Miracle-dz/UniFAR-FTUs huggingface dataset:
Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in the conservation flocks. The utility and limitations of the iselect chicken SNP60K in village chicken populations is discussed.
Grasp Stability Analysis of Two Objects in Two Dimensions

This paper analyzes grasp stability of two objects in two dimensions. In the previous researches on the grasp stability, the number of grasped objects is restricted to 1. For efficiency of tasks, multiple objects had better been grasped and manipulated by a robot hand. In order to design stable grasp, grasp stability of multiple objects must be quantitatively evaluated. In case of two grasped objects in two dimensions, the number of parameters of object displacement is 6. However, the displacement of the objects is constrained by each other, because the contact between the objects must be maintained. Independent parameters of the object displacement are provided and then finger displacement is derived. The grasp stability is evaluated from the viewpoint of the potential energy method. From numerical examples, the effect of curvature at contact point between two objects is demonstrated. The effect of this curvature stands for the feature of multiple objects.
Preventive Strategies against Bleeding due to Nonvitamin K Antagonist Oral Anticoagulants

Dabigatran etexilate (DE), rivaroxaban, and apixaban are nonvitamin K antagonist oral anticoagulants (NOACs) that have been compared in clinical trials with existing anticoagulants (warfarin and enoxaparin) in several indications for the prevention and treatment of thrombotic events. All NOACs presented bleeding events despite a careful selection and control of patients. Compared with warfarin, NOACs had a decreased risk of intracranial hemorrhage, and apixaban and DE (110 mg BID) had a decreased risk of major bleeding from any site. Rivaroxaban and DE showed an increased risk of major gastrointestinal bleeding compared with warfarin. Developing strategies to minimize the risk of bleeding is essential, as major bleedings are reported in clinical practice and specific antidotes are currently not available. In this paper, the following preventive approaches are reviewed: improvement of appropriate prescription, identification of modifiable bleeding risk factors, tailoring NOAC's dose, dealing with a missed dose as well as adhesion to switching, bridging and anesthetic procedures.
Managing chaos: models of turn-taking in character-multichild interactions

Turn-taking decisions in multiparty settings are complex, especially when the participants are children. Our goal is to endow an interactive character with appropriate turn-taking behavior using visual, audio and contextual features. To that end, we investigate three distinct turn-taking models: a baseline model grounded in established turn-taking rules for adults and two machine learning models, one trained with data collected in situ and the other trained with data collected in more controlled conditions. The three models are shown to have different profiles of behavior during silences, overlapping speech, and at the end of participants' turns. An exploratory user evaluation focusing on the decision points where the models differ showed clear preference for the machine learning models over the baseline model. The results indicate that the rules for language interactions with small groups of children are not simply an extension of the rules for interacting with small groups of adults.
Toucheo: multitouch and stereo combined in a seamless workspace

We propose a new system that efficiently combines direct multitouch interaction with co-located 3D stereoscopic visualization. In our approach, users benefit from well-known 2D metaphors and widgets displayed on a monoscopic touchscreen, while visualizing occlusion-free 3D objects floating above the surface at an optically correct distance. Technically, a horizontal semi-transparent mirror is used to reflect 3D images produced by a stereoscopic screen, while the user's hand as well as a multitouch screen located below this mirror remain visible. By registering the 3D virtual space and the physical space, we produce a rich and unified workspace where users benefit simultaneously from the advantages of both direct and indirect interaction, and from 2D and 3D visualizations. A pilot usability study shows that this combination of technology provides a good user experience.
Proton currents through amiloride-sensitive Na channels in hamster taste cells. Role in acid transduction

