Miracle-dz/UniFAR-FTUs huggingface dataset:
Out of the Black Sea: Phylogeography of the Invasive Killer Shrimp Dikerogammarus villosus across Europe

The amphipod Dikerogammarus villosus has colonized most of the European main inland water bodies in less than 20 years, having deteriorating effect on the local benthic communities. Our aim was to reveal the species phylogeography in the native Black Sea area, to define the source populations for the colonization routes in continental Europe and for the newly established UK populations. We tested for the loss of genetic diversity between source and invasive populations as well as along invasion route. We tested also for isolation by distance. Thirty three native and invasive populations were genotyped for mtDNA (COI, 16S) and seven polymorphic nuclear microsatellites to assess cryptic diversity (presence of deeply divergent lineages), historical demography, level of diversity within lineage (e.g., number of alleles), and population structure. A wide range of methods was used, including minimum spanning network, molecular clock, Bayesian clustering and Mantel test. Our results identified that sea level and salinity changes during Pleistocene impacted the species phylogeography in the Black Sea native region with four differentiated populations inhabiting, respectively, the Dnieper, Dniester, Danube deltas and Durungol liman. The invasion of continental Europe is associated with two sources, i.e., the Danube and Dnieper deltas, which gave origin to two independent invasion routes (Western and Eastern) for which no loss of diversity and no isolation by distance were observed. The UK population has originated in the Western Route and, despite very recent colonization, no drastic loss of diversity was observed. The results show that the invasion of the killer shrimp is not associated with the costs of loosing genetic diversity, which may contribute to the success of this invader in the newly colonized areas. Additionally, while it has not yet occurred, it might be expected that future interbreeding between the genetically diversified populations from two independent invasion routes will potentially even enhance this success.
Using artificial neural network to predict dry density of soil from thermal conductivity

Abstract Artificial neural network (ANN) was used to predict the dry density of soil from its thermal conductivity. The study area is a farmland located in Abeokuta, Ogun State, Southwestern Nigeria. Thirty points were sampled in a grid pattern, and the thermal conductivities were measured using KD-2 Pro thermal analyser. Samples were collected from 20 sample points to determine the dry density in the laboratory. MATLAB was used to perform the ANN analysis in order to predict the dry density of soil. The ANN was able to predict dry density with a root-mean-square error (RMSE) of 0.50 and a correlation coefficient (R2) of 0.80. The validation of our model between the actual and predicted dry densities shows R2 to be 0.99. This fit shows that the model can be applied to predict the dry density of soil in study areas where the thermal conductivities are known.
Evidence for Neandertal Jewelry: Modified White-Tailed Eagle Claws at Krapina

We describe eight, mostly complete white-tailed eagle (Haliaëtus [Haliaeetus] albicilla) talons from the Krapina Neandertal site in present-day Croatia, dating to approximately 130 kyrs ago. Four talons bear multiple, edge-smoothed cut marks; eight show polishing facets and/or abrasion. Three of the largest talons have small notches at roughly the same place along the plantar surface, interrupting the proximal margin of the talon blade. These features suggest they were part of a jewelry assemblage, --- the manipulations a consequence of mounting the talons in a necklace or bracelet. An associated phalanx articulates with one of the talons and has numerous cut marks, some of which are smoothed. These white-tailed eagle bones, discovered more than 100 years ago, all derive from a single level at Krapina and represent more talons than found in the entire European Mousterian period. Presence of eight talons indicates that the Krapina Neandertals acquired and curated eagle talons for some kind of symbolic purpose. Some have argued that Neandertals lacked symbolic ability or copied this behavior from modern humans. These remains clearly show that the Krapina Neandertals made jewelry well before the appearance of modern humans in Europe, extending ornament production and symbolic activity early into the European Mousterian.
Intersectin 1 is a component of the Reelin pathway to regulate neuronal migration and synaptic plasticity in the hippocampus

