Miracle-dz/UniFAR-FTUs huggingface dataset:
De Novo Assembly and Discovery of Genes That Are Involved in Drought Tolerance in Tibetan Sophora moorcroftiana

Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including ‘response to water ‘stimulus’ and ‘response to water deprivation’. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as ‘metabolic pathways’ and ‘plant hormone signal transduction’. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.
Improving the performance of quality-adaptive video streaming over multiple heterogeneous access networks

Devices capable of connecting to multiple, overlapping networks simultaneously are becoming increasingly common. For example, most laptops are equipped with LAN- and WLAN-interfaces, and smart phones can typically connect to both WLANs and 3G mobile networks. At the same time, streaming high-quality video is becoming increasingly popular. However, due to bandwidth limitations or the unreliable and unpredictable nature of some types of networks, streaming video can be subject to frequent periods of rebuffering and characterised by a low picture quality. In this paper, we present a client-side request scheduler that distributes requests for the video over multiple heterogeneous interfaces simultaneously. Each video is divided into independent segments with constant duration, enabling segments to be requested over separate links, utilizing all the available bandwidth. To increase performance even further, the segments are divided into smaller subsegments, and the sizes are dynamically calculated on the fly, based on the throughput of the different links. This is an improvement over our earlier subsegment approach, which divided segments into fixed size subsegments. Both subsegment approaches were evaluated with on-demand streaming and quasi-live streaming. The new subsegment approach reduces the number of playback interruptions and improves video quality significantly for all cases where the earlier approach struggled. Otherwise, they show similar performance.
Robust continuous speech recognition through combination of invariant-feature based systems

In the recent years, different types of invariant features have been proposed which promise to improve the robustness of speech recognition systems in mismatching training-test conditions with respect to the mean vocal tract lengths. Many state-of-the-art systems make use of system combination. By considering speech recognition systems with different front ends, this paper investigates whether the system combination of standard-feature and invariant-feature based systems with ROVER yields improvements in accuracy. Results show that the combination of the considered systems leads to clear accuracy improvements. An error analysis also shows that the considered invariant features carry different types of information than the standard ones. The performance achieved with our system combination is in the range of what the best systems achieve in literature, although our approach does not yet include discriminative training or heteroscedastic feature transformation.
Global Hypomethylation (LINE-1) and Gene-Specific Hypermethylation (GSTP1) on Initial Negative Prostate Biopsy as Markers of Prostate Cancer on a Rebiopsy

Purpose: Men at risk of missed prostate cancer on a negative biopsy often undergo a rebiopsy. We evaluated whether global hypomethylation, measured through LINE-1 methylation, and GSTP1 hypermethylation on a negative biopsy are associated with subsequent prostate cancer diagnosis. Experimental Design: We performed a case–control study nested in an unselected series of 737 men who received at least two prostate biopsies at least three months apart at the Molinette Hospital (Turin, Italy). Two pathology wards were included for replication purposes. The study included 67 cases and 62 controls in Ward 1 and 62 cases and 66 controls in Ward 2. We used pyrosequencing to analyze LINE-1 and GSTP1 methylation in the negative biopsies. Odds ratios (OR) of prostate cancer diagnosis were estimated using conditional logistic regression. Results: After mutual adjustment, GSTP1 hypermethylation was associated with an OR of prostate cancer diagnosis of 5.1 (95% confidence interval: 1.7–14.9) in Ward 1 and 2.0 (0.8–5.3) in Ward 2, whereas an association was suggested only for low LINE-1 methylation levels (<70% vs. 70%–74%) with an OR of 2.1 (0.5–9.1) in Ward 1 and 1.6 (0.4–6.1) in Ward 2. When the two wards were combined the association was stronger for tumors with Gleason score ≥4+3 [GSTP1 hypermethylation: 9.2 (2.0–43.1); LINE-1 (<70% vs. 70%–74%): 9.2 (1.4–59.3)]. GSTP-1 alone improved the predictive capability of the model (P = 0.007). Conclusions: GSTP1 hypermethylation on a negative biopsy is associated with the risk of prostate cancer on a rebiopsy, especially of high-grade prostate cancer. Consistent results were found only for extremely low LINE-1 methylation levels. Clin Cancer Res; 22(4); 984–92. ©2015 AACR.
Essential Matrix Estimation Using Adaptive Penalty Formulations

