Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Dynamics of Fucoid Populations (Ascophyllum nodosum and Fucus serratus): A Comparison between Central and Range Edge Populations

Persistence of populations at range edges relies on local population dynamics and fitness, in the case of geographically isolated populations of species with low dispersal potential. Focusing on spatial variations in demography helps to predict the long-term capability for persistence of populations across the geographical range of species’ distribution. The demography of two ecological and phylogenetically close macroalgal species with different life history characteristics was investigated by using stochastic, stage-based matrix models. Populations of Ascophyllum nodosum and Fucus serratus were sampled for up to 4 years at central locations in France and at their southern range limits in Portugal. The stochastic population growth rate (λs) of A. nodosum was lower and more variable in central than in southern sites whilst for F. serratus this trend was reversed with λs much lower and more variable in southern than in central populations. Individuals were larger in central than in southern populations for both species, which was reflected in the lower transition probabilities of individuals to larger size classes and higher probability of shrinkage in the southern populations. In both central and southern populations elasticity analysis (proportional sensitivity) of population growth rate showed that fertility elements had a small contribution to λs that was more sensitive to changes in matrix transitions corresponding to survival. The highest elasticities were found for loop transitions in A. nodosum and for growth to larger size classes in F. serratus. Sensitivity analysis showed high selective pressure on individual growth for both species at both locations. The results of this study highlight the deterministic role of species-specific life-history traits in population demography across the geographical range of species. Additionally, this study demonstrates that individuals’ life-transitions differ in vulnerability to environmental variability and shows the importance of vegetative compared to reproductive stages for the long-term persistence of populations.
Structural and Mechanistic Insights into the Improvement of the Halotolerance of a Marine Microbial Esterase by Increasing Intra- and Interdomain Hydrophobic Interactions

ABSTRACT Halotolerant enzymes are beneficial for industrial processes requiring high salt concentrations and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolabile esterase, E40, by increasing intraprotein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl, and its kcat and substrate affinity were both significantly reduced in 0.5 M NaCl. By introducing hydrophobic residues in loop 1 of the CAP domain and/or α7 of the catalytic domain in E40, we obtained several mutants with improved halotolerance, and the M3 S202W I203F mutant was the most halotolerant. (“M3” represents a mutation in loop 1 of the CAP domain in which residues R22-K23-T24 of E40 are replaced by residues Y22-K23-H24-L25-S26 of Est2.) Then we solved the crystal structures of the S202W I203F and M3 S202W I203F mutants to reveal the structural basis for their improved halotolerance. Structural analysis revealed that the introduction of hydrophobic residues W202 and F203 in α7 significantly improved E40 halotolerance by strengthening intradomain hydrophobic interactions of F203 with W202 and other residues in the catalytic domain. By further introducing hydrophobic residues in loop 1, the M3 S202W I203F mutant became more rigid and halotolerant due to the formation of additional interdomain hydrophobic interactions between the introduced Y22 in loop 1 and W204 in α7. These results indicate that increasing intraprotein hydrophobic interactions is also a way to improve the halotolerance of enzymes with industrial potential under high-salt conditions. IMPORTANCE Esterases and lipases for industrial application are often subjected to harsh conditions such as high salt concentrations, low water activity, and the presence of organic solvents. However, reports on halotolerant esterases and lipases are limited, and the underlying mechanism for their halotolerance is still unclear due to the lack of structures. In this study, we focused on the improvement of the halotolerance of a salt-sensitive esterase, E40, and the underlying mechanism. The halotolerance of E40 was significantly improved by introducing hydrophobic residues. Comparative structural analysis of E40 and its halotolerant mutants revealed that increased intraprotein hydrophobic interactions make these mutants more rigid and more stable than the wild type against high concentrations of salts. This study shows a new way to improve enzyme halotolerance, which is helpful for protein engineering of salt-sensitive enzymes.
Reconstitution by bone marrow grafting of the defective protective capacity at the migratory phase but not at the intestinal phase of Nippostrongylus brasiliensis infection in W/Wv mice

