Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward an Integrated Assessment of the Ecological and Chemical Status of European River Basins

Abstract EDITOR'S NOTE: This is 1 of 12 papers prepared by participants attending the workshop “Risk Assessment in European River Basins–State of the Art and Future Challenges” held in Liepzig, Germany on 12–14 November 2007. The meeting was organized within the framework of the European Commission's Coordination Action RISKBASE program. The objective of RISKBASE is to review and synthesize the outcome of European Commission FP4–FP6 projects, and other major initiatives, related to integrated risk assessment–based management of the water/sediment/soil environment at the river basin scale. Here, recommendations to improve ecological and chemical status assessments in accordance with the European Water Framework Directive (WFD) are made on the basis of experience gained from the MODELKEY project database, linking existing biological and chemical monitoring data of 3 case study river basins (Elbe, Scheldt, and Llobregat). The data analysis within and across river basins revealed major obstacles to be tackled, including scarcity of matching ecological and chemical monitoring sites for cause–effect relationships as well as a general lack of stressor-specific metrics for single biological quality elements (BQE) to enable a comprehensive risk assessment of all predominant stressors, including toxicity. An example of such a metric, which is recommended for the BQE of benthic macroinvertebrates, is the trait-based species-at-risk index (SPEAR) that correlated well with a respective measure for toxic stress, referred to as toxic units, based on simple mixture toxicity concepts. Surprisingly, the assessment of chemical status of a total of 695 monitoring sites for 2000 to 2004 showed that environmental quality standards (EQSs) were exceeded for at least 1 of the currently 41 priority pollutants (PPs) in 92% to 98% of the cases in all 3 of the river basins, which, according to definition, indicates potential effects on ecological status. A comparison of compliance with EQSs for 41 PPs with a respective effect threshold (derived for benthic macroinvertebrates) revealed that the rather conservative concept of chemical status is most likely not protective in all cases. Furthermore, to account for the many other compounds that are detected frequently in European surface waters and that may also have ecotoxicological effects, we introduced a provisional predicted no-effect concentration that is in accordance with the EQS methodology and is suggested to identify potential emerging compounds for which no or insufficient toxicity data exist. In conclusion, this study aims to support the implementation of the WFD by drawing conclusions from the analysis of heterogeneous data sets of various member states and by introducing new tools to move toward an integrated European assessment of ecological and chemical status.
Recurring surface fires cause soil degradation of forest land: A simulation experiment with the EFIMOD model

Renewal of pine forests is ecologically dependent on fires, but if fires become too frequent, they can disrupt the equilibrium and sustainability of these ecosystems. Field studies of the effects of fire are challenging because of the heterogeneity of forest ecosystems and because of the heterogeneous effect of fire on recovery of vegetation. As an alternative to complex field studies, mathematical models can be used as a tool to assess the complex dynamics of natural ecosystems as they recover after fire. The aim of this study was to apply the ecosystem model EFIMOD to analyse the effect of surface fires on soil degradation and its feedback on tree productivity in Scots pine forests on different soil types in Russia: Haplic Podzols in the Leningrad region and Psamment Entisols of the fragmented steppe in the Samara region. Simulation of the cumulative effects of fire cycles over 140 years showed that one fire did not affect growing stock but decreased soil organic matter by about 10% at both sites, and that three fires reduced the growing stock by 30% on the Haplic Podzols and 9% on the Psamment Entisols and decreased soil organic matter by about 30% on both sites. Forest fires led to the loss of soil carbon (C), as well as nitrogen (N), which is a principal limiting factor in forest ecosystems of boreal and temperate ecozones. The effect of repeated fire cycles on land degradation is similar to that of soil erosion, through the loss of soil C and N.
Contrast tuned responses in primary auditory cortex of the awake ferret

