Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Acute and Developmental Exposure to Bisphenol S on Chinese Medaka (Oryzias sinensis)

Bisphenol S (BPS), one of the substitutes for bisphenol A (BPA), is widely used in various commodities. The BPS concentrations in surface water have gradually increased in recent years, making it a predominant bisphenol analogue in the aquatic environment and raising concerns about its health and ecological effects on aquatic organisms. For this study, we conducted a 96 h acute toxicity test and a 15-day developmental exposure test to assess the adverse effects of BPS exposure in Chinese medaka (Oryzias sinensis), a new local aquatic animal model. The results indicate that the acute exposure of Chinese medaka embryos to BPS led to relatively low toxicity. However, developmental exposure to BPS was found to cause developmental abnormalities, such as decreased hatching rate and body length, at 15 dpf. A transcriptome analysis showed that exposure to different concentrations of bisphenol S often induced different reactions. In summary, environmental concentrations of BPS can have adverse effects on the hatching and physical development of Chinese medaka, and further attention needs to be paid to the potential toxicity of environmental BPS.
Multilingual Expert Search using Linked Open Data as Interlingual Representation

Most Information Retrieval models take documents as Bagof-Words and are thereby bound to the language of the documents. In this paper, we present an approach using Linked Open Data resources, i.e. URIs, as interlingual document representations. Documents and queries are summarized by the resources they contain. We show the applicability of our approach for multilingual retrieval with a case study on expert search.
Multi-Task Active Learning with Output Constraints

Many problems in information extraction, text mining, natural language processing and other fields exhibit the same property: multiple prediction tasks are related in the sense that their outputs (labels) satisfy certain constraints. In this paper, we propose an active learning framework exploiting such relations among tasks. Intuitively, with task outputs coupled by constraints, active learning can utilize not only the uncertainty of the prediction in a single task but also the inconsistency of predictions across tasks. We formalize this idea as a cross-task value of information criteria, in which the reward of a labeling assignment is propagated and measured over all relevant tasks reachable through constraints. A specific example of our framework leads to the cross entropy measure on the predictions of coupled tasks, which generalizes the entropy in the classical single-task uncertain sampling. We conduct experiments on two real-world problems: web information extraction and document classification. Empirical results demonstrate the effectiveness of our framework in actively collecting labeled examples for multiple related tasks.
Proteome approaches combined with Fourier transform infrared spectroscopy revealed a distinctive biofilm physiology in Bordetella pertussis

Proteome analysis was combined with whole‐cell metabolic fingerprinting to gain insight into the physiology of mature biofilm in Bordetella pertussis, the agent responsible for whooping cough. Recent reports indicate that B. pertussis adopts a sessile biofilm as a strategy to persistently colonize the human host. However, since research in the past mainly focused on the planktonic lifestyle of B. pertussis, knowledge on biofilm formation of this important human pathogen is still limited. Comparative studies were carried out by combining 2‐DE and Fourier transform infrared (FT‐IR) spectroscopy with multivariate statistical methods. These complementary approaches demonstrated that biofilm development has a distinctive impact on B. pertussis physiology. Results from MALDI‐TOF/MS identification of proteins together with results from FT‐IR spectroscopy revealed the biosynthesis of a putative acidic‐type polysaccharide polymer as the most distinctive trait of B. pertussis life in a biofilm. Additionally, expression of proteins known to be involved in cellular regulatory circuits, cell attachment and virulence was altered in sessile cells, which strongly suggests a significant impact of biofilm development on B. pertussis pathogenesis. In summary, our work showed that the combination of proteomics and FT‐IR spectroscopy with multivariate statistical analysis provides a powerful tool to gain further insight into bacterial lifestyles.
The Lipid Moiety of Haemozoin (Malaria Pigment) and P. falciparum Parasitised Red Blood Cells Bind Synthetic and Native Endothelin-1