After a primary infection by subcutaneous inoculation with the infective larvae (L3) of Nippostrongylus brasiliensis, the intestinal worm burden was higher and expulsion was slower in W/Wv mice than in +/+ mice. When the course of infection was segregated into the migratory and intestinal phases, protection during the migratory phase examined by the larval recovery from the lungs and that during the intestinal phase measured by worm burden after intraduodenal implantation with adult worms were both defective in W/Wv mice. The higher susceptibility of W/Wv mice during the migratory phase was normalized by bone marrow re constitution. On the other hand, higher susceptibility of W/Wv mice during the intestinal phase, which was measured by worm burden 24 h after intraduodenal implantation of the larvae recovered from the lungs of rats, was not normalized by bone marrow grafting. Furthermore, slower expulsion seen in W/Wv mice after intraduodenal implantation with adult worms was not hastened by bone marrow reconstitution. These results indicate that the protective mechanisms against N. brasiliensis operating during the migratory phase and those during the intestinal phase were different in terms of bone marrow dependency and that nonmyeloid cells utilizing c‐kit ligand/receptor system to express their functions are involved in the rnucosal defence against N. brasiliensis.
Ablation of Ca2+ Channel β3 Subunit Leads to Enhanced N-Methyl-d-aspartate Receptor-dependent Long Term Potentiation and Improved Long Term Memory*

The β subunits of voltage-dependent Ca2+ channels (VDCCs) have marked effects on the properties of the pore-forming α1 subunits of VDCCs, including surface expression of channel complexes and modification of voltage-dependent kinetics. Among the four different β subunits, the β3 subunit (Cavβ3) is abundantly expressed in the hippocampus. However, the role of Cavβ3 in hippocampal physiology and function in vivo has never been examined. Here, we investigated Cavβ3-deficient mice for hippocampus-dependent learning and memory and synaptic plasticity at hippocampal CA3-CA1 synapses. Interestingly, the mutant mice exhibited enhanced performance in several hippocampus-dependent learning and memory tasks. However, electrophysiological studies revealed no alteration in the Ca2+ current density, the frequency and amplitude of miniature excitatory postsynaptic currents, and the basal synaptic transmission in the mutant hippocampus. On the other hand, however, N-methyl-d-aspartate receptor (NMDAR)-mediated synaptic currents and NMDAR-dependent long term potentiation were significantly increased in the mutant. Protein blot analysis showed a slight increase in the level of NMDAR-2B in the mutant hippocampus. Our results suggest a possibility that, unrelated to VDCCs regulation, Cavβ3 negatively regulates the NMDAR activity in the hippocampus and thus activity-dependent synaptic plasticity and cognitive behaviors in the mouse.
Overriding errors in a speech and gaze multimodal architecture

This work explores how to use the gaze and the speech command simultaneously to select an object on the screen. Multimodal systems have long been a key mean to reduce the recognition errors of individual components. But the multimodal system generates errors as well. This present study tries to classify the multimodal errors, analyze the reasons causing these errors, and propose the solutions for eliminating them. The goal of this study is to gain insight into multimodal integration errors, and to develop an error self-recoverable multimodal architecture so as to make the error-prone recognition technologies perform at a more stable and robust level within multimodal architecture.
CHARACTERIZATION OF TWO HELA SUBLINES: TCRC-1 PRODUCES REGAN ISOENZYME AND TCRC-2, NON-REGAN ISOENZYME

HeLa Cells have been found to produce a placental form of alkaline phosphatase (1, 8, 17) which is very similar to the Regan isoenzyme, a carcinoplacental antigen found in cancer patients (7-9) . In order to investigate the nature of gene expression of carcinoplacental proteins, HeLa cells were cloned, and a subline (HeLa TCRC-1), monophenotypic for the Regan isoenzyme was selected . The properties of another line, HeLa TCRC-2 (HeLa 12-2), discovered by Kelly et al . (14) were studied with regard to non-Regan isoenzyme . MATERIALS AND METHODS
International Conference on Computational Science , ICCS 2011 Second-order Mining for Active Collaborative Filtering

