Miracle-dz/UniFAR-FTUs huggingface dataset:
The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics

The intracellular functions of myosin motors requires a number of adaptor molecules, which control cargo attachment, but also fine‐tune motor activity in time and space. These motor–adaptor–cargo interactions are often weak, transient or highly regulated. To overcome these problems, we use a proximity labelling‐based proteomics strategy to map the interactome of the unique minus end‐directed actin motor MYO6. Detailed biochemical and functional analysis identified several distinct MYO6‐adaptor modules including two complexes containing RhoGEFs: the LIFT (LARG‐Induced F‐actin for Tethering) complex that controls endosome positioning and motility through RHO‐driven actin polymerisation; and the DISP (DOCK7‐Induced Septin disPlacement) complex, a novel regulator of the septin cytoskeleton. These complexes emphasise the role of MYO6 in coordinating endosome dynamics and cytoskeletal architecture. This study provides the first in vivo interactome of a myosin motor protein and highlights the power of this approach in uncovering dynamic and functionally diverse myosin motor complexes.
Metal--slag--gas reactions and processes

Papers are presented concerning high-temperature chemical metallurgy. The four sections of the book are general aspects of kinetics and thermodynamics of metal--slag--gas reactions, high temperature oxidation and corrosion processes, electrochemical sensors in metal--slag--gas environment, and electrometallurgical processes and systems. Separate abstracts for some papers were prepared. (FS)
Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance

Determining which reproductive isolating barriers arise first between geographically isolated lineages is critical to understanding allopatric speciation. We examined behavioral isolation among four recently diverged allopatric species in the orangethroat darter clade (Etheostoma: Ceasia). We also examined behavioral isolation between each Ceasia species and the sympatric rainbow darter Etheostoma caeruleum. We asked (1) is behavioral isolation present between allopatric Ceasia species, and how does this compare to behavioral isolation with E. caeruleum, (2) does male color distance and/or genetic distance predict behavioral isolation between species, and (3) what are the relative contributions of female choice, male choice, and male competition to behavioral isolation? We found that behavioral isolation, genetic differentiation, and male color pattern differentiation were present between allopatric Ceasia species. Males, but not females, discerned between conspecific and heterospecific mates. Males also directed more aggression toward conspecific rival males. The high levels of behavioral isolation among Ceasia species showed no obvious pattern with genetic distance or male color distance. However, when the E. caeruleum was included in the analysis, an association between male aggression and male color distance was apparent. We discuss the possibility that reinforcement between Ceasia and E. caeruleum is driving behavioral isolation among allopatric Ceasia species.
Stage classification of IgG4-related dacryoadenitis and sialadenitis by the serum cytokine environment

Abstract Objectives: Patients with immunoglobulin-G4 related disease (IgG4-RD) diagnosed according to the comprehensive diagnostic criteria (CDC) show varied therapeutic responses and prognoses. We assumed that there are clinical stages in IgG4-RD and have verified it using serum cytokine levels in the groups classified by lesion distribution. Methods: Definite IgG4-related dacryoadenitis and sialadenitis (IgG4-DS) cases were divided according to the CDC for IgG4-RD into 11 cases with focal type and 30 cases with systemic type. The levels of serum interleukin (IL)-4, IL-5, IL-6, IL-10, IL-13, IL-15, IL-21, interferon (IFN)-α, IFN-γ, tumor necrosis factor (TNF)-α, transforming growth factor (TGF)-β1, and monocyte chemotactic protein (MCP)-1 were measured in healthy controls, allergic patients, probable IgG4-RD cases, and focal and systemic type cases. The cytokine environment was analyzed in each group. The 52 definite IgG4-RD cases were next classified into four groups with cluster analysis in terms of therapeutic responses and prognosis. The relationships between each cytokine level and therapeutic responses were also analyzed. Results: Both serum IL-5 and IFN-α concentrations were very low in healthy controls, but they increased in the allergic cases, probable cases, and focal and systemic type cases. The level of serum IL-5 was significantly higher in definite cases than in healthy controls. The serum IL-5 level was also significantly increased in the groups with a poor prognosis than in the good prognosis group. Conclusion: These results suggest that there are clinical stages in IgG4-RD, and serum IL-5 play roles in the pathogenesis of IgG4-RD.
Design and analysis of a query processor for brick