Given six or more pairs of corresponding points on two calibrated images, existing schemes for estimating the essential matrix (EsM) use some manifold representation to tackle the non-convex constraints of the problem. To the best of our knowledge, no attempts were made to use the more straightforward approach of integrating the EsM constraint functions directly into the optimization using Adaptive Penalty Formulations (APFs). One possible reason is that the constraints characterizing the EsM are nonlinearly dependent and their number exceeds the number of free parameters in the optimization variable. This paper presents an iterative optimization scheme based on penalty methods that integrates the EsM constraints into the optimization without the use of manifold-based techniques and differential geometry tools. The scheme can be used with algebraic, geometric, and/or robust cost functions. Experimental validations using synthetic and real data show that the proposed scheme outperforms manifold-based algorithms with either global or local parametrizations.
Multiple confusion network application in MT system combination

System combination has emerged as a powerful method for machine translation (MT). In the construction of word level confusion network (CN), the alignment and skeleton selection are two key issues of system combination. The paper introduces multi-CN for solving skeleton selection. We fail to yield the better performance through using simple prior score as CN-based feature, so we introduce more sophisticated CN-based and consensus-decoding-based features into combination framework to test multi-CN's validity. The approaches of multi-CN are shown to be superior to single-CN in the setting of the Chinese-to-English track of the 2008 NIST Open MT evaluation.
Developing Gratitude in Children and Adolescents

This important and timely volume provides the conceptual framework for studying the development of gratitude, with a comprehensive and international set of authors approaching the topic from philosophical, psychological, and educational perspectives. The first section provides the theoretical underpinnings for the study of gratitude as a virtue. In the next section, the authors examine the ways in which gratitude develops, including key cross-cultural variations and some possible effects of its development. The final section then considers the links between parent and child gratitude and the ways in which parents and teachers can help to encourage gratitude, both in their everyday practices and by using literary texts. Coming Soon!
Beginning teacher induction in secondary schools: A best practice case study

Beginning teacher induction is becoming an increasingly popular process in acculturating teachers to their new careers. The problems that teachers face early in their careers are well known, and effective and ongoing induction is one of the foremost practices for alleviating the pressures that teachers face early in their careers. While induction practices have become more common in recent years, there are still no mandated structures for inducting teachers into the profession throughout Australia. In a collective case study of six different programs in independent schools in Sydney, Australia, the author showcases one case in particular that illustrated best practice when matched against other wellknown, successful international programs. In the current article the induction program is viewed in light of best practice internationally, and best practice criteria that have been ascertained from a selection of local, national and international reports and an international review of induction programs. The article showcases what best practice looks like from the perspective of the teachers who have undertaken the program and the school leadership who implemented the program.
Cuts3vm: a fast semi-supervised svm algorithm

Semi-supervised support vector machine (S3VM) attempts to learn a decision boundary that traverses through low data density regions by maximizing the margin over labeled and unlabeled examples. Traditionally, S3VM is formulated as a non-convex integer programming problem and is thus difficult to solve. In this paper, we propose the cutting plane semi-supervised support vector machine (CutS3VM) algorithm, to solve the S3VM problem. Specifically, we construct a nested sequence of successively tighter relaxations of the original S3VM problem, and each optimization problem in this sequence could be efficiently solved using the constrained concave-convex procedure (CCCP). Moreover, we prove theoretically that the CutS3VM algorithm takes time O(sn) to converge with guaranteed accuracy, where n is the total number of samples in the dataset and s is the average number of non-zero features, i.e. the sparsity. Experimental evaluations on several real world datasets show that CutS3VM performs better than existing S3VM methods, both in efficiency and accuracy.
Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock

Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.
Conversational Databases: Explaining Structured Queries to Users

