Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination1[W][OPEN]

Gene expression profiling in two seed compartments uncovers two transcriptional phases during seed germination that are separated by testa rupture. Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high-resolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.
Perceptions, Attitudes and Behaviour around Climate Change Risks on Livelihood Activities: A Case Study of a Community in Takeo Province, Cambodia

This thesis investigates the Takeo community’s perception of climate change risks and their response strategies. It examines risks occurring in the regions and their impacts on the community. The thesis also explores how the perception of risks frames the community’s adaptation and mitigation strategies as well as how those perceptions influence climate change policies. This research draws on a range of risk perception theories. Employing a qualitative approach, this study uses semi-structured interviews, document analysis and participant observation as its research methods. Interviews were conducted individually with agricultural practitioners, mothers, community leaders, a local government officer and a government official from the Ministry of Environment. The thesis found that the Takeo’s community has a good perception of the issue and its impacts on their community. Droughts are the major concern for the majority of respondents, because these have become more severe and have the most direct impact on farmers’ lives, livelihoods and food security. The study reflects the view maintained by past and current theory, that individual perceptions of risks vary, and the perception of risk is influenced by media and peers. This study adds that farmers’ direct experience of climate change affects their consideration of such risks as an issue of great personal concern. Perception of climate change influences the community’s responses. Farmers employ a wide range of adaptation strategies such as increasing water storage and improving agricultural techniques. However, adaptation approaches are not enough to provide a long-term solution to the fast changing climate, because the community has limited knowledge of adaptation strategies, resources, and limited support from the government. The community, thus, needs to improve its water management by building more dams and sufficient irrigation that can store enough water for consumption and agriculture in the prolonged dry season. The government should provide more support and services to poor rural communities that rely on agriculture.
The influence of population size, noise strength and behavioral task on best-encoded stimulus for neurons with unimodal or monotonic tuning curves

Tuning curves and receptive fields are widely used to describe the selectivity of sensory neurons, but the relationship between firing rates and information is not always intuitive. Neither high firing rates nor high tuning curve gradients necessarily mean that stimuli at that part of the tuning curve are well represented by a neuron. Recent research has shown that trial-to-trial variability (noise) and population size can strongly affect which stimuli are most precisely represented by a neuron in the context of a population code (the best-encoded stimulus), and that different measures of information can give conflicting indications. Specifically, the Fisher information is greatest where the tuning curve gradient is greatest, such as on the flanks of peaked tuning curves, but the stimulus-specific information (SSI) is greatest at the tuning curve peak for small populations with high trial-to-trial variability. Previous research in this area has focussed upon unimodal (peaked) tuning curves, and in this article we extend these analyses to monotonic tuning curves. In addition, we examine how stimulus spacing in forced choice tasks affects the best-encoded stimulus. Our results show that, regardless of the tuning curve, Fisher information correctly predicts the best-encoded stimulus for large populations and where the stimuli are closely spaced in forced choice tasks. In smaller populations with high variability, or in forced choice tasks with widely-spaced choices, the best-encoded stimulus falls at the peak of unimodal tuning curves, but is more variable for monotonic tuning curves. Task, population size and variability all need to be considered when assessing which stimuli a neuron represents, but the best-encoded stimulus can be estimated on a case-by case basis using commonly available computing facilities.
Contextual Anatomic Mimesis Hybrid In-Situ Visualization Method for Improving Multi-Sensory Depth Perception in Medical Augmented Reality

The need to improve medical diagnosis and reduce invasive surgery is dependent upon seeing into a living human system. The use of diverse types of medical imaging and endoscopic instruments has provided significant breakthroughs, but not without limiting the surgeon's natural, intuitive and direct 3D perception into the human body. This paper presents a method for the use of augmented reality (AR) for the convergence of improved perception of 3D medical imaging data (mimesis) in context to the patient's own anatomy (in-situ) incorporating the physician's intuitive multi- sensory interaction and integrating direct manipulation with endoscopic instruments. Transparency of the video images recorded by the color cameras of a video see-through, stereoscopic head- mounted-display (HMD) is adjusted according to the position and line of sight of the observer, the shape of the patient's skin and the location of the instrument. The modified video image of the real scene is then blended with the previously rendered virtual anatomy. The effectiveness has been demonstrated in a series of experiments at the Chirurgische Klinik in Munich, Germany with cadaver and in-vivo studies. The results can be applied for designing medical AR training and educational applications.
Adaptive contrast enhancement using gain-controllable clipped histogram equalization