Endothelin1 (ET-1) is a 21-amino acid peptide produced by the vascular endothelium under hypoxia, that acts locally as regulator of vascular tone and inflammation. The role of ET-1 in Plasmodium falciparum malaria is unknown, although tissue hypoxia is frequent as a result of the cytoadherence of parasitized red blood cell (pRBC) to the microvasculature. Here, we show that both synthetic and endothelial-derived ET-1 are removed by parasitized RBC (D10 and W2 strains, chloroquine sensitive, and resistant, resp.) and native haemozoin (HZ, malaria pigment), but not by normal RBC, delipidized HZ, or synthetic beta-haematin (BH). The effect is dose dependent, selective for ET-1, but not for its precursor, big ET-1, and not due to the proteolysis of ET-1. The results indicate that ET-1 binds to the lipids moiety of HZ and membranes of infected RBCs. These findings may help understanding the consequences of parasite sequestration in severe malaria.
Exogenous stress hormones alter energetic and nutrient costs of development and metamorphosis

ABSTRACT Variation in environmental conditions during larval life stages can shape development during critical windows and have lasting effects on the adult organism. Changes in larval developmental rates in response to environmental conditions, for example, can trade off with growth to determine body size and condition at metamorphosis, which can affect adult survival and fecundity. However, it is unclear how use of energy and nutrients shape trade-offs across life-stage transitions because no studies have quantified these costs of larval development and metamorphosis. We used an experimental approach to manipulate physiological stress in larval amphibians, along with respirometry and 13C-breath testing to quantify the energetic and nutritional costs of development and metamorphosis. Central to larval developmental responses to environmental conditions is the hypothalamic–pituitary–adrenal/interrenal (HPA/I) axis, which regulates development, as well as energy homeostasis and stress responses across many taxa. Given these pleiotropic effects of HPA/I activity, manipulation of the HPA/I axis may provide insight into costs of metamorphosis. We measured the energetic and nutritional costs across the entire larval period and metamorphosis in a larval amphibian exposed to exogenous glucocorticoid (GC) hormones – the primary hormone secreted by the HPA/I axis. We measured metabolic rates and dry mass across larval ontogeny, and quantified lipid stores and nutrient oxidation via 13C-breath testing during metamorphosis, under control and GC-exposed conditions. Changes in dry mass match metamorphic states previously reported in the literature, but dynamics of metabolism were influenced by the transition from aquatic to terrestrial respiration. GC-treated larvae had lower dry mass, decreased fat stores and higher oxygen consumption during stages where controls were conserving energy. GC-treated larvae also oxidized greater amounts of 13C-labelled protein stores. These results provide evidence for a proximate cause of the physiological trade-off between larval growth and development, and provide insight into the energetic and nutrient costs that shape fitness trade-offs across life stages. Summary: The energetic and nutrient costs of glucocorticoid-accelerated development alter fitness trade-offs across life stages.
Color image processing system based on color/brightness constancy

This paper suggests a new color image processing system based on the human visual system. In human visual system, the brightness and chromaticity are processed independently. Thus, in the proposed system, first, the color signal is divided into brightness and chromaticity. Next, the brightness and chromaticity are processed in parallel. Arbitrary color image processing methods can be applied to the proposed system. We show a concrete processing procedure based on the constancy by using the proposed system. That is to say, the automatic white balance which is simulated color constancy and the retinex which is simulated brightness constancy are performed in the proposed system. We make clear that high quality color enhancement images can be obtained by the proposed system through the processing results.
Mitochondrial Release of Caspase-2 and -9 during the Apoptotic Process

