Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Different Rickettsial Bacteria Invading Volvox carteri

Background Bacteria of the family Rickettsiaceae are principally associated with arthropods. Recently, endosymbionts of the Rickettsiaceae have been found in non-phagotrophic cells of the volvocalean green algae Carteria cerasiformis, Pleodorina japonica, and Volvox carteri. Such endosymbionts were present in only C. cerasiformis strain NIES-425 and V. carteri strain UTEX 2180, of various strains of Carteria and V. carteri examined, suggesting that rickettsial endosymbionts may have been transmitted to only a few algal strains very recently. However, in preliminary work, we detected a sequence similar to that of a rickettsial gene in the nuclear genome of V. carteri strain EVE. Methodology/Principal Findings Here we explored the origin of the rickettsial gene-like sequences in the endosymbiont-lacking V. carteri strain EVE, by performing comparative analyses on 13 strains of V. carteri. By reference to our ongoing genomic sequence of rickettsial endosymbionts in C. cerasiformis strain NIES-425 cells, we confirmed that an approximately 9-kbp DNA sequence encompassing a region similar to that of four rickettsial genes was present in the nuclear genome of V. carteri strain EVE. Phylogenetic analyses, and comparisons of the synteny of rickettsial gene-like sequences from various strains of V. carteri, indicated that the rickettsial gene-like sequences in the nuclear genome of V. carteri strain EVE were closely related to rickettsial gene sequences of P. japonica, rather than those of V. carteri strain UTEX 2180. Conclusion/Significance At least two different rickettsial organisms may have invaded the V. carteri lineage, one of which may be the direct ancestor of the endosymbiont of V. carteri strain UTEX 2180, whereas the other may be closely related to the endosymbiont of P. japonica. Endosymbiotic gene transfer from the latter rickettsial organism may have occurred in an ancestor of V. carteri. Thus, the rickettsiae may be widely associated with V. carteri, and likely have often been lost during host evolution.
Spatial Variability of the Topsoil Organic Carbon in the Moso Bamboo Forests of Southern China in Association with Soil Properties

Understanding the spatial variability of soil organic carbon (SOC) must be enhanced to improve sampling design and to develop soil management strategies in terrestrial ecosystems. Moso bamboo (Phyllostachys pubescens Mazel ex Houz.) forests have a high SOC storage potential; however, they also vary significantly spatially. This study investigated the spatial variability of SOC (0-20 cm) in association with other soil properties and with spatial variables in the Moso bamboo forests of Jian’ou City, which is a typical bamboo hometown in China. 209 soil samples were collected from Moso bamboo stands and then analyzed for SOC, bulk density (BD), pH, cation exchange capacity (CEC), and gravel content (GC) based on spatial distribution. The spatial variability of SOC was then examined using geostatistics. A Kriging map was produced through ordinary interpolation and required sample numbers were calculated by classical and Kriging methods. An aggregated boosted tree (ABT) analysis was also conducted. A semivariogram analysis indicated that ln(SOC) was best fitted with an exponential model and that it exhibited moderate spatial dependence, with a nugget/sill ratio of 0.462. SOC was significantly and linearly correlated with BD (r = −0.373**), pH (r = −0.429**), GC (r = −0.163*), CEC (r = 0.263**), and elevation (r = 0.192**). Moreover, the Kriging method requires fewer samples than the classical method given an expected standard error level as per a variance analysis. ABT analysis indicated that the physicochemical variables of soil affected SOC variation more significantly than spatial variables did, thus suggesting that the SOC in Moso bamboo forests can be strongly influenced by management practices. Thus, this study provides valuable information in relation to sampling strategy and insight into the potential of adjustments in agronomic measure, such as in fertilization for Moso bamboo production.
Analysis of Cathepsin and Furin Proteolytic Enzymes Involved in Viral Fusion Protein Activation in Cells of the Bat Reservoir Host

