Miracle-dz/UniFAR-FTUs huggingface dataset:
What Happened to Gray Whales during the Pleistocene? The Ecological Impact of Sea-Level Change on Benthic Feeding Areas in the North Pacific Ocean

Background Gray whales (Eschrichtius robustus) undertake long migrations, from Baja California to Alaska, to feed on seasonally productive benthos of the Bering and Chukchi seas. The invertebrates that form their primary prey are restricted to shallow water environments, but global sea-level changes during the Pleistocene eliminated or reduced this critical habitat multiple times. Because the fossil record of gray whales is coincident with the onset of Northern Hemisphere glaciation, gray whales survived these massive changes to their feeding habitat, but it is unclear how. Methodology/Principal Findings We reconstructed gray whale carrying capacity fluctuations during the past 120,000 years by quantifying gray whale feeding habitat availability using bathymetric data for the North Pacific Ocean, constrained by their maximum diving depth. We calculated carrying capacity based on modern estimates of metabolic demand, prey availability, and feeding duration; we also constrained our estimates to reflect current population size and account for glaciated and non-glaciated areas in the North Pacific. Our results show that key feeding areas eliminated by sea-level lowstands were not replaced by commensurate areas. Our reconstructions show that such reductions affected carrying capacity, and harmonic means of these fluctuations do not differ dramatically from genetic estimates of carrying capacity. Conclusions/Significance Assuming current carrying capacity estimates, Pleistocene glacial maxima may have created multiple, weak genetic bottlenecks, although the current temporal resolution of genetic datasets does not test for such signals. Our results do not, however, falsify molecular estimates of pre-whaling population size because those abundances would have been sufficient to survive the loss of major benthic feeding areas (i.e., the majority of the Bering Shelf) during glacial maxima. We propose that gray whales survived the disappearance of their primary feeding ground by employing generalist filter-feeding modes, similar to the resident gray whales found between northern Washington State and Vancouver Island.
A Reassessment of Carbon Content in Tropical Trees

Accurate knowledge of carbon (C) content in live wood is essential for quantifying tropical forest C stocks, yet generic assumptions (such as biomass consisting of 50% carbon on a weight/weight basis) remain widely used despite being supported by little chemical analysis. Empirical data from stem cores of 59 Panamanian rainforest tree species demonstrate that wood C content is highly variable among co-occurring species, with an average (47.4±2.51% S.D.) significantly lower than widely assumed values. Prior published values have neglected to account for volatile C content of tropical woods. By comparing freeze- and oven-dried wood samples, we show that volatile C is non-negligible, and excluding the volatile fraction underestimates wood C content by 2.48±1.28% (S.D.) on average. Wood C content varied substantially among species (from 41.9–51.6%), but was neither strongly phylogenetically conserved, nor correlated to ecological (i.e. wood density, maximum tree height) or demographic traits (i.e. relative growth rate, mortality rate). Overall, assuming generic C fractions in tropical wood overestimates forest C stocks by ∼3.3–5.3%, a non-trivial margin of error leading to overestimates of 4.1–6.8 Mg C ha−1 in a 50-ha forest dynamics plot on Barro Colorado Island, Panama. In addition to addressing other sources of error in tropical forest C accounting, such as uncertainties in allometric models and belowground biomass, compilation and use of species-specific C fractions for tropical tree species would substantially improve both local and global estimates of terrestrial C stocks and fluxes.
Phytoremediation techniques of wastewater treatment

Heavy Metals in the Environment: Origin, Interaction and RemediationWastewater Engineering: Advanced Wastewater Treatment SystemsAdvances in Bioremediation and Phytoremediation for Sustainable Soil ManagementPhytoremediation: Role of Aquatic Plants in Environmental CleanUpEmerging Eco-friendly Green Technologies for Wastewater TreatmentBioremediation: Applications for Environmental Protection and ManagementHeavy Metals In The EnvironmentMethods for Bioremediation of Water and Wastewater PollutionEnvironmental Risk Assessment of Soil ContaminationRemoval of Refractory Pollutants from Wastewater Treatment PlantsPhysico-Chemical Wastewater Treatment and Resource RecoverySynergistic Application of a Municipal Waste Material and Phytoremediation Technique for Remediating Acid Mine Drainage and Impacted SoilPlant Ecophysiology and Adaptation under Climate Change: Mechanisms and Perspectives IIPhytoremediationRemoval of Refractory Pollutants from Wastewater Treatment PlantsSoil BioremediationCost Effective Technologies for Solid Waste and Wastewater TreatmentHandbook of Engineering Hydrology (Three-Volume Set)An Integration of Phycoremediation Processes in Wastewater TreatmentDevelopment in Wastewater Treatment Research and ProcessesPhytoremediationHandbook of Research on Microbial Tools for Environmental Waste ManagementRecent Advancements in Bioremediation of Metal ContaminantsEmerging and Eco-Friendly Approaches for Waste ManagementThe Role of Phytoremediation in Remediation of Industrial WastePhytoremediation Technology for the Removal of Heavy Metals and Other Contaminants from Soil and WaterPhytoremediationEcological Assessment of Wastewater Treatment TechnologiesSOUVENIR of 4th International Science CongressGreen Materials for Wastewater TreatmentBioremediation and Green TechnologiesWastewater Treatment EngineeringPhytoremediation of Contaminated Soil and WaterContamination of WaterApplication of Microalgae in Wastewater TreatmentNew Trends in Removal of Heavy Metals from Industrial WastewaterWastewater TreatmentAdvanced Treatment Techniques for Industrial WastewaterIntroduction to PhytoremediationPhytoremediation
The early response during the interaction of fungal phytopathogen and host plant

