Miracle-dz/UniFAR-FTUs huggingface dataset:
ADAPTIVE DIVERGENCE AND THE BALANCE BETWEEN SELECTION AND GENE FLOW: LAKE AND STREAM STICKLEBACK IN THE MISTY SYSTEM

Abstract We investigated the interplay between natural selection and gene flow in the adaptive divergence of threespine stickleback (Gasterosteus aculeatus) that reside parapatrically in lakes and streams. Within the Misty Lake system (Vancouver Island, British Columbia), stickleback from the inlet stream (flowing into the lake) have fewer gill rakers and deeper bodies than stickleback from the lake—differences thought to facilitate foraging (benthic macroinvertebrates in the stream vs. zooplankton in the open water of the lake). Common-garden experiments demonstrated that these differences have a genetic basis. Reciprocal transplant enclosure experiments showed that lake and inlet stickleback grow best in their home environments (although differences were subtle and often not significant). Release-recapture experiments in the inlet showed that lake fish are less well-suited than inlet fish for life in the stream (higher mortality or emigration in lake fish). Morphological divergence in the wild and under common rearing was greater between the lake and the inlet than between the lake and the outlet. Genetic divergence (mitochondrial DNA and microsatellites) was greatest between the lake and the upper inlet (1.8 km upstream from the lake), intermediate between the lake and the lower inlet (0.9 km upstream), and least between the lake and the outlet stream (1.2 km downstream). Relative levels of gene flow estimated from genetic data showed the inverse pattern. The negative association between morphological divergence and gene flow is consistent with the expectation that gene flow can constrain adaptation. Estimated absolute levels of gene flow also implied a constraint on adaptation in the outlet but not the inlet. Our results suggest that natural selection promotes the adaptive divergence of lake and stream stickleback, but that the magnitude of divergence can be constrained by gene flow.
GABAAR expression in brain noradrenergic and serotonergic centres and their plasticity in the context of stress induced behaviours

The broad intention of this thesis was to understand which factors regulate the release of serotonin and noradrenaline throughout the brain. Multiple factors, such as ion channels, transporters and neurotransmitter receptors shape the release of serotonin and noradrenaline within strict spatial and temporal windows. I was interested in how fast inhibition mediated by GABAARs may influence LC and DRN neuronal excitability. Therefore, within this thesis I localised distinct GABAAR subunits to the cellular and sub-cellular compartments of neurochemically diverse cell types which comprise the networks of two major monoaminergic brain centres, the noradrenergic Locus Coeruleus (LC) and the serotonergic Dorsal Raphe Nucleus (DRN). The GABAAR alpha1 subunit was predominantly localised to the non-principal, putative interneurons of the LC and DRN, whereas the GABAAR alpha2 and alpha3 subunits were mainly localised to the principal monoaminergic cells. This apparent segregation suggests that the precise targeting of certain GABAAR subunits to different cellular and sub-cellular compartments is important for shaping LC and DRN neuronal excitability, and thus the release of noradrenaline and serotonin. As these monoaminergic systems are engaged by stressor exposure (Swinny et al., 2010, Kirby et al., 2000, Kirby et al., 2007), and as they have been shown to have an important role in shaping mood (Stockmeier et al., 1998, Baumann et al., 2002), I was also interested to understand whether stressors engaged the GABAergic system to influence the release of monoamines. Moreover, I have demonstrated that a mild repeated stressor influences GABAAR expression at the transcriptomic level, in a brain region and subunit specific manner and thus 2 provide evidence for an important role of the GABAAR alpha3 subunit in the processing of stressor related information via the DRN. The finding that the stress neuropeptide CRH, contacts putative inhibitory synapses of serotonergic and non-serotonergic neurons of the DRN provides further evidence for the potential role of GABAergic neurotransmission in shaping DRN neuronal excitability in response to stressors. Finally, through behavioural phenotyping I have been able to demonstrate that a stressor induced increase in GABAAR alpha3 subunit expression in the DRN, parallels adaptive-like behavioural changes in response to a novel environment.
Localizing and Segmenting Objects with 3 D Objectness

