Miracle-dz/UniFAR-FTUs huggingface dataset:
Latitudinal and seasonal variation in space use by a large, predatory reef fish,
 Plectropomus leopardus

Temperature directly affects the metabolic rate and resource requirements of ectothermic animals, which is likely to influence their movement and habitat use. Space use is a fundamental component of an animal's ecology, and the extent of an animal's home range has consequences for individual distributions, community structure and ecosystem function. As ocean temperatures continue to rise as a result of global warming, determining the effects of temperature on space use and movement patterns of important fisheries species is vital. Our aim was to investigate the spatial and temporal variation in space use by a tropical fisheries species, the leopard coralgrouper (Plectropomus leopardus), from two latitudinally distinct locations on Australia's Great Barrier Reef to determine the potential response of large-bodied tropical fishes to ocean warming through behavioural modification. Using passive acoustic telemetry of 36 tagged individuals, we found that both core use areas (50%KUD) and home range extent (95%KUD) varied with respect to location, season, body size and temperature. Average home range extent (95%KUD) for tagged P. leopardus was 0.32 km(2) at the high-latitude location (Heron Island) compared to 0.23 km(2) at the low-latitude location (Opal Reef). However, core use areas (50%KUD) did not differ significantly between the two locations. Seasonal differences were also apparent at both locations with P. leopardusshowing contraction in home range extent during the summertime. This effect was most pronounced at the low-latitude location where home range was significantly reduced during summer when temperatures exceeded 27 degrees C. Taken together, our findings indicate that higher ambient temperature may elicit a sustained and significant decline in space use by a commercially important reef fish. Given projected increases in ocean temperature due to global climate change, large-bodied reef fishes may be increasingly constrained in their movement and space use, which will have ramifications for individual fitness, population viability, fisheries productivity and ecological function.
Dual language experience enhances neural activation variability during an fMRI reading and language task

Previous work has shown that experience speaking more than one language in childhood is associated with decreased intra-individual neural variability in electrophysiological responses during a low-level speech perception task. However, no study has yet evaluated the impact of dual language experience on variability in fMRI responses during a higher-level spoken and written language processing task. In the current study, we calculated trial-by-trial variability in neural activation during an fMRI task that involved deciding whether spoken or printed English words matched pictures of items. We compared trial-by-trial neural activation variability between two groups of 8–15 year-old children: a group of dual language learners (N = 24; 11 female) who were Spanish-dominant and acquiring English, and a group of monolingual learners who were English-dominant (N = 17; 9 female). We found that when controlling for a variety of language, general cognitive, and demographic measures, neural activation variability for printed words was greater in the dual language learners compared to the monolingual learners in the right middle frontal gyrus, a brain region previously associated with attentional control. This finding highlights how neural variability offers a window of opportunity to examine experience-dependent mechanisms during human development, and motivates future research on bilingual language processing.
Effect of imidazolium based silver nanoparticle irrigant on root canal dentin roughness in comparison with three common irrigants

Introduction : The aim of this study is to evaluate the effect of a newly introduced nanosilver based irrigant on dentin roughness in comparison with three commonly used root canal irrigants. Material and methods : Irrigants tested were: NaOCl 5.25%, EDTA 17%, CHX 2% and newly introduced imidazolium-based silver nanoparticle (Im AgNP) irrigant at 5.8×10 -8 mol/L. Distilled water was used as control. Roots of 25 human anterior teeth were sectioned longitudinally to obtain 50 dentin samples. Roughness values were evaluated by Atomic Force Microscopy analysis on 5 groups of 10 samples after each group were treated in one of the tested irrigant solutions for 10 minutes. Results: Dentin roughness significantly increased from 95.82 nm (control) to 136.02 nm, 187.07 nm, 142.29 nm and 150.92 nm by NaOCl, CHX, Im AgNP irrigant and EDTA respectively. CHX demonstrated a significantly higher roughness value compared to the other irrigants tested while no significant differences were seen in NaOCl, Im AgNP irrigant and EDTA groups. (P>0.05) Conclusions: Im AgNP irrigant affect physicochemical property of dentin and raised its surface roughness, thus, this irrigant could impact bacterial and restorative material adhesion to root canal dentin walls.
New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Radiomics-Assisted Presurgical Prediction for Surgical Portal Vein-Superior Mesenteric Vein Invasion in Pancreatic Ductal Adenocarcinoma