Significance The development and function of the brain depend on the migration of neurons from the proliferative zone in which they are born to their final position. Reelin, a signaling molecule implicated in the developmental disorder lissencephaly and associated with neurologic diseases in humans, plays an important role in directing neuronal migration and brain development. Here, we identify intersectin 1, a large scaffold protein genetically linked to Down syndrome, as a component of the Reelin signaling pathway that is important for brain development and Reelin-mediated augmentation of synaptic plasticity, a cellular model for learning and memory. Brain development and function depend on the directed and coordinated migration of neurons from proliferative zones to their final position. The secreted glycoprotein Reelin is an important factor directing neuronal migration. Loss of Reelin function results in the severe developmental disorder lissencephaly and is associated with neurological diseases in humans. Reelin signals via the lipoprotein receptors very low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), but the exact mechanism by which these receptors control cellular function is poorly understood. We report that loss of the signaling scaffold intersectin 1 (ITSN1) in mice leads to defective neuronal migration and ablates Reelin stimulation of hippocampal long-term potentiation (LTP). Knockout (KO) mice lacking ITSN1 suffer from dispersion of pyramidal neurons and malformation of the radial glial scaffold, akin to the hippocampal lamination defects observed in VLDLR or ApoER2 mutants. ITSN1 genetically interacts with Reelin receptors, as evidenced by the prominent neuronal migration and radial glial defects in hippocampus and cortex seen in double-KO mice lacking ITSN1 and ApoER2. These defects were similar to, albeit less severe than, those observed in Reelin-deficient or VLDLR/ ApoER2 double-KO mice. Molecularly, ITSN1 associates with the VLDLR and its downstream signaling adaptor Dab1 to facilitate Reelin signaling. Collectively, these data identify ITSN1 as a component of Reelin signaling that acts predominantly by facilitating the VLDLR-Dab1 axis to direct neuronal migration in the cortex and hippocampus and to augment synaptic plasticity.
Body sway reflects leadership in joint music performance

Significance People perform tasks in coordination with others in daily life, but the mechanisms are not well understood. Using Granger causality models to examine string quartet dynamics, we demonstrated that musicians assigned as leaders affect other performers more than musicians assigned as followers. These effects were present during performance, when musicians could only hear each other, but were magnified when they could also see each other, indicating that both auditory and visual cues affect nonverbal social interactions. Furthermore, the overall degree of coupling between musicians was positively correlated with ratings of performance success. Thus, we have developed a method for measuring nonverbal interaction in complex situations and have shown that interaction dynamics are affected by social relations and perceptual cues. The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers’ ratings of the “goodness” of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships.
Recombinant cytomegalovirus glycoprotein gB (UL55) induces an autoantibody response to the U1‐70 kDa small nuclear ribonucleoprotein

Human cytomegalovirus (CMV) infection can be life threatening in the immune compromised and is associated with congenital defects and / or mental retardation in the neonate. The demonstrated association between CMV infection and rheumatoid factor (RF) raised the possibility of an induction of an autoimmune response upon vaccination with a candidate CMV vaccine, glycoprotein gB (UL55). The antibody responses generated after injections of an adenovirus‐gB construct (Ad‐gB) were studied in autoimmune‐prone (MRL / mpj) and normal (BALB.k, C3H, and BALB / c) mice. Enzyme‐linked immunosorbent assay and immunoblot analyses were done to identify the autoantibodies produced following immunization. Immunization with Ad‐gB induced a significant IgG anti‐viral response in all strains tested (p < 0.0001) compared to phosphate‐buffered saline or HeLa controls. Ad‐gB induced a significant IgG autoantibody response (p > 0.005) to the U1‐70 kDa spliceosome protein in both autoimmune and normal strains whereas immunization with recombinant human La / SS‐B did not. Autoantibodies to U1‐70 kDa are part of the anti‐ribonucleoprotein response seen in systemic lupus erythematosus and mixed connective tissue disease. Low levels of IgG RF and anti‐double‐stranded DNA antibodies were also induced. This study raises concern that immunization with CMV gB in individuals genetically predisposed to autoimmunity could trigger the development or acceleration of an autoimmune disease.
Cultural Variation in the Use of Overimitation by the Aka and Ngandu of the Congo Basin

