Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Choice of Genetic Distance in Spatial-Genetic Studies

We look at how to choose genetic distance so as to maximize the power of detecting spatial structure. We answer this question through analyzing two population genetic models that allow for a spatially structured population in a continuous habitat. These models, like most that incorporate spatial structure, can be characterized by a separation of timescales: the history of the sample can be split into a scattering and a collecting phase, and it is only during the scattering phase that the spatial locations of the sample affect the coalescence times. Our results suggest that the optimal choice of genetic distance is based upon splitting a DNA sequence into segments and counting the number of segments at which two sequences differ. The size of these segments depends on the length of the scattering phase for the population genetic model.
L’encastrement institutionnel des procédures de recours internes en organisation

Cet article explore les limites de l’implantation d’une procedure organisationnelle anglo-saxonne de reglement de litiges interpersonnels dans le contexte francais. Visant a mieux integrer le souci d’equite, de telles procedures se sont tres largement developpes depuis les annees 1970 aux Etats-Unis ou elles prennent la denomination de « non union grievance procedures ». Elles donnent la possibilite pour un salarie, qui renonce alors a tout appui syndical, de remettre en cause la decision de ses superieurs hierarchiques et d’informer les dirigeants de l’existence d’une situation illegale ou contraire a la politique ethique de l’entreprise.
Automated Planning in Repeated Adversarial Games

Game theory's prescriptive power typically relies on full rationality and/or self-play interactions. In contrast, this work sets aside these fundamental premises and focuses instead on heterogeneous autonomous interactions between two or more agents. Specifically, we introduce a new and concise representation for repeated adversarial (constant-sum) games that highlight the necessary features that enable an automated planing agent to reason about how to score above the game's Nash equilibrium, when facing heterogeneous adversaries. To this end, we present TeamUP, a model-based RL algorithm designed for learning and planning such an abstraction. In essence, it is somewhat similar to R-MAX with a cleverly engineered reward shaping that treats exploration as an adversarial optimization problem. In practice, it attempts to find an ally with which to tacitly collude (in more than two-player games) and then collaborates on a joint plan of actions that can consistently score a high utility in adversarial repeated games. We use the inaugural Lemonade Stand Game Tournament1 to demonstrate the effectiveness of our approach, and find that TeamUP is the best performing agent, demoting the Tournament's actual winning strategy into second place. In our experimental analysis, we show hat our strategy successfully and consistently builds collaborations with many different heterogeneous (and sometimes very sophisticated) adversaries.
A robot for harvesting sweet-pepper in greenhouses

This paper describes the results of the development of a robot for harvesting sweet-peppers in greenhouses. A description is given of the working environment of the robot and its design objectives. The base of the robot consists out of two carrier modules. On the first, the manipulator, the control electronics and the computers are located. To assure maximum flexibility the realized manipulator prototype has nine degrees-of-freedom. On the second, the sensors and illumination are placed. The coupled modules can move in between the crop rows on the greenhouse rail system. The heights of the modules can be adjusted to match the height of the crop. On the sensor carrier module two 5 megapixel colour cameras and a Time of Flight camera are installed. The colour images and three dimensional (3D) data were calibrated and registered. Around the sensors, a lighting rig is placed to illuminate the scene. The sensor system is mounted on a linear motorized slide and can be horizontally moved in and out of the workspace of the manipulator. Machine vision software localises ripe fruits and obstacles in 3D. For fruit detection different approaches have been developed. One option is to initiate fruit detection by simple red colour blob detection. Another option is to perform fruit localization in two sequential steps. First Regions of Interest in the RGB image are selected which is suspected to contain target fruits. Next the fruit localization is performed in the corresponding 3D data, based on 3D point cloud template matching. Obstacle detection algorithms are used to localise plant stems and non-target fruits using the small baseline stereo images. In order to harvest the fruits, a motion planning module assures a collision free path for the manipulator to position the end-effector at the harvesting position. Two different types of end-effectors were designed and tested. The “Fin-Ray gripper” features a combined grip and cut mechanism. This end-effector first grips the fruit and after that the peduncle of the fruit is cut. The “Lip-type end-effector”, first stabilizes the fruit using a suction cup after which two rings enclose the fruit and cut the peduncle of the fruit. Both end effectors have a miniature RGB and a ToF camera for refining the fruit position and to determine the fruit pose. The main software platform of the robot was implemented for the Linux operating system and uses the open source middleware Robot Operating System (ROS). The coordinating control structure is based on a finite state machine and includes diagnostic tools and performance measures. The system was tested under simplified laboratory conditions in 2013. During these early tests 189 out of 194 fruit could be detected (97%), 167 fruits could be reached (86% of all fruits) and 154 picked (79% of all fruits). In spring 2014 final system integration took place. In a commercial greenhouse it was proven that the system is able to harvest pepper fruits fully autonomously.
Differential Trypanosome Surface Coat Regulation by a CCCH Protein That Co-Associates with procyclin mRNA cis-Elements