Objectives To develop a radiomics signature for predicting surgical portal vein-superior mesenteric vein (PV-SMV) in patients with pancreatic ductal adenocarcinoma (PDAC) and measure the effect of providing the predictions of radiomics signature to radiologists with different diagnostic experiences during imaging interpretation. Methods Between February 2008 and June 2020, 146 patients with PDAC in pancreatic head or uncinate process from two institutions were retrospectively included and randomly split into a training (n = 88) and a validation (n =58) cohort. Intraoperative vascular exploration findings were used to identify surgical PV-SMV invasion. Radiomics features were extracted from the portal venous phase CT images. Radiomics signature was built with a linear elastic-net regression model. Area under receiver operating characteristic curve (AUC) of the radiomics signature was calculated. A senior and a junior radiologist independently review CT scans and made the diagnosis for PV-SMV invasion both with and without radiomics score (Radscore) assistance. A 2-sided Pearson’s chi-squared test was conducted to evaluate whether there was a difference in sensitivity, specificity, and accuracy between the radiomics signature and the unassisted radiologists. To assess the incremental value of providing Radscore predictions to the radiologists, we compared the performance between unassisted evaluation and Radscore-assisted evaluation by using the McNemar test. Results Numbers of patients identified as presence of surgical PV-SMV invasion were 33 (37.5%) and 19 (32.8%) in the training and validation cohort, respectively. The radiomics signature achieved an AUC of 0.848 (95% confidence interval, 0.724–0.971) in the validation cohort and had a comparable sensitivity, specificity, and accuracy as the senior radiologist in predicting PV-SMV invasion (all p-values > 0.05). Providing predictions of radiomics signature increased both radiologists’ sensitivity in identifying PV-SMV invasion, while only the increase of the junior radiologist was significant (63.2 vs 89.5%, p-value = 0.025) instead of the senior radiologist (73.7 vs 89.5%, p-value = 0.08). Both radiologists’ accuracy had no significant increase when provided radiomics signature assistance (both p-values > 0.05). Conclusions The radiomics signature can predict surgical PV-SMV invasion in patients with PDAC and may have incremental value to the diagnostic performance of radiologists during imaging interpretation.
De novo Vessel Formation Through Cross-Talk of Blood-Derived Cells and Mesenchymal Stromal Cells in the Absence of Pre-existing Vascular Structures

Background The generation of functional blood vessels remains a key challenge for regenerative medicine. Optimized in vitro culture set-ups mimicking the in vivo perivascular niche environment during tissue repair may provide information about the biological function and contribution of progenitor cells to postnatal vasculogenesis, thereby enhancing their therapeutic potential. Aim We established a fibrin-based xeno-free human 3D in vitro vascular niche model to study the interaction of mesenchymal stromal cells (MSC) with peripheral blood mononuclear cells (PBMC) including circulating progenitor cells in the absence of endothelial cells (EC), and to investigate the contribution of this cross-talk to neo-vessel formation. Materials and Methods Bone marrow-derived MSC were co-cultured with whole PBMC, enriched monocytes (Mo), enriched T cells, and Mo together with T cells, respectively, obtained from leukocyte reduction chambers generated during the process of single-donor platelet apheresis. Cells were embedded in 3D fibrin matrices, using exclusively human-derived culture components without external growth factors. Cytokine secretion was analyzed in supernatants of 3D cultures by cytokine array, vascular endothelial growth factor (VEGF) secretion was quantified by ELISA. Cellular and structural re-arrangements were characterized by immunofluorescence and confocal laser-scanning microscopy of topographically intact 3D fibrin gels. Results 3D co-cultures of MSC with PBMC, and enriched Mo together with enriched T cells, respectively, generated, within 2 weeks, complex CD31+/CD34+ vascular structures, surrounded by basement membrane collagen type-IV+ cells and matrix, in association with increased VEGF secretion. PBMC contained CD31+CD34+CD45dimCD14– progenitor-type cells, and EC of neo-vessels were PBMC-derived. Vascular structures showed intraluminal CD45+ cells that underwent apoptosis thereby creating a lumen. Cross-talk of MSC with enriched Mo provided a pro-angiogenic paracrine environment. MSC co-cultured with enriched T cells formed “cell-in-cell” structures generated through internalization of T cells by CD31+CD45dim⁣/– cells. No vascular structures were detected in co-cultures of MSC with either Mo or T cells. Conclusion Our xeno-free 3D in vitro vascular niche model demonstrates that a complex synergistic network of cellular, extracellular and paracrine cross-talk can contribute to de novo vascular development through self-organization via co-operation of immune cells with blood-derived progenitor cells and MSC, and thereby may open a new perspective for advanced vascular tissue engineering in regenerative medicine.
Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea

Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.
Limited Contribution of Glacier Mass Loss to the Recent Increase in Tibetan Plateau Lake Volume

The Tibetan plateau plays an essential role in the water supply to Asia’s large river systems and, as the largest and highest mountain plateau in the world, it drives the Asian monsoon and influences global atmospheric circulation patterns. The increase in the Tibetan plateau lake volume since the mid-1990s is well documented, however the drivers of lake growth remain largely unexplained. In this study we investigate changes in lake and glacier volumes, together with changes in precipitation and evapotranspiration at basin scale. We calculate the contribution of glacier mass loss to the lake volume increase for the period 1994–2015. We demonstrate that glacier mass loss does have a limited contribution to the lake volume increase (19 ± 21% for the whole Tibetan plateau). Glacier mass loss is thus insufficient to explain all of the lake volume gain, and despite large spread in various products that estimate precipitation and evaporation, we suggest that an increase in precipitation excess (precipitation - evapotranspiration) may be sufficient to explain the lake volume gain.
Deep Learning for Understanding Satellite Imagery: An Experimental Survey

Translating satellite imagery into maps requires intensive effort and time, especially leading to inaccurate maps of the affected regions during disaster and conflict. The combination of availability of recent datasets and advances in computer vision made through deep learning paved the way toward automated satellite image translation. To facilitate research in this direction, we introduce the Satellite Imagery Competition using a modified SpaceNet dataset. Participants had to come up with different segmentation models to detect positions of buildings on satellite images. In this work, we present five approaches based on improvements of U-Net and Mask R-Convolutional Neuronal Networks models, coupled with unique training adaptations using boosting algorithms, morphological filter, Conditional Random Fields and custom losses. The good results—as high as A P = 0.937 and A R = 0.959 —from these models demonstrate the feasibility of Deep Learning in automated satellite image annotation.
Factors Associated With Falls Among Urban-Dwellers Aged 55 Years and Over in the Malaysian Elders Longitudinal Research (MELoR) Study

Falls are major issues affecting the older population with potentially serious complications, including fractures, head injury, institutionalization, fear of falling and depression. While risk factors for falls have been established across Western Europe and North America, geographical differences in falls risk have not been well researched. We aim to examine the clinical and physical risk factors for falls in a middle-income South East Asian country. Cross-sectional data from the Malaysian Elders Longitudinal Research (MELoR) study involving 1,362 community dwelling individuals aged 55 years and above was utilized. Information on sociodemographic and medical history was obtained by computer-assisted questionnaires completed during home visits and hospital-based detailed health checks. Univariate and multivariate analyses compared non-fallers and fallers in the previous 12 months. Urinary incontinence, hearing impairment, depression, arthritis and cognitive impairment were risk factors for falls in the past 12 months after adjustment for age in our study population. Awareness about the risk factors in a population helps the design of fall prevention strategies that target specific or multiple risk factors.
Effects of Water Addition on Reproductive Allocation of Dominant Plant Species in Inner Mongolia Steppe

