Miracle-dz/UniFAR-FTUs huggingface dataset:
Satellite Tracking of Sympatric Marine Megafauna Can Inform the Biological Basis for Species Co-Management

Context Systematic conservation planning is increasingly used to identify priority areas for protection in marine systems. However, ecosystem-based approaches typically use density estimates as surrogates for animal presence and spatial modeling to identify areas for protection and may not take into account daily or seasonal movements of animals. Additionally, sympatric and inter-related species are often managed separately, which may not be cost-effective. This study aims to demonstrate an evidence-based method to inform the biological basis for co-management of two sympatric species, dugongs and green sea turtles. This approach can then be used in conservation planning to delineate areas to maximize species protection. Methodology/Results Fast-acquisition satellite telemetry was used to track eleven dugongs and ten green turtles at two geographically distinct foraging locations in Queensland, Australia to evaluate the inter- and intra-species spatial relationships and assess the efficacy of existing protection zones. Home-range analysis and bathymetric modeling were used to determine spatial use and compared with existing protection areas using GIS. Dugong and green turtle home-ranges significantly overlapped in both locations. However, both species used different core areas and differences existed between regions in depth zone use and home-range size, especially for dugongs. Both species used existing protection areas in Shoalwater Bay, but only a single tracked dugong used the existing protection area in Torres Strait. Conclusions/Significance: Fast-acquisition satellite telemetry can provide evidence-based information on individual animal movements to delineate relationships between dugongs and green turtles in regions where they co-occur. This information can be used to increase the efficacy of conservation planning and complement more broadly based survey information. These species also use similar habitats, making complimentary co-management possible, but important differences exist between locations making it essential to customize management. This methodology could be applied on a broader scale to include other sympatric and inter-related species.
Where is time spent in message-passing and shared-memory programs?

Message passing and shared memory are two techniques parallel programs use for coordination and communication. This paper studies the strengths and weaknesses of these two mechanisms by comparing equivalent, well-written message-passing and shared-memory programs running on similar hardware. To ensure that our measurements are comparable, we produced two carefully tuned versions of each program and measured them on closely-related simulators of a message-passing and a shared-memory machine, both of which are based on same underlying hardware assumptions. We examined the behavior and performance of each program carefully. Although the cost of computation in each pair of programs was similar, synchronization and communication differed greatly. We found that message-passing's advantage over shared-memory is not clear-cut. Three of the four shared-memory programs ran at roughly the same speed as their message-passing equivalent, even though their communication patterns were different.
Content Modeling Using Latent Permutations

We present a novel Bayesian topic model for learning discourse-level document structure. Our model leverages insights from discourse theory to constrain latent topic assignments in a way that reflects the underlying organization of document topics. We propose a global model in which both topic selection and ordering are biased to be similar across a collection of related documents. We show that this space of orderings can be effectively represented using a distribution over permutations called the Generalized Mallows Model. We apply our method to three complementary discourse-level tasks: cross-document alignment, document segmentation, and information ordering. Our experiments show that incorporating our permutation-based model in these applications yields substantial improvements in performance over previously proposed methods.
A microtubule depolymerizing kinesin functions during both flagellar disassembly and flagellar assembly in Chlamydomonas

Cilia and flagella are dynamic organelles that are assembled and disassembled during cell differentiation, during stress, and during the cell cycle. Although intraflagellar transport (IFT) is well documented to be responsible for transport of ciliary/flagellar precursors from the cell body to the flagella, little is known about the molecular mechanisms for mobilizing the cell body-localized precursors to make them available for transport during organelle assembly or for disassembling the microtubule-based axoneme during shortening. Here, we show that Chlamydomonas kinesin-13 (CrKinesin-13), a member of the kinesin-13 family of microtubule depolymerizing kinesins best known for their roles in the cell cycle, functions in flagellar disassembly and flagellar assembly. Activation of a cell to generate new flagella induces rapid phosphorylation of CrKinesin-13, and activation of flagellar shortening induces the immediate transport of CrKinesin-13 via intraflagellar transport from the cell body into the flagella. Cells depleted of CrKinesin-13 by RNAi assemble flagella after cell division but are incapable of the rapid assembly of flagella that normally occurs after flagellar detachment. Furthermore, they are inhibited in flagellar shortening. Thus, CrKinesin-13 is dynamically regulated during flagellar assembly and disassembly in Chlamydomonas and functions in each.
Gaussian process-based algorithmic trading strategy identification

