Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel and Conserved Features of the Hox Cluster of Entoprocta (Kamptozoa)

Hox genes are highly conserved developmental genes involved in the patterning of the anterior-posterior axis of nearly all metazoan animals. While Hox genes have been characterized for many bilaterians, several cryptic taxa, often comprising microscopic specimens, have hitherto been neglected. We here present the first combined transcriptomic and genomic Hox gene study for Entoprocta (=Kamptozoa), a phylum of microscopic, sessile, tentacle-bearing animals with unresolved phylogenetic affinities. We identified 10 of the 11 Hox genes commonly found in other lophotrochozoans. The analyses of transcriptomic data of different developmental stages of three species (regenerating stages of the colonial species Pedicellina cernua, budding stages of the solitary species Loxosomella vivipara and embryos of the solitary species Loxosomella murmanica/atkinsae) yielded the Hox genes Labial, Hox3, Lox5, and Post2 in all species. Pb and Dfd were only found being expressed in the colonial species P. cernua. Lox4 was uniquely expressed in the solitary species L. vivipara and L. murmanica/atkinsae. Other homeobox genes belonging to the ANTP-class genes, e.g., ParaHox and NK-like genes, were also found. Thus, in addition to newly identified Hox genes (PceLox2-like & LviPost2-like), Entoporocta show the typical lophotrochozoan Hox pattern besides the loss of the posterior class Hox gene Post1.
Physiological Responses in Relation to Performance during Competition in Elite Synchronized Swimmers

Purpose We aimed to characterize the cardiovascular, lactate and perceived exertion responses in relation to performance during competition in junior and senior elite synchronized swimmers. Methods 34 high level senior (21.4±3.6 years) and junior (15.9±1.0) synchronized swimmers were monitored while performing a total of 96 routines during an official national championship in the technical and free solo, duet and team competitive programs. Heart rate was continuously monitored. Peak blood lactate was obtained from serial capillary samples during recovery. Post-exercise rate of perceived exertion was assessed using the Borg CR-10 scale. Total competition scores were obtained from official records. Results Data collection was complete in 54 cases. Pre-exercise mean heart rate (beats·min−1) was 129.1±13.1, and quickly increased during the exercise to attain mean peak values of 191.7±8.7, with interspersed bradycardic events down to 88.8±28.5. Mean peak blood lactate (mmol·L−1) was highest in the free solo (8.5±1.8) and free duet (7.6±1.8) and lowest at the free team (6.2±1.9). Mean RPE (0–10+) was higher in juniors (7.8±0.9) than in seniors (7.1±1.4). Multivariate analysis revealed that heart rate before and minimum heart rate during the routine predicted 26% of variability in final total score. Conclusions Cardiovascular responses during competition are characterized by intense anticipatory pre-activation and rapidly developing tachycardia up to maximal levels with interspersed periods of marked bradycardia during the exercise bouts performed in apnea. Moderate blood lactate accumulation suggests an adaptive metabolic response as a result of the specific training adaptations attributed to influence of the diving response in synchronized swimmers. Competitive routines are perceived as very to extremely intense, particularly in the free solo and duets. The magnitude of anticipatory heart rate activation and bradycardic response appear to be related to performance variability.
Bearded Reedlings Adjust Their Pair-Bond Behaviour in Relation to the Sex and Attractiveness of Unpaired Conspecifics

An individual's investment in mating or keeping a pair bond intact may be influenced not only by the attractiveness of its current mate, but also by that of other potential mates. In this study, we investigated the effect of relative attractiveness on pair-bond behaviour in bearded reedlings, Panurus biarmicus. We showed that mate attractiveness, in terms of beard length in males and tail length in females, influenced courtship behaviour when the pair was kept isolated. In the presence of a conspecific, contact initiations within a pair increased. This increment was mainly related to the sex of the unpaired conspecific, however, and less to differences in attractiveness between the current partner and the unpaired conspecific. Female contact initiations towards potential extra mates were independent of male attractiveness, whereas male contact behaviour was significantly influenced by female attractiveness. However, females displayed more contact initiations to their current mate when they were less attractive than the unpaired females. Males decreased their overtures towards other females with increasing attractiveness of their current mates. Overall, our results suggested that, when there was a risk of losing their mate, bearded reedlings adjust their pair-bond investment mainly in response to the presence or absence of a competitor, and fine-tune investment to a lesser extent in response to the attractiveness of that potential competitor.
Single-Channel Blind Separation Using Pseudo-Stereo Mixture and Complex 2-D Histogram