Plants can be infected by a variety of pathogens, most of which can cause severe economic losses. The plants resist the invasion of pathogens via the innate or acquired immune system for surviving biotic stress. The associations between plants and pathogens are sophisticated beyond imaging and the interactions between them can occur at a very early stage after their touching each other. A number of researchers in the past decade have shown that many biochemical events appeared even as early as 5 min after their touching for plant disease resistance response. The early molecular interactions of plants and pathogens are likely to involve protein phosphorylation, ion fluxes, reactive oxygen species (ROS) and other signalling transduction. Here, we reviewed the recent progress in the study for molecular interaction response of fungal pathogens and host plant at the early infection stage, which included many economically important crop fungal pathogens such as cereal rust fungi, tomato Cladosporium fulvum, rice blast and so on. By dissecting the earlier infection stage of the diseases, the avirulent/virulent genes of pathogen or resistance genes of plant could be defined more clearly and accurately, which would undoubtedly facilitate fungal pathogenesis study and resistant crop breeding.
Animal studies of the anaesthetic activity of ICI 35 868.

The activity of a new i.v. anesthetic agent ICI 35 868, a compound unrelated to currently used barbiturate, eugenol or steroid agents, has been examined in a range of animal species. Some of the properties of ICI 35 868 resemble those of thiopentone in that it is a rapidly acting agent which produces anaesthesia of short duration and without excitatory side-effects. Both agents have a similar therapeutic index and produce equivalent cardiovascular and respiratory effects. In the mouse ICI 35 868 is 1.8 times more potent than thiopentone as a hypnotic. However, the anaesthetic profile of ICI 35 868 differs from that of thiopentone in that recovery is rapid following repeated administration, no tissue damage is produced by perivascular or intra-arterial injection and greater reflex depression and more profound e.e.g. changes are produced at equipotent doses. This new agent has been shown to be compatible with a wide range of drugs used for preanaesthetic medication, inhalation anaesthetics, and neuromuscular blocking drugs.
Newcastle University E-prints Citation for Item: a Novel Extracellular Metallopeptidase Domain Shared by Animal Host-associated Mutualistic and Pathogenic Microbes

A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. Always use the definitive version when citing. The full-text may be used and/or reproduced and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not for profit purposes provided that: • A full bibliographic reference is made to the original source • A link is made to the metadata record in Newcastle E-prints • The full text is not changed in any way. The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Abstract The mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. Hence, there is considerable interest in identifying the molecular basis of human-microbe interactions. In this work we investigated the capacity of microbes to thrive on mucosal surfaces, either as mutualists, commensals or pathogens, using comparative genomics to identify co-occurring molecular traits. We identified a novel domain we named M60-like/PF13402 (new Pfam entry PF13402), which was detected mainly among proteins from animal host mucosa-associated prokaryotic and eukaryotic microbes ranging from mutualists to pathogens. Lateral gene transfers between distantly related microbes explained their shared M60-like/PF13402 domain. The novel domain is characterised by a zinc-metallopeptidase-like motif and is distantly related to known viral enhancin zinc-metallopeptidases. Signal peptides and/or cell surface anchoring features were detected in most microbial M60-like/PF13402 domain-containing proteins, indicating that these proteins target an extracellular substrate. A significant subset of these putative peptidases was further characterised by the presence of associated domains belonging to carbohydrate-binding module family 5/12, 32 and 51 and other glycan-binding domains, suggesting that these novel proteases are targeted to complex glycoproteins such as mucins. An in vitro mucinase assay demonstrated degradation of mammalian mucins by a recombinant form of an M60-like/PF13402-containing protein from the gut mutualist Bacteroides thetaiotaomicron. This study reveals that M60-like domains are peptidases targeting host glycoproteins. These peptidases likely play an important role in successful colonisation of both vertebrate mucosal surfaces and the invertebrate digestive tract by both mutualistic and pathogenic microbes. Moreover, 141 entries across various peptidase families described in the MEROPS database were also identified with carbohydrate-binding modules defining a new functional context for these glycan-binding domains and providing opportunities to engineer proteases targeting specific glycoproteins for both biomedical and …
Collective Intelligence in Multi-Agent Robotics: Stigmergy, Self-Organization and Evolution