Histogram equalization is a simple and effective method for contrast enhancement as it can automatically define the intensity transformation function based on statistical characteristics of the image. However, it tends to alter the brightness of the entire image, which it is not suitable for consumer electronic products, where preservation of the original brightness is essential to avoid annoying artifacts. This paper presents a new contrast enhancement method for generalization of the existing bihistogram equalization (BHE) and recursive mean-separate histogram equalization (RMSHE) methods. The proposed method is referred to gain-controllable clipped histogram equalization (GC-CHE) to provide both histogram equalization and brightness preservation. More specifically adaptive contrast enhancement is realized by using clipped histogram equalization with controllable gain. The clipping rate is determined based on the mean brightness, and the clipping threshold is determined based on the clipping rate. The clipping rate is adaptively controlled to enhance the contrast with preserving the mean brightness. It is mathematically proven that the mean brightness of the output image converges to that of the input image with adaptive controlled. Simulation results show that the proposed GC-CHE method outperforms existing histogram-based methods, such as HE, BHE, and RMSHE, in various situations.
Differential roles of STAT 1 and STAT 1 in fludarabine-induced cell cycle arrest and apoptosis in human B cells

Signal transducer and activator of transcription 1 (STAT1), a transcription factor known to participate in antiviral responses, acts as a tumor suppressor inhibiting cell growth and promoting apoptosis. To study the role of STAT1 in DNA damage–induced apoptosis in B lymphocytes, its active form, STAT1 , was specifically inhibited by the overexpression of STAT1 , the STAT1 truncated inhibitory isoform. An episomal vector with a tetracycline-inducible bidirectional promoter was created to induce the expression of 2 proteins, STAT1 and enhanced green fluorescence protein (EGFP). The same vector was used to overexpress STAT1 as a control. Expression of STAT1 inhibited the phosphorylation, the DNA-binding activity, and the transcriptional activity of STAT1 , as well as the expression of STAT1 target genes such as p21WAF1/ CIP1, TAP1, IRF1, and PKR. Inhibiting STAT1 by STAT1 increased the growth rate of transfected cells and their resistance to fludarabine-induced apoptosis and cell cycle arrest. Overexpressing STAT1 reversed the negative regulation of Mdm2 expression observed after treatment with interferon-gamma (IFN), which activates STAT1, or with fludarabine. Nuclear translocation of p53 after fludarabine treatment was decreased when STAT1 was overexpressed, and it was increased when STAT1 was induced. Oligonucleotide pull-down experiments showed a physical STAT1/p53 interaction. Our results show that imbalance between the antiproliferative/proapoptotic isoform STAT1 and the proliferative isoform STAT1 is likely to play a crucial role in the regulation of proliferation and apoptosis and that STAT1 may regulate p53 activity and sensitize B cells to fludarabine-induced apoptosis. (Blood. 2004;104:2475-2483)
Metabolic control as reflected by HbA1c in children, adolescents and young adults with type-1 diabetes mellitus: combined longitudinal analysis including 27,035 patients from 207 centers in Germany and Austria during the last decade.

INTRODUCTION While the central role of HbA1c levels for the prediction of micro- and macrovascular complications in patients with type 1 diabetes is generally accepted; recommendations in current guidelines and the level of metabolic control actually achieved during routine care differ widely. Limited information is available on factors that influence metabolic control in the pediatric age group and during the transition from pediatric to adult diabetes care. In a large prospective multicenter database (DPV-Wiss), 338,330 individual HbA1c measurements from 27,035 patients with type-1 diabetes (94,074 observation years) were recorded between 1995 and 2005. Data were anonymously transmitted from 207 institutions. HbA1c values were mathematically standardized to the DCCT normal range (4.05-6.05%). The SAS 9.1 software was used for statistical analysis using nonparametric statistics. Median HbA1c for all measurements was 7.8%, with a strong effect of diabetes duration: median HbA1c at onset was 9.1%, during the first 2 years of diabetes 7.1% with a subsequent increase to 7.9% in patients beyond the remission phase (>2 years, 20,314 patients); a strong age dependency was present. HbA1c above the recommended guidelines was found in 23%. For all age groups, girls/women had higher HbA1c values compared to boys (mean difference 0.1%, p<0.0001). Seasonal variation was remarkably small with the lowest HbA1c values in September (mean: 7.86%) and highest values in January (8.08%; p<0.0001). Some improvement in HbA1c was observed comparing three periods: 1995-1997, 1998-2000 and 2001-2005; after remission the median HbA1c decreases from 8.5% to 7.6%. In a multivariate model, a significant influence on HbA1c was detected for age (p<0001), duration of diabetes (p<0.0001), gender (p<0.02), minority status (p<0.0001), season (p<0.0001), treatment period (p<0.0001), insulin therapy (p<0.0001) and center effect (p<0.0001). CONCLUSIONS Both patient-related and treatment-related variables have a strong influence on metabolic control achieved in pediatric and young adult patients with T1DM. In contrast to wide-spread belief, metabolic control is only marginally better in summer compared to winter. Some improvement in metabolic control was observed during the last 10 years.
Preparation and characterization of a polystyrene/bovine serum albumin nanoparticle‐coated capillary for chiral separation using open‐tubular capillary electrochromatography

