Miracle-dz/UniFAR-FTUs huggingface dataset:
BIOINFORMATICS ORIGINAL PAPER

Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs), making use of the large number of processing cores to efﬁciently parallelize calculations even for large state-size models. Results: We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized CPU-based computation and a > 140-fold increase over the currently available implementation, making this the ﬁrst practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes. Availability and implementation: Source code provided in BEAGLE: Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (http://beast.bio.ed.ac.uk/).
Low-cost vertical coupling schemes for optical I/Os and 3D integration in CMOS photonic integrated circuits

Grating coupler structures have attracted prominent research and development efforts to address off-chip, vertical light coupling for wafer-level test and complex optical assemblies. In fact, three-dimensional (3D) integration is introduced as the key enabling technology for low footprint, high frequency and low loss silicon photonic and opto-electronic integrated circuits. Towards this direction, low-cost and CMOS compatible fabrication processes are required for the cost-effective mass-manufacturing of silicon photonic devices by CMOS foundries. This paper presents the recent research outcomes on effective perfectly normal grating couplers designed and fabricated on 340 nm thick silicon-on-insulator (SOI) following low cost methodologies that comply with CMOS fabrication processes while minimizing lithography and etching steps.
Predicting a bank's credit rating change using financial data and public financial news

This research integrated published financial news with accounting ratios to measure the viability of increasing the discriminatory power of a credit rating model. The aim was the utilization of information in news articles to create additional predictors of credit rating changes. Modal sentiment in news articles were integrated with calculated financial ratios from the published financial statements. The integrated data points were then analyzed in Eviews resulting in a model which was then used in determining credit rating. The model was found to be stable and having a good discriminatory power. Credit ratings of sample banks were then determined as at 31 December 2013. The output from the model was found to be almost the same as ratings assigned by GCR and RBZ. Data points from outside the sample were used to validate capability of the model in measuring ratings of banks outside the sample.
Multibranch Regenerative DF Wireless Relay Networks under Channel Uncertainty and Node Geometry

This paper studies channel uncertainty and node geometry influences on a regenerative distributed decode-and-forward (DF) wireless relay network. A network consisting of one-source-one-destination pair and N-multibranch relay nodes without a direct link between the source and the destination is investigated. A new proposed detection scheme employs the maximum ratio combiner (MRC) principle. The new detection scheme is applied at both relay nodes and the destination node, to optimally detect the original transmitted message from the source node. Monte-Carlo simulations were used to evaluate the bit error rate (BER) performance for the regenerative distributed DF wireless relay network using the new proposed MRC scheme.
Innovations and Market Value of Firms : Differential Effects of Leaders and Followers

We use a latent-factor patent count data model and a panel VAR model in order to analyze the lagged impact of observable and latent determinants of patent activity on the stock market value and patent activity of competitors for six industries – aircrafts, pharmaceuticals, computers, software, defense and oil sectors – in the U.S. during 1979-2000. We identify R&D leader and follower companies in each sector using alternative definitions. We find that the relative importance of the latent patent intensity component has increased in the pharmaceuticals, computers, software and defense sectors. We also find that the latent component has decreased in the aircrafts and oil industries. Regarding the observable patent intensity component, we find that it has increased in all sectors. Moreover, we evidence that R&D leader and follower firms have had significant and different influence on the market value and patent activity of competitors in each sector analyzed. JEL classification: C15; C31; C32; C33; C41
Predictors of progression from prehypertension to hypertension among rural Chinese adults: results from Liaoning Province

