Miracle-dz/UniFAR-FTUs huggingface dataset:
De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development

Natural stocks of Japanese eel (Anguilla japonica) have decreased drastically because of overfishing, habitat destruction, and changes in the ocean environment over the past few decades. However, to date, artificial mass production of glass eels is far from reality because of the lack of appropriate feed for the eel larvae. In this study, wild glass eel, leptocephali, preleptocephali, and embryos were collected to conduct RNA-seq. Approximately 279 million reads were generated and assembled into 224,043 transcripts. The transcript levels of genes coding for digestive enzymes and nutrient transporters were investigated to estimate the capacities for nutrient digestion and absorption during early development. The results showed that the transcript levels of protein digestion enzymes were higher than those of carbohydrate and lipid digestion enzymes in the preleptocephali and leptocephali, and the transcript levels of amino acid transporters were also higher than those of glucose and fructose transporters and the cholesterol transporter. In addition, the transcript levels of glucose and fructose transporters were significantly raising in the leptocephali. Moreover, the transcript levels of protein, carbohydrate, and lipid digestion enzymes were balanced in the glass eel, but the transcript levels of amino acid transporters were higher than those of glucose and cholesterol transporters. These findings implied that preleptocephali and leptocephali prefer high-protein food, and the nutritional requirements of monosaccharides and lipids for the eel larvae vary with growth. An online database (http://molas.iis.sinica.edu.tw/jpeel/) that will provide the sequences and the annotated results of assembled transcripts was established for the eel research community.
When do microswimmers exit the Stokes regime?

We compare fully-resolved, 3D lattice Boltzmann (LB) simulations of a three sphere microswimmer to analytical calculations, and show thereby that (i) LB simulations reproduce the motion very well in the Stokes regime, and (ii) the swimmer exits this regime at Reynolds numbers $Re \sim 10^{-2}$, significantly lower than previously realised. Below this $Re$ value Stokesian theory describes the motion accurately, but fails above it due to inertial effects. In the latter case, the swimmer's relaxation matches that of an underdamped harmonic oscillator, and this specifies its effective hydrodynamic radius in a narrow $Re$ range, as we show by calculating the radius analytically. The method can be used to determine the limit of the Stokes regime and the effective radius for a general mechanical microswimmer.
A Prospective Assessment of SRS-24 Scores After Endoscopic Anterior Instrumentation for Scoliosis

Study Design. Prospective clinical case series. Objective. To evaluate the clinical outcome of anterior endoscopic instrumention for scoliosis using the SRS-24 questionnaire and to examine how these scores change over a 2-year follow-up period. Summary of Background Data. Anterior endoscopic instrumentation correction has several advantages compared with open procedures. However, the clinical results of this technique using a validated outcome measure have rarely been reported in the literature. Methods. A total of 83 consecutive patients underwent endoscopic anterior instrumentation performed at a single unit. Patients completed the SRS-24 questionnaire before surgery and at 3, 6, 12, and 24 months after surgery. The SRS-24 scores were compared between each of the follow-up intervals. Results. The pain, general self-image, and function from back condition domains improved after surgery (P < 0.05). Activity level significantly improved between 3 and 6 months, and both function domains improved between 6 and 12 months (P < 0.05). None of the domains increased significantly after 1 year. Conclusions. Endoscopic anterior instrumentation for scoliosis significantly improved pain, self-image, and function. The greatest improvement in function occurred between 6 and 12 months after surgery. The SRS-24 scores at 1 year from surgery may provide a good indicator of patient outcome in the long-term.
Intestinal Nematode Infection Ameliorates Experimental Colitis in Mice

ABSTRACT Epidemiological studies suggest that inflammatory bowel disease (IBD) is common in developed countries and rare in countries where intestinal nematode infections are common. T cells are critical in many immune responses, including those associated with IBD and nematode infection. Among the distinct T helper (Th) cell subsets, Th1-type immune response is predominantly associated with Crohn's disease, while many nematode infections generate a strong Th2 response. The reciprocal cross regulation between Th1 and Th2 cells suggests that generation of a Th2 response by nematodes could prevent or reduce the effects of Th1-mediated diseases. In the present study, we investigated the effect of polarizing the immune response toward the Th2 type, using intestinal nematode infection, on subsequent experimental colitis. Mice were infected with the intestinal nematode Trichinella spiralis and allowed to recover before colitis was induced with dinitrobenzene sulfonic acid. The mice were sacrificed postcolitis to assess colonic damage macroscopically, histologically, and by myeloperoxidase (MPO) activity and Th cytokines. Prior nematode infection reduced the severity of colitis both macroscopically and histologically together with a decreased mortality and was correlated with a down-regulation of MPO activity, Th1-type cytokine expression in colonic tissue, and emergence of a Th2-type immune response. These results indicate a protective role of nematode infection in Th1 cell-driven inflammation and prompt consideration of a novel therapeutic strategy in IBD based on immunological distraction.
2 FDI INFLOW AND ICT EXPANSION 2 . 1 Impact of FDI Inflow and ICT Expansion in Developing Countries

