM device faults, achieving 20% higher accuracy than RRAM-based DNN on ISOLET dataset when 20% RRAM devices suffer from Stuck-At-Faults (SAFs).
Automata-Based Timed Event Program Comprehension for Real-Time Systems

In this paper, we extend the software space of program comprehension to real-time systems and introduce two orthogonal and hybrid paradigms that we refer to as timed event component comprehension and timed event program comprehension. The former, timed event component comprehension, with no role in the coding aspect, is a set of autonomous timed event components that provide a high-level system-specific functionality about the overall real-time system including its structure, components and their synchronized interrelationships at different level of granularity, and static and dynamic behaviors. The later, timed event program comprehension recovers high level of information from timed event component comprehension and then builds an automata-based model about the system. This process occurs before carrying any program comprehension. We show that both paradigms are intrinsically linked and neither of them can be explored in isolation. Importantly, we map the component comprehension paradigm into a distinguished component class that we refer to as timed event components (TeCmp) which, in turn, are formally modeled as timed event automata, a powerful canonical model for modeling and verifying real-time computations. Furthermore, to support this research towards an effective program comprehension geared towards real-time and embedded systems, we investigated and evaluated the effect of our approach through a practical Internet of Things (IoT) case study. Keywords–Program comprehension; program understanding; software modeling; real-time systems; embedded systems; IoT; timed event automata.
A Branch and Cut Algorithm for the Cycle Hub Location Problem

In this paper we present solution algorithms for the Cycle Hub Location Problem (CHLP), which seeks to locate p hub facilities that are connected by means of a cycle, and to assign non-hub nodes to hubs so as to minimize the total cost of routing flows through the network. This problem is useful in modeling applications in transportation and telecommunication systems, where large set-up costs on the links and reliability requirements make cycle topologies a prominent network architecture. We present a branch-andcut algorithm that uses a flow-based formulation and two families of mixeddicut inequalities as a lower bounding procedure at nodes of the enumeration tree. We also introduce a greedy randomized adaptive search algorithm that is used to obtain initial upper bounds for the exact algorithm and to obtain feasible solutions for large-scale instances of the CHLP. Numerical results on a set of benchmark instances with up to 100 nodes and 8 hubs confirm the efficiency of the proposed solution algorithms.
Analysing Cultural Events on Twitter

In this paper, we first present a model to represent message flows and their contents on Twitter, then a model and an instrumented methodology to describe and analyze these flows and their distribution among the various stakeholders. The aim is to explore the engagement and interactions between different types of stakeholders. We apply our methodology and tools to the 12th edition of the cultural event ”European Night of Museums” (NDM16).
Is the growth of Chinese firms constrained by internal finance?

Using a panel of 407,096 firms over the period 2000-2005, we examine the extent to which the growth of Chinese firms is affected by the availability of internal finance. We estimate dynamic assets growth equations augmented with cash flow and find that the growth of state owned enterprises is not affected by cash flow, while that of privately owned firms is most affected. Considering that they represent 63 percent of the observations in our sample and that, in spite of being typically discriminated against by financial institutions, private firms have experienced sensational growth rates, our results suggest that internal finance has fostered rather than constrained their growth.
Why myopic policies persist? Impact of growth opportunities and competition

Several case studies have documented myopic allocation of organizational resources among capabilities that payoff in short vs. long-term. We capture a general class of organizational resource allocation problems in a simple model that exhibits the typical worse-before-better dynamics commonly believed to be responsible for persistence of myopic policies. Next we examine the endogeneity of resources and the impact of competitive pressures on the efficiency of allocation policies. Endogenous resources and competition are both shown to significantly shift the optimal allocation towards myopic policies. Short-term policies become beneficial as they strengthen the positive loop between performance, resources, and capabilities. In fact strategic selection of allocation policy in a competitive market can force the firms to allocate all the resources to the short-term capability. These results provide an alternative explanation for the persistence of myopic organizational decision-rules that does not rest on psychological and learning arguments.
Automatic detection of cylindrical objects from unorganized point cloud

Extracting a 3D primitive geometric shape such as a sphere and a cylinder from a point cloud is an important research topic. Especially, most of CAD models are composed of such primitives, and extraction of geometric parameters of each primitive plays a key role in reverse engineering and registration. Among the primitives, cylinders are frequently used in practice to represent pipe-like objects. Recently, there are various methods for detecting multiple cylindrical objects from an unorganized point cloud, but they still have a limitation of detecting multiple cylinders and the elbow parts where two cylinders are connected. In this work, we present an automated robust method of detecting any types of multiple cylindrical objects from an unorganized point cloud and estimating a complete pipe structure consisting of multiple cylinders. We focus on a method of extracting a parabolic patch at each point using the points in the neighborhood and computing a radius from the patch to consider a virtual sphere of that radius at that point. We compute such spheres at all the other points and trace the centroids of the detected virtual spheres to find the axis of each cylinder. The orientation of the axis of the cylinder is computed from the mean-filtered centroids. Each cylinder is separately obtained, and the joints of the cylinders are estimated to form a complete pipe. The proposed method is tested with various examples.