This paper presents a novel method to localize and segment objects on close-range table-top scenarios sensed with a depth sensor. The method is based on a novel objectness measure that evaluates how likely a 3D region in space (defined by an oriented bounding box) could contain an object. Within a parametrized volume of interest placed above the table plane, a set of 3D bounding boxes is generated that exhaustively covers the parameter space. Efficiently evaluating — thanks to integral volumes and parallel computing — the 3D objectness at each sampled bounding box allows efficiently defining a set of regions in space with high probability of containing an object. Bounding boxes characterized by high objectness are then processed by means of a global optimization stage aimed at discarding inconsistent object hypotheses with respect to the scene. We evaluate the effectiveness of the method for the task of scene segmentation.
From the Selectedworks of Jeffrey A. Reinbolt Design of Patient-specific Gait Modifications for Knee Osteoarthritis Rehabilitation Design of Patient-specific Gait Modifications for Knee Osteoarthritis Rehabilitation

—Gait modification is a nonsurgical approach for reducing the external knee adduction torque in patients with knee osteoarthritis (OA). The magnitude of the first adduction torque peak in particular is strongly associated with knee OA progression. While toeing out has been shown to reduce the second peak, no clinically realistic gait modifications have been identified that effectively reduce both peaks simultaneously. This study predicts novel patient-specific gait modifications that achieve this goal without changing the foot path. The modified gait motion was designed for a single patient with knee OA using dynamic optimization of a patient-specific, full-body gait model. The cost function minimized the knee adduction torque subject to constraints limiting how much the new gait motion could deviate from the patient's normal gait motion. The optimizations predicted a " medial-thrust " gait pattern that reduced the first adduction torque peak between 32% and 54% and the second peak between 34% and 56%. The new motion involved three synergistic kinematic changes: slightly decreased pelvis obliquity, slightly increased leg flexion, and slightly increased pelvis axial rotation. After gait retraining, the patient achieved adduction torque reductions of 39% to 50% in the first peak and 37% to 55% in the second one. These reductions are comparable to those reported after high tibial osteotomy surgery. The associated kinematic changes were consistent with the predictions except for pelvis obliquity, which showed little change. This study demonstrates that it is feasible to design novel patient-specific gait modifications with potential clinical benefit using dynamic optimization of patient-specific, full-body gait models. Further investigation is needed to assess the extent to which similar gait modifications may be effective for other patients with knee OA.
Cloud Modeling for Computer Graphics

Realistic rendered images of clouds are important in architectural design, weather visualization, ight simulation, lm, art and entertainment. The extremely varied visual appearance of clouds and the complexity of the meteorological and optical processes that create clouds makes modeling and rendering di cult. This thesis presents a new visually-orientated technique for creating realistic images of convective clouds. The new technique is simple and very fast compared to physically-based methods, which makes it suitable for use on desktop workstations. The thesis also contains an overview of the meteorology and optics of clouds and a review of previous modeling and rendering techniques. Molnmodellering för datorgra k Referat Det är viktigt att ha tillgång till realistiska datorgenererade bilder av moln inom arkitekturdesign, vädervisualisering, ygsimulering, lm, konst och underhållning. Moln är dock svåra att modellera och rendera eftersom deras utseende varierar kraftigt. Samtidigt är det svårt att simulera de komplicerade fysiska processer som ger uppkomst till moln. I den här rapporten presenteras en ny, visuellt orienterad metod för att skapa realistiska bilder av cumulusmoln. Den nya tekniken är enkel och e ektiv jämfört med simuleringsbaserade metoder, vilket gör att den kan utnyttjas på persondatorer. Rapporten innehåller också en översikt över de delar av meteorologin och optiken som rör moln samt en genomgång av tidigare använda renderingsmetoder.
Can continuous glucose monitoring identify risk factors in type 1 and type 2 diabetes? A literature review

