Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear mechanism of the self-sustaining process in the buffer and logarithmic layer of wall-bounded flows

Abstract The nonlinear mechanism in the self-sustaining process (SSP) of wall-bounded turbulence is investigated. Resolvent analysis is used to identify the principal forcing mode that produces the maximum amplification of the velocities in numerical simulations of the minimal channel for the buffer layer and a modified logarithmic (log) layer. The wavenumbers targeted in this study are those of the fundamental mode, which is infinitely long in the streamwise direction and once-periodic in the spanwise direction. The identified mode is then projected out from the nonlinear term of the Navier–Stokes equations at each time step from the simulation of the corresponding minimal channel. The results show that the removal of the principal forcing mode of the fundamental wavenumber can inhibit turbulence in both the buffer and log layer, with the effect being greater in the buffer layer. Removing other modes instead of the principal mode of the fundamental wavenumber only marginally affects the flow. Closer inspection of the dyadic interactions in the nonlinear term shows that contributions to the principal forcing mode come from a limited set of wavenumber interactions. Using conditional averaging, the flow structures that are responsible for generating the nonlinear interaction to self-sustain turbulence are identified as spanwise rolls interacting with oblique streaks. This method, based on the equations of motion, validates the similarities in the SSP of the buffer and log layer, and characterises the underlying quadratic interactions in the SSP of the minimal channel.
Medical Image Segmentation via Unsupervised Convolutional Neural Network

For the majority of the learning-based segmentation methods, a large quantity of high-quality training data is required. In this paper, we present a novel learning-based segmentation model that could be trained semi- or un- supervised. Specifically, in the unsupervised setting, we parameterize the Active contour without edges (ACWE) framework via a convolutional neural network (ConvNet), and optimize the parameters of the ConvNet using a self-supervised method. In another setting (semi-supervised), the auxiliary segmentation ground truth is used during training. We show that the method provides fast and high-quality bone segmentation in the context of single-photon emission computed tomography (SPECT) image.
Action Language BC+: Preliminary Report

Action languages are formal models of parts of natural language that are designed to describe effects of actions. Many of these languages can be viewed as high level notations of answer set programs structured to represent transition systems. However, the form of answer set programs considered in the earlier work is quite limited in comparison with the modern Answer Set Programming (ASP) language, which allows several useful constructs for knowledge representation, such as choice rules, aggregates, and abstract constraint atoms. We propose a new action language called BC+, which closes the gap between action languages and the modern ASP language. Language BC+ is defined as a high level notation of propositional formulas under the stable model semantics. Due to the generality of the underlying language, BC+ is expressive enough to encompass many modern ASP language constructs and the best features of several other action languages, such as B, C, C+ and BC. Computational methods available in ASP solvers are readily applicable to compute BC+, which led us to implement the language by extending system Cplus2ASP.
The impact of short-term acute heat stress on the rumen microbiome of Hanwoo steers

Abstract Heat stress negatively affects cattle productivity by reducing feed intake. In the present study, we assessed if the rumen microbiome composition of Hanwoo steers was altered by exposure to heat stress. Rumen samples were collected from four Hanwoo steers that were individually housed in climate-controlled chambers with 60% humidity and environmental temperatures of: 1) 15°C (0-day group), 2) 35°C for 3 days (3-day group), and 3) 35°C for 6 days (6-day group). The total community DNA of samples was extracted, and 997,843 bacterial and 1,508,770 archaeal sequences were analyzed using next-generation sequencing. Assessment of the relative abundances revealed 15 major phyla of which Bacteroidetes was found to be the most dominant. After 3 days of heat stress exposure there were no significant changes in the rumen microbiome composition, except for a decrease in the Planctomycetes. However, after 6 days of heat stress exposure, we found that the relative abundance of fibrolytic Ruminococcaceae had decreased while that of lactate-producing Lactobacillaceae and amylolytic Prevotella and Ruminobacter had increased. The normal rumen microbiome of Hanwoo cattle was shown to be disrupted after 6 days of heat stress, which led to the decrease in fibrolytic bacteria that are sensitive to low pH and the increase in both lactate-producing and amylolytic bacteria. We have demonstrated that the microbiome composition of the rumen is affected by acute heat stress. Our findings may contribute to the development of different feeding strategies to restore heat stress-induced disruption of the rumen microbiome.
The Challenges of Ultrasound-guided Thoracic Paravertebral Blocks in Rib Fracture Patients