Nature has been able to evolve (several times) natural systems which produce complex spatio-temporal patterns from agents with very simple behaviours by exploiting the interactions between the agents and their environment. Surprisingly, the systematic use of these principles have been mostly neglected within the field of collective robotics. We study the use of these biological principles in nature and their application in artificial systems and hypothesize on the role between such principles and evolution. We conclude with future directions towards collective intelligence in multi-agent robotics.
Multimodal‐3D imaging based on μMRI and μCT techniques bridges the gap with histology in visualization of the bone regeneration process

Bone repair/regeneration is usually investigated through X‐ray computed microtomography (μCT) supported by histology of extracted samples, to analyse biomaterial structure and new bone formation processes. Magnetic resonance imaging (μMRI) shows a richer tissue contrast than μCT, despite at lower resolution, and could be combined with μCT in the perspective of conducting non‐destructive 3D investigations of bone. A pipeline designed to combine μMRI and μCT images of bone samples is here described and applied on samples of extracted human jawbone core following bone graft. We optimized the coregistration procedure between μCT and μMRI images to avoid bias due to the different resolutions and contrasts. Furthermore, we used an Adaptive Multivariate Clustering, grouping homologous voxels in the coregistered images, to visualize different tissue types within a fused 3D metastructure. The tissue grouping matched the 2D histology applied only on 1 slice, thus extending the histology labelling in 3D. Specifically, in all samples, we could separate and map 2 types of regenerated bone, calcified tissue, soft tissues, and/or fat and marrow space. Remarkably, μMRI and μCT alone were not able to separate the 2 types of regenerated bone. Finally, we computed volumes of each tissue in the 3D metastructures, which might be exploited by quantitative simulation. The 3D metastructure obtained through our pipeline represents a first step to bridge the gap between the quality of information obtained from 2D optical microscopy and the 3D mapping of the bone tissue heterogeneity and could allow researchers and clinicians to non‐destructively characterize and follow‐up bone regeneration.
Neuropathic Pain

ABSTRACT Purpose of Review: Neuropathic pain is a frequently encountered condition that is often resistant to treatment and is associated with poor patient satisfaction of their treatment. Several medications have been shown to be effective in treating neuropathic pain associated with diabetic neuropathy and postherpetic neuralgia, and these medications are often used to treat neuropathic pain associated with other conditions as well. This article summarizes the diagnosis and assessment of patients with neuropathic pain as well as available pharmacologic and interventional treatment options. Recent Findings: Evidence-based recommendations for the treatment of neuropathic pain have been published, and first-line medications include antidepressants, anticonvulsants, topical agents, as well as opioid analgesics. Interventional options include anesthetic and steroid injections, nerve blocks, and spinal cord stimulation. Essential to the treatment algorithm of neuropathic pain is the assessment and treatment of psychosocial comorbidities and the utilization of a multidisciplinary team approach, including cognitive-behavioral and rehabilitative therapies. Questions remain about the comparative effectiveness of various medications and combination therapies. Increasing interest also exists in the optimization and personalization of pharmacotherapy based upon the underlying mechanism(s) of neuropathic pain according to the quality of the patient’s symptoms. Summary: The management of chronic neuropathic pain is challenging and is best achieved with the use of a multidisciplinary team. Pain is a subjective experience, and it is important to validate a patient’s pain, address psychosocial comorbidities, and set realistic treatment goals. Evidence-based guidelines are available to guide treatment, but frequently, high-quality evidence-based recommendations are lacking.
A Diminutive T1 Cancer 4 mm in Size Resected by Cold Snare Polypectomy

Cold snare polypectomy (CSP) should be performed for benign lesions, though an accurate diagnosis is sometimes difficult with only white light observation. Irregular findings by narrow-band imaging (NBI) are useful for differentiating malignant lesions from benign lesions, and cases with this finding are not expected for CSP. We present a diminutive T1 cancer resected by CSP as a reflection case. A 68-year-old man underwent colonoscopy for surveillance after polypectomy. A reddish polyp 4 mm in size was detected at the rectum. White light observation showed no depression, but a slight, heterogeneous color change. NBI magnification showed irregular vessel and surface patterns. The polyp was diagnosed as intramucosal cancer. Even though cancerous lesions are regularly resected by endoscopic mucosal resection (EMR), this polyp was resected by CSP in daycare surgery because the patient requested not to be treated by EMR but by CSP, which needed an admission to our institution. The surgeon thought the polyp could be completely resected by CSP. It was thoroughly resected, and a histological examination showed submucosal cancer with a positive vertical margin. Additional surgical resection was not accepted by the patient, since he had received total gastrectomy for gastric cancer and a right hemicolectomy for colonic cancer in the past 7 years. He underwent follow-up colonoscopy 2 months after the CSP. Although there were no recurrent endoscopic findings, endoscopic submucosal dissection was performed to the scar area. The histological examination showed no residual tumor. In conclusion, CSP should only be adopted for benign cases, as cancerous lesions have a possibility for invading the submucosa, like in our case.
Beta-blockers for heart failure with reduced, mid-range, and preserved ejection fraction: an individual patient-level analysis of double-blind randomized trials