Brick is a recently proposed metadata schema and ontology for describing building components and the relationships between them. It represents buildings as directed labeled graphs using the RDF data model. Using the SPARQL query language, building-agnostic applications query a Brick graph to discover the set of resources and relationships they require to operate. Latency-sensitive applications, such as user interfaces, demand response and model-predictive control, require fast queries --- conventionally less than 100ms. We benchmark a set of popular open-source and commercial SPARQL databases against three real Brick models using seven application queries and find that none of them meet this performance target. This lack of performance can be attributed to design decisions that optimize for queries over large graphs consisting of billions of triples, but give poor spatial locality and join performance on the small dense graphs typical of Brick. We present the design and evaluation of HodDB, a RDF/SPARQL database for Brick built over a node-based index structure. HodDB performs Brick queries 3-700x faster than leading SPARQL databases and consistently meets the 100ms threshold, enabling the portability of important latency-sensitive building applications.
Heterogeneity of systolic dysfunction in patients with severe aortic stenosis and preserved ejection fraction

Left ventricular (LV) systolic strain has been shown to be an early marker of LV dysfunction in patients with severe aortic stenosis (AS) despite preserved ejection fraction (EF). Echocardiography has provided useful data on regional LV strain patterns, but is not as sensitive as magnetic resonance imaging (MRI). No prior studies have used MRI‐based strain analysis to characterize regional three‐dimensional strain in patients with severe AS.
Estimating Reaction Norms for Age and Size at Maturation with Reconstructed Immature Size Distributions: A New Technique Illustrated by Application to Northeast Arctic Cod

Reaction norms for age and size at maturation describe the probability of immature fish maturing at a certain age and size. Knowledge of such reaction norms is increasingly important, both for observing and understanding changes in maturation and for calibrating size- and age-structured population models. Estimating the reaction norms for age and size at maturation by logistic regression requires data on the size and age distribution of immature and maturing fish. To permit such estimation when measurements of the size and age distribution of immature fish are not available, the information can be reconstructed by means of a back-projection procedure. For the reconstruction, only the size and age distribution of maturing fish, or first-time spawners, together with the age-dependent proportion of mature fish, given in the form of maturity ogives, have to be known. The method of Gulland (1964) is used to generate maturity ogives in the absence of data on immature fish. The robustness of the estimation method is demonstrated by analysing artificial data generated with a known reaction norm. Application of the reconstruction method to a set of measurements on Northeast Arctic cod (Gadus morhua) collected between 1933 and 1944 illustrates how the approach allows new information to be extracted from real data. 2002 International Council for the Exploration of the Sea. Published by Elsevier Science Ltd.
Exploring Active Learning Approaches to Computer Science Classes

We present our experience in a Computer Science (CS) introductory course, where three teaching practices were implemented and compared: lectured-based learning, problem-based learning, and peer instruction. We chose Information Systems, a first-term undergraduate course, for this study. It overviews a variety of topics in CS, such as algorithms, data structures and programming logic. We initially conducted interviews with previous instructors, who assisted in the collection of data, requirements, and needs pertaining to both students and instructors. We also carried out a survey among students enrolled in the program, in order to identify suggestions on how the classes could become more dynamic and motivating. In sequence, the experiment was designed to format and evaluate classes in the chosen paradigms. We focused on assessing and analyzing how the students' motivation and learning process were affected, as well as how difficult it was for instructors to prepare classes and how much time they expended in doing so. Results indicate that a paradigm shift from traditional teaching is not only expected by students and instructor; it is well received, and had a positive influence on the students' learning and motivation. We also found, however, that the proposed changes brought on an unwelcome overhead for the instructors, as additional time and effort are required to implement such practices.
Markov chain analysis of an agent based growth model

In this paper we investigate the asymptotic behavior of a discrete and probabilistic dynamical system which can be described as a growth model where autonomous agents aggregates. The aim of this paper is to give a mathematical analysis of the dynamics. The analysis uses face homogeneous Markov chains and thanks to this study we validate a conjecture set by Laszlo Gulyas and Yuri Mansury concerning a growth model for cities where simulations had shown that the sizes of the cities asymptotically distribute as a Zipf's law. In light of our analysis, we discuss how the emergence of such a Zipf's law could be expected in Gulyas-Mansury' model and in its variants.
The Impacts of Heating Strategy on Soil Moisture Estimation Using Actively Heated Fiber Optics

Several recent studies have highlighted the potential of Actively Heated Fiber Optics (AHFO) for high resolution soil moisture mapping. In AHFO, the soil moisture can be calculated from the cumulative temperature (Tcum), the maximum temperature (Tmax), or the soil thermal conductivity determined from the cooling phase after heating (λ). This study investigates the performance of the Tcum, Tmax and λ methods for different heating strategies, i.e., differences in the duration and input power of the applied heat pulse. The aim is to compare the three approaches and to determine which is best suited to field applications where the power supply is limited. Results show that increasing the input power of the heat pulses makes it easier to differentiate between dry and wet soil conditions, which leads to an improved accuracy. Results suggest that if the power supply is limited, the heating strength is insufficient for the λ method to yield accurate estimates. Generally, the Tcum and Tmax methods have similar accuracy. If the input power is limited, increasing the heat pulse duration can improve the accuracy of the AHFO method for both of these techniques. In particular, extending the heating duration can significantly increase the sensitivity of Tcum to soil moisture. Hence, the Tcum method is recommended when the input power is limited. Finally, results also show that up to 50% of the cable temperature change during the heat pulse can be attributed to soil background temperature, i.e., soil temperature changed by the net solar radiation. A method is proposed to correct this background temperature change. Without correction, soil moisture information can be completely masked by the background temperature error.
Managing Risk and Marginalizing Identities