Polystyrene (PS) nanoparticles coated by BSA, hereafter denoted as PS/BSA, were prepared and chemically immobilized for the first time onto a capillary inner wall for open‐tubular CEC (OTCEC). EOF and scanning electron micrography were used to characterize the prepared nanoparticle‐coated capillaries. To investigate the performance of the prepared columns in OTCEC, chiral separation of d,l‐tryptophan (dl‐Trp) was performed in monolayer BSA‐modified capillary and PS/BSA nanoparticle‐coated columns. The results indicated that the nanoparticle‐modified column afforded a higher resolution compared with the monolayer type. Rapid enantioseparation of dl‐Trp (within 3 min) was achieved with the PS/BSA‐immobilized column using an electroosmotic pump‐assisted CEC. Enantiomer separations of other compounds like dl‐tyrosine and warfarin were also achieved with the column. Besides, run‐to‐run and column‐to‐column repeatabilities of the PS/BSA‐coated column in the chiral separation were systematically introduced.
Guide on Life Cycle Inventory (LCI) data generation for the Environmental Footprint

5 Acknowledgements . 6 Introduction . 7 1. Process data set types differentiated in ILCD format . 8 2. Procedure for updates of EF data sets and data stocks . 12 Conditions to update EF data sets and data stocks . 12 Frequency of the updates . 12 Procedure for updates that affect the core content of the data set (case A1) . 12 Procedure for updates from the data provider that do not affect the core content of the data set (case A2) . 13 Procedure for updates due to the EF reference package update (case B) . 13 3. Harmonization of EF data sets partly disaggregated at level-1 . 15 4. Requirements for meta-data information in EF data sets . 17 General information . 17 Conventions . 17 Information relevant for all data sets . 17 Data set LCA report, background info . 17 Type of process . 17 Reference year . 17 Default parameter values. 18 Regionalized elementary flows . 18 Duplicated elementary flows . 18 Allocation . 18 Element content . 18 CFF Parameters . 20 Modelling constants . 20 LCA methodology report . 20 Data sources used for this data set . 20 Reference to supported Impact methods: . 21 Compliance . 21 LCIA results . 21 Data quality criteria and rating . 21 Information relevant for partly disaggregated data sets . 24 Complementing processes . 24 Complete flow diagram . 24 Supporting sub-processes . 24
Modulation of KdpD phosphatase implicated in the physiological expression of the Kdp ATPase of Escherichia coli

The KdpD sensor kinase and the KdpE response regulator control the expression of the kdpFABC operon, encoding the KdpFABC high‐affinity K+ transport system of Escherichia coli. Low turgor pressure has been postulated to be the environmental stimulus to express KdpFABC. KdpD has autokinase, phosphotransferase and, like many sensor kinases, response regulator (phospho‐KdpE) specific phosphatase activity. To determine which of these activities are altered in response to the environmental stimulus, we isolated and analysed six kdpD mutants that cause constitutive expression of KdpFABC. In three of the mutants, phosphatase activity was undetectable and, in two, phosphatase was reduced. Kinase activity was unaffected in four of the mutants, but elevated in one. In one mutant, a pseudorevertant of a kdpD null mutation, kinase and phosphatase were both reduced to 20% of the wild‐type level. These findings suggest that initiation of signal transduction by KdpD is mediated by the inhibition of the phospho‐KdpE‐specific phosphatase activity of KdpD, leading to an accumulation of phospho‐KdpE, which in turn activates the expression of the KdpFABC system. The data also suggest that levels of activity in vitro may differ from what occurs in vivo, because in vitro conditions cannot replicate those in vivo.
Adaptive Path Planning for a Vision-Based quadrotor in an Obstacle Field : Beijing, China

This paper demonstrates a real life approach for quadrotor obstacle avoidance in indoor flight. A color-based vision approach for obstacle detection is used to good effect conjointly with an adaptive path planning algorithm. The presented task is to move about a set indoor space while avoiding randomly located obstacles and adapting a path to prevent future confrontation with the obstacles all together. The goal is to complete this task with a solution that is simple and efficient. The result is an adaptive path planning algorithm that evades obstacles when necessary and uses these interactions to find an obstaclefree path with simple logic. The whole task is implemented within Paparazzi, an open source autopilot software. Flight tests are performed in an indoor flight arena with simulated GPS from a camera tracking system. Through these flight tests, the approach proves to be reliable and efficient
Midgard Worms: Sudden Nasty Surprises from a Large Resilient Zombie Army

