Miracle-dz/UniFAR-FTUs huggingface dataset:
Host diversity and latitude drive trematode diversity patterns in the European freshwater fauna

Aim We investigated the relationship between host and parasite diversity as well as latitudinal gradients in parasite diversity on a continental scale in European freshwater trematodes. Location European freshwaters. Methods We extracted distributional data for 564 freshwater trematodes across 25 biogeographical regions in Europe from the Limnofauna Europaea and used multiple regression analyses to test for correlations between the diversity of definitive (vertebrates) or first intermediate (gastropods) hosts and that of trematodes, and for latitudinal gradients in trematode diversity. In particular, we investigated patterns in beta diversity among latitudinal bands and between trematode species that parasitize host groups with low (autogenic) and high (allogenic) dispersal capacity. We also tested for a latitudinal gradient in the proportional representation of these two trematode groups within regional faunas. Results Latitude or first intermediate host richness had no effect on trematode richness, but definitive host richness was a strong predictor of trematode richness, among both allogenic and autogenic parasites. We found that beta diversity of trematode faunas within latitudinal bands decreased to the north, with similar values for allogenic and autogenic trematodes. Finally, we observed an increasing proportion of autogenic species toward the north of Europe. Main conclusions The richness of definitive hosts appears to be the driver of trematode diversity at a continental scale. The latitudinal gradient in beta diversity reflects patterns observed in free-living species and probably results from recolonization in the aftermath of the ice ages. The similar beta-diversity patterns of allogenic and autogenic trematodes and the increasing proportion of autogenic trematodes with increasing latitude are surprising. We suggest that the geographical scale of our analysis or confounding factors such as differences in habitat utilization and specialization may partly explain these patterns.
Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

Wrapped DNA TAL effectors are proteins that bacterial pathogens inject into plant cells that bind to host DNA to activate expression of plant genes. The DNA-binding domain of TAL proteins is composed of tandem repeats within which a repeat-variable diresidue sequence confers nucleotide specificity. Deng et al. (p. 720, published online 5 January) report the structure of the TAL effector dHax3, containing 11.5 repeats, in DNA-free and DNA-bound states, and Mak et al. (p. 716, published online 5 January) report the structure of the PthXo1 TAL effector, containing 22 repeats, bound to its DNA target. Together, the structures reveal the conformational changes involved in DNA binding and provide the structural basis of DNA recognition. Structures show how a virulence factor in a plant pathogen recognizes and binds to host DNA. TAL (transcription activator–like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.
Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats.
The Limit of Information Propagation Speed in Large-Scale Multihop Wireless Networks

This paper investigates the speed limit of information propagation in large-scale multihop wireless networks, which provides fundamental understanding of the fastest information transportation and delivery that a wireless network is able to accommodate. We show that there exists a unified speed upper bound for broadcast and unicast communications in large-scale wireless networks. When network connectivity is considered, this speed bound is a function of node density. If the network noise is constant, the bound is a constant when node density exceeds a threshold; if the network noise is an increasing function of node density, the bound decreases to zero when node density approaches infinity. As achieving the speed bound places strict requirements on node locations, we also quantify the gap between the actual achieved speed and the desired bound in random networks in which the relay nodes are not located as desired. We find that the gap converges to zero exponentially as node density increases to infinity.
Interplay between ROS and Antioxidants during Ischemia-Reperfusion Injuries in Cardiac and Skeletal Muscle

Ischemia reperfusion (IR), present in myocardial infarction or extremity injuries, is a major clinical issue and leads to substantial tissue damage. Molecular mechanisms underlying IR injury in striated muscles involve the production of reactive oxygen species (ROS). Excessive ROS accumulation results in cellular oxidative stress, mitochondrial dysfunction, and initiation of cell death by activation of the mitochondrial permeability transition pore. Elevated ROS levels can also decrease myofibrillar Ca2+ sensitivity, thereby compromising muscle contractile function. Low levels of ROS can act as signaling molecules involved in the protective pathways of ischemic preconditioning (IPC). By scavenging ROS, antioxidant therapies aim to prevent IR injuries with positive treatment outcomes. Novel therapies such as postconditioning and pharmacological interventions that target IPC pathways hold great potential in attenuating IR injuries. Factors such as aging and diabetes could have a significant impact on the severity of IR injuries. The current paper aims to provide a comprehensive review on the multifaceted roles of ROS in IR injuries, with a focus on cardiac and skeletal muscle, as well as recent advancement in ROS-related therapies.
Attenuation of Mouse Hepatitis Virus by Deletion of the LLRKxGxKG Region of Nsp1