Auditory neurons are often characterized by their spectro‐temporal receptive field (STRF), a linear measure that captures overall trends of neural responses to modulations of the spectro‐temporal envelopes of sounds. We have previously shown that primary auditory cortex neurons of the awake ferret are better characterized by STRFs followed by a non‐trivial non‐linearity. This non‐linearity is a half‐wave rectification followed by a squaring function, indicating that cortical neurons probably encode higher‐order statistics of the spectrum of sounds. In this article, we introduce the concept of a contrast receptive field (CRF) and show that neurons in the auditory cortex encode quadratic statistics of the spectro‐temporal envelope of sounds, which we call auditory contrast. We reveal phase‐dependent contrast tuning in single units. Most units with a reliable STRF also possess a reliable CRF, such that the response to stimulus contrast complements the linear response described by the STRF. The relationship between the STRF and the CRF is analyzed in terms of orthogonality, co‐localization in time–frequency, feature orientation selectivity, and output non‐linearity interdependence. Our study shows that contrast can be used by auditory cortex neurons to sharpen, in a noise‐resistant fashion, their responses to dynamic spectral profiles.
Model Checking Concurrent Programs with Nondeterminism and Randomization

For concurrent probabilistic programs having process-level nondeterminism, it is often necessary to restrict the class of schedulers that resolve nondeterminism to obtain sound and precise model checking algorithms. In this paper, we introduce two classes of schedulers called view consistent and locally Markovian schedulers and consider the model checking problem of concurrent, probabilistic programs under these alternate semantics. Specifically, given a Buchi automaton Spec, a threshold x2 [0, 1], and a concurrent program P, the model checking problem asks if the measure of computations of P that satisfy Spec is at least x, under all view consistent (or locally Markovian) schedulers. We give precise complexity results for the model checking problem (for dierent classes of Buchi automata specifications) and contrast it with the complexity under the standard semantics that considers all schedulers.
An Optimal Broadcast of Warning Messages in Vehicular Ad Hoc Networks

—In vehicular ad hoc networks, multi-hop broadcast is a key technique to disseminate warning messages for safety applications. Due to the vehicle mobility and lossy wireless channel, highly reliable, scalable and fast multi-hop broadcast protocol is very challenging to design. A number of solutions have been proposed in the past few years. However, the tradeoff between reliability and efficiency in such solutions needs to be carefully considered. The scope of this paper is to present an optimal protocol for the broadcast of safety messages in VANETs. Optimality, in terms of delay and transmission count, is achieved using a broadcast strategy that exploits opposite vehicles. To carry out reliable and efficient broadcast coordination, intelligent periodic rebroadcasts, which effectively adapt our protocol to sparse and dense networks, are proposed. Simulations are conducted and results are presented to show that it has a better performance over existing competing protocols.
The Human Semicircular Canals Orientation Is More Similar to the Bonobos than to the Chimpanzees

For some traits, the human genome is more closely related to either the bonobo or the chimpanzee genome than they are to each other. Therefore, it becomes crucial to understand whether and how morphostructural differences between humans, chimpanzees and bonobos reflect the well known phylogeny. Here we comparatively investigated intra and extra labyrinthine semicircular canals orientation using 260 computed tomography scans of extant humans (Homo sapiens), bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Humans and bonobos proved more similarities between themselves than with chimpanzees. This finding did not fit with the well established chimpanzee – bonobo monophyly. One hypothesis was convergent evolution in which bonobos and humans produce independently similar phenotypes possibly in response to similar selective pressures that may be associated with postural adaptations. Another possibility was convergence following a “random walk” (Brownian motion) evolutionary model. A more parsimonious explanation was that the bonobo-human labyrinthine shared morphology more closely retained the ancestral condition with chimpanzees being subsequently derived. Finally, these results might be a consequence of genetic diversity and incomplete lineage sorting. The remarkable symmetry of the Semicircular Canals was the second major finding of this article with possible applications in taphonomy. It has the potential to investigate altered fossils, inferring the probability of post-mortem deformation which can lead to difficulties in understanding taxonomic variation, phylogenetic relationships, and functional morphology.
Adaptive Protection Scheme for a Distribution System Considering Grid-Connected and Islanded Modes of Operation