This study investigates the impact of foreign direct investment (FDI) inflow and trade openness on the expansion of information and communication technologies (ICTs) for the period of 1996 to 2005, in the Asia-Pacific and Middle East regions. Asia-Pacific countries cited in this study are: China (mainland & Hong Kong), Indonesia, Malaysia, Philippines, Singapore, Thailand and Vietnam. The Middle Eastern countries cited include: Bahrain, Iran, Jordan, Kuwait, Oman, Qatar, Saudi Arabia, Syria and the United Arab Emirates (UAE). The results of regression analyses conducted indicate that while dissimilarities exist among the countries included in this study in terms of their level of socio-economic and political development, factors such as trade openness, education and the growth of GDP had a positive impact on their ICT development. While FDI inflow had positive impact on the expansion of ICTs on Asia-Pacific countries its impact on Middle Eastern countries was not statistically significant. The study results also show that governmental intervention in economic activities has a negative impact on ICT expansion in both regions. In the Middle East, regional conflict imposes additional negative impact on FDI inflow and trade openness and consequently, ICT expansion. The regression results show that those countries that implemented liberalization of their ICT sector were able to not only reduce the digital divide with other developed countries, but also increase their operations in both local and global markets.
A Caching Approach to Reduce Communication in Graph Search Algorithms

In many scientific and computational domains, graphs are used to represent and analyze data. Such graphs often exhibit the characteristics of small-world networks: few high-degree vertexes connect many low-degree vertexes. Despite the randomness in a graph search, it is possible to capitalize on this characteristic and cache relevant information in high-degree vertexes. We applied this idea by caching remote vertex ids in a parallel breadth-first search implementation, and demonstrated 1.6x to 2.4x speedup over the reference implementation on 64 to 1024 cores. We proposed a system design in which resources are dedicated exclusively to caching, and shared among a set of nodes. Our evaluation demonstrates that this design has the potential to reduce communication and improve performance over large scale systems. Finally, we used a memcached system as the cache server finding that a generic protocol that does not match the usage semantics may hinder the potential performance improvements.
Coordinated autonomous vehicle formations: decentralization, control synthesis and optimization

This paper describes a novel methodology for high-level control and coordination of autonomous vehicle formations and its demonstration on high fidelity models of the organic air vehicle developed at Honeywell Laboratories. The scheme employs decentralized receding horizon controllers that reside on each vehicle to achieve coordination among team members. An appropriate graph structure describes the underlying communication topology between the vehicles. On each vehicle, information about neighbors is used to predict their behavior so that conflict-free trajectories that maintain coordination and achieve team objectives result. When feasibility of the decentralized control is lost, collision avoidance is ensured by invoking emergency maneuvers that are computed via invariant set theory
Improvements in Hip Flexibility Do Not Transfer to Mobility in Functional Movement Patterns

Abstract Moreside, JM and McGill, SM. Improvements in hip flexibility do not transfer to mobility in functional movement patterns. J Strength Cond Res 27(10): 2635–2643, 2013—The purpose of this study was to analyze the transference of increased passive hip range of motion (ROM) and core endurance to functional movement. Twenty-four healthy young men with limited hip mobility were randomly assigned to 4 intervention groups: group 1, stretching; group 2, stretching plus hip/spine disassociation exercises; group 3, core endurance; and group 4, control. Previous work has documented the large increase in passive ROM and core endurance that was attained over the 6-week interventions, but whether these changes transferred to functional activities was unclear. Four dynamic activities were analyzed before and after the 6-week interventions: active standing hip extension, lunge, a standing twist/reach maneuver, and exercising on an elliptical trainer. A Vicon motion capture system collected body segment kinematics, with hip and lumbar spine angles subsequently calculated in Visual 3D. Repeated measures analyses of variance determined group effects on various hip and spine angles, with paired t-tests on specific pre/post pairs. Despite the large increases in passive hip ROM, there was no evidence of increased hip ROM used during functional movement testing. Similarly, the only significant change in lumbar motion was a reduction in lumbar rotation during the active hip extension maneuver (p < 0.05). These results indicate that changes in passive ROM or core endurance do not automatically transfer to changes in functional movement patterns. This implies that training and rehabilitation programs may benefit from an additional focus on "grooving" new motor patterns if newfound movement range is to be used.
Efficient in-memory top-k document retrieval