Many market participants now employ algorithmic trading, commonly defined as the use of computer algorithms, to automatically make certain trading decisions, submit orders and manage those orders after submission. Identifying and understanding the impact of algorithmic trading on financial markets has become a critical issue for market operators and regulators. Advanced data feeds and audit trail information from market operators now allow for the full observation of market participants’ actions. A key question is the extent to which it is possible to understand and characterize the behaviour of individual participants from observations of trading actions. In this paper, we consider the basic problems of categorizing and recognizing traders (or, equivalently, trading algorithms) on the basis of observed limit orders. These problems are of interest to regulators engaged in strategy identification for the purposes of fraud detection and policy development. Methods have been suggested in the literature for describing trader behaviour using classification rules defined over a feature space consisting of summary trading statistics of volume and inventory, along with derived variables that reflect the consistency of buying or selling behaviour. Our principal contribution is to suggest an entirely different feature space that is constructed by inferring key parameters of a sequential optimization model that we take as a surrogate for the decision-making process of the traders. In particular, we model trader behaviour in terms of a Markov decision process. We infer the reward (or objective) function for this process from observations of trading actions using a process from machine learning known as inverse reinforcement learning (IRL). The reward functions learned through IRL then constitute a feature space that can be the basis for supervised learning (for classification or recognition of traders) or unsupervised learning (for categorization of traders). Making use of a real-world data-set from the E-Mini futures contract, we compare two principal IRL variants, linear IRL and Gaussian Process IRL, against a method based on summary trading statistics. Results suggest that IRL-based feature spaces support accurate classification and meaningful clustering. Further, we argue that, because they attempt to learn traders’ underlying value propositions under different market conditions, the IRL methods are more informative and robust than the summary statistic-based approach and are well suited for discovering new behaviour patterns of market participants.
Metallicity estimates for old star clusters in M 33

Using the theoretical stellar population synthesis models of BC96, Kong et al. (2003) showed that some BATC colors and color indices could be used to disentangle the age and metallicity effect. They found that there is a very good relation between the flux ratio of L 8 5 1 0 /L 9 1 7 0 and the metallicity for stellar populations older than 1 Gyr. In this paper, based on the Kong et al. results and on the multicolor spectrophotometry of Ma et al. (2001, 2002a,b,c), we estimate the metallicities of 31 old star clusters in the nearby spiral galaxy M 33, 23 of which are "true" globular clusters. The results show that most of these old clusters are metal poor. We also find that the ages and metal abundance for these old star clusters of M 33 do not vary with deprojected radial position.
Identification of Synapomorphic Characteris in the Genus Sarcocystis Based on 18S rDNA Sequence Comparison

ABSTRACT. In order to further investigate synapomorphic characters in the genus Sarcocystis, the small subunit ribosomal RNA gene sequences of Sarcocystis capracanis and Sarcocystis moulei were determined and used to infer the phylogenetic position of these two organisms within the cyst‐forming coccidia. Phylogenies derived using distance, maximum parsimony and maximum likelihood methods demonstrated that S. capracanis groups with Sarcoystis tenella and Sarcocystis arieticanis as a clade that shares the characteristic of using canids as their definitive host. S. moulei was shown to group with Sarcocystis gigantea and Sarcocystis fusiformis as a clade that shares the characteristic of using felids as their definitive host.
Effect of Drought Stress on Growth and Yield of Wheat Genotypes

