Miracle-dz/UniFAR-FTUs huggingface dataset:
Viruses and bacteria in floodplain lakes along a major Amazon tributary respond to distance to the Amazon River

In response to the massive volume of water along the Amazon River, the Amazon tributaries have their water backed up by 100s of kilometers upstream their mouth. This backwater effect is part of the complex hydrodynamics of Amazonian surface waters, which in turn drives the variation in concentrations of organic matter and nutrients, and also regulates planktonic communities such as viruses and bacteria. Viruses and bacteria are commonly tightly coupled to each other, and their ecological role in aquatic food webs has been increasingly recognized. Here, we surveyed viral and bacterial abundances (BAs) in 26 floodplain lakes along the Trombetas River, the largest clear-water tributary of the Amazon River’s north margin. We correlated viral and BAs with temperature, pH, dissolved inorganic carbon, dissolved organic carbon (DOC), phosphorus, nitrogen, turbidity, water transparency, partial pressure of carbon dioxide (pCO2), phytoplankton abundance, and distance from the lake mouth until the confluence of the Trombetas with the Amazon River. We hypothesized that both bacterial and viral abundances (VAs) would change along a latitudinal gradient, as the backwater effect becomes more intense with increased proximity to the Amazon River; different flood duration and intensity among lakes and waters with contrasting sources would cause spatial variation. Our measurements were performed during the low water period, when floodplain lakes are in their most lake-like conditions. Viral and BAs, DOC, pCO2, and water transparency increased as distance to the Amazon River increased. Most viruses were bacteriophages, as viruses were strongly linked to bacteria, but not to phytoplankton. We suggest that BAs increase in response to DOC quantity and possibly quality, consequently leading to increased VAs. Our results highlight that hydrodynamics plays a key role in the regulation of planktonic viral and bacterial communities in Amazonian floodplain lakes.
Unsupervised, automated segmentation of the normal brain using a multispectral relaxometric magnetic resonance approach

The purpose of this study was the development and testing of a method for unsupervised, automated brain segmentation. Two spin‐echo sequences were used to obtain relaxation rates and proton‐density maps from 1.5 T MR studies, with two axial data sets including the entire brain. Fifty normal subjects (age range, 16 to 76 years) were studied. A Three‐dimensional (3D) spectrum of the tissue voxels was used for automatic segmentation of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) and for calculation of their volumes. Accuracy and reproducibility were tested with a three‐compartment phantom simulating GM, WM, and CSF. In the normal subjects, a significant decrease of GM fractional volume and increased CSF volume with age were observed (P < 0.0001), with no significant changes in WM. This multi‐spectral segmentation method permits reproducible, operator‐independent volumetric measurements.
Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014

Objectives The hypothesis of the study was that if the gut microbiota is involved in the development of atherosclerotic cardiovascular and cerebrovascular diseases (CVDs), total colectomy may reduce the long-term risk of CVDs. The aim was therefore to investigate the risk of CVD in patients after a total colectomy compared with patients undergoing other types of surgery, which are not expected to alter the gut microbiota or the CVD risk. Setting The Danish National Patient Register including all hospital discharges in Denmark from 1996 to 2014. Participants Patients (n=1530) aged 45 years and above and surviving 1000 days after total colectomy without CVDs were selected and matched with five control patients who were also free of CVD 1000 days after other types of surgery. The five control patients were randomly selected from each of the three surgical groups: orthopaedic surgery, surgery in the gastrointestinal tract leaving it intact and other surgeries not related to the gastrointestinal tract or CVD (n=22 950). Primary and secondary outcome measures The primary outcome was the first occurring CVD event in any of the seven diagnostic domains (hypertensive disorders, acute ischaemic heart diseases, chronic ischaemic heart disease, cardiac arrhythmias, heart failure, cerebrovascular diseases and other arterial diseases) and the secondary outcomes were the first occurring event within each of these domains. Results Estimated by Cox proportional hazard models, the HRs of the composite CVD end point for patients with colectomy compared with the control patients were not significantly reduced (HR=0.94, 95% confidence limits 0.85 to 1.04). Among the seven CVD domains, only the risk of hypertensive disorders was significantly reduced (HR=0.85, 0.73 to 0.98). Conclusions Colectomy did not reduce the general risk of CVD, but reduced the risk of hypertensive disorders, most likely due to salt and water depletion induced by colectomy. These results encourage a reappraisal of the associations between gut microbiota and CVD.
Error Estimates for a Vectorial Second-Order Elliptic Eigenproblem by the Local L2 Projected C0 Finite Element Method