Background Individuals with prehypertension are at a high risk of developing hypertension. Little is known about the predictors of progression from prehypertesion to hypertension in rural Chinese adults. Methods A population-based sample of 15 061 rural Chinese aged ≥ 35 years with prehypertension free cardiovascular diseases at baseline were followed-up from 2004–2006 to 2008. Incident hypertension was defined as systolic blood pressure (BP) ≥ 140 mmHg, diastolic BP ≥ 90 mmHg, or current use of antihypertensive medications. Results During the 28-month follow-up period, 4917 individuals (32.6%) with prehypertension developed hypertension, in which only 1.5% (n = 73) of incident cases reached BP control target. After Cox stepwise regression analysis, baseline age (per 5 years) [hazard ratio (HR): 1.111; 95% confidence interval (CI): 1.095–1.126], Mongolian (HR: 1.079; 95% CI: 1.010–1.152), alcohol drinking, overweight and obese (HR: 1.349; 95% CI: 1.261–1.444), salt intake everyday, inappropriate physical activity, and family history of hypertension were associated with incident hypertension independent of initial systolic and diastolic BP. Among these predictors, current alcohol drinking (odds ratio: 1.126; 95% CI: 1.049–1.209), salt intake, and overweight and obese were associated only with increased systolic BP, whereas inappropriate physical activity contributed only to increase diastolic BP. Conclusion These data suggest a high incidence of hypertension in individuals with prehypertension. Lifestyle modifications such as cessation of drinking, healthy diet, and moderate physical activity are advised to prevent or delay the progression of prehypertension to hypertension in rural areas of China.
The Moderating Role of Perceived Regulatory Effectiveness of Online Marketplaces on the Role of Trust and Risk on Transaction Intentions

Past research has widely regarded trust as unconditionally facilitating behavioral intentions, and perceived risk as unconditionally detracting from them. This study advocates the necessity to examine trust and perceived risk within the broader perspective of the societal context. We propose that the perceived regulatory effectiveness of online marketplaces moderates the impact of trust and risk on transaction intentions. First, we hypothesize that the degree to which transaction intentions are affected by their trust in the marketplace, sellers will vary in an inverted-U manner depending on how effective the buyers perceive the online marketplace regulation to be. The impact of trust on transaction intentions will increase as the buyer’s perceived regulatory effectiveness increases from low to medium levels, but it will decrease as the buyer’s perceived effectiveness increases from medium to high levels. Second, the perceived regulatory effectiveness of the online marketplace is hypothesized to reduce the impact of perceived risk on transaction intentions. These moderating effects were examined and empirically supported in the context of eBay’s and Amazon’s online auction marketplaces. Implications for integrating the perceived regulatory effectiveness of online marketplaces into existing trust and risk models are discussed.
Photogeneration of singlet oxygen by humic substances: comparison of humic substances of aquatic and terrestrial origin

The singlet oxygen (^1O_2) luminescence of 27 isolated humic substances (HS), natural organic matter, ultrafiltrates, and the synthetic fulvic acid HS1500 has been investigated by time-resolved spectroscopy in buffered D_2O. The samples include both reverse osmosis isolates from lakes in Scandinavia, Canada, and Germany, and IHSS fulvic and humic acids of aquatic and terrestrial origin. The quantum yields of ^1O_2 formation ( Φ _Δ) obtained on laser excitation at 480 nm ranged between 0.06 (HS1500) and 2.7% (fulvic acid from soil, IHSS). In our study, a general trend towards higher Φ _Δ in terrestrial HS was observed. The comparison of reverse osmosis isolates from surface waters collected during fall 1999 and spring 2000 from five Scandinavian sites yielded, in all cases, higher Φ _Δ for the spring samples. For the aquatic sampling sites Hietajärvi and Birkenes, Φ _Δ even exceeded values of 0.6%, which were found to be typical for terrestrial or soil water material. Investigation of the excitation wavelength dependence of Φ _Δ in the spectral range 355–550 nm yielded different spectral shapes for aquatic HS and “non-aquatic” HS, respectively. On the basis of these excitation spectra, ^1O_2 production rates were calculated for eight representative HS.
Dynamic Modeling and Driving Cycle Prediction for a Racing Series Hybrid Car

This paper presents Noao, a plug-in series hybrid racing car equipped with an engine/generator set as range extender. To determine the velocity profile, i.e., performance of the car and its power profile, a dynamic model for this car is developed using pedal position as input. This value is easy to measure, representative for race cycles, and presents a novelty. The model is validated with the results from experiments. An analysis based on the map of Magny-Cours racing circuit and drivers pedal action on certain zones of the circuit is formulated and is used as a prediction tool to determine drivers inputs on other racing circuits and generate driving schedules. The results obtained from this analysis are essential to predict energy consumption of the system, estimate driving range, and inspect battery state-of-charge evolution of the car during races. Moreover, the generated driving cycle provides an optimum compromise between drivetime and energy consumption of the system.
Federalismo, drogas y violencia Por qué el conflicto partidista intergubernamental estimuló la violencia del narcotráfico en México / Federalism, drugs, and violence Why intergovernmental partisan conflict stimulated inter-cartel violence in Mexico

