Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling radiocesium bioaccumulation in a marine food chain

We measured the transfer of radiocesium in a marine food chain from phytoplankton to bivalves and finally to a predatory gastropod (Babylonia formosae habei). The assimilation efficiency (AE) of radiocesium in both green mussels (Perna viridis) and the gastropods feeding on different diets was measured by a pulse-chase feeding radiotracer technique. The AEs of 137 Cs in the green mussels ranged between 0.4 and 10%, and were the lowest for mussels feeding on natural sediment. The bioconcentration factor of 137 Cs ranged between 10 and 120 l kg -1 for 2 different phytoplankton species (diatom Thalassiosira pseudonana and green alga Chlorella autotrophica). The AEs of 137 Cs in the predatory gastropods were 44 to 58% of those feeding on mussels and clams (Ruditapes philip- pinarum). The efflux rate constant of 137 Cs in the gastropods was 0.074 d -1 . Using a simple kinetic model, we showed that the majority of 137 Cs in the mussels was due to uptake from the dissolved phase primarily because 137 Cs is not particle-reactive. Uptake due to ingestion of particulate materi- als contributed little to the overall 137 Cs accumulation in the mussels, except when the resuspended sediment constituted a major food source for mussels. In contrast, dietary ingestion (trophic transfer) can be an important source for radiocesium accumulation in the predatory gastropod because of its efficient assimilation. Our modeling results indicated that the trophic transfer factor was <1 in both bivalves and gastropods. Consequently, 137 Cs was not biomagnified during its transfer to filter-feed- ing bivalves and predatory gastropods. This was primarily due to the high turnover rate of radio- cesium in both bivalves and gastropods, even though the AE of radiocesium in the predators was high. However, the trophic transfer factor tended to increase with increasing trophic level, and a factor close to 1 may be reached when ingestion of the animals is high.
Story Point Approach based Agile Software Effort Estimation using Various SVR Kernel Methods

Agile software development process represents a major departure from traditional, plan-based approaches to software engineering. Estimating effort of agile software accurately in early stage of software development life cycle is a major challenge in the software industry. For improving the estimation accuracy, various optimization techniques are used. The Support Vector Regression (SVR) is one of these techniques that helps in getting optimal estimated values. The main objective of the research work carried out in this paper is to estimate the effort of agile softwares using story point approach. An attempt has been made to optimize the results obtained from story point approach using various SVR kernel methods to achieve better prediction accuracy. A performance comparison of the models obtained using various SVR kernel methods is also presented in order to highlight performance achieved by each method. Keywords—Agile Software Development; Software Effort Estimation; Story Point Approach; Support Vector Regression.
Dual-Polarized TerraSAR-X Data for Oil-Spill Observation

A study exploiting dual-polarimetric X-band synthetic aperture radar (SAR) data to observe oil at sea is undertaken for the first time. The polarimetric model exploits the interchannel correlation between the like polarized channels. Accordingly, two parameters related to the interchannel correlation, namely, the amplitude coherence and the copolarized phase difference (CPD) standard deviation, are accounted for, and their performances, with respect to sea oil slick observation, are carefully discussed. Single-look Slant range Complex dual-polarized TerraSAR-X SAR data, in which both certified oil slicks and weak-damping look-alikes are present, are used to verify the efficiency of the proposed approaches. Results show the advantage of the CPD approach and the effectiveness of TerraSAR-X dual-polarized products for such application.
Dual Frequency Head Maps: A New Method for Indexing Mental Workload Continuously during Execution of Cognitive Tasks