This article develops the constitutive features of the society-of-captives thesis as suggested by Arrigo and Milovanovic, and Arrigo, Bersot, and Sellers. The relevance of this thesis is briefly explored in relation to the institutional and community-based treatment philosophies that currently inform the mental health and criminal justice systems. This exploration specifies how risk (being human and doing humanness differently) is managed symbolically, linguistically, materially, and culturally. The management of this risk extends to the kept as well as to their keepers, regulators, and watchers (i.e., the society of captives). This article calls for a new clinical praxis (being/doing a critical mindfulness) designed to overcome the totalizing madness (the harm of social dis-ease) that follows from managing risk fearfully and marginalizing identities desperately as reified recursively through society’s captivity. The ethical underpinnings of this clinical praxis represent an emergent direction for undertaking correctional policy reform.
Towards improving the performance of chat oriented dialogue system

This paper is concerned with how to improve the overall performance of chat-oriented dialogue system. This research is motivated by the fact that majority of current chat engines are based on pattern matching. The knowledge base of this type of systems is predefined pattern-answer pairs such as the categories defined in Artificial Intelligent Markup Language (AIML). The inherent disadvantage of this kind of chat engines is that the interaction is carried out without any syntactic, semantic and contextual information. We propose a chat engine which is capable of dynamic knowledge acquisition and inference for a higher level of conversation intelligence. The dialogue engine leverages on natural language processing tasks such as syntactic and semantic parsing, named entity recognition, dialogue act detection, polarity analysis, etc., as well as dialogue history and heuristic rules for analysis and inference to achieve better understanding and intelligence.
In silico models of cancer

Cancer is a complex disease that involves multiple types of biological interactions across diverse physical, temporal, and biological scales. This complexity presents substantial challenges for the characterization of cancer biology, and motivates the study of cancer in the context of molecular, cellular, and physiological systems. Computational models of cancer are being developed to aid both biological discovery and clinical medicine. The development of these in silico models is facilitated by rapidly advancing experimental and analytical tools that generate information‐rich, high‐throughput biological data. Statistical models of cancer at the genomic, transcriptomic, and pathway levels have proven effective in developing diagnostic and prognostic molecular signatures, as well as in identifying perturbed pathways. Statistically inferred network models can prove useful in settings where data overfitting can be avoided, and provide an important means for biological discovery. Mechanistically based signaling and metabolic models that apply a priori knowledge of biochemical processes derived from experiments can also be reconstructed where data are available, and can provide insight and predictive ability regarding the behavior of these systems. At longer length scales, continuum and agent‐based models of the tumor microenvironment and other tissue‐level interactions enable modeling of cancer cell populations and tumor progression. Even though cancer has been among the most‐studied human diseases using systems approaches, significant challenges remain before the enormous potential of in silico cancer biology can be fully realized. Copyright © 2009 John Wiley & Sons, Inc.
MUTE: Sounding inhibition for MU-MIMO WLANs

In this paper, we present the design, implementation, and evaluation of the novel downlink Multi-User MIMO sounding protocol called MUTE. Our protocol decouples the sounding set selection used to collect Channel State Information (CSI), from the transmission set selection in order to minimize or even eliminate the overhead associated with sounding, while maximizing user selection performance. To this end, MUTE exploits channel statistics to all the different users to predict whether a particular user's channel will remain sufficiently stable, thereby allowing the access point to preclude channel sounding before a MU-MIMO transmission. We show that in indoor WLANs, MUTE can reduce sounding overhead by close to 73% under certain conditions while minimizing rate performance losses due to inaccurate channel estimation.
Bioengineering of microorganisms for C3 to C5 alcohols production

Production of renewable fuels and chemicals is an absolute requirement for the sustainability of societies. This fact has been neglected during the past century as cheap and abundant, yet not renewable, sources of hydrocarbons were available. Since fossil fuel availability is decreasing, biological production of fuels and chemicals has been proposed to be a potential alternative to fossil sources. Higher alcohols (from C3 to C5) are useful substitutes for gasoline because of their high energy density and low hygroscopicity and are important feedstocks for other chemicals. Some Clostridia species are known to naturally ferment sugars to isopropanol and 1‐butanol. However, other C3 to C5 alcohols are not produced in large quantities by natural microorganisms. A non‐fermentative strategy to produce a broad range of higher alcohols has been devised using the ubiquitous keto acid biosynthetic pathways. This review provides a current overview of these different strategies.
Stability and rheology of concentrated of concentrated O/W emulsions based on soybean oil/palm kernel olein blends.