Bats of different species play a major role in the emergence and transmission of highly pathogenic viruses including Ebola virus, SARS-like coronavirus and the henipaviruses. These viruses require proteolytic activation of surface envelope glycoproteins needed for entry, and cellular cathepsins have been shown to be involved in proteolysis of glycoproteins from these distinct virus families. Very little is currently known about the available proteases in bats. To determine whether the utilization of cathepsins by bat-borne viruses is related to the nature of proteases in their natural hosts, we examined proteolytic processing of several viral fusion proteins in cells derived from two fruit bat species, Pteropus alecto and Rousettus aegyptiacus. Our work shows that fruit bat cells have homologs of cathepsin and furin proteases capable of cleaving and activating both the cathepsin-dependent Hendra virus F and the furin-dependent parainfluenza virus 5 F proteins. Sequence analysis comparing Pteropus alecto furin and cathepsin L to proteases from other mammalian species showed a high degree of conservation; however significant amino acid variation occurs at the C-terminus of Pteropus alecto furin. Further analysis of furin-like proteases from fruit bats revealed that these proteases are catalytically active and resemble other mammalian furins in their response to a potent furin inhibitor. However, kinetic analysis suggests that differences may exist in the cellular localization of furin between different species. Collectively, these results indicate that the unusual role of cathepsin proteases in the life cycle of bat-borne viruses is not due to the lack of active furin-like proteases in these natural reservoir species; however, differences may exist between furin proteases present in fruit bats compared to furins in other mammalian species, and these differences may impact protease usage for viral glycoprotein processing.
Higher than reported adolescent and young adult clinical trial enrollment during the “Golden Age” of melanoma clinical trials

Clinical trial enrollments in adolescents and young adults (AYA) with cancer have historically been lower than those in pediatric and older adult populations. We sought to examine therapeutic trial enrollment rates at our cancer center. We performed a retrospective evaluation of AYA patients treated before and after the first checkpoint inhibitor trial opened at our cancer center in 2007. We examined gender, stage at presentation and insurance status in terms of trial enrollment. We compared the trial participation rate of AYA patients with that of older adults. In this adult facility, 12.7% (1,831) of total patients were between age 15 and 39. Overall therapeutic clinical trial rate was 17.6% which increased to 19.8% since 2007. Both nodal disease or metastatic disease at presentation was associated with increasing odds of trial enrollment (OR = 5.36 and P < 0.001 for nodal disease and OR = 7.96 and P < 0.001 for metastatic disease). There was a nonstatistically significant trend toward improved 3‐year overall survival in the AYA patients with advanced presentation that enrolled on clinical trials compared with those not enrolled on trials since 2007. AYA clinical trial enrollment at a comprehensive care center melanoma program was higher than reported in the literature overall for AYA patients. This 1,831 patient cohort may provide a foundation for more detailed investigation toward quantifying the effects of clinical trial enrollment in terms of age‐specific benefits and toxicities for AYA patients with malignancies that have their peak incidence in older adults.
Leptospira interrogans outer membrane protein LipL21 is a potent inhibitor of neutrophil myeloperoxidase

ABSTRACT Leptospirosis is a widespread zoonotic and neglected infectious disease of human and veterinary concern that is caused by pathogenic Leptospira species. After entrance in the host, pathogenic leptospires evade the host natural defense mechanisms in order to propagate and disseminate to multiple organs. Myeloperoxidase is an enzyme stored in neutrophils azurophilic granules, and is released upon neutrophil activation to produce mainly hypochlorous acid, a strong oxidant and potent antimicrobial agent. In the present investigation, we studied the modulation of myeloperoxidase activity by L. interrogans serovar Copenhageni. We show that leptospires and their culture supernatants are able to inhibit both peroxidase and chlorination activities of myeloperoxidase, without interfering with neutrophil degranulation. By leptospiral outer membrane protein extraction and fractionation, we identified the proteins LipL21 and LipL45 as myeloperoxidase inhibitors, constituting new Leptospira virulence factors. Accordingly, we propose a function for the protein LipL21, one of the most expressed leptospiral outer membrane proteins. Our results show a novel innate immune evasion mechanism by which leptospires interfere with the host response in order to cope with the host oxidative stress and efficiently achieve dissemination and colonization.
Intraspecific Autochthonous and Allochthonous Resource Use by Zooplankton in a Humic Lake during the Transitions between Winter, Summer and Fall

Seasonal patterns in assimilation of externally produced, allochthonous, organic matter into aquatic food webs are poorly understood, especially in brown-water lakes. We studied the allochthony (share biomass of terrestrial origin) in cladoceran, calanoid and cyclopoid micro-crustacean zooplankton from late winter to fall during two years in a small humic lake (Sweden). The use of allochthonous resources was important for sustaining a small population of calanoids in the water column during late winter. However, in summer the calanoids shifted to 100% herbivory, increasing their biomass several-fold by making efficient use of the pelagic primary production. In contrast, the cyclopoids and cladocerans remained at high levels of allochthony throughout the seasons, both groups showing the mean allochthony of 0.56 (range in mean 0.17-0.79 and 0.34-0.75, for the respective group, depending on model parameters). Our study shows that terrestrial organic matter can be an important resource for cyclopoids and cladocerans on an annual basis, forming a significant link between terrestrial organic matter and the higher trophic levels of the food web, but it can also be important for sustaining otherwise herbivorous calanoids during periods of low primary production in late winter.
A Model for Structured Information Representation in Neural Networks of the Brain