Future network intruders will probably use a zombie army to deliver many different attacks, rather than recruiting a new army per attack. We describe a Midgard Worm, which can build an extremely resilient and scalable overlay network to deliver attack code quickly. The worm's master could disseminate a 1-megabyte exploit or upgrade to a million zombies from any zombie in less than six minutes. Even if 80% of the zombies were disinfected, 70% of the remainder would remain connected and ready to receive new exploits. We discuss the basic design principles behind such a worm and methods of combating this kind of attack.
Comprehensive trend analysis of nutrients and related variables in a large eutrophic estuary: A decadal study of anthropogenic and climatic influences

We used a decadal data set, with weekly to biweekly sampling in April—October and monthly sampling in November—March, to characterize climatic (hurricane‐level storms, a sustained 3‐yr drought) and anthropogenic influences on N and P concentrations and loadings to a large eutrophic, poorly flushed estuary, the Neuse Estuary of the Albemarle—Pamlico Estuarine System. Mass volume transport data were obtained with cross‐estuary transect flow measurements taken near the entrance to the estuary. Although trends were minimally influenced by hurricanes, analyses were significantly affected by the sustained drought near the end of the study. As examples, decreasing trends in total N (TN), total P (TP), and bottom‐water dissolved oxygen concentrations, and in TN loadings were significant considering all data, but these trends were not significant when the sustained drought was excluded from analysis. In addition, the trend in TN loading was especially sensitive to the initial sampling period. NH4+ concentrations dramatically increased (overall by ~500%) as a persistent trend regardless of attempts to control for climatic events. An increasing trend in NH4+ also was documented in an adjacent, rapidly flushed Coastal Plain estuary, the Cape Fear. The NH4+ data suggest a regional‐scale effect of high inputs from inadequately controlled, increasing nonpoint sources. The fragility of TN loading trends, the striking increase in NH4+ concentrations, and the lack of management emphasis on controlling nonpoint sources such as “new” industrialized swine production collectively do not support recent reports of achievement of a 30% reduction in TN loading to the Neuse. Nonpoint sources remain a critical target for reduction to alleviate the negative effects of cultural eutrophication in this system, as in many estuaries throughout the world.
Learning from defect removals

Recent research has tried to identify changes in source code repositories that fix bugs by linking these changes to reports in issue tracking systems. These changes have been traced back to the point in time when they were previously modified as a way of identifying bug introducing changes. But we observe that not all changes linked to bug tracking systems are fixing bugs; some are enhancing the code. Furthermore, not all fixes are applied at the point in the code where the bug was originally introduced. We flesh out these observations with a manual review of several software projects, and use this opportunity to see how many defects are in the scope of static analysis tools.
Steps toward a cognitive engineering: Design rules based on analyses of human error

This paper uses the analysis of human error to provide a tool for the development of principles of system design, both to minimize the occurrence of error and to minimize its effects. Eventually, it should be possible to establish a systematic set of guidelines, with explicit, quantitative cost-benefit tradeoffs that can lead toward a design discipline—a “Cognitive Engineering. ” This short note starts the process.
Three-Way Analysis of Spectrospatial Electromyography Data: Classification and Interpretation

Classifying multivariate electromyography (EMG) data is an important problem in prosthesis control as well as in neurophysiological studies and diagnosis. With modern high-density EMG sensor technology, it is possible to capture the rich spectrospatial structure of the myoelectric activity. We hypothesize that multi-way machine learning methods can efficiently utilize this structure in classification as well as reveal interesting patterns in it. To this end, we investigate the suitability of existing three-way classification methods to EMG-based hand movement classification in spectrospatial domain, as well as extend these methods by sparsification and regularization. We propose to use Fourier-domain independent component analysis as preprocessing to improve classification and interpretability of the results. In high-density EMG experiments on hand movements across 10 subjects, three-way classification yielded higher average performance compared with state-of-the art classification based on temporal features, suggesting that the three-way analysis approach can efficiently utilize detailed spectrospatial information of high-density EMG. Phase and amplitude patterns of features selected by the classifier in finger-movement data were found to be consistent with known physiology. Thus, our approach can accurately resolve hand and finger movements on the basis of detailed spectrospatial information, and at the same time allows for physiological interpretation of the results.