Many applications offer a form-based environment for na\"{\i}ve users for accessing databases without being familiar with the database schema or a structured query language. Do-It-Yourself, database-driven web application platforms empower non-programmers to rapidly create applications. Users interactions are translated to structured queries and executed. However, as a user is unlikely to know the underlying semantic connections among the fields presented in a form, it is often useful to provide her with some feedback about the queries built without exposing her to the underlying query language, in order to assist her in forming queries correctly. Explaining queries may be also useful for users who explicitly use a structured query language for verification or debugging purposes. In this paper, we take a graph-based approach to the query translation problem. We represent various forms of structured queries as directed graphs and we annotate the graph edges with template labels using an extensible template mechanism. We present different graph traversal strategies for efficiently exploring these graphs and composing textual query descriptions. Finally, we present experimental results for the efficiency and effectiveness of the proposed methods.
Long-term effect of ropivacaine nanoparticles for sciatic nerve block on postoperative pain in rats

Purpose The analgesic effect of ropivacaine (Rop) for nerve block lasts only ~3–6 hours for single use. The aim of this study was to develop long-acting regional anesthetic Rop nanoparticles and investigate the effects of sciatic nerve block on postoperative pain in rats. Materials and methods Rop nanoparticles were developed using polyethylene glycol-co-polylactic acid (PELA). One hundred and twenty adult male Wistar rats were randomly divided into four groups (n=30, each): Con (control group; 0.9% saline, 200 µL), PELA (PELA group; 10 mg), Rop (Rop group; 0.5%, 200 µL), and Rop-PELA (Rop-PELA group; 10%, 10 mg). Another 12 rats were used for the detection of Rop concentration in plasma. The mechanical withdrawal threshold and thermal withdrawal latency were measured at 2 hours, 4 hours, 8 hours, 1 day, 2 days, 3 days, 5 days, and 7 days after incision. The expression of c-FOS was determined by immunohistochemistry at 2 hours, 8 hours, 48 hours, and 7 days. Nerve and organ toxicities were also evaluated at 7 days. Results The duration of Rop absorption in the plasma of the Rop-PELA group was longer (>8 hours) than that of the Rop group (4 hours). Mechanical withdrawal threshold and thermal withdrawal latency in the Rop-PELA group were higher than that in other groups (4 hours–3 days). c-FOS expression in the Rop-PELA group was lower than that in the control group at 2 hours, 8 hours, and 48 hours and lower than that in the Rop group at 8 hours and 48 hours after paw incision. Slight foreign body reactions were observed surrounding the sciatic nerve at 7 days. No obvious pathophysiological change was found in the major organs after Rop-PELA administration at 7 days. Conclusion Rop-PELA provides an effective analgesia for nerve block over 3 days after single administration, and the analgesic mechanism might be mediated by the regulation of spinal c-FOS expression. However, its potential long-term tissue toxicity needs to be further investigated.
Cranial Kinesis in Dinosaurs: Intracranial Joints, Protractor Muscles, and Their Significance for Cranial Evolution and Function in Diapsids

Abstract Different forms of intracranial mobility, including streptostyly, pleurokinesis, and prokinesis, have been postulated for many dinosaurs. The basis for inferring kinesis typically has included the presence of presumably synovial intracranial joints (otic and basal joints) and various ad hoc 'sliding joints' (many without modern parallels), whereas the protractor musculature that would have powered movement at these joints has received little attention. No study has reviewed the evidence underlying these inferences, and the functional mechanisms and evolution of kinesis among dinosaurs have remained unclear. We analyzed the relevant musculoskeletal structures in extant diapsids and extinct dinosaurs to evaluate in general the morphological support for inferences of cranial kinesis in dinosaurs. Four criteria (synovial otic joints, synovial basal joints, protractor muscles, and permissive kinematic linkages) were considered necessary but individually insufficient for the inference of kinesis. Assessing these criteria across dinosaurs reveals that synovial otic and basal joints are almost universally present (even in widely acknowledged akinetic taxa), and most taxa retained protractor musculature. However, unlike fully kinetic extant birds and squamates, almost all dinosaurs lacked the kinematic linkages that would have permitted movement (reduced palatal and temporal articulations, additional flexion zones). Thus, synovial basal and otic joints and protractor musculature are diapsid plesiomorphies, and, in the absence of permissive kinematic linkages, most formulations of nonavian dinosaur kinesis are currently problematic. Alternatively, persistent synovial joints may simply be cartilaginous sites that facilitate cranial growth during ontogeny.
Accuracy of Biometry for Intraocular Lens Implantation Using the New Partial Coherence Interferometer, AL-scan

