Miracle-dz/UniFAR-FTUs huggingface dataset:
Subsidies mediate interactions between communities across space

Most spatial ecology focuses on how species dispersal a ects community dynamics and coexistence. Ecosystems, however, are also commonly connected by ows of resources. We experimentally tested how neighbouring communities indirectly in uence each other in absence of dispersal, via resource exchanges. Using two-patch microcosm meta-ecosystems, we manipulated community composition and dynamics, by varying separately species key functional traits (autotroph versus heterotroph species and size of consumer species) and trophic structure of aquatic communities (species growing alone or in presence of competitors or predators). We then analysed the e ects of species functional traits and trophic structure on communities connected through spatial subsidies in the absence of actual dispersal. Both functional traits and trophic structure strongly a ected dynamics across neighbouring communities. Heterotroph communities connected to autotroph neighbours developed better than with heterotroph neighbours, such that coexistence of competitors was determined by the functional traits of the neighbouring community. Densities in autotroph communities were also strikingly higher when receiving subsidies from heterotroph communities compared to their own subsidies when grown in isolated ecosystems. In contrast, communities connected to predator-dominated ecosystems collapsed, without any direct contact with the predators. Our results demonstrate that because community composition and structure modify the distribution of biomass within a community, they may also a ect communities connected through subsidies through quantitative and qualitative changes of detritus ows. is stresses that ecosystem management should account for such interdependencies mediated by spatial subsidies, given that local community alterations cascade across space onto other ecosystems even if species dispersal is completely absent.
The Great Silk Alternative: Multiple Co-Evolution of Web Loss and Sticky Hairs in Spiders

Spiders are the most important terrestrial predators among arthropods. Their ecological success is reflected by a high biodiversity and the conquest of nearly every terrestrial habitat. Spiders are closely associated with silk, a material, often seen to be responsible for their great ecological success and gaining high attention in life sciences. However, it is often overlooked that more than half of all Recent spider species have abandoned web building or never developed such an adaptation. These species must have found other, more economic solutions for prey capture and retention, compensating the higher energy costs of increased locomotion activity. Here we show that hairy adhesive pads (scopulae) are closely associated with the convergent evolution of a vagrant life style, resulting in highly diversified lineages of at least, equal importance as the derived web building taxa. Previous studies often highlighted the idea that scopulae have the primary function of assisting locomotion, neglecting the fact that only the distal most pads (claw tufts) are suitable for those purposes. The former observations, that scopulae are used in prey capture, are largely overlooked. Our results suggest the scopulae evolved as a substitute for silk in controlling prey and that the claw tufts are, in most cases, a secondary development. Evolutionary trends towards specialized claw tufts and their composition from a low number of enlarged setae to a dense array of slender ones, as well as the secondary loss of those pads are discussed further. Hypotheses about the origin of the adhesive setae and their diversification throughout evolution are provided.
Lateral flow test strip based on colloidal selenium immunoassay for rapid detection of melamine in milk, milk powder, and animal feed

Although high melamine (MEL) intake has been proven to cause serious health problems, MEL is sometimes illegally added to milk products and animal feed, arousing serious food safety concerns. A satisfactory method of detecting MEL in onsite or in-home testing is in urgent need of development. This work aimed to explore a rapid, convenient, and cost-effective method of identifying MEL in milk products or other food by colloidal selenium-based lateral flow immunoassay. Colloidal selenium was synthesized by L-ascorbic acid to reduce seleninic acid at room temperature. After conjugation with a monoclonal antibody anti-MEL, a test strip was successfully prepared. The detection limit of the test strip reached 150 μg/kg, 1,000 μg/kg, and 800 μg/kg in liquid milk, milk powder, and animal feed, respectively. No cross-reactions with homologues cyanuric acid, cyanurodiamide, or ammelide were found. Moreover, the MEL test strip can remain stable after storage for 1 year at room temperature. Our results demonstrate that the colloidal selenium MEL test strip can detect MEL in adulterated milk products or animal feed conveniently, rapidly, and sensitively. In contrast with a colloidal gold MEL test strip, the colloidal selenium MEL test strip was easy to prepare and more cost-efficient.
Glaucoma detection using wavelet based contourlet transform

One of the leading retinal diseases which cause vision loss is Glaucoma. This paper presents the methodology to detect Glaucoma using wavelet based contourlet transform with Gabor filters. The input retinal fundus image is localized for its region of interest and enhanced using adaptive Gamma correction with weighted Distribution function (AGCWD). The blood vessels in ROI are removed using the Gabor filter and morphological operators. To the Region of Interest the wavelet based contourlet transform (WBCT) is applied to extract the features and then given to the Naïve Bayes (NB) classifiers for detecting the normal and glaucomatous image.
LAMTOR/Ragulator is a negative regulator of Arl8b- and BORC-dependent late endosomal positioning