A pot experiment on screening of wheat genotypes against drought stress was conducted at the research field of Sher-e-Bangla Agricultural University in earthen pots during rabi season of 2013-2014. Fifteen (15) wheat genotypes were evaluated under drought (stress was imposed by withdrawing irrigation after emergence) and well irrigated (control) condition. Exposure of plants to drought led to remarkable reduction in yield contributing characters which ultimate caused in reduced yield in all the genotypes. However, genotypes showed remarkable variability in yield reduction due to drought. The highest relative yield was observed in genotype SATYN-25 followed by SATYN-2, BARI Gom-26 and BARI Gom-28. However, yield reduction was less in SATYN-25 (about 20%) followed by BARI Gom-26 (21%) and SATYN-2 (25%). Besides yield performance of the genotypes, some drought tolerance indices like Geometric Mean Productivity (GMP), Stress Tolerance Index (STI), Yield Stability Index (YSI) and Stress Susceptible Index (SSI) were used to select the desirable genotypes. Among the genotypes, BARI Gom-26, BARI Gom-28 and SATYN-25 gave better yield with higher STI, GMP and YSI with lower SSI indicating that these genotypes would be suitable for growing under drought prone areas.Bangladesh Agron. J. 2017, 20(2): 97-105
The Muscle Chloride Channel ClC-1 Is Not Directly Regulated by Intracellular ATP

ClC-1 belongs to the gene family of CLC Cl− channels and Cl−/H+ antiporters. It is the major skeletal muscle chloride channel and is mutated in dominant and recessive myotonia. In addition to the membrane-embedded part, all mammalian CLC proteins possess a large cytoplasmic C-terminal domain that bears two so-called CBS (from cystathionine-β-synthase) domains. Several studies indicate that these domains might be involved in nucleotide binding and regulation. In particular, Bennetts et al. (J. Biol. Chem. 2005. 280:32452–32458) reported that the voltage dependence of hClC-1 expressed in HEK cells is regulated by intracellular ATP and other nucleotides. Moreover, very recently, Bennetts et al. (J. Biol. Chem. 2007. 282:32780–32791) and Tseng et al. (J. Gen. Physiol. 2007. 130:217–221) reported that the ATP effect was enhanced by intracellular acidification. Here, we show that in striking contrast with these findings, human ClC-1, expressed in Xenopus oocytes and studied with the inside-out configuration of the patch-clamp technique, is completely insensitive to intracellular ATP at concentrations up to 10 mM, at neutral pH (pH 7.3) as well as at slightly acidic pH (pH 6.2). These results have implications for a general understanding of nucleotide regulation of CLC proteins and for the physiological role of ClC-1 in muscle excitation.
Variance-minimizing transport plans for inter-surface mapping

We introduce an efficient computational method for generating dense and low distortion maps between two arbitrary surfaces of same genus. Instead of relying on semantic correspondences or surface parameterization, we directly optimize a variance-minimizing transport plan between two input surfaces that defines an as-conformal-as-possible inter-surface map satisfying a user-prescribed bound on area distortion. The transport plan is computed via two alternating convex optimizations, and is shown to minimize a generalized Dirichlet energy of both the map and its inverse. Computational efficiency is achieved through a coarse-to-fine approach in diffusion geometry, with Sinkhorn iterations modified to enforce bounded area distortion. The resulting inter-surface mapping algorithm applies to arbitrary shapes robustly, with little to no user interaction.
Highly Linear Predistortion Power Amplifiers With Phase-Controlled Error Generator

A simple predistortion technique to cancel the fifth-order intermodulation (IM5) as well as third-order intermodulation (IM3) components using a third-order predistorter (PD) is represented. The IM3 and IM5 components are cancelled out simultaneously by their same magnitude and phase difference in the PD and power amplifier (PA). Moreover, this phase difference is controlled by using the phase-controlled error generator in the PD. For experimental verification, a third-order PD has been implemented and tested in a 30-W class-AB PA at the wide-band code division multiple access (WCDMA) band of 2.11-2.17GHz. Two-tone test results show that significant cancellation of the IM3 and IM5 components can be obtained. For a four-carrier WCDMA application, significant adjacent channel leakage ratio improvement is achieved over a wide range of output power levels
Evaluation of Opinions Related to the Endangered Neopolis Wetland in North Cyprus