The renewable energy-based distributed generation (DG) implementation in power systems has been an active research area during the last few decades due to several environmental, economic and political factors. Although the integration of DG offers many advantages, several concerns, including protection schemes in systems with the possibility of bi-directional power flow, are raised. Thus, new protection schemes are strongly required in power systems with a significant presence of DG. In this study, an adaptive protection strategy for a distribution system with DG integration is proposed. The proposed strategy considers both grid-connected and islanded operating modes, while the adaptive operation of the protection is dynamically realized considering the availability of DG power production (related to faults or meteorological conditions) in each time step. Besides, the modular structure and fast response of the proposed strategy is validated via simulations conducted on the IEEE 13-node test system.
WaterCooler: exploring an organization through enterprise social media

As organizations scale up, their collective knowledge increases, and the potential for serendipitous collaboration between members grows dramatically. However, finding people with the right expertise or interests becomes much more difficult. Semi-structured social media, such as blogs, forums, and bookmarking, present a viable platform for collaboration-if enough people participate, and if shared content is easily findable. Within the trusted confines of an organization, users can trade anonymity for a rich identity that carries information about their role, location, and position in its hierarchy. This paper describes WaterCooler, a tool that aggregates shared internal social media and cross-references it with an organization's directory. We deployed WaterCooler in a large global enterprise and present the results of a preliminary user study. Despite the lack of complete social networking affordances, we find that WaterCooler changed users' perceptions of their workplace, made them feel more connected to each other and the company, and redistributed users' attention outside their own business groups.
Electrophysiology of Sodium Receptors in Taste Cells

Sodium intake is important to maintain proper osmolarity and volume of extracellular fluid in vertebrates. The ability to find sources of sodium ions for managing electrolyte homeostasis relies on the activity of the taste system to sense salt. Several studies have been performed to understand the mechanisms underlying Na+ reception in taste cells, the peripheral detectors for food chemicals. It is now generally accepted that Na+ interacts with specific ion channels in taste cell membrane, called sodium receptors. As ion channels, these proteins mediate transmembrane ion fluxes (that is, electrical currents) during their operation. Thus, a lot of information on the functional properties of sodium receptors has been obtained by using electrophysiological techniques. Here, I review our current knowledge on the biophysical and physiological features of these receptors obtained by applying the patch-clamp recording techniques to single taste cells.
Exercise-Induced Blood Lactate Increase Does Not Change Red Blood Cell Deformability in Cyclists

Background The effect of exercise-induced lactate production on red blood cell deformability and other blood rheological changes is controversial, given heavy-exercise induces biochemical processes (e.g., oxidative stress) known to perturb haemorheology. The aim of the present study was to examine the haemorheological response to a short-duration cycling protocol designed to increase blood lactate concentration, but of duration insufficient to induce significant oxidative stress. Methods Male cyclists and triathletes (n = 6; 27±7 yr; body mass index: 23.7±3.0 kg/m2; peak oxygen uptake 4.02±0.51 L/min) performed unloaded (0 W), moderate-intensity, and heavy-intensity cycling. Blood was sampled at rest and during the final minute of each cycling bout. Blood chemistry, blood viscosity, red blood cell aggregation and red blood cell deformability were measured. Results Blood lactate concentration increased significantly during heavy-intensity cycling, when compared with all other conditions. Methaemoglobin fraction did not change during any exercise bout when compared with rest. Blood viscosity at native haematocrit increased during heavy-intensity cycling at higher-shear rates when compared with rest, unloaded and moderate-intensity cycling. Heavy-intensity exercise increased the amplitude of red blood cell aggregation in native haematocrit samples when compared with all other conditions. Red blood cell deformability was not changed by exercise. Conclusion Acute exercise perturbs haemorheology in an intensity dose-response fashion; however, many of the haemorheological effects appear to be secondary to haemoconcentration, rather than increased lactate concentration.
Operationalizing Sen's Capability Approach