One goal of advanced information and communication technology is to simplify work. However, there is growing consensus regarding the negative consequences of inappropriate workload on employee's health and the safety of persons. In order to develop a method for continuous mental workload monitoring, we implemented a task battery consisting of cognitive tasks with diverse levels of complexity and difficulty. We conducted experiments and registered the electroencephalogram (EEG), performance data, and the NASA-TLX questionnaire from 54 people. Analysis of the EEG spectra demonstrates an increase of the frontal theta band power and a decrease of the parietal alpha band power, both under increasing task difficulty level. Based on these findings we implemented a new method for monitoring mental workload, the so-called Dual Frequency Head Maps (DFHM) that are classified by support vectors machines (SVMs) in three different workload levels. The results are in accordance with the expected difficulty levels arising from the requirements of the tasks on the executive functions. Furthermore, this article includes an empirical validation of the new method on a secondary subset with new subjects and one additional new task without any adjustment of the classifiers. Hence, the main advantage of the proposed method compared with the existing solutions is that it provides an automatic, continuous classification of the mental workload state without any need for retraining the classifier—neither for new subjects nor for new tasks. The continuous workload monitoring can help ensure good working conditions, maintain a good level of performance, and simultaneously preserve a good state of health.
Gatekeeping tests in dose-response clinical trials Alex Dmitrienko ( Eli Lilly )

This paper discusses multiple testing procedures in dose-response clinical trials with primary and secondary endpoints. A general gatekeeping framework for constructing multiple tests is proposed which extends the Dunnett test (Dunnett, 1955) and Bonferroni-based gatekeeping tests developed by Dmitrienko, Offen and Westfall (2003). The proposed procedure accounts for the hierarchical structure of the testing problem, for example, it restricts testing of secondary endpoints to the doses for which the primary endpoint is significant. The multiple testing approach is illustrated using a dose-response clinical trial in patients with diabetes. Monte-Carlo simulations demonstrate that the proposed procedure provides a power advantage over the Bonferroni gatekeeping procedure. The power gain generally increases with increasing correlation among the endpoints, especially when all primary dose-control comparisons are significant.
Design and Construction of Wireless Sensor Network Gateway with IPv4/IPv6 Support

6LoWPAN opens a great opportunity for wireless sensor networks (WSNs) to be operated from the Internet. However, 6LoWPAN requires a gateway in order to make the use of IPv6 feasible inside the WSN. In this paper, a gateway is designed and constructed to interconnect 6LoWPAN wireless sensor networks with IPv6 clients, enabling them to receive sensor nodes readings or send commands to the 6LoWPAN WSN at anytime through direct communication with the sensor nodes. Furthermore, this solution allows IPv4 clients to exchange information with the WSN through a bridge architecture implemented at the gateway. The experimental results show that the communication between 6LoWPAN WSN and IPv6/IPv4 clients is successful.
Hypothermic Preconditioning Increases Survival of Purkinje Neurons in Rat Cerebellar Slices after an In Vitro Simulated Ischemia

BackgroundA period of hypothermia before ischemia (hypothermic preconditioning) induces a delayed phase of ischemic tolerance in rat brain. However, whether hypothermic preconditioning induces an acute phase (within a few hours after the hypothermia) of ischemic tolerance remains unknown. This study was designed to determine the time window of the hypothermic preconditioning–induced acute phase of neuroprotection, which is useful information for situations during surgery with anticipated ischemic episodes, and its involved mechanisms. MethodsSurvival of Purkinje cells in rat cerebellar slices was evaluated after a 20-min oxygen-glucose deprivation (OGD, in vitro simulated ischemia) followed by a 4-h recovery. Mild hypothermia (33°C) for 20 min was applied at various times before the OGD. ResultsThe hypothermia applied immediately to 3 h before the OGD equally effectively reduced OGD-induced Purkinje cell death/injury. Glibenclamide, a selective KATP channel blocker; 8-cyclopentyl-1,3-dipropylxanthine, a selective adenosine A1 receptor antagonist; and farnesyl protein transferase inhibitor III, a selective inhibitor to reduce Ras farnesylation, abolished hypothermic preconditioning–induced neuroprotection when applied during the hypothermia. OGD increased the expression of high-mobility group I(Y) proteins, which are nuclear transcription factors to enhance the expression of putatively damaging proteins such as cyclooxygenase-2, in cerebellar slices. This increase was attenuated by hypothermic preconditioning. ConclusionsHypothermic preconditioning induces an acute phase of neuroprotection. This neuroprotection depends on activation of the signaling molecules, adenosine A1 receptors, KATP channels, and Ras. Inhibition of putatively damaging proteins via the effects of hypothermic preconditioning on high-mobility group I(Y) expression may also be involved in hypothermic preconditioning–induced neuroprotection.
Multiple agents rescue PC12 cells from serum-free cell death by translation- and transcription-independent mechanisms