In this paper, the complaints and expectations of people living around the Neopolis wetland, which is an endangered area with international importance in Famagusta, Cyprus, in terms of the present situation of the wetland. For this purpose, 88 people (self-employed, university students over 18 years of age, etc.) who live in the three streets and one main street parallel to the wetland were included in the working group. Open-ended questions were asked to the participants as required by qualitative research approaches. According to the research findings, it is seen that people have complaints about the present situation of the wetland and have expectations from the authorities and residents living there about its protection. It is observed that participants do not have sufficient awareness about the importance, protection and usage of the wetlands. In summary, it is found out that they required education about the environment and the wetland.
Chromosome 7 q Allelic Losses in Pancreatic Carcinoma 1

During our DNA fingerprinting studies of paired normal and pancre atic cancer tissues using arbitrarily primed PCR, we noticed a band showing an apparent homozygous deletion in a pancreatic cancer cell line and a decreased intensity in a number of primary cancers. That band was assigned to chromosome 7. Such information led us to analyze chromo some 7 loss of heterozygosity (LOH) in a panel of 12 cryostat-enriched primary pancreatic cancers and 2 pancreatic cancer cell lines, despite the reportedly low frequency of chromosome 7 LOH in xenograft-enriched pancreatic cancers. Seventeen PCR-amplified CA-microsatellite polymor phic sites were analyzed. One of the two cell lines and eight common-type cancers (including all five poorly differentiated and three of five moder ately differentiated cancers) showed chromosome 7q LOH, whereas the two uncommon types of ductal cancer (one adenosquamous and one mucinous noncystic) scored negative. Our data suggest that chromosome 7q LOH is a frequent event (80%) in cryostat-enrichable common pan creatic ductal carcinomas, that is, those primarily of high cellularity. The chromosome 7q smallest common deleted region described by our cases was between 7q31.1 and 7q32.
Characterization of Renal Ecto-Phosphodiesterase

In kidneys, stimulation of adenylyl cyclase causes egress of cAMP, conversion of cAMP to AMP by ecto-phosphodiesterase, and metabolism of AMP to adenosine by ecto-5′-nucleotidase. Although much is known about ecto-5′-nucleotidase, the renal ecto-phosphodiesterase remains uncharacterized. We administered cAMP (10 μM in the perfusate) to 12 different groups of perfused kidneys. AMP was measured in perfusate using ion trap mass spectrometry. In control kidneys (n = 19), basal renal secretion rate of AMP was 0.49 ± 0.08 and increased to 3.0 ± 0.2 nmol AMP/g kidney weight/min during administration of cAMP. A broad-spectrum phosphodiesterase (PDE) inhibitor (1,3-isobutyl-1-methylxanthine, 300 μM, n = 6) and an ecto-phosphodiesterase inhibitor (1,3-dipropyl-8-p-sulfophenylxanthine, 1 mM, n = 6) significantly attenuated cAMP-induced AMP secretion by 60 and 74%, respectively. Blockade of PDE1 (8-methoxymethyl-3-isobutyl-1-methylxanthine, 100 μM), PDE2 [erythro-9-(2-hydroxy-3-nonyl)adenine, 30 μM], PDE3 (milrinone, 10 μM; cGMP, 10 μM), PDE4 (Ro 20-1724 [4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one], 100 μM), PDE5 and PDE6 (zaprinast, 30 μM), and PDE7 [BRL-50481 (5-nitro-2,N,N-trimethylbenzenesulfonamide), 10 μM] did not alter renal ecto-phosphodiesterase activity. Administration of a concentration (100 μM) of dipyridamole that blocks PDE8 inhibited ecto-phosphodiesterase activity (by 44%). However, a lower concentration of dipyridamole (3 μM) that blocks PDE9, PDE10, and PDE11, but not PDE8, did not inhibit ecto-phosphodiesterase activity. These data support the conclusion that renal ecto-phosphodiesterase activity is not mediated by PDE1, PDE2, PDE3, PDE4, PDE5, PDE6, PDE7, PDE9, PDE10, or PDE11 and is inhibited by high concentrations of dipyridamole. Ecto-phosphodiesterase has some pharmacological characteristics similar to PDE8.
Short-term effect of egg-white hydrolysate products on the arterial blood pressure of hypertensive rats