For over forty years the dominant data structure for ranked document retrieval has been the inverted index. Inverted indexes are effective for a variety of document retrieval tasks, and particularly efficient for large data collection scenarios that require disk access and storage. However, many efficiency-bound search tasks can now easily be supported entirely in memory as a result of recent hardware advances. In this paper we present a hybrid algorithmic framework for in-memory bag of-words ranked document retrieval using a self-index derived from the FM-Index, wavelet tree, and the compressed suffix tree data structures, and evaluate the various algorithmic trade-offs for performing efficient queries entirely in-memory. We compare our approach with two classic approaches to bag-of-words queries using inverted indexes, term-at-a-time (TAAT) and document-at-a-time (DAAT) query processing. We show that our framework is competitive with state-of-the-art indexing structures, and describe new capabilities provided by our algorithms that can be leveraged by future systems to improve effectiveness and efficiency for a variety of fundamental search operations.
ATAC: A 1000-core cache-coherent processor with on-chip optical network

Based on current trends, multicore processors will have 1000 cores or more within the next decade. However, their promise of increased performance will only be realized if their inherent scaling and programming challenges are overcome. Fortunately, recent advances in nanophotonic device manufacturing are making CMOS-integrated optics a reality—interconnect technology which can provide significantly more bandwidth at lower power than conventional electrical signaling. Optical interconnect has the potential to enable massive scaling and preserve familiar programming models in future multicore chips. This paper presents ATAC, a new multicore architecture with integrated optics, and ACKwise, a novel cache coherence protocol designed to leverage ATAC's strengths. ATAC uses nanophotonic technology to implement a fast, efficient global broadcast network which helps address a number of the challenges that future multicores will face. ACKwise is a new directory-based cache coherence protocol that uses this broadcast mechanism to provide high performance and scalability. Based on 64-core and 1024-core simulations with Splash2, Parsec, and synthetic benchmarks, we show that ATAC with ACKwise out-performs a chip with conventional interconnect and cache coherence protocols. On 1024-core evaluations, ACKwise protocol on ATAC outperforms the best conventional cache coherence protocol on an electrical mesh network by 2.5x with Splash2 benchmarks and by 61% with synthetic benchmarks.
A flexible approach for extracting metadata from bibliographic citations

In this article we present FLUX-CiM, a novel method for extracting components (e.g., author names, article titles, venues, page numbers) from bibliographic citations. Our method does not rely on patterns encoding specific delimiters used in a particular citation style. This feature yields a high degree of automation and flexibility , and allows FLUX-CiM to extract from citations in any given format. Differently from previous methods that are based on models learned from user-driven training, our method relies on a knowledge base automatically constructed from an existing set of sample metadata records from a given field (e.g., computer science, health sciences , social sciences, etc.). These records are usually available on the Web or other public data repositories. To demonstrate the effectiveness and applicability of our proposed method, we present a series of experiments in which we apply it to extract bibliographic data from citations in articles of different fields. Results of these experiments exhibit precision and recall levels above 94% for all fields, and perfect extraction for the large majority of citations tested. In addition, in a comparison against a state-of-the-art information-extraction method, ours produced superior results without the training phase required by that method. Finally, we present a strategy for using bib-liographic data resulting from the extraction process with FLUX-CiM to automatically update and expand the knowledge base of a given domain. We show that this strategy can be used to achieve good extraction results even if only a very small initial sample of bibliographic records is available for building the knowledge base.
Validation of the Teacher Rating of Academic Achievement Motivation

The Teacher Rating of Academic Achievement Motivation (TRAAM) is a scale in development designed to measure children's academic motivation and to be used in a multifactored assessment. This study examined construct and criterion-related validity of the TRAAM with an elementary school sample. Gender and grade differences in academic motivation also were examined. Construct validity was established by investigating the relationship of the TRAAM with the Scale of Instrinsic vs. Extrinsic Orientation in the Classroom (SIEOC), the Children's Academic Intrinsic Motivation Inventory (CAIMI), and the Social Skills Rating System Teacher version, elementary level (SSRS-T). Criterion-related validity of the scale was demonstrated by using the TRAAM factors and Total Score, the SIEOC and CAIMI subscales, and the SSRS-T Social Skills subscales and Academic Competence domain to predict problem behaviors and academic achievement. A discussion of the TRAAM's limitations concludes the article.
Effect of reactive pharmacy intervention on quality of hospital prescribing.