Past studies revealed that NGF and fibroblast growth factor (FGF) prevent the death of PC 12 pheochromocytoma cells that otherwise occurs in serum-free medium. Additional agents were tested here for their abilities to promote long-term survival of naive and NGF-pretreated (primed) PC 12 cells in serum-free conditions. Forskolin and permeant cAMP analogs effectively prevented serum-free cell death, as did micromolar levels of insulin and 10–100-nM levels of insulin-like growth factors I and II. In contrast to NGF and FGF, none of these agents caused neuronal differentiation of naive cells or neurite regeneration by primed cells. Each of the agents also prevented rapid cell death in a balanced salt solution, thus apparently ruling out a mechanism dependent on regulation of nutrient uptake. Epidermal growth factor and elevated K+ appeared to slow the rate of cell death, but did not promote long-term survival; phorbol ester, dexamethasone, or vanadate did not prevent cell death. Each of the survival-promoting agents was effective even when macromolecular synthesis was blocked. Because the synthesis inhibitors themselves did not significantly prevent cell death, such findings indicate that survival was promoted by mechanisms that do not require synthesis of RNA or protein. In addition, various lines of experimental evidence (using the kinase inhibitor K-252a or PC 12 cell variants deficient either in protein kinase A activity or in responsiveness to NGF) further suggested that the effective agents maintain survival by independent initial pathways. Regulation of protein kinase activity appears to be a common feature of each pathway and may therefore play a key convergent role in mediating prevention of cell death.
Information: Currency of life?

In biology, the exception is mostly the rule, and the rule is mostly the exception. However, recent results indicate that known universal concepts in biology such as the genetic code or the utilization of ATP as a source of energy may be complemented by a large class of principles based on Shannon's concept of information. The present position paper discusses various promising pathways toward the formulation of such generic informational principles and their relevance for the realm of biology.
Robust methodologies for modeling web click distributions

Metrics such as click counts are vital to online businesses but their measurement has been problematic due to inclusion of high variance robot traffic. We posit that by applying statistical methods more rigorous than have been employed to date that we can build a robust model of thedistribution of clicks following which we can set probabilistically sound thresholds to address outliers and robots. Prior research in this domain has used inappropriate statistical methodology to model distributions and current industrial practice eschews this research for conservative ad-hoc click-level thresholds. Prevailing belief is that such distributions are scale-free power law distributions but using more rigorous statistical methods we find the best description of the data is instead provided by a scale-sensitive Zipf-Mandelbrot mixture distribution. Our results are based on ten data sets from various verticals in the Yahoo domain. Since mixture models can overfit the data we take care to use the BIC log-likelihood method which penalizes overly complex models. Using a mixture model in the web activity domain makes sense because there are likely multiple classes of users. In particular, we have noticed that there is a significantly large set of "users" that visit the Yahoo portal exactly once a day. We surmise these may be robots testing internet connectivity by pinging the Yahoo main website. Backing up our quantitative analysis is graphical analysis in which empirical distributions are plotted against heoretical distributions in log-log space using robust cumulative distribution plots. This methodology has two advantages: plotting in log-log space allows one to visually differentiate the various exponential distributions and secondly, cumulative plots are much more robust to outliers. We plan to use the results of this work for applications for robot removal from web metrics business intelligence systems.
Cryo-Transmission Electron Microscopy of Frozen-Hydrated Sections of Escherichia coli and Pseudomonas aeruginosa