A novel single-channel blind source separation (SCBSS) algorithm is presented. The proposed algorithm yields at least three benefits of the SCBSS solution: 1) resemblance of a stereo signal concept given by one microphone; 2) independent of initialization and a priori knowledge of the sources; and 3) it does not require iterative optimization. The separation process consists of two steps: 1) estimation of source characteristics, where the source signals are modeled by the autoregressive process and 2) construction of masks using only the single-channel mixture. A new pseudo-stereo mixture is formulated by weighting and time-shifting the original single-channel mixture. This creates an artificial mixing system whose parameters will be estimated through our proposed weighted complex 2-D histogram. In this paper, we derive the separability of the proposed mixture model. Conditions required for unique mask construction based on maximum likelihood are also identified. Finally, experimental testing on both synthetic and real-audio sources is conducted to verify that the proposed algorithm yields superior performance and is computationally very fast compared with existing methods.
The complete mitochondrial genome of Octopus bimaculatus Verrill, 1883 from the Gulf of California

Abstract The complete mitochondrial genome of Octopus bimaculatus is 16 085 bp in length and includes 13 protein-codes genes, 2 ribosomal RNA genes, 22 transfers RNA genes, and a control region. The composition of genome is A (40.9%), T (34.7%), C (16.9%), and G (7.5%). The control region of O. bimaculatus contains a VNTR locus not present in the genomes from other octopus species. A phylogenetic analysis shows a closer relationship between the mitogenomes from O. bimaculatus and O. vulgaris.
A Model for the Size Distribution of Product from a Granulating Drum

Carefully controlled granulation experiments were carried out on a haematite ore with a wide size distribution (0-8mm) over a range of moisture contents. At any one moisture content, the finest size fractions could be classified solely as layering particles whilst the largest size fractions acted only as nuclei particles. Between these two extremes, a proportion of particles in any one size fraction behaved as nuclei particles, the remainder being layering particles. Hence each particle size fraction could he characterised by a partition coefficient. The partitioning of an individual size range between nuclei and adhering particles was shown to be dependent on the moisture content. For each moisture content, the partition curve could be modelled using a log-normal function. The variation of adhering layer mass with granule size was investigated and it was found that adhering layer thickness was approximately proportional to nuclei diameter at lower moisture contents. At higher moisture contents there was an optimum nuclei particle size for which the ratio of granule mass to total nuclei mass was a maximum.A population balance model to predict granule size distribution was developed and tested against experimental data. The important model parameters were those describing the particle partition curve. Excellent agreement was found between experimental and model predicted granule size distributions for the full range of moisture contents covered.
Interface Prostheses With Classifier-Feedback-Based User Training

It is evident that user training significantly affects performance of pattern-recognition-based myoelectric prosthetic device control. Despite plausible classification accuracy on offline datasets, online accuracy usually suffers from the changes in physiological conditions and electrode displacement. The user ability in generating consistent electromyographic (EMG) patterns can be enhanced via proper user training strategies in order to improve online performance. This study proposes a clustering-feedback strategy that provides real-time feedback to users by means of a visualized online EMG signal input as well as the centroids of the training samples, whose dimensionality is reduced to minimal number by dimension reduction. Clustering feedback provides a criterion that guides users to adjust motion gestures and muscle contraction forces intentionally. The experiment results have demonstrated that hand motion recognition accuracy increases steadily along the progress of the clustering-feedback-based user training, while conventional classifier-feedback methods, i.e., label feedback, hardly achieve any improvement. The result concludes that the use of proper classifier feedback can accelerate the process of user training, and implies prosperous future for the amputees with limited or no experience in pattern-recognition-based prosthetic device manipulation.
A Statistical NLP Approach for Feature and Sentiment Identification from Chinese Reviews

Existing methods for extracting features from Chinese reviews only use simplistic syntactic knowledge, while those for identifying sentiments rely heavily on a semantic dictionary. In this paper, we present a systematic technique for identifying features and sentiments, using both syntactic and statistical analysis. We firstly identify candidate features using a proposed set of common syntactic rules. We then prune irrelevant candidates with topical relevance scores below a cut-off point. We also propose an association analysis method based on likelihood ratio test to infer the polarity of opinion word. The sentiment of a feature is finally adjusted by analyzing the negative modifiers in the local context of the opinion word. Experimental re-sults show that our system performs significantly better than a well-known opinion mining system.
An Alignment-Free Approach for Eukaryotic ITS2 Annotation and Phylogenetic Inference