Studies in Western cultures have observed that both children and adults tend to overimitate, copying causally irrelevant actions in the presence of clear causal information. Investigation of this feature in non-Western groups has found little difference cross-culturally in the frequency or manner with which individuals overimitate. However, each of the non-Western populations studied thus far has a history of close interaction with Western cultures, such that they are now far removed from life in a hunter-gatherer or other small-scale culture. To investigate overimitation in a context of limited Western cultural influences, we conducted a study with the Aka hunter-gatherers and neighboring Ngandu horticulturalists of the Congo Basin rainforest in the southern Central African Republic. Aka children, Ngandu children, and Aka adults were presented with a reward retrieval task similar to those performed in previous studies, involving a demonstrated sequence of causally relevant and irrelevant actions. Aka children were found not to overimitate as expected, instead displaying one of the lowest rates of overimitation seen under similar conditions. Aka children copied fewer irrelevant actions than Aka adults, used a lower proportion of irrelevant actions than Ngandu children and Aka adults, and had less copying fidelity than Aka adults. Measures from Ngandu children were intermediate between the two Aka groups. Of the participants that succeeded in retrieving the reward, 60% of Aka children used emulation rather than imitation, compared to 15% of Ngandu children, 11% of Aka adults, and 0% of Western children of similar age. From these results, we conclude that cross-cultural variation exists in the use of overimitation during childhood. Further study is needed under a more diverse representation of cultural and socioeconomic groups in order to investigate the cognitive underpinnings of overimitation and its possible influences on social learning and the biological and cultural evolution of our species.
Investigation into the production flaws in thin solid carbon laminates by using the ultrasonic phased array method

Composites are used in a wide variety of markets, including the aerospace, architecture, automotive and military sectors. Along with the increased use of composites, multiple non-destructive testing (NDT) methods have been further developed specifically for inspecting them. Among them, one can single out ultrasonic phased arrays. Research described in this article focuses on the use of ultrasonic PAs for production flaw investigations into an aileron. The examined part was made of up to 16 layers of BAER 3068 epoxy carbon prepreg. The investigation was carried out by using the tap test, conventional ultrasonic measurement and phased array methods. The phased array method allowed us to thoroughly check the affected specimen and confirm the presence of a production flaw in the form of epoxy resin build-up. The results show how effective this method can be and emphasize its advantages over traditional ultrasonic inspections.
Specific Medicinal Plant Polysaccharides Effectively Enhance the Potency of a DC-Based Vaccine against Mouse Mammary Tumor Metastasis

Dendritic cell (DC) vaccines are a newly emerging immunotherapeutic approach for the treatment and prevention of cancer, but major challenges still remain particularly with respect to clinical efficacy. Engineering and optimization of adjuvant formulations for DC-based vaccines is one strategy through which more efficacious treatments may be obtained. In this study, we developed a new ex vivo approach for DC vaccine preparation. We evaluated two highly purified mixed polysaccharide fractions from the root of Astragalus membranaceus and Codonopsis pilosulae, named Am and Cp, for their use in enhancing the efficiency of a DC-based cancer vaccine against metastasis of 4T1 mammary carcinoma in mice. Mixed lymphocyte reaction showed all Am-, Cp- and [Am+Cp]-treated DCs enhanced mouse CD4+ and CD8+ T-cell proliferation. [Am+Cp]-treated DCs exhibited the strongest anti-4T1 metastasis activity in test mice. Treatments with Am, Cp and [Am+Cp] also resulted in augmented expression of CD40, CD80 and CD86 markers in test DCs. Bioinformatics analysis of the cytokine array data from treated DCs identified that [Am+Cp] is efficacious in activation of specific immune functions via mediating the expression of cytokines/chemokines involved in the recruitment and differentiation of defined immune cells. Biochemical analysis revealed that Am and Cp are composed mainly of polysaccharides containing a high level (70–95%) glucose residues, but few or no (< 1%) mannose residues. In summary, our findings suggest that the specific plant polysaccharides Am and Cp extracted from traditional Chinese medicines can be effectively used instead of bacterial LPS as a potent adjuvant in the formulation of a DC-based vaccine for cancer immunotherapies.
The Effect on the Transcriptome of Anemone coronaria following Infection with Rust (Tranzschelia discolor)