Self-monitoring of blood glucose has been used for many years to control glucose levels in diabetic patients. This method is a quick and easy way for taking pre/postprandial and pre-sleep glucose measurements and it is very simple for most of the patients. However, it does not allow collecting detailed information about excursions of hyperglycemia or hypoglycemia since most of the samples are widely spaced in time, which leads to lose important information for the treatment of diabetes. Nowadays, Continuous Glucose Monitoring System (CGMS) is used to solve such problem. CGMS devices take blood glucose samples continuously (normally every 5 minutes) from patients having type 1 or type 2 diabetes. This paper presents a literature review exploring the current CGMS applications and the role of this signal in the identification of risk factor for diabetic patients.
Antioxidant, Liver Protective and Angiotensin I-converting Enzyme Inhibitory Activities of Old Laying Hen Hydrolysate in Crab Meat Analogue

The purpose of this study was to evaluate the antioxidative activities of Crab meat analogue prepared with protein hydrolysates obtained from mechanically deboned chicken meat (MDCM) from spent laying hens. 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH) radical-scavenging activity was increased by adding MDCM hydrolysates during storage, and activity correlated with the concentration of DPPH added up to 6 weeks of storage. Hydroxyl radical-scavenging activity was increased in all analogues containing MDCM hydrolysates. At 0 days of storage, angiotensin I-converting enzyme (ACE)-inhibitory activity was increased by the addition of MDCM hydrolysates. Activity did not correlate after 6 weeks of storage, in which ACE-inhibitory activity was increased with low concentrations of MDCM hydrolysates, but no ACE-inhibitory activity was observed at higher concentrations. The liver-protecting activity of crab meat analogue was shown to be around 60% of the positive control; however, it was not significantly different among the samples during storage. These results support the use of MDCM as a source of health-promoting constituents in crab meat analogue.
Accepted for Publication in Ieee Transactions on Visualization and Computer Graphics, Authors' Personal Copy a Model for Structure-based Comparison of Many Categories in Small-multiple Displays

—Many application domains deal with multi-variate data that consist of both categorical and numerical information. Small-multiple displays are a powerful concept for comparing such data by juxtaposition. For comparison by overlay or by explicit encoding of computed differences, however, a specification of references is necessary. In this paper, we present a formal model for defining semantically meaningful comparisons between many categories in a small-multiple display. Based on pivotized data that are hierarchically partitioned by the categories assigned to the x and y axis of the display, we propose two alternatives for structure-based comparison within this hierarchy. With an absolute reference specification, categories are compared to a fixed reference category. With a relative reference specification, in contrast, a semantic ordering of the categories is considered when comparing them either to the previous or subsequent category each. Both reference specifications can be defined at multiple levels of the hierarchy (including aggregated summaries), enabling a multitude of useful comparisons. We demonstrate the general applicability of our model in several application examples using different visualizations that compare data by overlay or explicit encoding of differences.
Expression of dicistronic transcriptional units in transgenic tobacco

We investigated whether the two cistrons of a dicistronic mRNA can be translated in plants to yield both gene products. The coding sequences of various reporter genes were combined in dicistronic units, and their expression was analyzed in stably transformed tobacco plants at the RNA and protein levels. The presence of an upstream cistron resulted in all cases in a drastically reduced expression of the downstream cistron. The translational efficiency of the gene located downstream in the dicistronic units was 500- to 1,500-fold lower than that in a monocistronic control; a 500-fold lower value was obtained with a dicistronic unit in which both cistrons were separated by 30 nucleotides, whereas a 1,500-fold lower value was obtained with a dicistronic unit in which the stop codon of the upstream cistron and the start codon of the downstream cistron overlapped. As a strategy to select indirectly for transformants with enhanced levels of expression of a gene which is by itself nonselectable, the gene of interest can be cloned upstream from a selectable marker in a dicistronic configuration. This strategy can be used provided that the amount of dicistronic mRNA is high. If, on the other hand, the expression of the dicistronic unit is too low, selection of the downstream cistron will primarily give clones with rearranged dicistronic units.
Heart-rate complexity for prediction of prehospital lifesaving interventions in trauma patients.