Extreme events such as extreme drought and precipitation are expected to increase in intensity and/or duration in the face of climate change. Such changes significantly affect plant productivity and the biomass allocation between reproductive and vegetation organs (i.e., reproductive allocation). Our aims are to test the effects of water addition on the trade-offs in allocation of plant biomass and whether such effects are modified by species. A manipulative experiment was conducted from May 2000 to October 2001, where four dominant plant species (i.e., Leymus chinensis, Stipa grandis, Artemisia frigida, and Potentilla acaulis) in the Inner Mongolia steppe in China were treated with 8 levels of water addition. Results demonstrated that water addition significantly affected the reproductive allocation of plants, and such effects were modified by species. Specifically, with increasing water availability, L. chinensis was not impacted, while A. frigida allocated more biomass to reproductive organs than to vegetative organs, while such allocation in S. grandis and P. acaulis first decreased, and then increased after reaching a peak. Our results indicated that plant species can adjust their reproductive allocation patterns to deal with water availability gradients. Climatic factors such as rainfall and temperature usually co-appearing, thus future research should explore the joint effects of several climate change factors on grasslands in order to maintain the health and sustainability of grasslands.
Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

Intestine microbiota is tightly associated with host health status. Increasing studies have focused on assessing how host intestine microbiota is affected by biotic factors but ignored abiotic factors. Here, we aimed to understand the effects of salinity on shrimp intestine microbiota, by comparing the differences of intestine bacterial signatures of shrimp under low-salinity (LS) and high-salinity (HS) culture conditions. Our results found that intestine core bacterial taxa of shrimp under LS and HS culture conditions were different and that under HS contained more opportunistic pathogen species. Notably, compared with LS culture conditions, opportunistic pathogens (e.g., Vibrio species) were enriched in shrimp intestine under HS. Network analysis revealed that shrimp under HS culture conditions exhibited less connected and lower competitive intestine bacterial interspecies interactions compared with LS. In addition, under HS culture conditions, several opportunistic pathogens were identified as keystone species of intestine bacterial network in shrimp. Furthermore, the ecological drift process played a more important role in the intestine bacterial assembly of shrimp under HS culture conditions than that under LS. These above traits regarding the intestine microbiota of shrimp under HS culture conditions might lead to host at a higher risk of disease. Collectively, this work aids our understanding of the effects of salinity on shrimp intestine microbiota and helps for shrimp culture.
PCSK9 Inhibition: Insights From Clinical Trials and Future Prospects

In 2003, clinical observations led to the discovery of the involvement of proprotein convertase subtilisin/kexin type 9 (PCSK9) in lipid metabolism. Functional studies demonstrated that PCSK9 binds to the low-density lipoprotein (LDL) receptor directing it to its lysosomal degradation. Therefore, carriers of gain-of-function mutations in PCSK9 exhibit decreased expression of LDL receptors on the hepatocyte surface and have higher LDL cholesterol (LDL-C) levels. On the contrary, loss-of-function mutations in PCSK9 are associated with low LDL-C concentrations and significantly reduced lifetime risk of cardiovascular disease. These insights motivated the search for strategies to pharmacologically inhibit PCSK9. In an exemplary rapid development, fully human monoclonal antibodies against PCSK9 were developed and found to effectively reduce LDL-C. Administered subcutaneously every 2–4 weeks, the PCSK9 antibodies evolocumab and alirocumab reduce LDL-C by up to 60% in a broad range of populations either as monotherapy or in addition to statins. Two large cardiovascular outcome trials involving a total of ∼46,000 cardiovascular high-risk patients on guideline-recommended lipid-lowering therapy showed that treatment with evolocumab and alirocumab led to a relative reduction of cardiovascular risk by 15% after 2.2 and 2.8 years of treatment, respectively. These findings expanded the armamentarium of pharmacological approaches to address residual cardiovascular risk associated with LDL-C. Furthermore, the unprecedented low LDL-C concentrations achieved (e.g., 30 mg/dL in the FOURIER study) suggest that the relationship between LDL-C and cardiovascular risk is without a lower threshold, and without associated adverse events during the timeframe of the studies. The side effect profile of PCSK9 antibodies is favorable with few patients exhibiting injection-site reactions. Currently, the access to PCSK9 antibodies is limited by high treatment costs. The development of novel approaches to inhibit PCSK9 such as the use of small interfering RNA to inhibit PCSK9 synthesis seems promising and may soon become available.