The genome of Trypanosoma brucei is unusual in being regulated almost entirely at the post-transcriptional level. In terms of regulation, the best-studied genes are procyclins, which encode a family of major surface GPI-anchored glycoproteins (EP1, EP2, EP3, GPEET) that show differential expression in the parasite's tsetse-fly vector. Although procyclin mRNA cis-regulatory sequences have provided the paradigm for post-transcriptional control in kinetoplastid parasites, trans-acting regulators of procyclin mRNAs are unidentified, despite intensive effort over 15 years. Here we identify the developmental regulator, TbZFP3, a CCCH-class predicted RNA binding protein, as an isoform-specific regulator of Procyclin surface coat expression in trypanosomes. We demonstrate (i) that endogenous TbZFP3 shows sequence-specific co-precipitation of EP1 and GPEET, but not EP2 and EP3, procyclin mRNA isoforms, (ii) that ectopic overexpression of TbZFP3 does not perturb the mRNA abundance of procyclin transcripts, but rather that (iii) their protein expression is regulated in an isoform-specific manner, as evidenced by mass spectrometric analysis of the Procyclin expression signature in the transgenic cell lines. The TbZFP3 mRNA–protein complex (TbZFP3mRNP) is identified as a trans-regulator of differential surface protein expression in trypanosomes. Moreover, its sequence-specific interactions with procyclin mRNAs are compatible with long-established predictions for Procyclin regulation. Combined with the known association of TbZFP3 with the translational apparatus, this study provides a long-sought missing link between surface protein cis-regulatory signals and the gene expression machinery in trypanosomes.
SecA Dimer Cross-Linked at Its Subunit Interface Is Functional for Protein Translocation

ABSTRACT SecA facilitates protein transport across the eubacterial plasma membrane by its association with cargo proteins and the SecYEG translocon, followed by ATP-driven conformational changes that promote protein translocation in a stepwise manner. Whether SecA functions as a monomer or a dimer during this process has been the subject of considerable controversy. Here we utilize cysteine-directed mutagenesis along with the crystal structure of the SecA dimer to create a cross-linked dimer at its subunit interface, which was normally active for in vitro protein translocation.
Ecological Risk Assessment of a Metal-Contaminated Area in the Tropics. Tier II: Detailed Assessment