Signaling from lysosomes controls cellular clearance and energy metabolism. Lysosomal malfunction has been implicated in several pathologies, including neurodegeneration, cancer, infection, immunodeficiency, and obesity. Interestingly, many functions are dependent on the organelle position. Lysosomal motility requires the integration of extracellular and intracellular signals that converge on a competition between motor proteins that ultimately control lysosomal movement on microtubules. Here, we identify a novel upstream control mechanism of Arl8b-dependent lysosomal movement toward the periphery of the cell. We show that the C-terminal domain of lyspersin, a subunit of BLOC-1–related complex (BORC), is essential and sufficient for BORC-dependent recruitment of Arl8b to lysosomes. In addition, we establish lyspersin as the linker between BORC and late endosomal/lysosomal adaptor and mitogen activated protein kinase and mechanistic target of rapamycin activator (LAMTOR) complexes and show that epidermal growth factor stimulation decreases LAMTOR/BORC association, thereby promoting BORC- and Arl8b-dependent lysosomal centrifugal transport.
GLP-1 and Insulin Recruit Muscle Microvasculature and Dilate Conduit Artery Individually But Not Additively in Healthy Humans

Abstract Context: Glucagon-like peptide-1 (GLP-1) and insulin increase muscle microvascular perfusion, thereby increasing tissue endothelial surface area and nutrient delivery. Objective: To examine whether GLP-1 and insulin act additively on skeletal and cardiac microvasculature and conduit artery. Design: Healthy adults underwent three study protocols in random order. Setting: Clinical Research Unit at the University of Virginia. Methods: Overnight-fasted participants received an intravenous infusion of GLP-1 (1.2 pmol/kg/min) or normal saline for 150 minutes with or without a 2-hour euglycemic insulin clamp (1 mU/kg/min) superimposed from 30 minutes onward. Skeletal and cardiac muscle microvascular blood volume (MBV), flow velocity, and flow; brachial artery diameter, flow velocity, and blood flow; and pulse wave velocity (PWV) were measured. Results: GLP-1 significantly increased skeletal and cardiac muscle MBV and microvascular blood flow (MBF) after 30 minutes; these remained elevated at 150 minutes. Insulin also increased skeletal and cardiac muscle MBV and MBF. Addition of insulin to GLP-1 did not further increase skeletal and cardiac muscle MBV and MBF. GLP-1 and insulin increased brachial artery diameter and blood flow, but this effect was not additive. Neither GLP-1, insulin, nor GLP-1 and insulin altered PWV. Combined GLP-1 and insulin infusion did not result in higher whole-body glucose disposal. Conclusion: GLP-1 and insulin at physiological concentrations acutely increase skeletal and cardiac muscle microvascular perfusion and dilate conduit artery in healthy adults; these effects are not additive. Thus, GLP-1 and insulin may regulate skeletal and cardiac muscle endothelial surface area and nutrient delivery under physiological conditions.
Modelling the effects of toxic metal mixtures on the reproduction of Eisenia veneta in different types of soil

Previously, toxicity studies have mainly focused on the responses of organisms to single toxicants; however the importance of studying mixtures of toxicants is now being recognised, along with the importance of speciation as a modifier of toxic effect. The aim of this study was to improve our understanding of the toxic response of the compost worm Eisenia veneta to cadmium, copper and zinc by integrating understanding of speciation effects into existing mixture models. Adult earthworm tests were carried out in four soils with different pH and organic matter contents, spiked with varying single and mixed doses of Cu/Zn and Cd/Zn. The reproduction rate of the earthworms after a four week exposure was studied. The three metals had different levels of toxicity in different soils. There were clear differences in the responses of the earthworms to the toxic metals in the different soils, and the extent of metal mixture interaction found depended on the form of metal (total metal, free ion (M2+) or diffusive gradient in thin film (DGT) effective concentrations) used to express the dose to the organisms. Mixture interactions were different when expressed in different metal forms and in the four soils. Detailed analysis of the different chemical species provides further insight into how the soil environment instigates the observed mixture effects. The results from this study support the need to consider bioavailability and mixture effects in toxicity studies.
Förster Resonance Energy Transfer between Core/Shell Quantum Dots and Bacteriorhodopsin

An energy transfer relationship between core-shell CdSe/ZnS quantum dots (QDs) and the optical protein bacteriorhodopsin (bR) is shown, demonstrating a distance-dependent energy transfer with 88.2% and 51.1% of the QD energy being transferred to the bR monomer at separation distances of 3.5 nm and 8.5 nm, respectively. Fluorescence lifetime measurements isolate nonradiative energy transfer, other than optical absorptive mechanisms, with the effective QD excited state lifetime reducing from 18.0 ns to 13.3 ns with bR integration, demonstrating the Förster resonance energy transfer contributes to 26.1% of the transferred QD energy at the 3.5 nm separation distance. The established direct energy transfer mechanism holds the potential to enhance the bR spectral range and sensitivity of energies that the protein can utilize, increasing its subsequent photocurrent generation, a significant potential expansion of the applicability of bR in solar cell, biosensing, biocomputing, optoelectronic, and imaging technologies.
Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations

Background Many health organizations allow patients to access their own electronic health record (EHR) notes through online patient portals as a way to enhance patient-centered care. However, EHR notes are typically long and contain abundant medical jargon that can be difficult for patients to understand. In addition, many medical terms in patients’ notes are not directly related to their health care needs. One way to help patients better comprehend their own notes is to reduce information overload and help them focus on medical terms that matter most to them. Interventions can then be developed by giving them targeted education to improve their EHR comprehension and the quality of care. Objective We aimed to develop a supervised natural language processing (NLP) system called Finding impOrtant medical Concepts most Useful to patientS (FOCUS) that automatically identifies and ranks medical terms in EHR notes based on their importance to the patients. Methods First, we built an expert-annotated corpus. For each EHR note, 2 physicians independently identified medical terms important to the patient. Using the physicians’ agreement as the gold standard, we developed and evaluated FOCUS. FOCUS first identifies candidate terms from each EHR note using MetaMap and then ranks the terms using a support vector machine-based learn-to-rank algorithm. We explored rich learning features, including distributed word representation, Unified Medical Language System semantic type, topic features, and features derived from consumer health vocabulary. We compared FOCUS with 2 strong baseline NLP systems. Results Physicians annotated 90 EHR notes and identified a mean of 9 (SD 5) important terms per note. The Cohen’s kappa annotation agreement was . 51. The 10-fold cross-validation results show that FOCUS achieved an area under the receiver operating characteristic curve (AUC-ROC) of 0.940 for ranking candidate terms from EHR notes to identify important terms. When including term identification, the performance of FOCUS for identifying important terms from EHR notes was 0.866 AUC-ROC. Both performance scores significantly exceeded the corresponding baseline system scores (P<.001). Rich learning features contributed to FOCUS’s performance substantially. Conclusions FOCUS can automatically rank terms from EHR notes based on their importance to patients. It may help develop future interventions that improve quality of care.
Peak perihemorrhagic edema correlates with functional outcome in intracerebral hemorrhage

Objective To evaluate the association of perihemorrhagic edema (PHE) evolution and peak edema extent with day 90 functional outcome in patients with intracerebral hemorrhage (ICH) and identify pathophysiologic factors influencing edema evolution. Methods This retrospective cohort study included patients with spontaneous supratentorial ICH between January 2006 and January 2014. ICH and PHE volumes were studied using a validated semiautomatic volumetric algorithm. Multivariable logistic regression and propensity score matching (PSM) accounting for age, ICH volume, and location were used for assessing measures associated with functional outcome and PHE evolution. Clinical outcome on day 90 was assessed using the modified Rankin Scale (0–3 = favorable, 4–6 = poor). Results A total of 292 patients were included. Median age was 70 years (interquartile range [IQR] 62–78), median ICH volume on admission 17.7 mL (IQR 7.9–40.2). Besides established factors for functional outcome, i.e., ICH volume and location, age, intraventricular hemorrhage, and NIH Stroke Scale score on admission, multivariable logistic regression revealed peak PHE volume (odds ratio [OR] 0.984 [95% confidence interval (CI) 0.973–0.994]) as an independent predictor of day 90 outcome. Peak PHE volume was independently associated with initial PHE increase up to day 3 (OR 1.060 [95% CI 1.018–1.103]) and neutrophil to lymphocyte ratio on day 6 (OR 1.236 [95% CI 1.034–1.477; PSM cohort, n = 124]). Initial PHE increase (PSM cohort, n = 224) was independently related to hematoma expansion (OR 3.647 [95% CI 1.533–8.679]) and fever burden on days 2–3 (OR 1.456 [95% CI 1.103–1.920]). Conclusion Our findings suggest that peak PHE volume represents an independent predictor of functional outcome after ICH. Inflammatory processes and hematoma expansion seem to be involved in PHE evolution and may represent important treatment targets.
A high-fat diet containing whole walnuts ( Juglans regia ) reduces tumour size and growth along with plasma insulin-like growth factor 1 in the transgenic adenocarcinoma of the mouse prostate model Paul