The activity of taste cells maintained in the intact hamster tongue was monitored in response to acid stimulation by recording action currents from taste receptor cells with an extracellular "macro" patch pipette: a glass pipette was pressed over the taste pore of fungiform papillae and perfused with citric acid, hydrochloric acid, or NaCl. Because this technique restricted stimulus application to the small surface area of the apical membranes of the taste cells, many nonspecific, and potentially detrimental, effects of acid stimulation could be avoided. Acid stimulation reliably elicited fast transient currents (action currents of average amplitude, 9 pA) which were consistently smaller than those elicited by NaCl (29 pA). The frequency of action currents elicited by acid stimuli increased in a dose-dependent manner with decreasing pH from a threshold of about pH 5.0. Acid-elicited responses were independent of K+, Na+, Cl-, or Ca2+ at physiological (salivary) concentrations, and were unaffected by anthracene-9-carboxylic acid, tetraethylammonium bromide, diisothiocyanate-stilbene-2,2'-disulfonic acid, vanadate, or Cd2+. In contrast, amiloride (< or = 30 microM) fully and reversibly suppressed acid-evoked action currents. At submaximal amiloride concentrations, the frequency and amplitude of the action currents were reduced, indicating a reduction of the taste cell apical conductance concomitant with a decrease in cell excitation. Exposure to low pH elicited, in addition to transient currents, an amiloride-sensitive sustained d.c. current. This current is apparently carried by protons instead of Na+ through amiloride-sensitive channels. When citric acid was applied while the taste bud was stimulated by NaCl, the action currents became smaller and the response resembled that produced by acid alone. Because of the strong interdependence of the acid and salt (NaCl) responses when both stimuli are applied simultaneously, and because of the similarity in the concentration dependence of amiloride block, we conclude that amiloride-sensitive Na+ channels on hamster taste receptor cells are permeable to protons and may play a role in acid (sour) taste.
Calsequestrin interacts directly with the cardiac ryanodine receptor luminal domain

ABSTRACT Cardiac muscle contraction requires sarcoplasmic reticulum (SR) Ca2+ release mediated by the quaternary complex comprising the ryanodine receptor 2 (RyR2), calsequestrin 2 (CSQ2), junctin (encoded by ASPH) and triadin. Here, we demonstrate that a direct interaction exists between RyR2 and CSQ2. Topologically, CSQ2 binding occurs at the first luminal loop of RyR2. Co-expression of RyR2 and CSQ2 in a human cell line devoid of the other quaternary complex proteins results in altered Ca2+-release dynamics compared to cells expressing RyR2 only. These findings provide a new perspective for understanding the SR luminal Ca2+ sensor and its involvement in cardiac physiology and disease. Summary: Direct physical and functional calsequestrin 2 association with the ryanodine receptor luminal domain is the minimal requirement to form the sarcoplasmic reticulum Ca2+ sensor, which governs cardiac Ca2+ homeostasis and reliable heartbeat.
Perception of the population about climate change inprotected natural areas of ‘Baja California Sur’, Mexico

This work shows the perception of the human population settled in the seven federal natural protected areas of ‘Baja California Sur’, from the point of view of empirical knowledge about changes in the environment and natural resources in front of the effects of climate change (CC). Data was collected from the application of 250 qualitative surveys in 2011. The results show that most of the people know the meaning of CC and that the effects they perceive are reduction of forest surface by changes of land use, reduction of fishing activity by changes in Polis, Revista Latinoamericana, Volumen 12, No 35, 2013, p. 459-481 Polis, Revista Latinoamericana, Volumen 12, No 35, 2013 460 sea conditions, negative effects on the cattle herds and frequency and intensity of hurricanes, increased droughts, lack of water and reduction of ecotourism by changes in the beaches. Studies have shown that subjective valuation of the population contributes to behavioral change through a strategy of adaptation and of citizen awareness.
Trajectory of Topsoil Nitrogen Transformations Along a Thermo‐Erosion Gully on the Tibetan Plateau

Permafrost thaw, especially thermokarst formation, that is, ground collapse due to thawing of ice‐rich permafrost, is expected to alter soil gross nitrogen (N) transformations, which can regulate plant productivity and ecosystem carbon cycle. However, it remains unclear how thermokarst formation modifies soil N processes in permafrost ecosystems. Here 15N pool dilution techniques were used to evaluate changes in topsoil gross N transformations during various thaw stages (early, middle, and late stages) along a thermo‐erosion gully on the Tibetan Plateau. Structural equation modeling was then conducted to explore the relative importance of biotic and abiotic factors in affecting soil gross N transformations. The results showed that topsoil gross N mineralization (GNM) decreased at the three stages, reflecting declined inorganic N production after permafrost collapse. In contrast, topsoil gross nitrification increased only during the early stage. Additionally, the ratio of microbial N immobilization to GNM was enhanced during the middle and late stages, indicating a stronger microbial N limitation after thermokarst formation. The structural equation modeling analysis revealed that soil moisture played an important role in modulating gross N transformations. For GNM, decreased soil moisture had inhibiting effects via regulating the microbial biomass, microbial community, and enzyme activities along the thaw sequence. For gross nitrification, declined soil moisture exerted facilitating effects directly by improving oxygen availability and indirectly by modulating the abundances of ammonia‐oxidizing archaea and bacteria during the early stage. Overall, these results demonstrated that thermokarst formation altered soil N processes, potentially triggering interactions between ecosystem N and carbon cycles after permafrost thaw.
A neural network approach for a single-camera based Artificial Compound Eye System (ACES)