Active learning for collaborative filtering tasks draws many attentions from the research community. It can capture the user’s interest with greatly reduced labeling burden for the online user. High quality recommendation can thus be made with good user experience. In this paper we address the efficiency challenge of current active learning methods for online and interactive applications by using the second-order mining techniques. According to the global latent semantic model learnt from the feedbacks of historical users to items, we propose an intuitive and efficient query strategy for the item selection for new active user. The time complexity in each query is reduced greatly to constant O(1). Experimental results on the public available data sets show the efficiency and effectiveness of our method.
Agent-Agnostic Human-in-the-Loop Reinforcement Learning

Providing Reinforcement Learning agents with expert advice can dramatically improve various aspects of learning. Prior work has developed teaching protocols that enable agents to learn efficiently in complex environments; many of these methods tailor the teacher's guidance to agents with a particular representation or underlying learning scheme, offering effective but specialized teaching procedures. In this work, we explore protocol programs, an agent-agnostic schema for Human-in-the-Loop Reinforcement Learning. Our goal is to incorporate the beneficial properties of a human teacher into Reinforcement Learning without making strong assumptions about the inner workings of the agent. We show how to represent existing approaches such as action pruning, reward shaping, and training in simulation as special cases of our schema and conduct preliminary experiments on simple domains.
Bimanual Word Gesture Keyboards for Mid-air Gestures

Mid-air hand gestural interaction has generally been researched as a pointing device. However, recent research has shown potential for text input with the use of word gesture keyboards (WGK), where these forms of interactions require the input system to identify when the gesture has started and when it has stopped. Previous research has had success where the same hand moved the cursor, and performed the activation gesture. In this paper we introduce bimanual interaction for gestural interaction to perform text input with WGK, where one hand moves the cursor while the other hand performs the activation. In our user studies, the bimanual method demonstrated significantly higher results than the state-of-the-art single handed method. We achieved 16 words per minute; about 39% higher than the benchmark, and with significantly lower error rates.
Hamilton–Jacobi Skeleton on Cortical Surfaces

In this paper, we propose a new method to construct graphical representations of cortical folding patterns by computing skeletons on triangulated cortical surfaces. In our approach, a cortical surface is first partitioned into sulcal and gyral regions via the solution of a variational problem using graph cuts, which can guarantee global optimality. After that, we extend the method of Hamilton-Jacobi skeleton to subsets of triangulated surfaces, together with a geometrically intuitive pruning process that can trade off between skeleton complexity and the completeness of representing folding patterns. Compared with previous work that uses skeletons of 3-D volumes to represent sulcal patterns, the skeletons on cortical surfaces can be easily decomposed into branches and provide a simpler way to construct graphical representations of cortical morphometry. In our experiments, we demonstrate our method on two different cortical surface models, its ability of capturing major sulcal patterns and its application to compute skeletons of gyral regions.
Increased gravitational force reveals the mechanical, resonant nature of physiological tremor

Physiological hand tremor has a clear peak between 6 and 12 Hz, which has been attributed to both neural and resonant causes. A reduction in tremor frequency produced by adding an inertial mass to the limb has usually been taken as a method to identify the resonant component. However, adding mass to a limb also inevitably increases the muscular force required to maintain the limb's position against gravity, so ambiguous results have been reported. Here we measure hand tremor at different levels of gravitational field strength using a human centrifuge, thereby increasing the required muscular force to preserve limb position without changing the limb's inertia. By comparing the effect of added mass (inertia + force) versus solely added force upon hand acceleration, we conclude that tremor frequency can be almost completely explained by a resonant mechanical system.
Electroencephalographic spectral analysis: detection of cortical activity changes in sleep apnoea patients