In this paper, a theoretical framework with a completely new theory is presented for the general curlcurl-graddiv second-order elliptic eigenproblem when discretized by the recently developed local $L^2$ projected $C^0$ finite element method. The theoretical framework consists of two Fortin-type interpolations and an Inf-Sup inequality associated with a trilinear curl/div form. From this framework, error estimates are readily derived for the source problem as well as the eigenproblem. The new theory is verified for the local $L^2$ projected $C^0$ finite element method with elementwise linear element $L^2$ projections applied to div and curl operators and the $C^0$ linear elements enriched with some face-bubbles and element-bubbles for the singular solution. The challenging question is whether $C^0$ elements can give spectrally correct approximations when eigenfunctions are singular (not in $(H^1(\Omega))^d$ space). It is shown that optimal error bounds can be obtained from this theoretical framework with .
Neural Network Control for Position Tracking of a Two-Axis Inverted Pendulum System: Experimental Studies

In this paper, experimental studies of a decentralized neural network control scheme of the reference compensation technique applied to control a 2-degrees-of-freedom (2-DOF) inverted pendulum on an x-y plane are presented. Each axis is controlled by two separate neural network controllers to have a decoupled control structure. Neural network controllers are applied not only to balance the angle of pendulum, but also to control the position tracking of the cart. The decoupled control structure can compensate for uncertainties and cancel coupling effects. Especially, a circular trajectory tracking task is tested for position tracking control of the cart while maintaining the angle of the pendulum. Experimental result shows that position control of the inverted pendulum and cart is successful.
Automatic Generation of Graphical User Interfaces for Simulation of Modelica Models

For a certain class of applications simulation models are developed and then rolled out for standalone usage without the tool with which they have been developed. The user is intended to perform simulation runs, to inspect results, to change selected parameters within given bounds, but not to inspect or even change the model itself. The reasons for such a usage scenario are manifold: The simulation is intended to be used as a black-box tool by non simulation specialists, a component vendor (electric drives, pneumatic or hydraulic components, etc.) likes to demonstrate the performance of his components in the context of a simulation or the model developer may hide model details. If a model development tool includes code generation the model specific simulator can be setup fully automatic. However, a GUI (graphical user interface) for such a simulator must be developed manually. We developed a tool which automatically generates a simulator GUI from a Modelica model and data definition.
An Evaluation of the Effectiveness of an FE/HE Partnership in the Delivery of a Preparation for Practice Module within an Undergraduate Social Work Degree Programme

The Preparation for Practice module at the University of Ulster is delivered to 170 first year students via a collaborative arrangement between higher and further education institutions. In each of the five sites, students receive large group and small group teaching facilitated by social work training agency workers and academic tutor dyads. An evaluation of the module sought the perceptions of the agency and academic facilitators regarding the overall collaborative arrangement and the model of co-teaching involving social work academics and agency partners. Respondents were asked to complete a semi-structured questionnaire, which generated data from a Likert scale and also invited qualitative commentary. The Likert scale data were analysed via SPSS and the qualitative information was scrutinised using a manual thematic analysis technique. Findings indicated that continuous communication, consistency in programme content and the acknowledgement of the differences in organisation resources were key to a successful collaborative arrangement. It was also noted that a co-teaching model should be viewed as a positive vehicle for achieving module objectives in a safe learning environment.
An empirical comparison of three variants of the AHP and two variants of conjoint analysis

This paper provides an empirical comparison of two methods of attribute valuation: the analytic hierarchy process (AHP) and conjoint analysis. Variants within each approach are also examined. The results of two empirical studies indicate that the methods differ in their predictive and convergent validity. Within the AHP methods no significant difference in predictive validity was found. Within the conjoint methods, the ranking method significantly outperformed the rating method. The difference in predictive validity between the AHP and conjoint methods was significant in the second study but not in the first study, suggesting superior performance of the AHP over conjoint analysis in complex problems. Copyright© 1998 John Wiley & Sons, Ltd.
Effects of camptothecin on double-strand break repair by non-homologous end-joining in DNA mismatch repair-deficient human colorectal cancer cell lines