Professor Amartya Sen (1993: 30) once observed that “Capability is not an awfully attractive word”. One wonders what might be said of the word “Operationalizing” and of “Operationalizing Capabilities”? Operationalizing is definitely an awfully unattractive word that has no clear or unambiguous meaning. It can be used in a very broad sense, meaning “something that can be put into practice or used” or something narrowly defined, meaning “quantification” restricted to a particular level of analysis. There are many different ways through which any theory can be used or applied and it does not seem correct to limit the ‘processes of putting these theories into operation’ to one or two particular modes. Thus, by ‘operationalizing’ we mean the diverse sequence of transforming a theory into an object of practical value. To simplify matters, it could be suggested that operationalization consists of four sequences/alternatives:
Elevated White Blood Cell Count Is Associated with Higher Risk of Glucose Metabolism Disorders in Middle-Aged and Elderly Chinese People

White blood cell (WBC) count has been associated with diabetic risk, but whether the correlation is independent of other risk factors has hardly been studied. Moreover, very few such studies with large sample sizes have been conducted in Chinese. Therefore, we investigated the relationship between WBC count and glucose metabolism in china. We also examined the relevant variables of WBC count. A total of 9,697 subjects (mean age, 58.0 ± 9.1 years) were recruited. The subjects were classified into four groups, including subjects with normal glucose tolerance, isolated impaired fasting glucose, impaired glucose tolerance and type 2 diabetes mellitus (T2DM). We found that WBC count increased as glucose metabolism disorders exacerbated. WBC count was also positively correlated with waist hip ratio, body mass index, smoking, triglycerides, glycosylated haemoglobin A1c (HbA1c) and 2-h postprandial glucose. In addition, high density lipoprotein and the female gender were inversely correlated with WBC levels. In patients with previously diagnosed T2DM, the course of T2DM was not correlated with WBC count. Our findings indicate that elevated WBC count is independently associated with worsening of glucose metabolism in middle-aged and elderly Chinese. In addition, loss of weight, smoking cessation, lipid-modifying therapies, and control of postprandial plasma glucose and HbA1c may ameliorate the chronic low-grade inflammation.
Hypoxia response element‐driven cytosine deaminase/5‐fluorocytosine gene therapy system: a highly effective approach to overcome the dynamics of tumour hypoxia and enhance the radiosensitivity of prostate cancer cells in vitro

We proposed to exploit hypoxia‐inducible factor (HIF)‐1α overexpression in prostate tumours and use this transcriptional machinery to control the expression of the suicide gene cytosine deaminase (CD) through binding of HIF‐1α to arrangements of hypoxia response elements. CD is a prodrug activation enzyme, which converts inactive 5‐fluorocytosine to active 5‐fluorouracil (5‐FU), allowing selective killing of vector containing cells.
Adrenocortical hypertrophy: establishing cause and toxicological significance

The primary cause of adrenocortical hypertrophy is increased adrenocorticotrophic hormone (ACTH) stimulation. In toxicology studies, such a condition can arise as a result of the stress response, but it may also occur due to deficient glucocorticoid feedback regulation of ACTH due to toxicity to the adrenal cortex. This latter condition is defined as adrenocortical insufficiency and represents a serious adverse toxic effect on the function of the adrenal cortex. Adrenocortical hypertrophy may occur in the absence of other adrenocortical lesions such that a toxicopathological mechanism is not obvious, for example by pharmacological inhibition of steroidogenesis at the biochemical level. This review discusses the different aetiological factors and mechanisms producing adrenocortical hypertrophy. The need for further evidence in ascribing findings to stress is discussed, as is a protocol for establishing differential diagnoses between stress‐induced and toxicity‐induced adrenocortical hypertrophy, which is useful in cases where there are no other histopathological lesions in the adrenal cortex. It is concluded that all cases of adrenocortical hypertrophy require further investigation or evidence to ascribe such findings to either stress or adrenocortical inhibition/insufficiency, and that all cases of adrenocortical insufficiency (whether due to a histopathological lesion or reversible pharmacological enzyme inhibition) represent a serious adverse effect that must be properly considered in toxicological risk assessment. Copyright © 2010 John Wiley & Sons, Ltd.
HIV infection awareness and willingness to participate in future HIV vaccine trials across different risk groups in Abuja, Nigeria