The dominant view of the dramatic increase of criminal violence in Mexico following the 2007 federal intervention in the War on Drugs suggests that inter-cartel violence became particularly intense in subnational regions where the president could not coordinate the federal government’s actions with subnational opposition rulers but came under control where the president worked with his co-partisans. In this article we challenge the “coordination” argument and claim that in contexts of acute political polarization between Left and Right —like the one Mexico experienced before the War on Drugs— partisan conflict can motivate federal authorities to develop cooperative military and policing interventions in regions where the president’s co-partisans rule, but to deliberately neglect effective assistance to the president’s main political rivals and then blame the violence on them. Based on an original dataset of inter-cartel violence in Mexico (2006-2012), we show that while criminal violence was more intense in municipalities from states ruled by opposition parties, it was five times greater in cities ruled by the Left —the president’s political nemesis. We use case studies to show how Mexico’s conservative federal government followed differentiated strategies to deal with spirals of drug violence: it worked together and protected subnational co-partisans (PAN); partially cooperated with centrist opposition authorities (PRI); but confronted leftist governors and mayors (PRD) and left them at the mercy of drug cartels. Our results are consistent with findings in conflict studies showing that state agents do not always seek the monopoly on violence and sometimes tolerate violence to punish their political enemies.
8 × 2-Element 60-GHz-Band Circularly Polarized Post-Wall Waveguide Slot Array Antenna Loaded With Dipoles

In this paper, an <inline-formula> <tex-math notation="LaTeX">$8\times 2$ </tex-math></inline-formula>-element 60-GHz band circularly polarized post-wall waveguide slot array antenna loaded with dipoles is proposed. The antenna is composed of a feeding circuit, radiating slots on radiating waveguides, and dipoles for polarization conversion. By integrating the feeding circuit and the radiating waveguides into a single dielectric layer, the total number of dielectric layers is reduced to two which greatly increases ease of mass production. The feeding circuit divides power into two and feeds the two radiating waveguides from their center. <inline-formula> <tex-math notation="LaTeX">$8\times 2$ </tex-math></inline-formula> radiating elements are composed of a slot and a dipole placed on the radiating waveguides. The elements are designed by standing-wave excitation. The antenna is fabricated by printed circuit board technology and its dimensions are <inline-formula> <tex-math notation="LaTeX">$44.5\times 20.0\times2.16$ </tex-math></inline-formula> mm<sup>3</sup>. The measured results show a 2.1-dB axial ratio, 15.6-dBi gain, and 57.2% efficiency at 61.5 GHz. The proposed antenna realizes a circular polarized array antenna with the minimum number of dielectric layers and electric performance comparable to conventional antennas.
Cognitive load of learner control: extraneous or germane load?

Computer-based learning environments become more tailored when learners can exert control over one or more parts of the learning process. Learner control (LC) demands additional efforts of learners because, in addition to learning, they also have to monitor that learning. As a consequence, LC may cause additional cognitive load and even cognitive overload. The central question in this study is what type of cognitive load is induced by LC and whether the experienced load is related to learning outcomes. For this study, half of the students had control over task selection, while the other half had not. Within each condition, students were assigned to a single treatment, with the primary task to solely focus on the learning content, and a dual treatment, comprising a primary task and a secondary task. The results indicate that LC did not impose higher cognitive load as measured by secondary task scores and mental effort ratings.
Comparing Mattis Dementia Rating Scale – initiation / perseveration subset and frontal assessment battery in stroke associated with small vessel disease

Forty-two controls and 32 patients with stroke associated with small vessel disease (SSVD) were administered the Mattis Dementia Rating Scale Initiation / Perseveration subset (MDRS I/P) and Frontal Assessment Battery (FAB). Both tests showed comparably good ability in Receiver Operating Characteristics curves analysis (AUCMDRS I/P = 0.887; AUC FAB = 0.854, p = .833) in discriminating between controls and patients and correctly classified over 78% of subjects. Verbal fluency and motor programming contributed most to the discriminating power in the two tests. The MDRS I/P and FAB are useful in discriminating between controls and SSVD patients in a hospital setting.
Factors influencing students' perceptions of their teachers' interpersonal behaviour: A multilevel analysis