Coronaviruses are a family of large positive-sense RNA viruses that are responsible for a wide range of important veterinary and human diseases. Nsp1 has been shown to have an important role in the pathogenetic mechanisms of coronaviruses in vivo. To assess the function of a relatively conserved domain (LLRKxGxKG) of MHV nsp1, a mutant virus, MHV-nsp1-27D, with a 27 nts (LLRKxGxKG) deletion in nsp1, was constructed using a reverse genetic system with a vaccinia virus vector. The mutant virus had similar growth kinetics to MHV-A59 wild-type virus in 17CI-1 cells, but was highly attenuated in vivo. Moreover, the mutant virus completely protected C57BL/6 mice from a lethal MHV-A59 challenge. To further analyze the mechanism of the attenuation of the mutant virus, changes in reporter gene expression were measured in nsp1- or nsp1-27D-expressing cells; the results showed that nsp1 inhibited reporter gene expression controlled by different promoters, but that this inhibition was reduced for nsp1-27D. The research in vivo and in vitro suggests that the LLRKxGxKG region of nsp1 may play an important role in this process.
The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data

Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog, Craugastor fitzingeri. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found that Pseudomonas was a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found genes enriched either in Sapo or Sob. We then focused our study on five functional classes of genes: biosynthesis of secondary metabolites, metabolism of terpenoids and polyketides, membrane transport, cellular communication and antimicrobial drug resistance. These gene classes are potentially involved in bacterial communication, bacterial-host and bacterial-pathogen interactions among other functions. We found that C. fitzingeri metagenomes have a wide array of genes that code for secondary metabolites, including antibiotics and bacterial toxins, which may be involved in bacterial communication, but could also have a defensive role against pathogens. Several genes involved in bacterial communication and bacterial-host interactions, such as biofilm formation and bacterial secretion systems were found. We identified specific genes and pathways enriched at the different sites and determined that gene co-occurrence networks differed between sites. Our results suggest that skin microbiomes are composed of distinct bacterial taxa with a wide range of metabolic capabilities involved in bacterial defense and communication. Differences in taxonomic composition and pathway enrichments suggest that skin microbiomes from different sites have unique functional properties. This study strongly supports the need for shotgun metagenomic analyses to describe the functional capacities of skin microbiomes and to tease apart their role in host defense against pathogens.
Time Course and Magnitude of Synthesis of Heat‐Shock Proteins in Congeneric Marine Snails (Genus Tegula) from Different Tidal Heights

The time course and magnitude of the heat‐shock response in relation to severity of thermal stress are important, yet poorly understood, aspects of thermotolerance. We examined patterns of protein synthesis in congeneric marine snails (genus Tegula) that occur at different heights along the subtidal to intertidal gradient after a thermal exposure (30°C for 2.5 h, followed by 50 h recovery at 13°C) that induced the heat‐shock response. We monitored the kinetics and magnitudes of protein synthesis by quantifying incorporation of 35S‐labeled methionine and cysteine into newly synthesized proteins and observed synthesis of putative heat‐shock proteins (hsp's) of size classes 90, 77, 70, and 38 kDa. In the low‐ to mid‐intertidal species, Tegula funebralis, whose body temperature frequently exceeds 30°C during emersion, synthesis of hsp's commenced immediately after heat stress, reached maximal levels 1–3 h into recovery, and returned to prestress levels by 6 h, except for hsp90 (14 h). In contrast, in the low‐intertidal to subtidal species, Tegula brunnea, for which 2.5 h at 30°C represents a near lethal heat stress, synthesis of hsp's commenced 2–14 h after heat stress; reached maximal levels after 15–30 h, which exceeded magnitudes of synthesis in T. funebralis; and returned to prestress levels in the case of hsp90 (50 h) and hsp77 (30 h) but not in the case of hsp70 and hsp38. Exposures to 30°C under aerial (emersion) and aquatic (immersion) conditions resulted in differences in hsp synthesis in T. brunnea but not in T. funebralis. The different time courses and magnitudes of hsp synthesis in these congeners suggest that the vertical limits of their distributions may be set in part by thermal stress.
Sox2 is required for olfactory pit formation and olfactory neurogenesis through BMP restriction and Hes5 upregulation