Prostate cancer (PCa) has been linked to fat intake, but the effects of both different dietary fat levels and types remain inconsistent and incompletely characterised. The effects on PCa in the transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model of an elevated fat (20 % of energy as fat) diet containing 155 g of whole walnuts were compared to those of an elevated fat (20 % of energy as soyabean oil) diet with matched macronutrients, tocopherols as well as a low-fat (8 % of energy as soyabean oil) diet. Mice, starting at 8 weeks of age, consumed one of the three different diets ad libitum; and prostates, livers and blood were obtained after 9, 18 or 24 weeks of feeding. No differences were observed in whole animal growth rates in either high-fat (HF) diet group, but prostate tumour weight and growth rate were reduced in the walnut diet group. Walnut diet group prostate weight, plasma insulin-like growth factor 1, resistin and LDL were lower at 18 weeks, while no statistically significant prostate weight differences by diet were seen at 9 or 24 weeks. Multiple metabolites in the livers differed by diet at 9 and 18 weeks. The walnut diet’s beneficial effects probably represent the effects of whole walnuts’ multiple constituents and not via a specific fatty acid or tocopherols. Moreover, as the two HF diets had dissimilar effects on prostate tumour growth rate and size, and yet had the same total fat and tocopherol composition and content, this suggests that these are not strongly linked to PCa growth.
Metformin inhibits proliferation and growth hormone secretion of GH3 pituitary adenoma cells

Metformin is an anti-hyperglycemic agent used to treat diabetes, and recent evidence suggests it has antitumor efficacy. Because growth hormone-secreting pituitary adenoma (GH-PA) patients have a high incidence of diabetes frequently treated with metformin, we assessed the antitumor effect of metformin on GH-PA. We found that metformin effectively inhibited proliferation and induced apoptosis in the GH-PA cell line GH3. We detected a decrease in mitochondrial membrane potential (MMP), an increase in expression of pro-apoptotic proteins, and a decrease in expression of an anti-apoptotic protein in metformin-treated GH3 cells, which suggests involvement of the mitochondrial-mediated apoptosis pathway. Inhibition of AMPK, which is activated by metformin, failed to reverse the antiproliferative effect. ATF3 was upregulated by metformin, and its knockdown significantly reduced metformin-induced apoptosis. In addition, GH secretion was inhibited by metformin through suppression of STAT3 activity independently of AMPK. Metformin also significantly suppressed cellular proliferation and GH secretion in primary human GH-PA cells. Metformin also significantly inhibited GH3 cell proliferation and GH secretion in vivo. ATF3 upregulation and p-STAT3 downregulation were confirmed in xenografts. These findings suggest metformin is a potentially promising therapeutic agent for the treatment of GH-PA, particularly in patients with diabetes.
Molecular Cloning and Characterization of a Newly Isolated Pyrethroid-Degrading Esterase Gene from a Genomic Library of Ochrobactrum anthropi YZ-1

A novel pyrethroid-degrading esterase gene pytY was isolated from the genomic library of Ochrobactrum anthropi YZ-1. It possesses an open reading frame (ORF) of 897 bp. Blast search showed that its deduced amino acid sequence shares moderate identities (30% to 46%) with most homologous esterases. Phylogenetic analysis revealed that PytY is a member of the esterase VI family. pytY showed very low sequence similarity compared with reported pyrethroid-degrading genes. PytY was expressed, purified, and characterized. Enzyme assay revealed that PytY is a broad-spectrum degrading enzyme that can degrade various pyrethroids. It is a new pyrethroid-degrading gene and enriches genetic resource. Kinetic constants of Km and Vmax were 2.34 mmol·L−1 and 56.33 nmol min−1, respectively, with lambda-cyhalothrin as substrate. PytY displayed good degrading ability and stability over a broad range of temperature and pH. The optimal temperature and pH were of 35°C and 7.5. No cofactors were required for enzyme activity. The results highlighted the potential use of PytY in the elimination of pyrethroid residuals from contaminated environments.
Adaptive video coding selection scheme for solar-powered wireless video sensor networks

Recently, the use of wireless sensor networks to collect video data for environmental observation or monitoring has been increasing, but they are not suitable for transmitting large video data due to the limitation of node energy. Energy-harvesting node could be used to overcome this limitation, but the harvested energy is also limited. Therefore, an efficient energy utilization method is required to transmit a large amount of video data. This paper proposes a scheme to reduce the number of blackout nodes and increase the amount of collected data by selecting an appropriate video encoding method according to energy condition of the node in a solar-powered wireless sensor network. To collect data continuously regardless of day or night, this scheme allocates the amount of energy that can be used by time, and selects a coding with a high-compression ratio if the allocated amount is large, or a coding with a low-compression ratio if it is small. In this way, the blackouts of relay nodes are reduced and data can be transmitted continuously, which increases the amount of data arriving at the sink node. The simulation results verified confirmed that the proposed scheme prevented the energy exhaustion of the relay nodes and collected more data compared to using one coding only.
The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus) including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1) a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2) blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case of orthology prediction methods like HaMStR it is likewise decreased by using more than one reference taxon.