There are no visible electroencephalographic (EEG) changes at the termination of some apnoeas and hypopnoeas. This study tests the hypothesis that cortical activity fluctuates at apnoea/hypopnoea termination, despite the lack of visible changes. To detect these changes, EEG spectral analysis was performed and centred around the end of apnoeas/hypopnoeas in 15 sleepy patients. Ten second windows were applied and comparisons were conducted between the normalised power of the same frequency bands before and after termination of each apnoea/hypopnoea. Comparisons were performed within patients between apnoeas/hypopnoeas and periods of undisturbed sleep as well as between patients and healthy subjects during sleep. Normalised theta power (4–8 Hz) decreased significantly at apnoea/hypopnoea termination. No significant changes were found between consecutive periods of undisturbed sleep across the 15 patients. During nonrapid eye movement sleep, changes were detected irrespective of arousal visibility. During rapid eye movement sleep, nonarousal apnoeas/hypopnoeas were not accompanied by any significant spectral power changes. Theta power was significantly lower across patients compared to healthy subjects (p=0.03) and was correlated to the apnoea/hypopnoea index (rho=0.6, p=0.008). The authors conclude that electroencephalographic spectral analysis improves detection of changes at apnoea/hypopnoea termination. Further validation is needed to determine whether it improves correlation between nocturnal measures and daytime symptoms.
A scalable computational approach for modeling dynamic fracture of brittle solids in three dimensions

In this thesis a new parallel computational method is proposed for modeling threedimensional dynamic fracture of brittle solids. The method is based on a combination of the discontinuous Galerkin (DG) formulation of the continuum elastodynamic problem with Cohesive Zone Models (CZM) of fracture. In the proposed framework, discontinuous displacement jumps are allowed to occur at all element boundaries in the pre-fracture regime in a manner similar to "intrinsic" cohesive element methods. However, owing to the DG framework, consistency and stability of the finite element solution are guaranteed prior to fracture. This in stark contrast to the intrinsic cohesive element methods which suffer wave propagation and stability issues as a result of allowing discontinuous displacement jumps in the pre-fracture regime without properly accounting for them in the weak statement of the problem. In the new method, a fracture criterion is evaluated at all element boundaries throughout the calculation and upon satisfaction of this criterion, cracks are allowed to nucleate and propagate in the finite element mesh, governed by a cohesive tractionseparation law (TSL). This aspect of the method is similar to existing "extrinsic" cohesive element methods which introduce new fracture surfaces in the mesh through the adaptive insertion of cohesive elements subsequent to the onset of fracture. Typically this requires the mesh topology to be modified on-the-fly, a process which is highly complex and hinders the scalability of parallel implementations. However, for the DG method, discontinuities exist at element boundaries from the start of the calculation and so modifications of the mesh topology are unnecessary for introducing new fracture surfaces. As a result, the parallel computational framework is highly scalable and algorithmically simple. In this thesis, the formulation and numerical implementation of the method is described in detail. The method is then applied to simulate two practical problems. First a ceramic spall test is simulated. In this example, the DG method is shown to accurately capture the propagation of longitudinal elastic waves and the formation of a spall plane. Mesh dependency of the predicted spall plane and the dissipated cohesive energy is investigated for refined meshes resolving the size of the fracture process zone and the results are shown to be highly mesh-sensitive for the range of mesh sizes used. The spall test is also simulated using an existing intrinsic cohesive approach which is shown to alter the propagation of elastic stress waves, leading to the spurious result that no spallation occurs. In a second numerical example, the proposed DG method is applied to simulate high-velocity impact of an unconfined ceramic plate with a rigid spherical projectile. The method is shown to capture some of the basic fundamental aspects of the impact response of unconfined ceramics including the formation of conical and radial cracking patterns. Thesis Supervisor: Radil A. Radovitzky Title: Associate Professor
Diffuse Large B cell Lymphoma with Primary Spleen Involvement: Report of Three Cases