This work studies an Artificial Compound Eye System (ACES) which consists of a camera, a main lens, and a lenslet array. Similar to the compound eye systems in arthropods, one single shot of the ACES can simultaneously capture the visual image of an object from hundreds of different viewpoints, which essentially record the object's 3D information. Due to the special optics of the ACES, traditional imaging models based on a pinhole assumption can not be directly applied to the system. In this work, we propose to use artificial neural network (NN) to model the mapping from the image observation of the ACES to the object's 3D information. To deal with the incomplete observation problem in the ACES, a sliding frame based method is proposed to construct the input and target data to train the neural network. Experimental results show that with the proposed method, position of an object in 3D can be effectively extracted from a single image input and the object's motion in 3D can be extracted from a 2D optical flow. This work may inspire related efforts in exploring the ACES for novel 3D imaging applications.
New generation Systran translation system

In this paper, we present the design of the new generation Systran translation systems, currently utilized in the development of English-Hungarian, English-Polish, English-Arabic, French-Arabic, Hungarian-French and Polish-French language pairs. The new design, based on the traditional Systran machine translation expertise and the existing linguistic resources, addresses the following aspects: efficiency, modularity, declarativity, reusability, and maintainability. Technically, the new systems rely on intensive use of state-of-the-art finite automaton and formal grammar implementation. The finite automata provide the essential lookup facilities and the natural capacity of factorizing intuitive linguistic sets. Linguistically, we have introduced a full monolingual description of linguistic information and the concept of implicit transfer. Finally, we present some by-products that are directly derived from the new architecture: intuitive coding tools, spell checker and syntactic tagger.
Mitochondrial Haplogroups and Polymorphisms Reveal No Association with Sporadic Prostate Cancer in a Southern European Population

Background It is known that mitochondria play an important role in certain cancers (prostate, renal, breast, or colorectal) and coronary disease. These organelles play an essential role in apoptosis and the production of reactive oxygen species; in addition, mtDNA also reveals the history of populations and ancient human migration. All these events and variations in the mitochondrial genome are thought to cause some cancers, including prostate cancer, and also help us to group individuals into common origin groups. The aim of the present study is to analyze the different haplogroups and variations in the sequence in the mitochondrial genome of a southern European population consisting of subjects affected (n = 239) and non-affected (n = 150) by sporadic prostate cancer. Methodology and Principal Findings Using primer extension analysis and DNA sequencing, we identified the nine major European haplogroups and CR polymorphisms. The frequencies of the haplogroups did not differ between patients and control cohorts, whereas the CR polymorphism T16356C was significantly higher in patients with PC compared to the controls (p = 0.029). PSA, staging, and Gleason score were associated with none of the nine major European haplogroups. The CR polymorphisms G16129A (p = 0.007) and T16224C (p = 0.022) were significantly associated with Gleason score, whereas T16311C (p = 0.046) was linked with T-stage. Conclusions and Significance Our results do not suggest that mtDNA haplogroups could be involved in sporadic prostate cancer etiology and pathogenesis as previous studies performed in middle Europe population. Although some significant associations have been obtained in studying CR polymorphisms, further studies should be performed to validate these results.
Feature Articles: Multimedia Communications

A key challenge to the vision of ubiquitous mobile multi-media access is the communication resource limitation in multiple access wireless channels. In this paper we review several source adaptation techniques and wireless collaboration schemes. We then formulate the multiuser video communication problem as a network utility maximiza-tion (NUM) problem. , and solve it using a pricing scheme. The pricing scheme coordinates resource allocation, source adaptation in a distributed manner, and leads to efficient packet scheduling to achieve better utilization of communication resources and end-to-end video quality.
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

