Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression Patterns of Atlantic Sturgeon (Acipenser oxyrinchus) During Embryonic Development

During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular backgrounds of the development of economically important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) have not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using an Illumina HiSequation 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of prelarval development [2 d posthatching (dph)] were investigated applying an Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts upregulated at the two early stages were mainly enriched in transcripts linked to developmental processes, while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore, important stage-specific expression has been detected for the hatching stage with transcripts enriched in molecule transport, and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development, and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture.
The Enactive equation: Exploring How Multiple External Representations are Integrated, Using a Fully Controllable Interface and Eye-Tracking

Representational competence (RC), defined as "the ability to simultaneously process and integrate multiple external representations (MERs) in a domain", is a marker of expertise in science and engineering. However, the cognitive mechanisms underlying this ability and how this ability develops in learners, is poorly understood. In this paper, we report a fully controllable interface, designed to help school students develop RC. Further, as the design emerged from the application of distributed and embodied cognition theory to the RC problem, the design also seeks to shed light on the cognitive mechanisms underlying the integration of MERs. Here we report a preliminary eye and mouse tracking study, which sought to develop a detailed understanding of how students interacted with our interface, under self and text-guided exploration conditions. We also examined how the interaction process related to students' ability to integrate the representations in the interface. Results highlighted several desirable student behaviors, and potential points of modification of the interface to improve integration of MERs.
Continuous-Time, Discrete-Event Simulation from Counting Processes

This is a method for discrete event simulation specified by survival analysis. It presents a sequence of steps. First, hazard rates from survival analysis specify the rates of a set of counting processes. Second, those counting processes define a transition kernel. Third, there are four different ways to sample that transition kernel, including a first-principles derivation of exact stochastic simulation algorithms (SSA) in continuous time. This simulation allows time-dependent intensities which include both continuous and atomic components. Separating the steps involved makes a clear correspondence between mathematical formulation and algorithmic implementation.
Production of lymphocyte-activating factor (Interleukin 1) by macrophages activated with colony-stimulating factors.

Murine peritoneal exudate macrophages incubated with medium conditioned by L929 cells were stimulated to produce lymphocyte-activating factor (LAF, Interleukin 1). This stimulatory activity was partially neutralized by antiserum prepared against partially purified L cell colony-stimulating factor (CSF) and comigrated upon gel filtration with the myeloproliferative activity. LAF-inducing activity of three different L cell CSF preparations, including one purified to homogeneity, was dependent upon the concentration of CSF. A minimum of 1,000 to 3,000 units of CSF activity was required to stimulate macrophagfes to produce LAF. Concanavalin A (Con A) stimulated splenic supernatants also contained CSF and LAF-inducing activities that co-eluted upon gel filtration. LAF-inducing activities co-eluting with the two Con A CSF peaks (apparent m.w. of 25,000 and 35,000) were effective at minimum dilutions containing 1,000 to 3,000 units of CSF activity correlating in potency with L cell-derived CSF. Based on these data, it is proposed that CSF, whether of L cell or lymphoid origin, not only has myeloproliferative activities but also is capable of stimulating macrophages to produce LAF.
Endocardial-to-mesenchymal transformation and mesenchymal cell colonization at the onset of human cardiac valve development

The elucidation of mechanisms in semilunar valve development might enable the development of new therapies for congenital heart disorders. Here, we found differences in proliferation-associated genes and genes repressed by VEGF between human semilunar valve leaflets from first and second trimester hearts. The proliferation of valve interstitial cells and ventricular valve endothelial cells (VECs) and cellular density declined from the first to the second trimester. Cytoplasmic expression of NFATC1 was detected in VECs (4 weeks) and, later, cells in the leaflet/annulus junction mesenchyme expressing inactive NFATC1 (5.5-9 weeks) were detected, indicative of endocardial-to-mesenchymal transformation (EndMT) in valvulogenesis. At this leaflet/annulus junction, CD44+ cells clustered during elongation (11 weeks), extending toward the tip along the fibrosal layer in second trimester leaflets. Differing patterns of maturation in the fibrosa and ventricularis were detected via increased fibrosal periostin content, which tracked the presence of the CD44+ cells in the second trimester. We revealed that spatiotemporal NFATC1 expression actively regulates EndMT during human valvulogenesis, as early as 4 weeks. Additionally, CD44+ cells play a role in leaflet maturation toward the trilaminar structure, possibly via migration of VECs undergoing EndMT, which subsequently ascend from the leaflet/annulus junction. Summary: Global gene expression analyses on semilunar valve leaflets from embryonic human hearts reveals significant differences in the expression profiles of EndMT-associated and proliferation-associated genes.
Kombination und Integration qualitativer und quantitativer Analyse