This study presents data on the detailed evaluation (tier 2) of a site-specific ecological risk assessment (ssERA) in a former smelter area contaminated with metals (Santo Amaro, Bahia, Brazil). Combining information from three lines of evidence (LoE), chemical (ChemLoE), ecotoxicological (EcotoxLoE) and ecological (EcoLoE), in the Triad approach, integrated risk values were calculated to rank sites and confirm the potential risk disclosed with tier 1. Risk values were calculated for the habitat and for the retention functions in each sampling point. Habitat function included the ChemLoE calculated from total metal concentrations. The EcotoxLoE was based on reproduction tests with terrestrial invertebrates (Folsomia candida, Enchytraeus crypticus, Eisenia andrei), shoot length and plant biomass (Avena sativa, Brassica rapa). For the EcoLoE, ecological parameters (microbial parameters, soil invertebrate community, litter breakdown) were used to derive risk values. Retention function included the ChemLoE, calculated from extractable metal concentrations, and the EcotoxLoE based on eluate tests with aquatic organisms (Daphnia magna reproduction and Pseudokirchneriella subcapitata growth). Results related to the habitat function indicated that the metal residues are sufficient to cause risk to biota, while the low metal levels in extracts and the general lack of toxicity in aquatic tests indicated a high soil retention capacity in most sampling points. Integrated risk of tier 2 showed the same trend of tier 1, suggesting the need to proceed with remediation actions. The high risk levels were related to direct toxicity to organisms and indirect effects, such as failure in the establishment of vegetation and the consequent loss of habitat quality for microorganisms and soil fauna. This study shed some light on the selection of tools for the tier 2 of an ssERA in tropical metal-contaminated sites, focusing on ecological receptors at risk and using available chemical methods, ecological surveys and ecotoxicity tests.
Pattern Based User Interface Generation in Pervasive Computing

In a dynamic heterogeneous environment, such as pervasive computing, context-aware adaptation is a key concept to meet the varying requirements of different clients. However, this newfound versatility poses difficult challenges for user-interface design. The traditional UI development measures seem insufficient toward this situation. As the concept of design pattern in architecture and software engineering, we propose a pattern based UI generation approach that is context sensitive. It can create the specific UI dynamically based on the certain context and the whole procedure is automatic. An implementation example based on Web application will be given at last to illustrate our idea.
Perceptual Knowledge Retrieval Activates Sensory Brain Regions

Although knowledge indexes our experiences of the world, the neural basis of this relationship remains to be determined. Previous neuroimaging research, especially involving knowledge biased to visual and functional information, suggests that semantic representations depend on modality-specific brain mechanisms. However, it is unclear whether sensory cortical regions, in general, support retrieval of perceptual knowledge. Using neuroimaging methods, we show that semantic decisions that index tactile, gustatory, auditory, and visual knowledge specifically activate brain regions associated with encoding these sensory experiences. Retrieval of tactile knowledge was specifically associated with increased activation in somatosensory, motor, and premotor cortical regions. In contrast, decisions involving flavor knowledge increased activation in an orbitofrontal region previously implicated in processing semantic comparisons among edible items. Perceptual knowledge retrieval that references visual and auditory experiences was associated with increased activity in distinct temporal brain regions involved in the respective sensory processing. These results indicate that retrieval of perceptual knowledge relies on brain regions used to mediate sensory experiences with the referenced objects.
Density Mining Based Resilient Data Aggregation for Wireless Sensor Network

Data aggregation is generally used to reduce data streams and save energy consumption in cluster-based wireless sensor networks (CWSNs). However the vulnerable deployment environment of CWSN challenge the data aggregation in terms of data privacy and resiliency. If a node or a group of nodes are compromised or the sensing environment is manipulated by an adversary, the aggregation result will be changed easily. Therefore, it is essential to design a resilient data aggregation scheme with data privacy and security guarantees. This paper proposes a scheme that provides privacy-preserving data fusion, and tolerate data disruption and node compromise as well. We make use of subgroup within each cluster to improve the resiliency against node compromise; and we employ a novel encryption algorithm that support secure comparison between concealed data, which will be further used for density mining against the manipulating data disruption. The simulation results show that this scheme can preserve relatively accurate average aggregation with malicious data filtering. And the mathematical evaluation and comparison show better effectiveness and fitness of our scheme for CWSN in terms of fault tolerance and process efficiency than the previous data aggregation schemes.
Using the Johnson-Lindenstrauss lemma in linear and integer programming

The Johnson-Lindenstrauss lemma allows dimension reduction on real vectors with low distortion on their pairwise Euclidean distances. This result is often used in algorithms such as $k$-means or $k$ nearest neighbours since they only use Euclidean distances, and has sometimes been used in optimization algorithms involving the minimization of Euclidean distances. In this paper we introduce a first attempt at using this lemma in the context of feasibility problems in linear and integer programming, which cannot be expressed only in function of Euclidean distances.
Are kinesins required for organelle trafficking in plant cells?