Thoracic paravertebral blocks (TPVBs) provide an effective pain relief modality in conditions where thoracic epidurals are contraindicated. Historically, TPVBs were placed relying solely on the landmark-based technique, but the availability of ultrasound imaging makes it a valuable and practical tool during the placement of these blocks. TPVBs also provide numerous advantages over thoracic epidurals, namely, minimal hypotension, absence of urinary retention, lack of motor weakness, and remote risk of an epidural hematoma. Utilization of both landmark-based and ultrasound-guided techniques may increase the successful placement of a TPVB. This article reviews relevant sonoanatomy as it pertains to TPVBs. However, certain patient-related issues, including pneumothoraces, surgical emphysema, body habitus, and transverse process fractures, all may make imaging with ultrasound challenging. The changes noted on ultrasound imaging as a result of these issues will be further described in this review.
A new Stamnodes from the southwestern United States (Lepidoptera, Geometridae, Larentiinae)

Abstract Stamnodes fergusonisp. nov. occurs from extreme southeastern Arizona through southern New Mexico east into western Texas, USA. Identity of the new species can be reliably determined by external features, genitalic characters, and COI haplotypes. Larvae are believed to be specialists on Salvia pinguifolia and S. ballotiflora. The adult and larval stages and male and female genitalia are illustrated, available DNA barcode data that support the recognition of the new Stamnodes are reviewed, and its life history briefly characterized.
Bioactive Peptide Tempe Made from Mucuna pruriens (L) DC as an Inhibitor of Angiotensin-I-Converting Enzyme (ACE) in a Digestion Simulation

Mucuna pruriens (L) DC tempe is a food that functions as an inhibitor of the angiotensin-I-converting enzyme (ACE). The purpose of this research was to study the activity of M. pruriens tempe peptides during the digestive process in vitro with pepsin-pancreatin, and absorption of peptides in the small intestine using the inverted intestinal sac method. Our results show that M. pruriens had the highest ACE-inhibiting activity after digestion in vitro after fermentation for 72 h (F72). F72 peptide absorption (%) and ACE-inhibitory activity of the absorbed peptides did not significantly differ between the different segments of the small intestine (duodenum, jejunum, and ileum). These results demonstrate that F72 tempe maintains ACE-inhibitory activity in each segment of the small intestine after both digestion and absorption.
RNA-seq profiling of skin in temperate and tropical cattle

Abstract Skin is a major thermoregulatory organ in the body controlling homeothermy, a critical function for climate adaptation. We compared genes expressed between tropical- and temperate-adapted cattle to better understand genes involved in climate adaptation and hence thermoregulation. We profiled the skin of representative tropical and temperate cattle using RNA-seq. A total of 214,754,759 reads were generated and assembled into 72,993,478 reads and were mapped to unique regions in the bovine genome. Gene coverage of unique regions of the reference genome showed that of 24,616 genes, only 13,130 genes (53.34%) displayed more than one count per million reads for at least two libraries and were considered suitable for downstream analyses. Our results revealed that of 255 genes expressed differentially, 98 genes were upregulated in tropically-adapted White Fulani (WF; Bos indicus) and 157 genes were down regulated in WF compared to Angus, AG (Bos taurus). Fifteen pathways were identified from the differential gene sets through gene ontology and pathway analyses. These include the significantly enriched melanin metabolic process, proteinaceous extracellular matrix, inflammatory response, defense response, calcium ion binding and response to wounding. Quantitative PCR was used to validate six representative genes which are associated with skin thermoregulation and epithelia dysfunction (mean correlation 0.92; p < 0.001). Our results contribute to identifying genes and understanding molecular mechanisms of skin thermoregulation that may influence strategic genomic selection in cattle to withstand climate adaptation, microbial invasion and mechanical damage.
Thrombophilic Risk of Factor V Leiden, Prothrombin G20210A, MTHFR, and Calreticulin Mutations in Essential Thrombocythemia Egyptian Patients

Objectives Essential thrombocythemia (ET) is one of the myeloproliferative neoplasms characterized by a sustained elevation of platelet numbers with a tendency for thrombosis and hemorrhage. The aim of this work is to establish the relation between calreticulin, factor V Leiden, prothrombin G20210A, and MTHFR mutations in ET patients and the thrombotic risk of these patients. Methods This study was carried out on 120 ET patients and 40 apparently healthy individuals as a control group. Results There were increases in WBCs, PLT counts, PT, fibrinogen concentration factor V Leiden, and MTHFR mutation in ET patients as compared to the control group (P < 0.05). Also, there were increases in WBCs, PLT counts, and hematocrit value in thrombosed ET patients as compared to the nonthrombosed ones (P < 0.05). On the contrary, there was no significantly statistical difference in ET patients with JAK2 V617F positive mutation versus the JAK2 negative group (P > 0.05) and in patients with cardiovascular risk factors versus patients with noncardiovascular risk factors (P > 0.05). ET patients with factor V Leiden, prothrombin gene, and CALR mutations were more prone to thrombosis (odds ratio 5.6, 5.7 and 4.7, respectively). On the contrary, JAk2V 617F and MTHFR mutations have no effect on the thrombotic state of those patients. Conclusion There is a significant increase risk of thrombosis in ET patients with CALR mutation, thrombophilic mutations, as well as factor V Leiden and prothrombin gene mutation with a risk of developing leukemic transformation.
Using model checkers in an introductory course on operating systems