Zusammenfassung: Moglichkeiten der Kombination qualitativer und quantitativer Analyseschritte werden auf funf unterschiedlichen Ebenen gezeigt: Auf technischer Ebene bieten die Programme computerunterstutzter qualitativer Analyse diverse Kombinationsmoglichkeiten. Auf der Ebene der Daten stellt das Arbeiten mit Kategorien, z.B. mittels qualitativer Inhaltsanalyse, Moglichkeiten qualitativer und quantitativer Verarbeitung zu Verfugung. Auf der Personenebene ermoglichen Typisierungen und induktive Fallverallgemeinerungen den Schritt von Einzelfallmaterial zu quantitativen Generalisierungen. Auf der Ebene des Forschungsdesigns lassen sich verschiedene Modelle differenzieren (Vorstudienmodell, Verallgemeinerungsmodell, Vertiefungsmodell, Triangulationsmodell), die qualitative und quantitative Analyseschritte miteinander kombinieren. Auf der Ebene der Forschungslogik schlieslich lasst sich zeigen, dass ein gemeinsames Ablaufmodell des Forschungsprozesses in einer erweiterten Form fur qualitative und quantitative Forschung angemessen sein kann und so zu einer Integration der Forschungsansatze fuhren kann.
Representations for Cognitive Vision:A Review of Appearance-Based, Spatio-Temporal, and Graph-Based Approaches

The emerging discipline of cognitive vision requires a proper representation of visual information including spatial and temporal relationships, scenes, events, semantics and context. This review article summarizes existing representational schemes in computer vision which might be useful for cognitive vision, and discusses promising future research directions. The various approaches are categorized according to appearance-based, spatio-temporal, and graph-based representations for cognitive vision. While the representation of objects has been covered extensively in computer vision research, both from a reconstruction as well as from a recognition point of view, cognitive vision will also require new ideas how to represent scenes. We introduce new concepts for scene representations and discuss how these might be efficiently implemented in future cognitive vision systems.
Incorporating Users' Perceptions of Site Quality in a Recreation Travel Cost Model

The travel cost method is used to analyze the recreation demand for North Carolina trails. Incorporated in the demand model are users' perceptions of trail quality and their stated number of annual trips. Trail demand is specified with panel data that consists of two separate observations per respondent. Users' behaviors are analyzed by combining both data on the observed trip counts and stated trips. Stated trips are the number of trips a user would have taken to the last trail used had the site quality been ideal. Since both users and non users of trails during the past 12 months were asked their stated trips if quality improved, the non-participation effect was incorporated into the estimates of trail demand. Study findings showed users' ratings of trail quality can be successfully incorporated into a demand model to evaluate a hypothetical improvement in trail conditions. The estimated $15 increase in consumer surplus per trip is of practical importance to policy analyses aimed at improving social and environmental conditions averse to trail users.
Production of aflatoxins by Aspergillus flavus and of fumonisins by Fusarium species isolated from Brazilian sorghum

Fifty-nine Aspergillus flavus and 35 Fusarium verticillioides strains, isolated from freshly harvested (10) and stored (130) Brazilian sorghum samples, were tested regarding their ability to produce aflatoxins (coconut milk agar) and fumonisins (rice culture), respectively. Aflatoxins B1 and B2 were detected by TLC, and fumonisins B1 and B2 were analyzed by HPLC. Thirty-eight (64.4%) A. flavus strains produced detectable levels of aflatoxins at concentrations ranging from 12.00 to 3282.50 µg/kg (AFB1 + AFB2), while thirty two (91%) F. verticillioides strains produced FB1 at concentrations ranging from 0.12 to 5.38 µg/g. Two F. proliferatum strains produced low fumonisin levels. The toxigenic potential of A. flavus (64.4%) and F. verticillioides (91.5%) strains observed in sorghum samples indicates that rigorous control should be directed at the storage conditions of these products to minimize contamination with toxigenic deteriorating fungi, preventing further hazard to human and animal health.
Dual-rate sampled-data H∞ control for vehicle active suspension systems

This paper investigates the problem of dual-rate sampled-data H∞ control for a vehicle active suspension system. In the system, the state variables are sampled by two types of sensors, and the ratio of two sampling rates is assumed to be a positive integer. Depending on whether the sampled states at two sampling rates are available simultaneously or separately, a periodic switched controller is proposed. Then, by using an input delay approach, the closed-loop system is modeled as a switched system with different input delays. A delay-dependent criterion on the existence of the switched controller is established such that the system is exponentially stable with a prescribed H∞ performance. The effectiveness of the proposed method is shown by a numerical example.
Influence of carer expressed emotion and affect on relapse in non-affective psychosis