The sc-PDB is a collection of 6 415 three-dimensional structures of binding sites found in the Protein Data Bank (PDB). Binding sites were extracted from all high-resolution crystal structures in which a complex between a protein cavity and a small-molecular-weight ligand could be identified. Importantly, ligands are considered from a pharmacological and not a structural point of view. Therefore, solvents, detergents, and most metal ions are not stored in the sc-PDB. Ligands are classified into four main categories: nucleotides (< 4-mer), peptides (< 9-mer), cofactors, and organic compounds. The corresponding binding site is formed by all protein residues (including amino acids, cofactors, and important metal ions) with at least one atom within 6.5 angstroms of any ligand atom. The database was carefully annotated by browsing several protein databases (PDB, UniProt, and GO) and storing, for every sc-PDB entry, the following features: protein name, function, source, domain and mutations, ligand name, and structure. The repository of ligands has also been archived by diversity analysis of molecular scaffolds, and several chemoinformatics descriptors were computed to better understand the chemical space covered by stored ligands. The sc-PDB may be used for several purposes: (i) screening a collection of binding sites for predicting the most likely target(s) of any ligand, (ii) analyzing the molecular similarity between different cavities, and (iii) deriving rules that describe the relationship between ligand pharmacophoric points and active-site properties. The database is periodically updated and accessible on the web at http://bioinfo-pharma.u-strasbg.fr/scPDB/.
Lead-free, high-powered rifl e bullets and their applicability in wildlife management

In recent years, concern over the use of lead-based ammunition for hunting has been growing, primarily due to consumption of discarded offal by scavengers and donated game meat for human consumption. While there are alternative bullet technologies on the market that are suitable for hunting, these alternatives have not been adequately researched and tested for use in professional wildlife damage management (WDM). Differences between hunting and WDM include an increased level of precision necessary for safe WDM work, potentially greater distances for shots fi red at targets, a need for instant incapacitation, and overall cost-effectiveness. To determine the applicability of lead-free bullets for WDM, we reviewed current lead-free bullet technologies and examined their limitations and benefi ts based on ballistic theory and available research. We found that there has not been suffi cient research or experience with lead-free ammunition in the unique shooting scenarios used in WDM. Some of the issues identifi ed by our review include a reduced theoretical precision of lead-free bullets due to a mismatch between bullet length and twist rate of the rifl e barrel, lower performance of lead-free ammunition at greater ranges compared with lead-based bullets, and greater chance of bullets passing through targets and striking a nontarget object or animal. While some of these defi ciencies may be overcome with new equipment and decreased target ranges, there are still situations where lead-based ammunition may be the safest and most practical option.
Modeling error-based Adaptive User Interfaces

vi CHAPTER 1. OVERVIEW AND MOTIVATION . 1 1.
In High-Light-Acclimated Coffee Plants the Metabolic Machinery Is Adjusted to Avoid Oxidative Stress Rather than to Benefit from Extra Light Enhancement in Photosynthetic Yield

Coffee (Coffea arabica L.) has been traditionally considered as shade-demanding, although it performs well without shade and even out-yields shaded coffee. Here we investigated how coffee plants adjust their metabolic machinery to varying light supply and whether these adjustments are supported by a reprogramming of the primary and secondary metabolism. We demonstrate that coffee plants are able to adjust its metabolic machinery to high light conditions through marked increases in its antioxidant capacity associated with enhanced consumption of reducing equivalents. Photorespiration and alternative pathways are suggested to be key players in reductant-consumption under high light conditions. We also demonstrate that both primary and secondary metabolism undergo extensive reprogramming under high light supply, including depression of the levels of intermediates of the tricarboxylic acid cycle that were accompanied by an up-regulation of a range of amino acids, sugars and sugar alcohols, polyamines and flavonoids such as kaempferol and quercetin derivatives. When taken together, the entire dataset is consistent with these metabolic alterations being primarily associated with oxidative stress avoidance rather than representing adjustments in order to facilitate the plants from utilizing the additional light to improve their photosynthetic performance.
Establishment and Molecular Cytogenetic Characterization of a Cell Culture Model of Head and Neck Squamous Cell Carcinoma (HNSCC)

Cytogenetic analysis of head and neck squamous cell carcinoma (HNSCC) established several biomarkers that have been correlated to clinical parameters during the past years. Adequate cell culture model systems are required for functional studies investigating those potential prognostic markers in HNSCC. We have used a cell line, CAL 33, for the establishment of a cell culture model in order to perform functional analyses of interesting candidate genes and proteins. The cell line was cytogenetically characterized using array CGH, spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH). As a starting point for the investigation of genetic markers predicting radiosensitivity in tumor cells, irradiation experiments were carried out and radiation responses of CAL 33 have been determined. Radiosensitivity of CAL 33 cells was intermediate when compared to published data on tumor cell lines.