BACKGROUND Traditional vital signs often fail to identify critically injured patients soon enough to permit timely intervention. To improve our ability to forecast the need for prehospital lifesaving interventions (LSIs), we applied heart-rate complexity (HRC) analysis to the electrocardiogram (ECG) of patients en route to trauma centers. METHODS Analysis of ECG and clinical data from 374 patients en route by helicopter to three urban Level I trauma centers was conducted. Waveforms from 182 patients were excluded (because of ectopy, noise, or inadequate length). Of the remaining 192 patients, 54 received 66 LSIs in the field (LSI group): intubation (n = 52), cardiopulmonary resuscitation (n = 5), cricothyroidotomy (n = 2), and pneumothorax decompression (n = 7); 138 patients did not (non-LSI group). In the field, heart rate, blood pressure, and the Glasgow Coma Scale score (GCS(TOTAL)) and its motor component (GCS(MOTOR)) were recorded. ECG was recorded during flight. Ectopy-free, 800-beat sections of ECG were identified off-line and analyzed by HRC methods including Sample Entropy (SampEn) and Detrended Fluctuations Analysis (DFA). RESULTS There was no difference between LSI and non-LSI patients in heart rate or blood pressure. SampEn was lower in LSI than in non-LSI (0.88 +/- 0.03 vs. 1.11 +/- 0.03), as was DFA (1.09 +/- 0.05 vs. 1.33 +/- 0.03) and GCS(MOTOR) (3.4 +/- 0.4 vs. 5.7 +/- 0.1) (all p < 0.0001). By logistic regression, SampEn, DFA, and GCS(MOTOR) were independently associated with LSIs (area under the receiver operating characteristic curve, 0.897). CONCLUSIONS Decreased HRC is associated with LSIs in prehospital trauma patients. HRC may be useful as a new vital sign for identification of the severely injured.
New appearance models for natural image matting

Image matting is the task of estimating a fore- and background layer from a single image. To solve this ill posed problem, an accurate modeling of the scene's appearance is necessary. Existing methods that provide a closed form solution to this problem, assume that the colors of the foreground and background layers are locally linear. In this paper, we show that such models can be an overfit when the colors of the two layers are locally constant. We derive new closed form expressions in such cases, and show that our models are more compact than existing ones. In particular, the null space of our cost function is a subset of the null space constructed by existing approaches. We discuss the bias towards specific solutions for each formulation. Experiments on synthetic and real data confirm that our compact models estimate alpha mattes more accurately than existing techniques, without the need of additional user interaction.
Incidence Rate of and Factors Associated with Loss to Follow-up in a Longitudinal Cohort of Antiretroviral-Treated HIV-Infected Persons: An AIDS Clinical Trials Group (ACTG) Longitudinal Linked Randomized Trials (ALLRT) Analysis

Abstract Purpose: Examine incidence and factors associated with loss to follow-up (LTFU) in the AIDS Clinical Trials Group (ACTG) Longitudinal Linked Randomized Trials (ALLRT) cohort.Method: ALLRT is a prospective cohort of HIV-infected persons randomized to antiretroviral (ARV) regimens/strategies in ACTG trials and followed long-term after the trial ends. Person-years were calculated from ALLRT entry until loss to follow-up (LTFU; defined using off-study reasons or ≥3 consecutive missed visits), death/ severe debilitation/site closures, or June 2009 (censored). Poisson regression was used to examine LTFU factors separately among participants who were ARV naïve or ARV experienced at trial entry.Results: Among 4,630 participants (22,524 person-years), 1,140 were lost to follow-up, 237 died, 29 were severely debilitated, and 443 were at sites that closed. The LTFU incidence was 5.5 and 4.2 per 100 person-years among previously ARV-naïve and ARV-experienced participants, respectively. In both groups, age ≤50, site location, being off ARVs, and viral load ≥400 copies/mL were associated with a higher risk of LTFU. Among ARV-naïve participants, male sex, education <16 years, intravenous drug use, and cigarette smoking were also associated with LTFU.Conclusion: Knowledge of differential LTFU can help researchers identify participants at risk of LTFU in longitudinal HIV cohorts and design retention strategies, thereby limiting study bias. The identified factors should be included in inverse probability of weighting models to account for LTFU.
Reliable Paths with Pose SLAM