Background High expressed emotion in carers predicts relapse in psychosis, but it is not known why this is so. In our cognitive model of psychosis, we postulated that the effect is mediated through affective changes. Aims To investigate the relationships between carer expressed emotion, patients' symptoms and carer characteristics during a recent relapse of psychosis. Method A total of 86 patients and carers were investigated in a cross-sectional design. Results Patients whose carers showed high expressed emotion had significantly higher levels of anxiety and depression, but not more psychotic symptoms or lower self-esteem. Linear regression showed that carers' critical comments predicted anxiety in patients. Critical comments were related to low carer self-esteem and avoidant coping strategies. Low carer self-esteem was also related to carer depression, stress and carer ‘burden’, and to low patient self-esteem. Conclusions Our hypothesis was partially supported. Carer criticism was associated with patient anxiety, low carer self-esteem and poor carer coping strategies. Family interventions should focus on improving these after a relapse of symptoms of psychosis.
Neural Networks Based Navigation and Control of a Mobile Robot in a Partially Known Environment

Developing mobile robots able to move autonomously and staying operational in unexplored environments is one of the most important aims of intelligent robotics research. Navigation (here in the sense: collision-free goal following behaviour) depends on the amount of a priori available information. It could be assumed that this information comes in the following three categories: (I) complete information about the robot's workspace is available, (II) a priori knowledge about the environment is not available and the robot would have to rely on its sensors at execution time to obtain the information needed to accomplish the task, (III) partial knowledge of the environment is available and sensors are used at the execution time to acquire additional information. The robot may interweave planning and execution monitoring activities, but the more incomplete the prior knowledge, the less important the role of global planning. Most of the global path-planning methods, which assume a static and completely known to the robot environment, are considered to belong to or to be variations of a few basic approaches: roadmap, cell decomposition, and potential field methods (Latombe, 1991; Choset et al., 2005). However, the dynamic and complex features of robot environments make their accurate modelling and predicting fundamentally impossible. Hence, during path following a local re-planning is needed in order to make the robot avoid collisions with unknown obstacles. By combining global and local path-planning methods mobile robots are able to operate in dynamic environments (Yahja et al., 2000). Each of the path-planning methods has its own advantages and drawbacks and is more or less proper to be used in a particular situation. How to select the most suitable approach and how to use local pathplanning in collaboration with the global one in a practical example, related to a partially known or fast-changing environment these are still open research problems. Navigation relies on the tracking and regulation capabilities of the feedback control design (the lower control level of the robot). Standard approaches to non-holonomic control design often deal only with the kinematic steering system, but good performance cannot be obtained without taking into account the vehicle dynamics. A stable control algorithm that considers the complete vehicle dynamics has been developed using back stepping 10
Lossless Compression Techniques in Wireless Sensor Networks: Monitoring Microacoustic Emissions

Collapse of rock faces and stability assessment of buildings is related to the geological substrate or the nature of the concrete and the presence of fractures which influence the stability properties of the envisaged material. A wireless sensor network-based approach has been suggested to monitor crack formation which, due to the high sampling rate of sensors, requires both online temporal identification of the event and compression of the same before transmittal to a remote control room (the action containing the energy consumption of the unit by triggering and reducing the radio activity). The paper proposes a simple -yet effective-algorithm for detecting microacoustic emissions generated by formation/organization of cracks and identifies a suitable lossless technique for microacoustic event compression. Finally, to satisfy real time performance, the optimal processing chain has been implemented on a FPGA chip to be mounted onto the WSN units.
Embodied design of full bodied interaction with virtual humans

This paper presents a system that allows end users to design full body interactions with 3D animated virtual character through a process we call Interactive Performance Capture. This process is embodied in the sense that users design directly by moving and interacting using an interactive machine learning method. Two people improvise an interaction based only on their movements, one plays the part of the virtual character the other plays a real person. Their movements are recorded and they label it with metadata that identifies certain actions and responses. This labeled data is then used to train a Gaussian Mixture Model that is able to recognize new actions and generate suitable responses from the virtual character. A small study showed that users do indeed design in a very embodied way using movement directly as a means of thinking through and designing interactions.
Reclaiming Performance and Energy Efficiency from Variability