The barrier function of mitochondrial membranes is perturbed early during the apoptotic process. Here we show that the mitochondria contain a caspase-like enzymatic activity cleaving the caspase substrate Z-VAD.afc, in addition to three biological activities previously suggested to participate in the apoptotic process: (a) cytochrome c; (b) an apoptosis-inducing factor (AIF) which causes isolated nuclei to undergo apoptosis in vitro; and (c) a DNAse activity. All of these factors, which are biochemically distinct, are released upon opening of the permeability transition (PT) pore in a coordinate, Bcl-2–inhibitable fashion. Caspase inhibitors fully neutralize the Z-VAD.afc–cleaving activity, have a limited effect on the AIF activity, and have no effect at all on the DNase activities. Purification of proteins reacting with the biotinylated caspase substrate Z-VAD, immunodetection, and immunodepletion experiments reveal the presence of procaspase-2 and -9 in mitochondria. Upon induction of PT pore opening, these procaspases are released from purified mitochondria and become activated. Similarly, upon induction of apoptosis, both procaspases redistribute from the mitochondrion to the cytosol and are processed to generate enzymatically active caspases. This redistribution is inhibited by Bcl-2. Recombinant caspase-2 and -9 suffice to provoke full-blown apoptosis upon microinjection into cells. Altogether, these data suggest that caspase-2 and -9 zymogens are essentially localized in mitochondria and that the disruption of the outer mitochondrial membrane occurring early during apoptosis may be critical for their subcellular redistribution and activation.
Exploring How to Get at--and Eradicate--Hidden HIV

AIDS THERAPIESDEDHAM, MASSACHUSETTS-- The remarkable success achieved by various combinations of anti-HIV drugs has allowed researchers not only to think about whether the last bits of virus can be eliminated from the body, but also to speculate about how it might be done. The main obstacle is that even in people whose viral load is "undetectable," the virus continues to lurk in "latently" infected blood cells and in sites such as the brain, eyes, and testes. Although not everyone agrees that eradication is possible, researchers proposed several strategies at a recent conference, including injecting people with immune system messengers that could flush out the virus so that the patient's own immune system could pick it off and looking for ways to sneak drugs past borders such as the one that protects the brain.
Heterogenous Agents , Time-varying Macro Fundamental and Asset Market Dynamics

This paper proposes a new channel to explain the positive price-volume correlation in the housing market. I study a simple overlapping generations model in the presence of heterogeneous agents. In the model, (i) consumer investors are forward looking and heterogeneous both in their holding periods and in their ownership preference, (ii) the underlying time varying macro fundamental is persistent, (iii) there are no transaction costs/frictions, and (iv) an auction is the micro-mechanism for price formation. In equilibrium, short horizon buyers are more likely to win the asset when prices are high whereas long horizon buyers on average win more when prices are low. This state-dependent ownership structure then naturally leads to a higher expected turnover rate in good times given a (positively) persistent macro dynamics. Empirically I document novel findings that are consistent with my model’s asset pricing implications. Owners’ ex ante holding horizons co-vary negatively with asset prices. Owners’ expected durations also have predictive power on future returns, particularly the return component that is forecastable by macro conditions. ∗I am very grateful to Jonathan Berk, Thomas Davidoff, Bob Edelstein, Dwight Jaffee and Nancy Wallace for their guidance, comments and suggestions. I also thank Stefano Corradin and seminar participants at the University of California, Berkeley for helpful discussions and comments. All errors are mine alone. This is a preliminary version and I appreciate all comments. Correspondence: Wenlan Qian, Haas School of Business, S545, #1900, University of California, Berkeley CA 94720. Email: qian@haas.berkeley. edu.
[Third generation oral contraceptives and risk of venous thrombosis].

The third-generation pill was introduced as a better option than the second-generation pill due to its improved effect on the lipid profile of the user. It thus came as a surprise that the great international case control study of the WHO showed a greater risk of venous thrombosis associated with the use of the third-generation pill compared to the second-generation pill. (excerpt)
Assessment of shifting cultivation dynamics in East Garo Hills District, Meghalaya, India