Abstract The purpose of this survey is to generate baseline data on the level of HIV infection awareness and willingness to participate (WTP) in hypothetical vaccine trials, ahead of any trial conduct in Nigeria. In a cross-sectional survey, 500 respondents were interviewed, including sex workers, male motorcycle taxi drivers, students, and the general public. About 153 (30.6%) of the respondents did not believe that correct and consistent use of condom can protect people from getting HIV, while about 66 (13.2%) respondents believed it is possible to get HIV by sharing meal with an infected person. Population groups considered at high risk for HIV were less aware of the disease, however, they were more willing to participate in HIV vaccine trials compared those at low risk of the disease. A total of 55% expressed WTP in a hypothetical vaccine trial after they were informed about it. Age, population group, and ethnicity were significantly associated with WTP.
Squeezing succinct data structures into entropy bounds

Consider a sequence <i>S</i> of <i>n</i> symbols drawn from an alphabet <i>A</i> = {1, 2,. ,σ}, stored as a binary string of <i>n</i>log σ bits. A <i>succinct</i> data structure on <i>S</i> supports a given set of primitive operations on <i>S</i> using just <i>f (n)</i> = <i>o</i>(<i>n</i> log σ) extra bits. We present a technique for transforming succinct data structures (which do not change the binary content of <i>S</i>) into <i>compressed</i> data structures using <i>nH</i><inf><i>k</i></inf> + <i>f(n)</i> + <i>O</i>(<i>n</i> log σ + log log<inf>σ</inf> <i>n</i> + <i>k</i>)/ log<inf>σ</inf> <i>n</i>) bits of space, where <i>H</i><inf><i>k</i></inf> ≤ log σ is the <i>k</i>th-order empirical entropy of <i>S</i>. When <i>k</i> + log σ = o(log <i>n</i>), we improve the space complexity of the succinct data structure from <i>n</i> log σ + <i>o</i>(<i>n</i> log σ) to <i>n</i> <i>H</i><inf><i>k</i></inf> + <i>o</i>(<i>n</i>log σ) bits by keeping <i>S</i> in compressed format, so that any substring of <i>O</i>(log σ <i>n</i>) symbols in <i>S</i> (i.e. <i>O</i>(log <i>n</i>) bits) can be decoded on the fly in constant time. Thus, the time complexity of the supported operations does not change asymptotically. Namely, if an operation takes <i>t</i>(<i>n</i>) time in the succinct data structure, it requires <i>O</i>(<i>t</i>(<i>n</i>)) time in the resulting compressed data structure. Using this simple approach we improve the space complexity of some of the best known results on succinct data structures We extend our results to handle another definition of entropy.
LIME, a Novel Transmembrane Adaptor Protein, Associates with p56lck and Mediates T Cell Activation

In this study, we identify and characterize a novel transmembrane adaptor protein, designated Lck-interacting membrane protein (LIME), as a binding partner of the Lck Src homology (SH)2 domain. LIME possesses a short extracellular domain, a transmembrane domain, and a cytoplasmic tail containing five tyrosine-based motifs. The protein is primarily expressed in hematopoietic cells and lung. Interestingly, LIME expression is up-regulated by TCR stimulation and sustained up to 24 h, suggesting that LIME acts throughout the early to late stages of T cell activation. LIME is localized to membrane rafts and distributed within the T cell–APC contact site. Upon TCR stimulation of Jurkat T cells, LIME associates with Lck as a tyrosine-phosphorylated protein. Experiments using Jurkat T cells expressing CD8–LIME chimera reveal that the protein associates with phosphatidylinositol 3-kinase, Grb2, Gads, and SHP2, and activates ERK1/2 and JNK but not p38. Moreover, overexpression of LIME in Jurkat T cells induces transcriptional activation of the IL-2 promoter. Our data collectively show that LIME is a raft-associated transmembrane adaptor protein linking TCR stimuli to downstream signaling pathways via associations with Lck.