Abstract Humans can reason at an abstract level and structure information into abstract categories, but the underlying neural processes have remained unknown. Recent experimental data provide the hint that this is likely to involve specific subareas of the brain from which structural information can be decoded. Based on this data, we introduce the concept of assembly projections, a general principle for attaching structural information to content in generic networks of spiking neurons. According to the assembly projections principle, structure-encoding assemblies emerge and are dynamically attached to content representations through Hebbian plasticity mechanisms. This model provides the basis for explaining a number of experimental data and provides a basis for modeling abstract computational operations of the brain.
WHISPER: Wirelessly Synchronized Distributed Audio Sensor Platform

This paper describes a distributed wireless acoustic sensor network (WASN) platform called WHISPER that is capable of synchronous multichannel sampling at different spatial locations with a sampling clock whose relative jitter is less than 300 ns. The platform comprises up to four data acquisition modules with onboard computing capabilities, and that can form an ad-hoc Wi-Fi network allowing an additional processing module such as a laptop or a smartphone to be connected if needed. Each acquisition module holds four digital SPI microphones with a total of 16 microphones for the entire system. Wireless synchronization of the sampling on each platform is implemented using a separate wireless module operating in the 902-928 MHz ISM band. Usage of this system is demonstrated in a real-time application involving spatial sound filtering through a beamforming algorithm.
Effect of bacterial growth rate on bacteriophage population growth rate

It is important to understand how physiological state of the host influence propagation of bacteriophages (phages), due to the potential higher phage production needs in the future. In our study, we tried to elucidate the effect of bacterial growth rate on adsorption constant (δ), latent period (L), burst size (b), and bacteriophage population growth rate (λ). As a model system, a well‐studied phage T4 and Escherichia coli K‐12 as a host was used. Bacteria were grown in a continuous culture operating at dilution rates in the range between 0.06 and 0.98 hr−1. It was found that the burst size increases linearly from 8 PFU·cell−1 to 89 PFU·cell−1 with increase in bacteria growth rate. On the other hand, adsorption constant and latent period were both decreasing from 2.6∙10‐9 ml·min−1 and 80 min to reach limiting values of 0.5 × 10‐9 ml·min−1 and 27 min at higher growth rates, respectively. Both trends were mathematically described with Michaelis–Menten based type of equation and reasons for such form are discussed. By applying selected equations, a mathematical equation for prediction of bacteriophage population growth rate as a function of dilution rate was derived, reaching values around 8 hr−1 at highest dilution rate. Interestingly, almost identical description can be obtained using much simpler Monod type equation and possible reasons for this finding are discussed.
Pancreatic and Pancreatic-Like Microbial Proteases Accelerate Gut Maturation in Neonatal Rats

Objectives Postnatal gut maturation in neonatal mammals, either at natural weaning or after precocious inducement, is coinciding with enhanced enzymes production by exocrine pancreas. Since the involvement of enzymes in gut functional maturation was overlooked, the present study aimed to investigate the role of enzymes in gut functional maturation using neonatal rats. Methods Suckling rats (Rattus norvegicus) were instagastrically gavaged with porcine pancreatic enzymes (Creon), microbial-derived amylase, protease, lipase and mixture thereof, while controls received α-lactalbumin or water once per day during 14–16 d of age. At 17 d of age the animals were euthanized and visceral organs were dissected, weighed and analyzed for structural and functional properties. For some of the rats, gavage with the macromolecular markers such as bovine serum albumin and bovine IgG was performed 3 hours prior to blood collection to assess the intestinal permeability. Results Gavage with the pancreatic or pancreatic-like enzymes resulted in stimulated gut growth, increased gastric acid secretion and switched intestinal disaccharidases, with decreased lactase and increased maltase and sucrase activities. The fetal-type vacuolated enterocytes were replaced by the adult-type in the distal intestine, and macromolecular transfer to the blood was declined. Enzyme exposure also promoted pancreas growth with increased amylase and trypsin production. These effects were confined to the proteases in a dose-dependent manner. Conclusion Feeding exogenous enzymes, containing proteases, induced precocious gut maturation in suckling rats. This suggests that luminal exposure to proteases by oral loading or, possibly, via enhanced pancreatic secretion involves in the gut maturation of young mammals.
Low Molecular Weight Heparin (LMWH) Improves Peritoneal Function and Inhibits Peritoneal Fibrosis Possibly through Suppression of HIF-1α, VEGF and TGF-β1