Purpose To compare the refractive results of cataract surgery measured by applanation ultrasound and the new partial coherence interferometer, AL-scan. Methods Medical records of 76 patients and 104 eyes who underwent cataract surgery from January 2013 to June 2013 were retrospectively reviewed. Biometries were measured using ultrasound and AL-scan and intraocular lens power was calculated using the SRK-T formula. Automatic refraction examination was done 1 month after the operation, and differences between the ultrasound group and AL-scan group were compared and analyzed by mean absolute error. Results Mean axial length measured preoperatively by the ultrasound method was 23.53 ± 1.17 mm while the lengths measured using the AL-scan were 0.03 mm longer than that of the ultrasound group (23.56 ± 1.15 mm). However, there was not a significant difference in this finding (p = 0.638). Mean absolute error was 0.34 ± 0.27 diopters in the ultrasound group and 0.36 ± 0.31 diopters in AL-scan group, which showed no significant difference (p = 0.946) in precision of predicting postoperative refraction. Conclusions Although the difference was not statistically significant, intraocular lens calculations done by the AL-scan were nearly similar in predicting postoperative refraction compared to those of applanation ultrasound, however more precise measurements may be obtained if the axial length is longer than 24.4 mm. Except in the case of opacity in the media, which makes obtaining measurements with the AL-scan difficult, AL-scan could be a useful biometry in cataract surgery.
A Projection-Based Multi-view Time-multiplexed Autostereoscopic 3D Display System

This paper presents our implementation of a multi-view autostereoscopic 3D display system by using time-multiplexing approach, digital micro-mirror devices (DMD), and the optical Wedgereg. The whole system consists of three major parts: high frame rate DMD projector, an active shutter, and an optical Wedgereg. This research investigates and develops the approaches to interface and control DMDs at very high bit rates and ultra-high frame rates to drive a novel flicker-free 3D flat panel device, with a wide viewing area and without need of special viewing glasses or head-tracking system. It needs to design a digital interface circuit capable of receiving video image data in a conventional format and translating it into a form appropriate for display on a DMD light modulator. This approach differs from existing ones in that it facilitates the modulation of the DMD to achieve much high frame rates, though with a trade-off in greyscale resolution. The outcomes of this research will have the great potential for commercialising the autostereoscopic display systems
On the stiffening effect of magneto-rheological elastomers

Magneto-rheological elastomers (MREs), a class of polymer-based composites with dispersed magnetic filler particles, are known for their tunable stiffness. The magnetic-field-induced stiffening effect, namely the magneto-rheological (MR) effect, is often attributed to the magnetic dipolar interaction. The direct attraction between two magnetic dipoles could increase the shear modulus of the material, but not the tensile modulus, while experiments showed increases in both. In this paper, we investigate the possible mechanisms of the MR effect using two different methods: a dipolar interaction model and a micromechanics model based on a continuum field theory. It is found that while the magnetic dipolar interaction is indeed the major cause of the MR effect, the specific microstructure of an MRE is the key to the modulus increase. An MRE of straight chains has a negative MR effect in tension, but one of wavy chains can have tensile modulus increase under a magnetic field. While the chain-chain magnetic interaction is shown to be insignificant, the filler concentration plays an important role on the strength of MR effect, just as observed in experiments.
Virtual Page Placement Guided by DRAM Locality and Latency

The organization of modern DRAM containing multiple banks per device or module allows for non-uniform access latencies. By including the physical organization of the memory system in virtual page allocation algorithms, program execution time can be reduced through aggregate changes in memory access latency. Four virtual page allocation mechanisms are incorporated into the Linux 2.6 kernel and evaluated for impact upon benchmark execution times. These modified kernels are able to better utilize the available parallelism and multiple latency states of DRAM in the main memory system. Each of these mechanisms uses a different approach, or a combination of approaches, to distribute virtual pages across the available DRAM banks. An analysis utilizing several benchmark suites demonstrates that these modifications to page placement algorithms provide a moderate increase in performance in most benchmarks. These modified virtual page allocation mechanisms require limited changes to the code base, with no modifications to the hardware.