Shifting cultivation is an ancient traditional system of cultivation in the slopes of the northeastern region of India, where it is locally known as Jhum cultivation. In these regions, this system of cultivation is at subsistence level. For the study, the area selected is the East Garo Hills district in Meghalaya, one of the states in the region. In the study, a probe is made on the dynamics of parameters, temperature, and rainfall data. The period of study is taken from 1980-2016. Two types of shifting cultivation - current and regenerating shifting cultivation have been distinguished using object-based image analysis. From the study, it is noticed that the area under shifting cultivation is showing an overall decreasing trend. Maximum area under shifting cultivation was mostly found in gentle, strong slopes and mainly at east facing slopes. While moving towards extreme, steep and west facing slopes the area under cultivation was found to be decreasing. The study also reveals more amount of rainfall received there is a decrease in the area of shifting cultivation. Further, a correlation was not being able to establish between temperature and shifting cultivation.
Throughput Limits in Spectrum Sensing Cognitive Radio Networks Using Point Processes

Spectrum sensing in cognitive wireless networks is important for Secondary nodes to avoid interference with the Primaries. In this paper, considering a spectrum sensing framework, we develop models for bounding interference levels from Secondary network to the Primary nodes. First, we assume that both networks are distributed according to Poisson point processes. Subsequently, we consider a more practical model which takes into account the medium access control regulations and where the Secondary Poisson process is judiciously thinned in two phases to avoid interference with the Secondary as well as the Primary nodes. The resulting process will be a modified version of the Mat\`ern point process. For both of these models, we obtain bounds for CCDF of interference and present simulation results which show the developed analytical bounds are quite tight. Moreover, we use these bounds to find the operation regions of the Secondary network such that the interference constraint is satisfied on receiving Primary nodes for the two cases. We then obtain theoretical results on the Primary and Secondary throughput and find the throughput limits under interference constraint.
Autonomous Requirements Specification Processing using Natural Language Processing

We describe our ongoing research that centres on the application of natural language processing (NLP) to software engineering and systems development activities. In particular, this paper addresses the use of NLP in the requirements analysis and systems design processes. We have developed a prototype toolset that can assist the systems analyst or software engineer to select and verify terms relevant to a project. In this paper we describe the processes employed by the system to extract and classify objects of interest from requirements documents. These processes are illustrated using a small example.
Population status, threats, and evolutionary conservation genetics of Bengal tigers in the Sundarbans of Bangladesh

The Sundarbans is a Tiger Conservation Landscape of global priority that supports one of the most important tiger populations across their current range. In Bangladesh, Sundarbans is the last stronghold of the critically endangered tiger, therefore conserving this flagship species will help to ensure the long-term future of the Sundarbans which has been providing significant economic and ecosystem services to human communities for centuries. However, scientific information is lacking on many aspects of the Sundarbans tigers, including population and genetic status, and detailed patterns of tiger and prey poaching. The objectives of this study were therefore to improve the knowledge base to help design better management strategies for long-term persistence of the Sundarbans tigers. As a consequence of challenges faced in applying conventional census methods in the Sundarbans mangrove habitat, a non-invasive genetic approach was applied to collect samples that were then screened using polymorphic microsatellite markers to estimate density and population size of tigers within the spatially explicit capture-recapture model. DNA analyses provided reasonable population estimates, indicating that a non-invasive genetic approach is a viable method for monitoring tigers and can be applied to monitor tiger populations elsewhere. Bayesian and Maximum likelihood inferences using mitochondrial DNA sequences supported a polyphyletic relationship between tiger population in the Sundarbans and the populations in central India. Together, microsatellite and mitochondrial DNA analyses revealed a signal of fine-scale genetic structure and significant genetic differentiation on a spatial scale which is probably the consequence of limited tiger dispersal due to the presence of wide rivers in the Sundarbans landscape. Systematic field survey across sample areas detected a range of snaring methods used to catch tiger prey and evidence of killing tigers by poisoning prey carcasses with the Carbofuran pesticide. Spatial analysis showed that poachers selected sites that tended to be further away from guard posts, and close to river banks. Based on these results, a range of future management interventions were recommended including the reduction of water-based commercial and resource collection activities to allow tiger dispersal, and regulation of Carbofuran and snare materials to better tackle tiger and prey poaching in the Sundarbans.
A 12-bit High-Speed Time-Interleaved Pipelined Asynchronous Successive-Approximation ADC in 22-nm FDSOI CMOS