ABSTRACT The transcription factor Sox2 is necessary to maintain pluripotency of embryonic stem cells, and to regulate neural development. Neurogenesis in the vertebrate olfactory epithelium persists from embryonic stages through adulthood. The role Sox2 plays for the development of the olfactory epithelium and neurogenesis within has, however, not been determined. Here, by analysing Sox2 conditional knockout mouse embryos and chick embryos deprived of Sox2 in the olfactory epithelium using CRISPR-Cas9, we show that Sox2 activity is crucial for the induction of the neural progenitor gene Hes5 and for subsequent differentiation of the neuronal lineage. Our results also suggest that Sox2 activity promotes the neurogenic domain in the nasal epithelium by restricting Bmp4 expression. The Sox2-deficient olfactory epithelium displays diminished cell cycle progression and proliferation, a dramatic increase in apoptosis and finally olfactory pit atrophy. Moreover, chromatin immunoprecipitation data show that Sox2 directly binds to the Hes5 promoter in both the PNS and CNS. Taken together, our results indicate that Sox2 is essential to establish, maintain and expand the neuronal progenitor pool by suppressing Bmp4 and upregulating Hes5 expression. Summary: Analysis of Sox2 mutant mouse and Sox2 CRISPR-targeted chick embryos reveals that Sox2 controls the establishment of sensory progenitors in the olfactory epithelium by suppressing Bmp4 and upregulating Hes5 expression.
A novel conduit-based coaptation device for primary nerve repair*

ABSTRACT Background: Conduit-based nerve repairs are commonly used for small nerve gaps, whereas primary repair may be performed if there is no tension on nerve endings. We hypothesize that a conduit-based nerve coaptation device will improve nerve repair outcomes by avoiding sutures at the nerve repair site and utilizing the advantages of a conduit-based repair. Methods: The left sciatic nerves of female Sprague-Dawley rats were transected and repaired using a novel conduit-based device. The conduit-based device group was compared to a control group of rats that underwent a standard end-to-end microsurgical repair of the sciatic nerve. Animals underwent behavioral assessments at weekly intervals post-operatively using the sciatic functional index (SFI) test. Animals were sacrificed at four weeks to obtain motor axon counts from immunohistochemistry. A sub-group of animals were sacrificed immediately post repair to obtain MRI images. Results: SFI scores were superior in rats which received conduit-based repairs compared to the control group. Motor axon counts distal to the injury in the device group at four weeks were statistically superior to the control group. MRI tractography was used to demonstrate repair of two nerves using the novel conduit device. Conclusions: A conduit-based nerve coaptation device avoids sutures at the nerve repair site and leads to improved outcomes in a rat model. Conduit-based nerve repair devices have the potential to standardize nerve repairs while improving outcomes.
The cost of Lyme borreliosis

Background Lyme borreliosis (LB) is the most frequently reported tick-borne infection in Europe and North America. The aim of this study was to estimate the cost-of-illness of LB in the Netherlands. We used available incidence estimates from 2010 for tick bite consultations and three symptomatic LB outcomes: erythema migrans (EM), disseminated LB and Lyme-related persisting symptoms. The cost was estimated using these incidences and the average cost per patient as derived from a patient questionnaire. We estimated the cost from a societal perspective, including healthcare cost, patient cost and production loss, using the friction cost method and a 4% annual discount rate. Tick bites and LB in 2010 led to a societal cost of €19.3 million (95% CI 15.6-23.4; 16.6 million population) for the Netherlands. Healthcare cost and production loss each constituted 48% of the total cost (€9.3 and €9.2 million/year), and patient cost 4% (€0.8 million/year). Of the total cost, 37% was related to disseminated LB, followed by 27% for persisting symptoms, 22% for tick bites and 14% for EM. Per outcome, for an individual case the mean cost of disseminated LB and Lyme-related persisting symptoms was both around €5700; for EM and GP consultations for tick bites this was €122 and €53. As an alternative to the friction cost method, the human capital method resulted in a total cost of €23.5 million/year. LB leads to a substantial societal cost. Further research should therefore focus on additional preventive interventions.
On the throughput of two-way relay systems under queueing constraints