Background Peritoneal fibrosis is the major cause of ultrafiltration failure, and intraperitoneal administration of Low Molecular Weight Heparin (LMWH) was reported to protect peritoneal function. But the exact mechanism of its influence on peritoneal structure and function is still unknown. Methods A fibrosis model of rat was established by intraperitoneal (IP) administration of PD fluid and Erythromycin Lactobionate. Fifty-two rats were randomly divided into 6 groups: (1) normal control group (CON, n = 6); (2) normal saline group (NS, n = 10); (3) high-glucose group (GLU, n = 10); (4) heparin group (HEP, n = 6); (5) low dose LMWH group (LLMWH, n = 10); (6) high dose LMWH group (HLMWH, n = 10). Two hour peritoneal equilibration test was performed after 28 days of intervention. The peritoneum, mesentery and omentum were harvested, and evaluated by Hematoxylin-Eosin and Masson Trichrome staining. The expressions of HIF-1α, VEGF and TGF-β1 in parietal peritoneum were detected by IHC and RT-PCR (Reverse Transcriptase Polymerase Chain Reaction). Results Compared with group CON and NS, ultrafiltration volume and D2/D0 glucose in group GLU decreased significantly, D/Purea (Dialysate-Plasma ratio of urea), D/Palb (Dialysate-Plasma ratio of albumin), peritoneal thickness, neoangiogenesis and inflammatory reaction increased significantly (all P<0.05). Administration of heparin and LMWH markedly alleviated these above pathological changes. The protein and mRNA levels of HIF-1α, VEGF and TGF-β1 increased significantly in group GLU, and decreased significantly after administration of LMWH in a dose-dependent manner. Conclusions LMWH ameliorates peritoneal function and inhibits peritoneal fibrosis, possibly through suppression of HIF-1α, VEGF and TGF-β1.
Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells

Proteomic profiling plays a decisive role in the elucidation of molecular signatures representative of a specific clinical context. MuStem cell based therapy represents a promising approach for clinical applications to cure Duchenne muscular dystrophy (DMD). To expand our previous studies collected in the clinically relevant DMD animal model, we decided to investigate the skeletal muscle proteome 4 months after systemic delivery of allogenic MuStem cells. Quantitative proteomics with isotope‐coded protein labeling was used to compile quantitative changes in the protein expression profiles of muscle in transplanted Golden Retriever muscular dystrophy (GRMD) dogs as compared to Golden Retriever muscular dystrophy dogs. A total of 492 proteins were quantified, including 25 that were overrepresented and 46 that were underrepresented after MuStem cell transplantation. Interestingly, this study demonstrates that somatic stem cell therapy impacts on the structural integrity of the muscle fascicle by acting on fibers and its connections with the extracellular matrix. We also show that cell infusion promotes protective mechanisms against oxidative stress and favors the initial phase of muscle repair. This study allows us to identify putative candidates for tissue markers that might be of great value in objectively exploring the clinical benefits resulting from our cell‐based therapy for DMD. All MS data have been deposited in the ProteomeXchange with identifier PXD001768 (http://proteomecentral.proteomexchange.org/dataset/PXD001768).
Large-Scale Geographic Variation in Distribution and Abundance of Australian Deep-Water Kelp Forests

Despite the significance of marine habitat-forming organisms, little is known about their large-scale distribution and abundance in deeper waters, where they are difficult to access. Such information is necessary to develop sound conservation and management strategies. Kelps are main habitat-formers in temperate reefs worldwide; however, these habitats are highly sensitive to environmental change. The kelp Ecklonia radiate is the major habitat-forming organism on subtidal reefs in temperate Australia. Here, we provide large-scale ecological data encompassing the latitudinal distribution along the continent of these kelp forests, which is a necessary first step towards quantitative inferences about the effects of climatic change and other stressors on these valuable habitats. We used the Autonomous Underwater Vehicle (AUV) facility of Australia’s Integrated Marine Observing System (IMOS) to survey 157,000 m2 of seabed, of which ca 13,000 m2 were used to quantify kelp covers at multiple spatial scales (10–100 m to 100–1,000 km) and depths (15–60 m) across several regions ca 2–6° latitude apart along the East and West coast of Australia. We investigated the large-scale geographic variation in distribution and abundance of deep-water kelp (>15 m depth) and their relationships with physical variables. Kelp cover generally increased with latitude despite great variability at smaller spatial scales. Maximum depth of kelp occurrence was 40–50 m. Kelp latitudinal distribution along the continent was most strongly related to water temperature and substratum availability. This extensive survey data, coupled with ongoing AUV missions, will allow for the detection of long-term shifts in the distribution and abundance of habitat-forming kelp and the organisms they support on a continental scale, and provide information necessary for successful implementation and management of conservation reserves.