This paper presents methods for addressing two sources of variability in the context of microprocessors within-die process variability and dynamic thermal variability and shows the improvements in performance and energy efficiency obtained by applying them to a globally asynchronous, locally synchronous (GALS) microprocessor design. The GALS design style partitions the core into several independently-clocked domains, which provides a natural granularity for variability to be addressed at. Process variability is addressed by observing that each domain has fewer critical paths than the processor as a whole, shifting their maximum frequency distributions towards higher speeds. Meanwhile, the detrimental effects of thermal variability are reduced by isolating the effects of thermal hotspots on delay to the domains they occur in. We simulate a subset of the SPEC2000 benchmarks, comparing the baseline GALS architecture against a version that accounts for the reduction in the number of critical paths per domain, a version that scales the clock speed of each domain based on the slack between its temperature and the maximum operating temperature of the core, and a final version that does both. These schemes achieve improvements of 2.0%, 9.5%, and 11.4% in execution time and 4.4%, 16.0%, and 20.0% in energy-delay, respectively.
Tensor Switching Networks

We present a novel neural network algorithm, the Tensor Switching (TS) network, which generalizes the Rectified Linear Unit (ReLU) nonlinearity to tensor-valued hidden units. The TS network copies its entire input vector to different locations in an expanded representation, with the location determined by its hidden unit activity. In this way, even a simple linear readout from the TS representation can implement a highly expressive deep-network-like function. The TS network hence avoids the vanishing gradient problem by construction, at the cost of larger representation size. We develop several methods to train the TS network, including equivalent kernels for infinitely wide and deep TS networks, a one-pass linear learning algorithm, and two backpropagation-inspired representation learning algorithms. Our experimental results demonstrate that the TS network is indeed more expressive and consistently learns faster than standard ReLU networks.
Acidic and basic hair/nail ("hard") keratins: their colocalization in upper cortical and cuticle cells of the human hair follicle and their relationship to "soft" keratins

Although numerous hair proteins have been studied biochemically and many have been sequenced, relatively little is known about their in situ distribution and differential expression in the hair follicle. To study this problem, we have prepared several mouse monoclonal antibodies that recognize different classes of human hair proteins. Our AE14 antibody recognizes a group of 10-25K hair proteins which most likely corresponds to the high sulfur proteins, our AE12 and AE13 antibodies define a doublet of 44K/46K proteins which are relatively acidic and correspond to the type I low sulfur keratins, and our previously described AE3 antibody recognizes a triplet of 56K/59K/60K proteins which are relatively basic and correspond to the type II low sulfur keratins. Using these and other immunological probes, we demonstrate the following. The acidic 44K/46K and basic 56-60K hair keratins appear coordinately in upper corticle and cuticle cells. The 10-25K, AE14-reactive antigens are expressed only later in more matured corticle cells that are in the upper elongation zone, but these antigens are absent from cuticle cells. The 10-nm filaments of the inner root sheath cells fail to react with any of our monoclonal antibodies and are therefore immunologically distinguishable from the cortex and cuticle filaments. Nail plate contains 10-20% soft keratins in addition to large amounts of hair keratins; these soft keratins have been identified as the 50K/58K and 48K/56K keratin pairs. Taken together, these results suggest that the precursor cells of hair cortex and nail plate share a major pathway of epithelial differentiation, and that the acidic 44K/46K and basic 56-60K hard keratins represent a co- expressed keratin pair which can serve as a marker for hair/nail-type epithelial differentiation.
Nitric oxide modulates regional blood flow differences in the fetal gastrointestinal tract.

We studied the role of endogenous nitric oxide (NO) in the regulation of gastrointestinal (GI) circulation in 11 chronically instrumented and unanesthetized late-gestation fetal sheep. Systemic and GI blood flows were measured by the radiolabeled microsphere technique. Mean arterial pressure (MAP), heart rate, blood flows, oxygen delivery, and vascular resistance were determined before and after infusion of the specific NO synthase inhibitor, N omega-nitro-L-arginine (L-NNA), to cumulative doses of 10 and 25 mg/kg. At both L-NNA doses, MAP increased, and combined ventricular output and heart rate decreased. GI blood flow and oxygen delivery decreased and vascular resistance increased for the stomach, all segments of the small intestine, and proximal colon and cecum but were unchanged in the middle and distal colon and rectum. Because blood flow reduction in the small intestine was pronounced (from 176 to 107 ml.min-1.100 g-1, P < 0.001) and blood flow in the large intestine was unchanged, distribution of intestinal blood flow became more uniform. Overall, blood flow reduction was proportionally greater in GI circulation than in the remainder of fetal circulation. In three additional animals we established that L-NNA reduced blood flow to the mucosal-submucosal layer (P < 0.02) but not to the muscularis serosa of the small intestine. In the same animals, L-arginine (250 mg/kg) restored systemic hemodynamics and partially restored small intestinal blood flow. Our results suggest that NO is an important differential regulator of vascular tone in the developing GI circulation.