In this paper, throughput of two-way relaying under buffer constraints is studied. In the two-way relay system, source nodes initially send their messages to the relay in the multiple-access phase. Relay decodes and stores the messages from different sources in different buffers and subsequently broadcasts a superimposed signal. It is assumed that both source nodes and the relay operate in the presence of statistical queueing constraints. Under these assumptions, arrival rates that can be supported in this system are investigated through the logarithmic moment generating functions of the arrival and service processes. In particular, after identifying the service rates in the multiple-access and broadcast phases and addressing the stability conditions, characterizations of the maximum arrival rates are provided in terms of system resource allocation parameters, signal-to-noise ratios, and quality-of-service exponents. Impact of different parameters on the performance is investigated through numerical results.
MAPx (Mobility Aid Personalization): examining why older adults “pimp their ride” and the impact of doing so

Abstract We all do this. We personalize things. We buy leopard-printed seat covers and fuzzy dice for our cars, and display action figures and photographs in our offices. Studying older adults who have extended this process of personalization to their mobility devices, the purpose of the mobility aid personalization (MAPx) project is to examine MAPx and its impact on the health and mobility of older adults. Using a qualitative research design, field observations and interviews were conducted with 72 older adults to gain an in-depth understanding of device customization from an emic (insider’s) perspective. Findings illustrate that older adults personalize their devices for reasons of fun, function and fashion. MAPx – the process of purposefully selecting or modifying a mobility device to suit individual needs and preferences – was also found to promote health and mobility by encouraging device acceptance, increasing social participation, enhancing joy and preserving identity. MAPx makes an important contribution to our understanding of the complex relationship between older adults and assistive devices and provides a new approach to some old problems including falls, inactivity and social isolation. Encouraging MAPx is a promising rehabilitation strategy for promoting health and community mobility among the older adult population. Implications for Rehabilitation Personalizing an assistive device facilitates device acceptance, promotes health and well-beingand should be supported and encouraged in rehabilitative care. Choice, variety and access are critical aspects of assistive devices; vendors, manufacturers andpractitioners should work together to provide clients with a greater range of affordable optionsfor new devices. Function is more than mechanical or physical; social factors including social identity, stigma andsocial roles must be adequately considered and explicit in rehabilitative practice.
Aplicación del método de bisección para la mejora automática del comportamiento a-todo-momento del algoritmo ASO

Resumen. El comportamiento a-todo-momento dota a un algoritmo de robustez al permitirle ser interrumpido en cualquier punto del proceso, mientras que se garantiza que se entregara la mejor respuesta posible cuando suceda la solicitud de paro. Este trabajo propone una m´etodo-log´ıa para identiﬁcar la relaci´on de los par´ametros de un algoritmo de optimizaci´on por colonia de hormigas con su comportamiento a-todo-momento, permitiendo implementar una t´ecnica de mejora autom´atica del comportamiento a-todo-momento utilizando una reducci´on en factores logaritmos del espacio de
Mobility Management in Ultra-Dense Networks: Handover Skipping Techniques

Ultra-dense network deployment is a key technology for potentially achieving the capacity target of next-generation wireless communication systems. However, such a deployment results in cell proliferation and cell size decrement, leading to an increased number of handovers and limited sojourn time within a cell, which severely degrade the user’s quality of service (QoS). In this paper, we propose two intelligent handover skipping techniques to overcome the high handover rates. The first technique considers a user associated with a single base station (BS) and the decision to skip a handover is based on the upcoming cell’s topology; we consider three criteria: 1) the area of the cell; 2) the trajectory distance within the cell; and 3) the distance of the BS from the cell edge. The second technique exploits BS cooperation and enables a dynamic handover skipping scheme, where the skipping decision is taken based on the BSs of three consecutive cells in the user’s trajectory. This technique achieves a balance between BS cooperation and single BS transmission and manages to maintain a good QoS during the skipping phase. We show that the proposed techniques reduce both the handover rate and handover cost and outperform the conventional techniques for moderate to high-velocity values.