The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge. net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp. fungal isolate.
Index of cardiometabolic health: a new method of measuring allostatic load using electronic health records

Abstract Objective: We developed a measure of allostatic load from electronic medical records (EMRs), which we named “Index of Cardiometabolic Health” (ICMH). Methods: Data were collected from participants’ EMRs and a written survey in 2005. We computed allostatic load scores using the ICMH score and two previously described approaches. Results: We included 1865 employed adults who were 25–59 years old. Although the magnitude of the association was small, all methods of were predictive of SF-12 physical component subscales (all p < 0.001). Conclusion: We found that the ICMH had similar relationships with health-related quality of life as previously reported in the literature.
Chinese Word Sense Induction with Basic Clustering Algorithms

Word Sense Induction (WSI) is an important topic in natural langage processing area. For the bakeoff task Chinese Word Sense Induction (CWSI), this paper proposes two systems using basic clustering algorithms, k-means and agglomerative clustering. Experimental results show that k-means achieves a better performance. Based only on the data provided by the task organizers, the two systems get FScores of 0.7812 and 0.7651 respectively.
Developmental Localization and Methylesterification of Pectin Epitopes during Somatic Embryogenesis of Banana (Musa spp. AAA)

Background The plant cell walls play an important role in somatic embryogenesis and plant development. Pectins are major chemical components of primary cell walls while homogalacturonan (HG) is the most abundant pectin polysaccharide. Developmental regulation of HG methyl-esterification degree is important for cell adhesion, division and expansion, and in general for proper organ and plant development. Methodology/Principal Findings Developmental localization of pectic homogalacturonan (HG) epitopes and the (1→4)-β-D-galactan epitope of rhamnogalacturonan I (RG-I) and degree of pectin methyl-esterification (DM) were studied during somatic embryogenesis of banana (Musa spp. AAA). Histological analysis documented all major developmental stages including embryogenic cells (ECs), pre-globular, globular, pear-shaped and cotyledonary somatic embryos. Histochemical staining of extracellularly secreted pectins with ruthenium red showed the most intense staining at the surface of pre-globular, globular and pear-shaped somatic embryos. Biochemical analysis revealed developmental regulation of galacturonic acid content and DM in diverse embryogenic stages. Immunodots and immunolabeling on tissue sections revealed developmental regulation of highly methyl-esterified HG epitopes recognized by JIM7 and LM20 antibodies during somatic embryogenesis. Cell walls of pre-globular/globular and late-stage embryos contained both low methyl-esterified HG epitopes as well as partially and highly methyl-esterified ones. Extracellular matrix which covered surface of early developing embryos contained pectin epitopes recognized by 2F4, LM18, JIM5, JIM7 and LM5 antibodies. De-esterification of cell wall pectins by NaOH caused a decrease or an elimination of immunolabeling in the case of highly methyl-esterified HG epitopes. However, immunolabeling of some low methyl-esterified epitopes appeared stronger after this base treatment. Conclusions/Significance These data suggest that both low- and highly-methyl-esterified HG epitopes are developmentally regulated in diverse embryogenic stages during somatic embryogenesis. This study provides new information about pectin composition, HG methyl-esterification and developmental localization of pectin epitopes during somatic embryogenesis of banana.
Anisotropic, lightweight, strong, and super thermally insulating nanowood with naturally aligned nanocellulose

Researchers transformed natural wood into a super thermal insulation structural material with aligned cellulose nanofibers. There has been a growing interest in thermal management materials due to the prevailing energy challenges and unfulfilled needs for thermal insulation applications. We demonstrate the exceptional thermal management capabilities of a large-scale, hierarchal alignment of cellulose nanofibrils directly fabricated from wood, hereafter referred to as nanowood. Nanowood exhibits anisotropic thermal properties with an extremely low thermal conductivity of 0.03 W/m·K in the transverse direction (perpendicular to the nanofibrils) and approximately two times higher thermal conductivity of 0.06 W/m·K in the axial direction due to the hierarchically aligned nanofibrils within the highly porous backbone. The anisotropy of the thermal conductivity enables efficient thermal dissipation along the axial direction, thereby preventing local overheating on the illuminated side while yielding improved thermal insulation along the backside that cannot be obtained with isotropic thermal insulators. The nanowood also shows a low emissivity of <5% over the solar spectrum with the ability to effectively reflect solar thermal energy. Moreover, the nanowood is lightweight yet strong, owing to the effective bonding between the aligned cellulose nanofibrils with a high compressive strength of 13 MPa in the axial direction and 20 MPa in the transverse direction at 75% strain, which exceeds other thermal insulation materials, such as silica and polymer aerogels, Styrofoam, and wool. The excellent thermal management, abundance, biodegradability, high mechanical strength, low mass density, and manufacturing scalability of the nanowood make this material highly attractive for practical thermal insulation applications.
A systematic framework for analyzing the dynamic e!ects of permanent and transitory shocks