A 12-bit time-interleaved (TI) analog-to-digital converter (ADC) with pipelined successive-approximation (SAR) channels is presented in this paper. The ADC consists of four TI channels, each incorporating a two-stage pipelined asynchronous SAR ADC. To facilitate clock distribution, a common bootstrapped sampler in front of the four channels is employed. The reset switch in the capacitive digital-to-analog converter (CDAC) of each channel is also bootstrapped to enhance the speed and linearity. A prototype ADC has been designed and implemented in a 22-nm FDSOI CMOS technology, with a core occupation area of 0.43 mm2. Measurements show that the ADC achieves a signal-to-noise-and-distortion ratio of 50dB with a low-frequency input, and of 48.5 dB at Nyquist. The total power consumption is 37.5 mW; the core ADC consumes 19.3 mW from a 0.8V supply. With a 1.4 GS/s sampling rate and input at Nyquist, the ADC achieves a Walden’s figure of merit of 114 fJ/conversion.
Nutrition Discussion Forum

The reaction of M. J. Arnaud, which is more a bibliographic review (67 references) than a letter, was expected. Arnaud accepts our experimental results, i.e. a higher urinary Ca excretion with a CaSO4-rich mineral water than with milk for identical Ca intake, but he argues against our interpretation on the responsibility of sulphate. The pertinence of many of the cited references could be criticized, but, to avoid a long and fastidious polemic, we propose a shorter response focusing on the most important points and without a list of bibliographic references, which would be redundant with the ones included in our article and/or Arnaud’s letter.
Top-down Tree Long Short-Term Memory Networks

Long Short-Term Memory (LSTM) networks, a type of recurrent neural network with a more complex computational unit, have been successfully applied to a variety of sequence modeling tasks. In this paper we develop Tree Long Short-Term Memory (TreeLSTM), a neural network model based on LSTM, which is designed to predict a tree rather than a linear sequence. TreeLSTM defines the probability of a sentence by estimating the generation probability of its dependency tree. At each time step, a node is generated based on the representation of the generated sub-tree. We further enhance the modeling power of TreeLSTM by explicitly representing the correlations between left and right dependents. Application of our model to the MSR sentence completion challenge achieves results beyond the current state of the art. We also report results on dependency parsing reranking achieving competitive performance.
Biodiversity of culturable heterotrophic bacteria in the Southern Adriatic Sea Italian coastal waters*

A large number of studies in the past two decades show that heterotrophic bacteria not only function as decomposers, but also channel dissolved organic substrates and inorganic nutrients into higher trophic levels through the microbial food web (Pomeroy, 1980; Azam et al., 1983; Azam, 1998) hence facilitating the cycling of bioelements. The paramount importance of microbial life for the cycling of matSCI. MAR., 68 (Suppl. 1): 31-41 SCIENTIA MARINA 2004
Building a spindle of the correct length in human cells requires the interaction between TPX2 and Aurora A

To assemble mitotic spindles, cells nucleate microtubules from a variety of sources including chromosomes and centrosomes. We know little about how the regulation of microtubule nucleation contributes to spindle bipolarity and spindle size. The Aurora A kinase activator TPX2 is required for microtubule nucleation from chromosomes as well as for spindle bipolarity. We use bacterial artificial chromosome–based recombineering to introduce point mutants that block the interaction between TPX2 and Aurora A into human cells. TPX2 mutants have very short spindles but, surprisingly, are still bipolar and segregate chromosomes. Examination of microtubule nucleation during spindle assembly shows that microtubules fail to nucleate from chromosomes. Thus, chromosome nucleation is not essential for bipolarity during human cell mitosis when centrosomes are present. Rather, chromosome nucleation is involved in spindle pole separation and setting spindle length. A second Aurora A–independent function of TPX2 is required to bipolarize spindles.