In the present study we evaluate the blood pressure-lowering effect of the following products: the hydrolysate obtained from egg white (EW) by enzymatic treatment with pepsin (HEW), the peptide fraction of HEW with molecular mass lower than 3000 Da (HEW<3000 Da), and three peptide sequences isolated from HEW<3000 Da (Tyr-Ala-Glu-Glu-Arg-Tyr-Pro-Ile-Leu: YAEERYPIL); (Arg-Ala-Asp-His-Pro-Phe-Leu: RADHPFL); and (Ile-Val-Phe (IVF)). These peptides, and also HEW and HEW<3000 Da, had been characterized previously in vitro as potent inhibitors of angiotensin-converting enzyme (ACE). EW and the products mentioned earlier were orally administered by gastric intubation, to 17–20-week-old male spontaneously hypertensive rats (SHR) and normotensive Wistar–Kyoto (WKY) rats. We measured the systolic blood pressure (SBP) and the diastolic blood pressure (DBP) of the rats by the tail cuff method before administration and also 2, 4, 6, 8 and 24h post-administration. Distilled water served as negative control, and we used captopril (50mg/kg) as positive control to carry out similar experiments with a known ACE inhibitor. HEW, HEW<3000 Da and the three peptide sequences decreased SBP and DBP in SHR but they did not modify these variables in WKY rats. The peptide sequences YAEERYPIL, RADHPFL and IVF showed a potency to decrease blood pressure greater than HEW or HEW<3000 Da. The results obtained suggest that the studied products could be used as a functional food with potential therapeutic benefit in the prevention and treatment of hypertension.
Face-to-Face and Online Interactions--Is a Task a Task?.

This study contrasts two different ways of analysing interaction and participation in language learning tutorials: Social network analysis of frequency and QSR analysis of type of interaction. One task from three German beginners' language tutorials (one delivered face-to-face and two online) is analysed. A description of the background and method of the study is provided together with some examples of the findings. As this is work in progress, only tentative conclusions can be provided at this stage.
Retinal vessel dilatation and elongation precedes diabetic macular oedema

AIMS/BACKGROUND Retinal vessel dilatation is a well known phenomenon in diabetes. In this study, the theory of whether excessive changes in diameter and length of retinal vessels occur in the development of diabetic macular oedema was tested, supporting a hypothesis that the development of diabetic macular oedema may be linked to hydrostatic pressure changes described in Starling’s law. METHODS From fundus photographs of diabetic patients attending a regular eye screening programme, the diameter and segment length of retinal vessels were measured in three retinopathy groups (12 patients each) with diabetic macular oedema (DMO), background retinopathy and no retinopathy, over a period of approximately 4 years, ending at the time of diagnosis of diabetic macular oedema in the DMO group. RESULTS A statistically significant dilatation and elongation of retinal arterioles, venules, and their macular branches was found before the diagnosis of macular oedema in the DMO group. No significant changes were found in the other two groups. CONCLUSION It is suggested that Starling’s law applies to the formation of oedema in the retina as in other tissues.
Disulfide connectivity prediction using recursive neural networks and evolutionary information

MOTIVATION We focus on the prediction of disulfide bridges in proteins starting from their amino acid sequence and from the knowledge of the disulfide bonding state of each cysteine. The location of disulfide bridges is a structural feature that conveys important information about the protein main chain conformation and can therefore help towards the solution of the folding problem. Existing approaches based on weighted graph matching algorithms do not take advantage of evolutionary information. Recursive neural networks (RNN), on the other hand, can handle in a natural way complex data structures such as graphs whose vertices are labeled by real vectors, allowing us to incorporate multiple alignment profiles in the graphical representation of disulfide connectivity patterns. RESULTS The core of the method is the use of machine learning tools to rank alternative disulfide connectivity patterns. We develop an ad-hoc RNN architecture for scoring labeled undirected graphs that represent connectivity patterns. In order to compare our algorithm with previous methods, we report experimental results on the SWISS-PROT 39 dataset. We find that using multiple alignment profiles allows us to obtain significant prediction accuracy improvements, clearly demonstrating the important role played by evolutionary information. AVAILABILITY The Web interface of the predictor is available at http://neural.dsi. unifi.it/cysteines