This study investigates which student, teacher and class characteristics are associated with students' perceptions of their science teachers' interpersonal behaviour. Using the Questionnaire on Teacher Interaction (QTI), two important dimensions of teacher interpersonal behaviour were investigated: influence (dominance vs. submission) and proximity (cooperation vs. opposition). Earlier work with the QTI in the USA and The Netherlands has shown that, in those countries, several factors affect students’ perceptions of their teachers. These factors include student and teacher gender, student and teacher ethnic background, student age, teacher experience, class size, student achievement and subject. It has been found that each of these variables has a distinctive effect, but also that they interact with each other when determining students' perceptions. For the present study, an analysis was performed on a large Australian QTI data set of secondary science teachers and their students. QTI dimension scores were examined against factors such as: gender, class size and subject. To investigate separate and combined effects of variables, a hierarchical analysis of variance (distinguishing between the school, class and student level) was conducted. This paper reports for the first time on the effect sizes and variance explained by these variables with respect to the Australian context.
Streaming XPath Subquery Evaluation

We describe a method for the streaming evaluation of XPath queries that have subqueries in predicates. Our method rewrites XPath queries into a set of predicate-free labeled linear-form expressions (LFEs). These LFEs are used to generate a pushdown transducer that enables efficient management of a buffer and hierarchical index at runtime. To the best of our knowledge, our method is the first to support XPath subqueries in a streaming environment. Our method also provides optimal buffering, minimum-latency output, and optimal predicate evaluation. The method has been fully implemented and publicly released in the XSQ system. We present an experimental study of XSQ and related systems on both real-life and synthetic datasets, and investigate how subqueries and other features affect the performance of these systems.
A location based QoS routing protocol for ad hoc networks

An ad hoc system with high topology changing rate makes routing extremely unstable. However stability is an important issue, especially for designing a routing with QoS provision. Recently, the availability of small, inexpensive, and low-power GPS receivers realizes location based routing for ad hoc networks. With the help of location information, the routing stability is significantly improved. The paper investigates the QoS routing problem in ad hoc networks. We propose a location based routing protocol with QoS provision. The proposed scheme, named QoS-GRID, considers a two-tier-grid system configuration to reduce each mobile transmission power so as to enhance the bandwidth utilization. Simulation results show that QoS-GRID establishes a stable QoS guaranteed route and meanwhile saves bandwidth.
Artificial selection for determinate growth habit in soybean

Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas Glycine soja, the wild progenitor of soybean, is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype, but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However, the GmTfl1 homeolog, despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1, appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
Altered Amplitude of Low-Frequency Fluctuation Induced by Acupuncture at Baihui Acupoint: A Pilot Functional MRI Study

Baihui (GV20), an important acupoint of the Governor Vessel according to the traditional Chinese medicine (TCM) theory of acupuncture, is usually used for treatments of psychiatric disorders. However, studies about relationships between the brain activities and GV20 are limited. In the present study, we thereby tried to investigate specific pattern of brain activities induced by electroacupuncture stimulation (EAS) at GV20. Thirty three healthy subjects were enrolled in this study for MRI scanning. Each subject underwent EAS at GV20 and at sham acupoint, separately. Based on sustained effects of acupuncture, amplitude of low-frequency fluctuation and fractional amplitude of low-frequency fluctuation (ALFF/fALFF) methods were used to examine different ALFF and fALFF patterns of the whole brain induced by GV20 with comparison to the ones induced by sham acupoint. Results showed that GV20 induced altered ALFF/fALFF in the brain regions, including the medial prefrontal cortex (mPFC), orbital frontal cortex (OFC), dorsolateral prefrontal cortex (dlPFC) and middle cingulate cortex (MCC), temporal cortex (TC), supplementary motor area (SMA), precuneus, thalamus, hippocampus (HIPP), insula, putamen and cerebellum compared to sham acupoint. Our findings might present the specific neural responses to EAS at GV20 using ALFF and fALFF methods, and may further provide preliminary evidence for understanding the mechanisms of GV20.