Plant cells exhibit active movement of membrane-bounded materials, which is more pronounced in large cells but is also appreciable in medium-sized cells and in tip-growing cells (such as pollen tubes and root hairs). Trafficking of organelles (such as Golgi bodies, endoplasmic reticulum, peroxisomes, and mitochondria) and vesicles is essential for plant cell physiology and allows a more or less homogeneous distribution of the cell content. It is well established that the long-range trafficking of organelles is dependent essentially on the network of actin filaments and is powered by the enzyme activity of myosins. However, some lines of evidence suggest that microtubules and members of the kinesin microtubule-based motor superfamily might have a role in the positioning and/or short-range movement of cell organelles and vesicles. Data collected in different cells (such as trichomes and pollen tubes), in specific stages of the plant cell life cycle (for example, during phragmoplast development) and for different organelle classes (mitochondria, Golgi bodies, and chloroplasts) encourage the hypothesis that microtubule-based motors might play subtle yet unclarified roles in organelle trafficking. In some cases, this function could be carried out in cooperation with actin filaments according to the model of “functional cooperation” by which motors of different families are associated with the organelle surface. Since available data did not provide an unambiguous conclusion with regard to the role of kinesins in organelle transport, here we want to debate such hypothesis.
A Simulator for Distributed Cache Managementin Friend-to-Friend Networks

Multimedia streaming services such as YouTube and Netflix consume a staggering amount of Internet bandwidth [1]. Furthermore, traditional mechanisms such as proxy caches, content distribution networks, and redundant traffic elimination are rendered ineffective by copyright concerns, regulatory issues, and the growing prevalence of end-to-end encryption. One possible solution is a peer-to-peer caching system with social relationships at the core of its topology construction. A social topology carries an implicit level of trust, and induces a relatively high degree of correlation between users that can be exploited by the system as a whole. For example, two users with shared interests are more likely to have relevant videos in cache for each other. This short paper discusses the design of a simulator for such a system to provide insight into the performance of different cache management policies.
Studies on Tolfenamic Acid–Chitosan Intermolecular Interactions: Effect of pH, Polymer Concentration and Molecular Weight

Solid-state properties of tolfenamic acid (TA) and its complexes with chitosan (CT) have been studied. Effect of medium pH, molecular weight of polymer and its different concentrations on these TA–CT complexes were studied in detail. Low and medium molecular weight CT have been used in different ratios at pH ranging from 4 to 6 and freeze-drying technique has been employed to modify the appearance of crystalline TA. Physical properties of the formed complexes have been studied by employing X-ray diffraction, differential scanning calorimetry and scanning electron microscopy; chemical structure has been studied using Fourier transform infrared spectroscopy. The results showed that both forms of the polymer exhibited complete conversion in 1:8 ratio at pH 4, 1:4 at pH 5 and 1:1 at pH 6 indicating a marked effect of pH on drug–polymer complexation. The percent crystallinity calculations indicated low molecular weight CT slightly more effective than the other form. No changes in the complexes have been observed during the 12 week storage under controlled conditions. Both forms of CT at different pH values indicated retardation of recrystallization in TA during cooling of the melt from 1:1 ratios exhibiting formation of strong intermolecular hydrogen bonding between the drug and the polymer.
Expression of a Chimeric Magainin Gene in Potato Confers Improved Resistance to the Phytopathogen Erwinia carotovora