ABSTRACT High-pressure freezing of Escherichia coli K-12 and Pseudomonas aeruginosa PAO1 in the presence of cryoprotectants provided consistent vitrification of cells so that frozen-hydrated sections could be cut, providing ∼2-nm resolution of structure. The size and shape of the bacteria, as well as their surface and cytoplasmic constituents, were nicely preserved and compared well with other published high-resolution techniques. Cells possessed a rich cytoplasm containing a diffuse dispersion of ribosomes and genetic material. Close examination of cells revealed that the periplasmic space was compressed during cryosectioning, a finding which provided supporting evidence that this space is filled by a compressible gel. Since the outer membrane and peptidoglycan layer are bonded together via lipoproteins, the space between them (although still part of the periplasmic space) was not as compacted. Even when this cryosectioning compression was taken into account, there was still substantial variability in the width of the periplasmic space. It is possible that the protoplast has some capacity to float freely within the periplasm.
A Quadratic Modeling-Based Framework for Accurate Statistical Timing Analysis Considering Correlations

The impact of parameter variations on timing due to process variations has become significant in recent years. In this paper, we present a statistical timing analysis (STA) framework with quadratic gate delay models that also captures spatial correlations. Our technique does not make any assumption about the distribution of the parameter variations, gate delays, and arrival times. We propose a Taylor-series expansion-based quadratic representation of gate delays and arrival times which are able to effectively capture the nonlinear dependencies that arise due to increasing parameter variations. In order to reduce the computational complexity introduced due to quadratic modeling during STA, we also propose an efficient linear modeling driven quadratic STA scheme. We ran two sets of experiments assuming the global parameters to have uniform and Gaussian distributions, respectively. On an average, the quadratic STA scheme had 20.5times speedup in runtime as compared to Monte Carlo simulations with an rms error of 0.00135 units between the two timing cummulative density functions (CDFs). The linear modeling driven quadratic STA scheme had 51.5times speedup in runtime as compared to Monte Carlo simulations with an rms error of 0.0015 units between the two CDFs. Our proposed technique is generic and can be applied to arbitrary variations in the underlying parameters under any spatial correlation model
p107 regulates neural precursor cells in the mammalian brain

Here we show a novel function for Retinoblastoma family member, p107 in controlling stem cell expansion in the mammalian brain. Adult p107-null mice had elevated numbers of proliferating progenitor cells in their lateral ventricles. In vitro neurosphere assays revealed striking increases in the number of neurosphere forming cells from p107−/− brains that exhibited enhanced capacity for self-renewal. An expanded stem cell population in p107-deficient mice was shown in vivo by (a) increased numbers of slowly cycling cells in the lateral ventricles; and (b) accelerated rates of neural precursor repopulation after progenitor ablation. Notch1 was up-regulated in p107−/− neurospheres in vitro and brains in vivo. Chromatin immunoprecipitation and p107 overexpression suggest that p107 may modulate the Notch1 pathway. These results demonstrate a novel function for p107 that is distinct from Rb, which is to negatively regulate the number of neural stem cells in the developing and adult brain.
CTRL+Z: Recovering Anonymized Social Graphs

Social graphs derived from online social interactions contain a wealth of information that is nowadays extensively used by both industry and academia. However, due to the sensitivity of information contained in such social graphs, they need to be properly anonymized before release. Most of the graph anonymization techniques that have been proposed to sanitize social graph data rely on the perturbation of the original graph's structure, more specifically of its edge set. In this paper, we identify a fundamental weakness of these edge-based anonymization mechanisms and exploit it to recover most of the original graph structure. First, we propose a method to quantify an edge's plausibility in a given graph by relying on graph embedding. Our experiments on three real-life social network datasets under two widely known graph anonymization mechanisms demonstrate that this method can very effectively detect fake edges with AUC values above 0.95 in most cases. Second, by relying on Gaussian mixture models and maximum a posteriori probability estimation, we derive an optimal decision rule to detect whether an edge is fake based on the observed graph data. We further demonstrate that this approach concretely jeopardizes the privacy guarantees provided by the considered graph anonymization mechanisms. To mitigate this vulnerability, we propose a method to generate fake edges as plausible as possible given the graph structure and incorporate it into the existing anonymization mechanisms. Our evaluation demonstrates that the enhanced mechanisms not only decrease the chances of graph recovery (with AUC dropping by up to 35%), but also provide even better graph utility than existing anonymization methods.
Clustering-based Approach for Categorizing Pregnant Women in Obstetrics and Maternity Care