The maps built by standard feature-based SLAM methods cannot be directly used to compute paths for navigation, unless enriched with obstacle or traversability information with the consequent increase in complexity. Here, we propose a method that directly uses the Pose SLAM graph of constraints to determine the path between two robot configurations with lowest accumulated pose uncertainty, i.e., the most reliable path to the goal. The method shows improved navigation results when compared to standard path planning strategies, both over datasets and real world experiments.
Pressure + X/Z two-axis acceleration composite sensors monolithically integrated in non-soi wafer for upgraded production of TPMS (tire pressure monitoring systems)

The paper reports a novel low-cost batch fabrication technique for monolithically integrated pressure plus two-axis (X/Z) acceleration composite sensors for upgraded production of automobile TPMS (tire-pressure monitoring systems). The newly added X-axis accelerometer is used for automatically identifying and positioning each of the four wheels. Benefited from the single-wafer front-side fabrication technique on non-SOI wafers, the sensor has the advantages of small chip-size of 1.9mm∗1.9mm, low cross-talk interference, low-cost and compatible process with IC-foundries. Testing results of the TPMS sensor meet the requirements of upgraded TPMS application.
A coarse-to-precise matching strategy in navigation

In order to ensure that SAR scene matching aided navigation system can acquire the position errors and yawing errors simultaneously, it is important to select the matching method carefully. In this paper, a coarse-to-precise matching strategy is proposed to be applied in navigation. The proposed method combines area-based and feature-based matching method. Specifically, in the coarse phase, a wavelet-based pyramid multi-resolution technique is adopted to reduce the number of calculated pixels, and then the robustness of the strategy is achieved by a multi-scale circular template fusion. In the precise stage, a nonlinear scale space method is recommended to accomplish the high matching performance. Two experimental results, matching real-time images with reference image and matching multiple real-time subimages with reference image, are listed to validate the proposed strategy.
Visualising concurrent programs with dynamic dependence graphs

Atropos is a software tool for visualising concurrent program executions intended to help students debug concurrent programs and learn how concurrency works. Atropos supports a slicing debugging strategy by providing a visualisation of dynamic dependence graphs that can be explored to trace the chain of events backwards from a symptom to its cause. In this paper, we present the reasoning behind the design of Atropos and summarise how we evaluated it with students.
Ultrasonication effect on size distribution of functionalized porous silicon microparticles

Sponge-like luminescent mesoporous silicon microparticles are produced from crystalline silicon with a simple and cheap top-down fabrication process which, however, offers scarce control of structural features such size, size distribution and pore dimensions of the final product. Herein, we report on a post-fabrication procedure based on ultrasonic treatment to get more homogeneous size distribution and much more control on the average dimension of the microparticles. We investigated the effect of variable ultrasonic treatments on the structural and optical properties of the microparticles. The structure was analysed both at micro and nano scale and for microparticles in dried state and in solution. We proved that few minutes of sonication strongly limits the heterogeneity of the sample size, without affecting the optical properties and porous structure. This simple post-fabrication step offers new opportunities for successful use of silicon microparticles in biomedicine.
Tactile temporal discrimination in patients with blepharospasm

Background: Blepharospasm is an adult-onset focal dystonia that causes involuntary blinking and eyelid spasms. Studies have shown the presence of sensory deficits associated with dystonia. Aim: To rule out any confounding effect of muscle spasms on sensory performance in affected and unaffected body regions of patients with blepharospasm and with hemifacial spasm. Methods: Participants (19 patients with blepharospasm, 19 patients with hemifacial spasm and 19 control subjects) were asked to discriminate between two stimuli that were either simultaneous or sequential (temporal discrimination threshold, TDT). Pairs of tactile stimuli were delivered with increasing or decreasing inter-stimulus intervals from 0 to 400 ms (in 10-ms steps) to the hands or on the skin over the orbicularis oculi muscle. Results: Tactile stimuli elicited similar TDTs in control subjects and patients with hemifacial spasm, but significantly higher TDTs in patients with blepharospasm, regardless of whether stimuli were applied to the orbicularis muscle or the hand. Conclusions: As TDT was abnormal in unaffected body regions of patients with blepharospasm, and patients with hemifacial spasm processed tactile stimuli normally, TDT deficits in blepharospasm depend on central rather than peripheral factors. This study further supports the link between focal dystonia and impaired temporal processing of somatosensory inputs.