Droplet size distribution and rheological properties of egg yolk-stabilized emulsions were studied before and after storage (25 °C, 30 days). The dispersed phase (70%) of the emulsions was based on soybean oil (SBO) and 10–40% palm kernel olein (PKO) replacements of SBO. Replacement of PKO resulted in a significant increase in droplet mean diameters and a decrease in rheological properties of the emulsions. All emulsion exhibited a gel-like characteristic with storage modulus higher than loss modulus and tan δ greater than 0.3. Significant increase (p < 0.05) was found for droplet mean diameters and rheological properties of the emulsions after storage. Emulsion with fully SBO and the highest PKO replacement (40%) were found to be the most unstable, which was ascribed to a strong flocculation. With 10–30% PKO replacements, the emulsions displayed a better stability after storage, most probably promoted by significant content of short-medium chain fatty acids in PKO.
Polymorphism and separation in hoare type theory

In previous work, we proposed a Hoare Type Theory (HTT) which combines effectful higher-order functions, dependent types and Hoare Logic specifications into a unified framework. However, the framework did not support polymorphism, and ailed to provide a modular treatment of state in specifications. In this paper, we address these shortcomings by showing that the addition of polymorphism alone is sufficient for capturing modular state specifications in the style of Separation Logic. Furthermore, we argue that polymorphism is an essential ingredient of the extension, as the treatment of higher-order functions requires operations not encodable via the spatial connectives of Separation Logic.
A novel mechanism underlies atrazine toxicity in quails (Coturnix Coturnix coturnix): triggering ionic disorder via disruption of ATPases

The widely used atrazine has been reported to exhibit extensive ecological hazards. Due to the biological accumulation, atrazine elicits widespread toxic effects on different organisms. However, true proof for the mechanism of atrazine-induced toxicity is lacking. To determine the potential mechanism by which atrazine exerted toxic effects, quails were treated with atrazine (0, 50, 250 and 500 mg/kg) by gavage administration for 45 days. Atrazine significantly increased the histological alterations and serum creatine kinase, lactate dehydrogenase and choline esterase levels. A marked disorder in ionic (Na+, K+, Ca2+ and Mg2+)contents and the decrease of ATPases (Na+-K+-ATPase, Ca2+-ATPase, Mg2+-ATPase and Ca2+-Mg2+-ATPase) activities were observed in the heart and liver of atrazine-exposed quails. Of note, it was also observed that atrazine suppressed the transcription of Na+, K+ transfer associated genes (Na+-K+-ATPase subunits) and Ca2+ transfer associated genes (Ca2+-ATPase subunits, solute carriers) in heart and liver. In conclusion, atrazine induced cardiac and hepatic damage via causing the ionic disorder, triggering the transcription of the ion transporters and leading the histopathological and functional alternations in the heart and liver of quails. This study demonstrated atrazine significantly induced the ionic disorder via decreasing the ATPases activities and disturbing the transcription of the ion transporters.
Smartphone-Based Cooperative Indoor Localization with RFID Technology

In GPS-denied indoor environments, localization and tracking of people can be achieved with a mobile device such as a smartphone by processing the received signal strength (RSS) of RF signals emitted from known location beacons (anchor nodes), combined with Pedestrian Dead Reckoning (PDR) estimates of the user motion. An enhacement of this localization technique is feasible if the users themselves carry additional RF emitters (mobile nodes), and the cooperative position estimates of a group of persons incorporate the RSS measurements exchanged between users. We propose a centralized cooperative particle filter (PF) formulation over the joint state of all users that permits to process RSS measurements from both anchor and mobile emitters, as well as PDR motion estimates and map information (if available) to increase the overall positioning accuracy, particularly in regions with low density of anchor nodes. Smartphones are used as a convenient mobile platform for sensor measurements acquisition, low-level processing, and data transmission to a central unit, where cooperative localization processing takes place. The cooperative method is experimentally demonstrated with four users moving in an area of 1600 m2, with 7 anchor nodes comprised of active RFID (radio frequency identification) tags, and additional mobile tags carried by each user. Due to the limited coverage provided by the anchor beacons, RSS-based individual localization is inaccurate (6.1 m median error), but this improves to 4.9 m median error with the cooperative PF. Further gains are produced if the PDR information is added to the filter: median error of 3.1 m (individual) and 2.6 m (cooperative); and if map information is also considered, the results are 1.8 m (individual) and 1.6 m (cooperative). Thus, for each version of the particle filter, cooperative localization outperforms individual localization in terms of positioning accuracy.