Loss of a functional mismatch repair (MMR) system in colorectal cancer (CRC) cells is associated with microsatellite instability and increased sensitivity to topoisomerase inhibitors. In this study, we have investigated whether a defect in double-strand break (DSB) repair by non-homologous end-joining (NHEJ) could explain why MMR-deficient CRC cells are hypersensitive to camptothecin (CPT), a topoisomerase I inhibitor. To evaluate the efficiency and the fidelity of DSB repair, we have transiently transfected plasmids containing cohesive or non-complementary ends in cells with various MMR defects. We have observed that the repair efficiency of DSB with cohesive and non-complementary ends is comparable in all cell lines. In contrast to the MMR-proficient cell line HT29, the MMR-deficient cell lines were highly accurate in repairing DSB with cohesive ends, but this characteristic could not be directly assigned to the primary MMR deficiency. Furthermore, CPT treatment had no detectable effect on the repair of cohesive ends but significantly decreased the repair efficiency of non-complementary DSB. In conclusion, although our observations show that DSB repair efficiency by NHEJ decreases upon treatment with CPT, which possibly contributes to its cytotoxicity, it is quite unlikely that it accounts for the hypersensitivity of MMR-deficient cells to topoisomerase inhibitors.
Characterization of driver nodes: Network of discrete-time agents

A network of discrete-time agents (nodes) which can be controlled by different nodes, acting independently, is considered. When a network can be controlled through several nodes, it is important to understand differences in choosing a particular node as driver node (node which control the entire network). This work considers limited actuator amplitude of driver node and characterizes driver node based on Region of Attraction (ROA) obtained corresponding to a particular chosen driver node. The presented theory and algorithms enable to find an appropriate node such that Region of Attraction maximizes. Theoretical developments are verified through numerical simulation.
Cross-Cultural Invariance in Story Recall.

MANDLER, JEAN M. ; SCRIBNER, SYLVIA; COLE, MICHAEL; and DEFOREST, MARSHA. CrOSs-cultural Invariance in Story Recall. CHILD DEVELOPMENT, 1980, 51, 19-26. A comparison was made of recall of stories by Liberian nonschooled children, nonliterate adults, nonschooled literate adults, and schooled literate adults. These data were then compared to similar data from American children and adults. Highly similar patterns of recall were found for all groups, although there was improvement in performance from childhood to adulthood. The data were used to support a hypothesis of the universality of certain kinds of schematic organization and their control of memorial processes.
Hand gesture recognition: self-organising maps as a graphical user interface for the partitioning of large training data sets

Gesture recognition is a difficult task in computer vision due to the numerous degrees of freedom of a human hand. Fortunately, human gesture covers only a small part of the theoretical "configuration space" of a hand, so an appearance based representation of human gesture becomes tractable. A major problem, however, is the acquisition of appropriate labelled image data from which an appearance based representation can be built. In This work we apply self-organising maps for a visualisation of large amounts of segmented hands performing pointing gestures. Using a graphical interface, an easy labelling of the data set is facilitated. The labelled set is used to train a neural classification system, which is itself embedded in a larger architecture for the recognition of gestural reference to objects.
Validity of two wearable monitors to estimate breaks from sedentary time.

UNLABELLED Investigations using wearable monitors have begun to examine how sedentary time behaviors influence health. PURPOSE The objective of this study is to demonstrate the use of a measure of sedentary behavior and to validate the activPAL (PAL Technologies Ltd., Glasgow, Scotland) and ActiGraph GT3X (Actigraph, Pensacola, FL) for estimating measures of sedentary behavior: absolute number of breaks and break rate. METHODS Thirteen participants completed two 10-h conditions. During the baseline condition, participants performed normal daily activity, and during the treatment condition, participants were asked to reduce and break up their sedentary time. In each condition, participants wore two ActiGraph GT3X monitors and one activPAL. The ActiGraph was tested using the low-frequency extension filter (AG-LFE) and the normal filter (AG-Norm). For both ActiGraph monitors, two count cut points to estimate sedentary time were examined: 100 and 150 counts per minute. Direct observation served as the criterion measure of total sedentary time, absolute number of breaks from sedentary time, and break rate (number of breaks per sedentary hour (brk·sed-h)). RESULTS Break rate was the only metric sensitive to changes in behavior between baseline (5.1 [3.3-6.8] brk·sed-h) and treatment conditions (7.3 [4.7-9.8] brk·sed-h) (mean (95% confidence interval)). The activPAL produced valid estimates of all sedentary behavior measures and was sensitive to changes in break rate between conditions (baseline, 5.1 [2.8-7.1] brk·sed-h; treatment, 8.0 [5.8-10.2] brk·sed-h). In general, the AG-LFE and AG-Norm were not accurate in estimating break rate or the absolute number of breaks and were not sensitive to changes between conditions. CONCLUSION This study demonstrates the use of expressing breaks from sedentary time as a rate per sedentary hour, a metric specifically relevant to free-living behavior, and provides further evidence that the activPAL is a valid tool to measure components of sedentary behavior in free-living environments.
The Dalhousie Career Portfolio Programme: A multi-faceted approach to transition to work