The spleen is the primary organ of lymphoma in only 1–2 % of all lymphoma patients. We presented three cases of primary splenic involvement of lymphoma that were treated. Presentation of cases: In the first case, four solid lesions were detected, and in the second case, a hypodense lesion of 3 cm was detected in the spleen. Two cases underwent splenectomy. No complication and recurrence were observed during 22 - 21 months follow-up, respectively. In the third case, a splenic mass invading pancreas was detected. Splenectomy and distal pancreatectomy were performed. No recurrence was observed during 8-year follow-up. In postoperative period, all cases were treated with cyclophosphamide, vincristine, doxorubicin, prednisone plus rituximab for 6 cycles. Primary splenic lymphoma refers to the involvement of the spleen only or with splenic hilar lymph node or local invasion without liver involvement. The pathologic diagnosis was diffuse large B-cell non-Hodgkin’s lymphoma in the all cases. Splenic mass biopsy has some complication risks. Aspiration biopsy of splenic mass was performed in one of the three cases. Invasions should be evaluated in terms of malignity during splenectomy, and liver biopsy and biopsies of lymph nodes can be performed in case of lymphoma. Additionally diagnosis should be confirmed via post-operative bone marrow biopsy and positron emission tomography screening. Primary splenic involved lymphoma must be kept in mind for differential diagnosis in cases with splenic mass. Splenectomy is one of the most common modality for primary splenic lymphomas in terms of both diagnostic and curative treatment.
The Necessity of Placebo Application in Psychotropic Drug Trials

Psychopharmacological research is handicapped by the lack of unequivocal guidelines on the methodology of the evaluation of psychotropic drugs. In particular, the need for placebo-controlled trials for evidencing the efficacy of drugs is controversial; although a number of investigators are arguing for the need for placebo-controlled trials, such studies have found only very limited acceptance in German-speaking countries, as both the legal conditions and the ethical committees require placebo-controlled trials to be conducted under unrealistic conditions. These \imitations make trials capable of determining the efficacy of new drugs impossible in a substantial number of countries. This situation requires discussion, especially in view ofthe fact that it has become increasingly difficult to recruit patients for c1inical trials.
Cyogenetics effects in AG01522 human primary fibroblasts exposed to low doses of radiations with different quality

Abstract Purpose: Biological effects produced by low doses of ionizing radiations, though relevant for the risk assessment, have not been fully elucidated. The aim of the present work was to evaluate cytogenetic endpoints, as telomere dysfunctions and chromosome instability in the low-dose range as a function of radiation quality. In particular, we analyzed whether the telomere length was modulated, as well as the involvement of telomeres in chromosomal alterations at anaphase, and the yield of stable simple and complex chromosome aberrations. Materials and methods: AG01522 human primary fibroblasts were irradiated with 0.1–1 Gy of X-rays, protons (28.5 keV/μm), and 4He2+ ions (62 keV/μm). Frequency of chromosome bridges carrying or not telomeric signals and telomere length were measured in irradiated samples up to 72 h. Moreover, chromosome instability was measured using multicolor fluorescence in situ hybridization (mFISH). Results: The results evidenced a linear energy transfer (LET)- and dose-dependent response in the frequency of anaphase bridges induction and in their persistence as a function of time. However, neither variation in telomere length and telomere loss, nor in the proportion of bridges bearing telomeric signals, was detected, thus indicating a minor role of telomeres in the generation of the radiation-induced chromosome bridges. Chromosome instability followed a linear-dependence with dose and LET, showing a far higher extent of complex translocations in helium-ion-irradiated cells than in proton- or X-ray-irradiated samples. Conclusions: Altogether, the results indicated the lack of telomere involvement in cytogenetic effects induced by low-dose ionizing radiation. On the contrary, chromosome aberration yield and spectrum were LET- and dose-dependent.