This paper proposes a systematic framework for analyzing the dynamic e! ects of permanent and transitory shocks on a system of n economic variables. We consider a two-step orthogonolization on the residuals of a VECM with r cointegrating vectors. The "rst step separates the permanent from the transitory shocks, and the second step isolates n! r mutually uncorrelated permanent shocks and r transitory shocks. The decomposition is computationally straightforward and entails only a minor modi"cation to the Choleski decomposition commonly used in the literature. We then show how impulse response functions can be constructed to trace out the propagating mechanism of shocks distinguished by their degree of persistence. In an empirical example, the dynamic responses to the identi"ed permanent shocks have properties similar to shocks to productivity, the real interest rate, and money growth, even though no economic
SLAM: scalable locality-aware middleware for I/O in scientific analysis and visualization

Whereas traditional scientific applications are computationally intensive, recent applications require more data-intensive analysis and visualization. As the computational power and size of compute clusters continue to increase, the I/O read rates and associated network cost for these data-intensive applications create a serious performance bottleneck when faced with the massive data sets of today's "big data" era. In this paper, we present "Scalable Locality-Aware Middleware" (SLAM) for scientific data analysis applications. SLAM leverages a distributed file system (DFS) to provide scalable data access for scientific applications. To reduce data movement and enforce data process locality, a data-centric scheduler (DC-scheduler) is proposed to enable scientific applications to read data locally from a DFS. We prototype our proposed SLAM system along with the Hadoop distributed file system (HDFS) on two well-known scientific applications. We find in our experiments that SLAM can greatly reduce I/O cost and double the overall performance, as compared to existing approaches.
Decentralization of Control Loop for Self-Adaptive Software through Reinforcement Learning

In a decentralized self-adaptive software, multiple control loops provide self-adaptation capabilities to the components these manage. For this, these control loops need to coordinate to continuously satisfy some local QoS goals of each managed component and global QoS goals concerning the whole system in a changing environment. This is accomplished by choosing variants of the managed system (component) that satisfy these goals. As goal conformance requires coordination, a control loop requires choosing the variant that leads to maximum goal conformance considering the variant selection strategies by other control loops. An overall goal conformance calculation mechanism is also needed that captures the local and global goal violations. This paper proposes a decentralized reinforcement learning-based self-adaptation technique considering these issues. A reinforcement learning technique, Q-learning helps to learn the maximum achievable goal conformance choosing a specific variant. The other control loop strategies are estimated by observing their variant selection and incorporated with Q-learning for better variant selection. An overall goal conformance calculation technique is also proposed that dynamically adjusts weights on the local and global goals to emphasize violated goals. The proposed approach was evaluated using a service-based Tele Assistance System. It was compared with two approaches - random variant selection and variant selection ignoring other control loop strategies. The proposed technique outperformed both with maximum overall goal conformance. The proposed dynamic weight update mechanism was compared with a static weight-based one. The dynamic technique outperformed the static one continuously satisfying all the goals.
Combustion Visualization of Paraffin-Based Hybrid Rocket Fuel at Elevated Pressures

The discovery of high regression rate liquefying fuels for hybrid motors has generated a renewed interest in visualization experiments. In 2012, the Stanford Combustion Visualization Facility was developed to investigate the combustion of these fuels with gaseous oxygen. A major upgrade of this facility was recently completed. Details of the changes made to the facility are provided. Visual and schlieren images of the combustion of paraffin wax and oxygen at a range of operating pressures are presented, including the first schlieren images of the combustion of paraffin wax and oxygen at supercritical pressures. The nature of the combustion and the boundary layer thickness were seen to change dramatically with increasing chamber pressure, up to approximately the critical pressure of the fuel. Droplet entrainment from the surface of the fuel grain was observed at all pressures. At elevated pressures the combustion of the fuel grain was characterized by very strong surface blowing events comprised of numerous droplets.