During the last three years, we have been experimenting with the use of the Uppaal model checker in an introductory course on operating systems for first-year Computer Science students at the Radboud University Nijmegen. The course uses model checkers as a tool to explain, visualize and solve concurrency problems. Our experience is that students enjoy to play with model checkers because it makes concurrency issues tangible. Even though it is hard to measure objectively, we think that model checkers really help students to obtain a deeper insight into concurrency. In this article, we report on our experiences in the classroom, explain how mutual exclusion algorithms, semaphores and monitors can conveniently be modeled in Uppaal, and present some results on properties of small, concurrent patterns.
The decline of native fishes and fisheries and the rise of aquaculture in lakes and rivers in the Philippines.

This paper reviews historical and recent data on biodiversity, fisheries, exotic fishes, and aquaculture in Philippine lakes and rivers. The country's lakes and rivers are poor in primary freshwater fishes because the Philippines' only connection with the Asian mainland had been through land bridges between Borneo, the Sulu islands, Mindanao, Palawan and Mindoro in which islands endemic carps have evolved. Philippine lakes and rivers instead have secondary freshwater fishes such as gobies, migratory marine fishes such as mullets, and some snails, clams, and prawns. Most lakes and rivers have been severely degraded and their biodiversity reduced by siltation, pollution, overfishing, and the establishment of exotic fishes from other countries or elsewhere in the country. Many fishes first described in the Philippines in 1910-1940 by Seale, Herre, and Filipino ichthyologists have not been collected in recent years. The Laguna de Bay fishery in the early 1960s was largely dependent on the 'ayungin' Therapon plumbeus, 'biyang puti' Glossogobius giurus, and the 'kanduli' Arius manilensis that together comprised 95% of the annual 83,000 mt; another 19,000 mt came from shrimps and 245,000 mt from snails. Fishing and snail-dredging were so intense that catches declined and the whole lake fishery collapsed around 1970. After the collapse, the primary production of the lake increased and milkfish and tilapia became natural choices for aquaculture. Lake Lanao became famous for its species flock of 18 endemic carps, but these are now extinct, except perhaps two species. In 1963, these carps contributed 981 mt to the fishery, other native fishes 269 mt, shrimps and snails 257 mt, and introduced fishes 479 mt. Twenty years later, endemic carps have made up only 92 mt, native fishes 141 mt, shrimps and snails 164 mt, and introduced fishes 312 mt of the harvest from the lake. The 'kadurog' G. giurus, probably stocked in the lake with milkfish larvae in 1955, proliferated in the 1960s and apparently drove the endemic carps to extinction. The 'katolong' Hypseleotris agilis was first seen in the lake in 1977 and has since outcompeted the 'kadurog'. In Lakes Taal and Naujan, migratory marine fishes have been caught by fish corrals set across the outlets, but the catch along Pansipit River has fallen since the turn of the century and that in Butas River fell from 62 mt in 1977 to 17 mt in 1983. Catches of the endemic sardine Harengula tawilis in Lake Taal fluctuated between 4,400 mt in 1983 to 11,300 mt in 1990 and 1,400 mt in 1994. Cage culture of tilapia and milkfish has been going on in Lake Taal for 10 years. In Lakes Buhi and Bato, the endemic 'sinarapan' Mistichthys luzonensis almost disappeared due to fine-net fishing and tilapia stocking; catches have been 50-90 mt in 1983-93 but zero in 1994. D ow nl oa de d by [1 22 . 5 5. 1. 77 ] f ro m h tt p: // re po si to ry . s ea fd ec . o rg . p h on Ju ly 2 7, 2 01 6 at 1 2: 11 P M C ST
Bridging formal models : an engineering perspective