When a pregnant woman is guided to a hospital for obstetrics purposes, many outcomes are possible, depending on her current conditions. An improved understanding of these conditions could provide a more direct medical approach by categorizing the different types of patients, enabling a faster response to risk situations, and therefore increasing the quality of services. In this case study, the characteristics of the patients admitted in the maternity care unit of Centro Hospitalar of Porto are acknowledged, allowing categorizing the patient women through clustering techniques. The main goal is to predict the patients' route through the maternity care, adapting the services according to their conditions, providing the best clinical decisions and a cost-effective treatment to patients. The models developed presented very interesting results, being the best clustering evaluation index: 0.65. The evaluation of the clustering algorithms proved the viability of using clustering based data mining models to characterize pregnant patients, identifying which conditions can be used as an alert to prevent the occurrence of medical complications.
HiReD: a high-resolution multi-window visualisation environment for cluster-driven displays

High-resolution, wall-size displays often rely on bespoke software for performing interactive data visualisation, leading to interface designs with little or no consistency between displays. This makes adoption for novice users difficult when migrating from desktop environments. However, desktop interface techniques (such as task- and menu- bars) do not scale well and so cannot be relied on to drive the design of large display interfaces. In this paper we present HiReD, a multi-window environment for cluster-driven displays. As well as describing the technical details of the system, we also describe a suite of low-precision interface techniques that aim to provide a familiar desktop environment to the user while overcoming the scalability issues of high-resolution displays. We hope that these techniques, as well as the implementation of HiReD itself, can encourage good practice in the design and development of future interfaces for high-resolution, wall-size displays.
EPOCH chemotherapy: toxicity and efficacy in relapsed and refractory non-Hodgkin's lymphoma.

PURPOSE Based on in vitro evidence that tumor cells are less resistant to prolonged exposure to low concentrations of the natural product class, compared with brief higher concentration exposure, we developed a chemotherapy regimen (etoposide, vincristine, doxorubicin, cyclophosphamide, and prednisone [EPOCH]) in which the natural products are administered as a continuous infusion. PATIENTS AND METHODS This is a phase II study of etoposide, vincristine, and doxorubicin, administered as a 96-hour continuous infusion, with intravenous (IV) bolus cyclophosphamide and oral prednisone (EPOCH) in 74 consecutive patients who relapsed from or failed to respond to most of the same drugs administered on a bolus schedule. Patients with aggressive lymphomas who achieved a good response after EPOCH were eligible to undergo bone marrow transplantation. RESULTS Patients with intermediate- or high-grade lymphoma comprised 76% of this series and 77% had stage IV disease. Seventy-one percent had previously received all of the drugs contained in the EPOCH regimen and 92% had received at least four of the drugs. Seventy patients were assessable for response, of whom 19 (27%) achieved a complete remission (CR) and 42 (60%) a partial remission (PR). Among 21 patients who had no response to prior chemotherapy, 15 (71%) responded, but only one achieved a CR. Patients who relapsed from an initial CR had a 100% response rate, with 76% CRs. With a median potential follow-up duration of 19 months, there was a 28% probability of being event-free at 1 year. Toxicity was primarily hematologic with neutropenia during 51% of cycles, but only a 17% incidence of febrile neutropenia. Gastrointestinal, neurologic, and cardiac toxicity were minimal. CONCLUSION EPOCH chemotherapy was well tolerated and highly effective in patients who were resistant to or relapsed from the same drugs administered on a bolus schedule, suggesting that continuous infusion of the natural drug component of this regimen is capable of partially reversing drug resistance and reducing toxicity. Dose-intensity (DI) was > or = that achieved in primary treatment regimens for aggressive lymphomas.