Magainin peptides originally identified from Xenopus laevis have cytotoxic effects against a range of prokary- otic organisms without harmful effects on higher eukaryotes. The mechanism of cytotoxicity of the peptides is by disrup- tion of membranes, which causes osmolysis. Magainin peptides are known to inhibit the in vitro growth of many phytopa- thogens including Erwinia carotovora, the causative agent of soft rot disease in potato. A synthetic gene was constructed based on the antimicrobial peptide magainin II. The coding sequence for the modified magainin II, magaininD, was con- structed using potato codon preference. Modifications included a point mutation previously shown to reduce proteolytic cleavage, and three substitutions known to increase activity of the peptide against prokaryotic organisms. Agrobacterium- mediated transformation was used to generate transgenic potato plants. Each line was tested for expression of the trans- gene at RNA and protein levels using RT-PCR and western analyses. Lines were identified that expressed both RNA and protein of the magaininD transgene. Field trials with the transgenic magaininD potato plants were conducted over three seasons, and harvested tubers were evaluated in bioassays for resistance to Erwinia carotovora ssp. atroseptica. Results from bioassays identified potato lines with significantly improved resistance to soft rot compared with control lines. The same lines were determined to have higher levels of expression of the transgene-derived peptide. The result demonstrated that the design, construction and transformation of a synthetic antimicrobial magainin gene was a successful strategy in introducing a novel form of disease resistance in potato plants.
A Micropositioning System with Real-Time Feature Extraction Capability for Quantifying C. elegans Locomotive Behavior

Tracking C. elegans and extracting locomotive features of the nematode allow the investigation of how genes control behavioral phenotypes. Existing systems require large storage space for image data recording and significant time for off-line processing. This paper presents a visually servoed micropositioning system capable of extracting locomotive features on line at a full 30 Hz. The employment of Gaussian pyramid Level-2 images significantly reduces the image size by 16 folds and permits real-time feature extraction, without sacrificing accuracy due to the cubic smoothing spline fitting. Enabled by the capability of the micropositioning system in revealing subtle differences in locomotive behavior across strains, the relationship between C. elegans locomotive behavior and the number of muscle arms, for the first time, was investigated. A total of 128 worms of four C. elegans strains with different numbers of muscle arms were continuously tracked for 3 minutes per sample, and locomotive features were extracted on line. The potential impact of this research extends beyond revealing subtle phenotypic differences in C. elegans locomotive behavior across strains by demonstrating how automation techniques can be used to provide valuable tools for genetic investigations of C. elegans.
Identification and Molecular Characterization of Nkp30, a Novel Triggering Receptor Involved in Natural Cytotoxicity Mediated by Human Natural Killer Cells

Two major receptors involved in human natural cytotoxicity, NKp46 and NKp44, have recently been identified. However, experimental evidence suggested the existence of additional such receptor(s). In this study, by the generation of monoclonal antibodies (mAbs), we identified NKp30, a novel 30-kD triggering receptor selectively expressed by all resting and activated human natural killer (NK) cells. Although mAb-mediated cross-linking of NKp30 induces strong NK cell activation, mAb-mediated masking inhibits the NK cytotoxicity against normal or tumor target cells. NKp30 cooperates with NKp46 and/or NKp44 in the induction of NK-mediated cytotoxicity against the majority of target cells, whereas it represents the major triggering receptor in the killing of certain tumors. This novel receptor is associated with CD3ζ chains that become tyrosine phosphorylated upon sodium pervanadate treatment of NK cells. Molecular cloning of NKp30 cDNA revealed a member of the immunoglobulin superfamily, characterized by a single V-type domain and a charged residue in the transmembrane portion. Moreover, we show that NKp30 is encoded by the previously identified 1C7 gene, for which the function and the cellular distribution of the putative product were not identified in previous studies.
Adaption feedback of precoding matrix indicator for 3GPP LTE/LTE-A system

Limited feedback of channel state information (CSI), which is made up of rank indicator (RI), precoding matrix indicator (PMI) and channel quality indicator (CQI), is an important part in closed-loop transmission for 3GPP Long Time Evolution (LTE)/LTE-Advanced standard. In this paper, an efficient way, where PMI granularity selection method is used in PMI feedback mechanism, is presented to adaptively choose PMI granularity to track the channel variation, especially for fast fading channel. Simulation results show that the adaption feedback of PMI can get a better spectral efficiency and lower BER without much computational cost.