The thesis presents different techniques that can be used to build formal behavioral models. If modal properties are formulated, the models can be subjected to verification techniques to determine whether a model possesses the desired properties. However many native environments do not facilitate tools or techniques to verify them. Hence, these models need to be transformed into other models that provide suitable techniques for a formal analysis. The transformations are classified into two engineering approaches, namely syntactically engineered models and semantically engineered models. Syntactically engineered models are constructed from input specifications without explicitly considering the semantics. Semantically engineered models are constructed from input specifications by explicitly considering the semantics. The syntactic engineering approach presents four dedicated modeling techniques that construct or disseminate verification results for formal models. The first modeling technique describes a way to create models from system descriptions that specify concurrent behavior. Here, we model three variations of a 2×2 switch, for which the models are subsequently compared to models created in the specification languages: TLA+, Bluespec, Statecharts, and ACP. The comparison validates that mCRL2 is a suitable specification language to model descriptions or specify the behavior for prototype systems. The second syntactic technique constructs an mCRL2 model from a software implementation that operates a printer for printing Printed Circuit Boards. The model is used to advise (other) software engineers on dangerous language constructs in the control software. Hence, the model is model checked for various safety properties. The implementation is modeled through an over-approximation on the behavior by abstracting from program variables, such that only interface calls between processes and non-deterministic choices in procedures remain. The third modeling technique describes a language transformation from the language Chi 2.0 language to the mCRL2 language. The purpose of the transformation is to facilitate model checking techniques to the discrete part of the Chi 2.0 language.
Multilingual Projection for Parsing Truly Low-Resource Languages

We propose a novel approach to cross-lingual part-of-speech tagging and dependency parsing for truly low-resource languages. Our annotation projection-based approach yields tagging and parsing models for over 100 languages. All that is needed are freely available parallel texts, and taggers and parsers for resource-rich languages. The empirical evaluation across 30 test languages shows that our method consistently provides top-level accuracies, close to established upper bounds, and outperforms several competitive baselines.
Faster optimization through adaptive importance sampling

The current state of the art stochastic optimization algorithms (SGD, SVRG, SCD, SDCA, etc.) are based on sampling one active datapoint uniformly at random in each iteration. Changing these probabilities to better reflect the importance of each datapoint is a natural and powerful idea. In this thesis we analyze Stochastic Coordinate Descent methods with fixed non-uniform and adaptive sampling. We consider problems with strongly convex (e.g. SVM) and general convex (e.g. Lasso) regularizers and obtain new upper bounds on the number of iterations needed to reach given duality gap or suboptimality. Experiments on smoothed hinge loss SVM and Lasso are provided to confirm the theoretical analysis.
Exploring Social Interaction With a Tangible Music Interface

This article presents a video-based field study of the Reactable, a tabletop tangible user interface (TUI) for music performance, in a hands-on science centre. The goal was to investigate visitors’ social interactions in a public setting. We describe liminality and cross-group interaction, both synchronous with fluid transitions and overlaps in use between groups and asynchronous. Our findings indicate the importance of: (i) facilitating smooth transitions and overlaps between groups and (ii) supporting not only synchronous but also asynchronous group interaction. We discuss the lessons learned on how best to enable liminal situations in the design of interactive tabletops and TUIs for social interaction and particularly collaborative tangible music in public museum settings. • Presentation of a video-based field study describing cross-group interaction. • Description of exemplar vignettes of video for illustrating liminal situations in social interaction. • Discussion of the nature of different levels of cross-group interaction and their relevance for social interaction and collaboration. • Lessons learned in how best to enable liminal situations in the design of collaborative tangible user interfaces for promoting social interaction and collaboration.
Conjunctive and Elemental Representations of a Context in Humans

Abstract The dual-process theory assumes that contexts are encoded in an elemental and in a conjunctive representation. However, this theory was developed from animal studies, and we still have to explore if and how elemental and conjunctive representations contribute to, for example, contextual anxiety in humans. Therefore, 28 participants underwent differential context conditioning in a newly developed flip-book paradigm. Virtual rooms were presented similar to a flip-book, that is, as a stream of 49 consecutive screenshots creating the impression of walking through the rooms. This allowed registration of event-related brain potentials triggered by specific screenshots. During two acquisition phases, two rooms were shown in this way for six times each. In one room, the anxiety context (CTX+), mildly painful electric stimuli (unconditioned stimuli [USs]) were administered unpredictably after 12 distinct screenshots, which became threat elements, whereas 12 selected comparable screenshots became nonthreat elements (elemental representation); all screenshots represented the anxiety context (conjunctive representation). In the second room, the safety context (CTX−), no USs were applied; thus, all screenshots created the safety context whereby 12 preselected screenshots represented safety elements. Increased US expectancy ratings for threat versus nonthreat or safety elements reflected elemental representation. Conjunctive representation was evident in differential ratings (arousal and contingency) and increased P100 and early posterior negativity amplitudes for threat and nonthreat CTX+ versus safety CTX− screenshots. These differences disappeared during two test phases without US delivery indicating successful extinction. In summary, we revealed the first piece of evidence for the simultaneous contributions of elemental and conjunctive representation during context conditioning in humans.