This article describes a well-established Canadian university's new programme to prepare students for the world of work while enhancing the undergraduate educational experience. The overall purpose of the 'Dalhousie Career Portfolio' programme is to help students understand the value and transferability of their learning, knowledge and skills to their personal and career development. The multi-faceted aspect of the programme is emphasised, as is the voluntary nature of participation by academic staff and students. Surveys and focus groups report a relatively high level of satisfaction among early participants in the programme. To ensure a sustainable impact on educational quality, this employability project must integrate observations and lessons from the international arena, instil 'portfolio thinking' throughout the campus community, and thoroughly monitor teaching, learning and employment outcomes.
Temporally controlled targeted somatic mutagenesis in skeletal muscles of the mouse

To generate temporally controlled targeted somatic mutations selectively and efficiently in skeletal muscles, we established a transgenic HSA‐Cre‐ERT2 mouse line in which the expression of the tamoxifen‐dependent Cre‐ERT2 recombinase is under the control of a large genomic DNA segment of the human skeletal muscle α‐actin gene, contained in a P1‐derived artificial chromosome. In this transgenic line Cre‐ERT2 is selectively expressed in skeletal muscles, and Cre‐ERT2‐mediated alteration of LoxP flanked (floxed) target genes is skeletal muscle‐specific and strictly tamoxifen‐dependent. HSA‐Cre‐ERT2 mice should be of great value to analyze gene function in skeletal muscles, and to establish animal models of human skeletal muscle disorders. genesis 41:165–170, 2005. © 2005 Wiley‐Liss, Inc.
Wide‐field tracking with zenith‐pointing telescopes

Equipped with a suitable optical relay system, telescopes employing low-cost fixed primary mirrors could point and track while delivering high-quality images to a fixed location. Such an optical tracking system would enable liquid-mirror telescopes to access a large area of sky and employ infrared detectors and adaptive optics. Such telescopes could also form the elements of an array in which light is combined either incoherently or interferometrically. Tracking of an extended field requires correction of all aberrations including distortion, field curvature and tilt. A specific design is developed that allows a 10-m liquid-mirror telescope to track objects for as long as 30 min and to point as far as 4° from the zenith, delivering a distortion-free diffraction-limited image to a stationary detector, spectrograph or interferometric beam combiner.
Humanoid Gait Stabilization based on Omnidirectional Visual Gyroscope

Omnidirectional vision has already been used for attitude and heading estimation, thanks to its wide field of view. We adapt some existing methods in order to obtain a simple vision system capable to estimate pitch, roll and yaw angles for a real time application, using the parallel lines of the environment. We test this visual gyroscope and visual compass in some common environments to show that the proposed sensor continues to work even if the number of detected lines is small. We mount the catadioptric sensor in place of the head of a humanoid robot and use the measured angles to stabilize the walk, allowing the robot to keep a vertical position also if the terrain changes its slope. In this way we also stabilize the robot's perception, reducing camera oscillations.
Ecologically valid long-term mood monitoring of individuals with bipolar disorder using speech

Speech patterns are modulated by the emotional and neurophysiological state of the speaker. There exists a growing body of work that computationally examines this modulation in patients suffering from depression, autism, and post-traumatic stress disorder. However, the majority of the work in this area focuses on the analysis of structured speech collected in controlled environments. Here we expand on the existing literature by examining bipolar disorder (BP). BP is characterized by mood transitions, varying from a healthy euthymic state to states characterized by mania or depression. The speech patterns associated with these mood states provide a unique opportunity to study the modulations characteristic of mood variation. We describe methodology to collect unstructured speech continuously and unobtrusively via the recording of day-to-day cellular phone conversations. Our pilot investigation suggests that manic and depressive mood states can be recognized from this speech data, providing new insight into the feasibility of unobtrusive, unstructured, and continuous speech-based wellness monitoring for individuals with BP.
Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.