Aims Recent guidelines recommend that patients with heart failure and left ventricular ejection fraction (LVEF) 40-49% should be managed similar to LVEF ≥ 50%. We investigated the effect of beta-blockers according to LVEF in double-blind, randomized, placebo-controlled trials. Methods and results Individual patient data meta-analysis of 11 trials, stratified by baseline LVEF and heart rhythm (Clinicaltrials.gov: NCT0083244; PROSPERO: CRD42014010012). Primary outcomes were all-cause mortality and cardiovascular death over 1.3 years median follow-up, with an intention-to-treat analysis. For 14 262 patients in sinus rhythm, median LVEF was 27% (interquartile range 21-33%), including 575 patients with LVEF 40-49% and 244 ≥ 50%. Beta-blockers reduced all-cause and cardiovascular mortality compared to placebo in sinus rhythm, an effect that was consistent across LVEF strata, except for those in the small subgroup with LVEF ≥ 50%. For LVEF 40-49%, death occurred in 21/292 [7.2%] randomized to beta-blockers compared to 35/283 [12.4%] with placebo; adjusted hazard ratio (HR) 0.59 [95% confidence interval (CI) 0.34-1.03]. Cardiovascular death occurred in 13/292 [4.5%] with beta-blockers and 26/283 [9.2%] with placebo; adjusted HR 0.48 (95% CI 0.24-0.97). Over a median of 1.0 years following randomization (n = 4601), LVEF increased with beta-blockers in all groups in sinus rhythm except LVEF ≥50%. For patients in atrial fibrillation at baseline (n = 3050), beta-blockers increased LVEF when < 50% at baseline, but did not improve prognosis. Conclusion Beta-blockers improve LVEF and prognosis for patients with heart failure in sinus rhythm with a reduced LVEF. The data are most robust for LVEF < 40%, but similar benefit was observed in the subgroup of patients with LVEF 40-49%.
A Microwave and Microfluidic Planar Resonator for Efficient and Accurate Complex Permittivity Characterization of Aqueous Solutions

A microwave resonator is presented as a microfabricated sensor dedicated to liquid characterization with perspectives for chemistry and biology. The nanolitter range aqueous solution under investigation is located on top of the planar resonator thanks to a microfluidic channel compatible with a future lab-on-a-chip integration. The interaction between the electric field and the liquid translates into a predictable relationship between electrical characteristics of the resonator (resonant frequency and associated insertion loss) and the complex permittivity of the fluid (real and imaginary parts). A prototype of the resonator has been fabricated and evaluated with de-ionized water/ethanol mixtures with ethanol volume fraction ranging from 0% to 20%. Good agreement has been reached between theoretical and measured electrical parameters of the resonator. The discrepancy on the resonant frequency is estimated to 0.5%, whereas the one on the associated transmission coefficient is lower than 1%. This translates into a maximum relative error on the real and imaginary part of the predicted relative permittivity of less than 6.5% and 4%, respectively, validating the principle of this accurate permittivity characterization methodology.
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis

The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of feedbacks from the metabolic network (MN) has received relatively little attention. Here we study the causal structure of the GRNs, namely the chain of influence of one component on the other, taking into account feedback from the MN. First we consider the GRNs of E. coli and B. subtilis without feedback from MN and illustrate their causal structure. Next we augment the GRNs with feedback from their respective MNs by including (a) links from genes coding for enzymes to metabolites produced or consumed in reactions catalyzed by those enzymes and (b) links from metabolites to genes coding for transcription factors whose transcriptional activity the metabolites alter by binding to them. We find that the inclusion of feedback from MN into GRN significantly affects its causal structure, in particular the number of levels and relative positions of nodes in the hierarchy, and the number and size of the strongly connected components (SCCs). We then study the functional significance of the SCCs. For this we identify condition specific feedbacks from the MN into the GRN by retaining only those enzymes that are essential for growth in specific environmental conditions simulated via the technique of flux balance analysis (FBA). We find that the SCCs of the GRN augmented by these feedbacks can be ascribed specific functional roles in the organism. Our algorithmic approach thus reveals relatively autonomous subsystems with specific functionality, or regulatory modules in the organism. This automated approach could be useful in identifying biologically relevant modules in other organisms for which network data is available, but whose biology is less well studied.