In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3’end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.
Columnar Architecture Improves Noise Robustness in a Model Cortical Network

Cortical columnar architecture was discovered decades ago yet there is no agreed upon explanation for its function. Indeed, some have suggested that it has no function, it is simply an epiphenomenon of developmental processes. To investigate this problem we have constructed a computer model of one square millimeter of layer 2/3 of the primary visual cortex (V1) of the cat. Model cells are connected according to data from recent paired cell studies, in particular the connection probability between pyramidal cells is inversely proportional both to the distance separating the cells and to the distance between the preferred parameters (features) of the cells. We find that these constraints, together with a columnar architecture, produce more tightly clustered populations of cells when compared to the random architecture seen in, for example, rodents. This causes the columnar network to converge more quickly and accurately on the pattern representing a particular stimulus in the presence of noise, suggesting that columnar connectivity functions to improve pattern recognition in cortical circuits. The model also suggests that synaptic failure, a phenomenon exhibited by weak synapses, may conserve metabolic resources by reducing transmitter release at these connections that do not contribute to network function.
A Simple Chamber for Long-term Confocal Imaging of Root and Hypocotyl Development

Several aspects of plant development, such as lateral root morphogenesis, occur on time spans of several days. To study underlying cellular and subcellular processes, high resolution time-lapse microscopy strategies that preserve physiological conditions are required. Plant tissues must have adequate nutrient and water supply with sustained gaseous exchange but, when submerged and immobilized under a coverslip, they are particularly susceptible to anoxia. One strategy that has been successfully employed is the use of a perfusion system to maintain a constant supply of oxygen and nutrients. However, such arrangements can be complicated, cumbersome, and require specialized equipment. Presented here is an alternative strategy for a simple imaging system using perfluorodecalin as an immersion medium. This system is easy to set up, requires minimal equipment, and is easily mounted on a microscope stage, allowing several imaging chambers to be set up and imaged in parallel. In this system, lateral root growth rates are indistinguishable from growth rates under standard conditions on agar plates for the first two days, and lateral root growth continues at reduced rates for at least another day. Plant tissues are supplied with nutrients via an agar slab that can be used also to administer a range of pharmacological compounds. The system was established to monitor lateral root development but is readily adaptable to image other plant organs such as hypocotyls and primary roots.
Mechanisms of Basin-Scale Nitrogen Load Reductions under Intensified Irrigated Agriculture

Irrigated agriculture can modify the cycling and transport of nitrogen (N), due to associated water diversions, water losses, and changes in transport flow-paths. We investigate dominant processes behind observed long-term changes in dissolved inorganic nitrogen (DIN) concentrations and loads of the extensive (465,000 km2) semi-arid Amu Darya River basin (ADRB) in Central Asia. We specifically considered a 40-year period (1960–2000) of large irrigation expansion, reduced river water flows, increased fertilizer application and net increase of N input into the soil-water system. Results showed that observed decreases in riverine DIN concentration near the Aral Sea outlet of ADRB primarily were due to increased recirculation of irrigation water, which extends the flow-path lengths and enhances N attenuation. The observed DIN concentrations matched a developed analytical relation between concentration attenuation and recirculation ratio, showing that a fourfold increase in basin-scale recirculation can increase DIN attenuation from 85 to 99%. Such effects have previously only been observed at small scales, in laboratory experiments and at individual agricultural plots. These results imply that increased recirculation can have contributed to observed increases in N attenuation in agriculturally dominated drainage basins in different parts of the world. Additionally, it can be important for basin scale attenuation of other pollutants, including phosphorous, metals and organic matter. A six-fold lower DIN export from ADRB during the period 1981–2000, compared to the period 1960–1980, was due to the combined result of drastic river flow reduction of almost 70%, and decreased DIN concentrations at the basin outlet. Several arid and semi-arid regions around the world are projected to undergo similar reductions in discharge as the ADRB due to climate change and agricultural intensification, and may therefore undergo comparable shifts in DIN export as shown here for the ADRB. For example, projected future increases of irrigation water withdrawals between 2005 and 2050 may decrease the DIN export from arid world regions by 40%.