OBJECTIVE--To evaluate the medical impact of reactive pharmacy intervention. DESIGN--Analysis of all interventions during 28 days by all 35 pharmacists in hospitals in Nottingham. SETTING--All (six) hospitals in the Nottingham health authority (a teaching district), representing 2530 mainly acute beds, 781 mental illness beds, and 633 mainly health care of the elderly beds. PATIENTS--Hospital inpatients and outpatients. INTERVENTIONS--Recording of every important intervention made by pharmacists to prescriptions for both inpatients and outpatients when they perceived inadequacies of drug prescription or administration, including characterisation of the problem, coding of outcome, recording of time taken to initiate and resolve intervention, and grade of prescribing doctor. The problems were independently assessed for their potential to cause medical harm. RESULTS--769 Interventions (about 2.9% of prescriptions) were made, of which 60 concerned prescriptions rated as having a major potential for medical harm. The commonest problems concerned dosage, which was wrong in 280 prescriptions (102 for antibiotics) and not stated in 50 (one for antibiotics), especially those associated with a major potential for medical harm (32 prescriptions). These concerned sedatives; analgesics; cardiovascular drugs or diuretics; and iron, vitamin, or mineral preparations. Also common were overprolonged prescription of antibiotics (48 prescriptions), confusion of drug names (nine), and inadvertent coprescription of excessive quantities of aspirin or paracetamol in plain and compound preparations (seven). The pharmacist's recommendation was accepted in 639 instances (86%), and the prescription was altered in 575, leading to an appreciable (246 cases) or minor (231 cases) improvement. Interventions had little effect on costs; 427/646 had no effect and 130 produced savings less than 50p. Pharmacy intervention (730/769 interventions) occupied on average 41 minutes per pharmacist per week. CONCLUSIONS--Most reactive pharmacy interventions concerned prescribing errors with a limited potential for medical harm, but a small number of detected errors with a major potential for medical harm; cost savings were not appreciable.
InCtrl HD: Intuitive User Interface Control Using Wii Remote for High Definition Videoconferencing

There is an increasing rise in High Definition (HD) videoconferencing solutions, due to the increase in demand for HD media and the availability of inexpensive Internet services. However, there is a need for simpler but effective user interface (UI) design and devices so that nontechnical people will be able to use a videoconferencing system with minimal training. The objective of this paper was to develop an HD videoconferencing system - InCtrl HD - with an intuitive UI. A media streamer using HDV format and a media player was integrated to support an HD resolution of 1920x1080 pixels at 30 fps. The UI was designed so that it can be effectively controlled by the Nintendo Wii Remote (Wiimote), which is a wireless device that can act both as a remote and a mouse pointer. As an added feature, InCtrl HD can also support sending and receiving of an HD multicast stream. Quality of Experience (QoE) metrics such as end-to-end delay measurement, audiovisual and conversational quality were done to evaluate the performance of the system, while usability and task analysis tests were performed to evaluate the usability and ease of using the UI with the Wiimote as its control device. InCtrl HD was able to establish HD video calls, and effectively control a graphical UI using the Wiimote. InCtrl HD obtained scores higher than the acceptable scores, indicating that the system has acceptable usability and had successfully achieved its objectives.
Sex-Based Differences as a Predictor of Recovery Trajectories in Young Athletes After a Sports-Related Concussion

Background: To date, few studies have delineated clear sex-based differences in symptom resolution after a sports-related concussion (SRC), and equivocal results have been identified in sex-based differences on baseline assessments. Purpose: To assess whether female athletes displayed prolonged recovery and more symptoms at baseline and after an SRC compared with male athletes. Study Design: Cohort study; Level of evidence, 3. Methods: The current study assessed 135 male and 41 female athletes (10-18 years old) who participated in high-impact sports in metropolitan Atlanta middle and high schools. All athletes completed a baseline assessment and at least 1 postconcussion assessment from the Immediate Post-Concussion Assessment and Cognitive Testing battery. Longitudinal hierarchical linear modeling was employed to examine individual-level variables and their associations with adolescents’ rates of recovery in concussive symptoms after controlling for age and number of prior concussions. Results: Aggregate symptoms were rated as higher in female athletes compared with male athletes at baseline (mean ± SD: females, 13.49 ± 11.20; males, 4.88 ± 8.74; F(1,175) = 10.59, P < . 001) and immediately after a concussion (females: 16.75 ± 18.08; males: 10.58 ± 14.21; F(1,175) = 3.99, P = . 05). There were no group differences in the slope of recovery between male and female athletes, indicating generally similar trajectories of change for both groups. Post hoc analyses revealed higher baseline levels of migraine and neuropsychological symptoms in female athletes. Conclusion: Although female athletes in the current study reported increased symptoms, identical recovery patterns were observed in both sexes, suggesting that sex-based differences in concussion recovery are better explained by increased symptom frequency among female athletes when compared with their male counterparts.