Miracle-dz/UniFAR-FTUs huggingface dataset:
Anthropogenic fragmentation may not alter pre‐existing patterns of genetic diversity and differentiation in perennial shrubs

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird‐pollinated shrub Grevillea caleyi R.Br. , by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F′ST = 0.615 and 0.454; Sp = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long‐term effects of inbreeding in self‐compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self‐compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.
Transmission of Plasmodium vivax in South-Western Uganda: Report of Three Cases in Pregnant Women

Plasmodium vivax is considered to be rare in the predominantly Duffy negative populations of Sub-Saharan Africa, as this red blood cell surface antigen is essential for invasion by the parasite. However, despite only very few reports of molecularly confirmed P. vivax from tropical Africa, serological evidence indicated that 13% of the persons sampled in Congo had been exposed to P. vivax. We identified P. vivax by microscopy in 8 smears from Ugandan pregnant women who had been enrolled in a longitudinal study of malaria in pregnancy. A nested polymerase chain reaction (PCR) protocol was used to detect and identify the Plasmodium parasites present. PCR analysis confirmed the presence of P. vivax for three of the women and analysis of all available samples from these women revealed clinically silent chronic low-grade vivax infections for two of them. The parasites in one woman carried pyrimethamine resistance-associated double non-synonymous mutations in the P. vivax dihydrofolate reductase gene. The three women found infected with P. vivax were Duffy positive as were nine of 68 women randomly selected from the cohort. The data presented from these three case reports is consistent with stable transmission of malaria in a predominantly Duffy negative African population. Given the substantial morbidity associated with vivax infection in non-African endemic areas, it will be important to investigate whether the distribution and prevalence of P. vivax have been underestimated in Sub-Saharan Africa. This is particularly important in the context of the drive to eliminate malaria and its morbidity.
Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1

Ssd1 targets mRNAs to daughter cells for translation or to stress granules (SGs) and P-bodies (PBs) for storage or decay. PB components also assist in its nuclear export. If Ssd1 fails to localize to the nucleus, it is targeted to IPOD. IPOD and PB/SG association requires a prion-like domain, whose activity is differentially regulated by Cbk1 phosphorylation.
Large-Scale Changes in Community Composition: Determining Land Use and Climate Change Signals

Human land use and climate change are regarded as the main driving forces of present-day and future species extinction. They may potentially lead to a profound reorganisation of the composition and structure of natural communities throughout the world. However, studies that explicitly investigate both forms of impact—land use and climate change—are uncommon. Here, we quantify community change of Dutch breeding bird communities over the past 25 years using time lag analysis. We evaluate the chronological sequence of the community temperature index (CTI) which reflects community response to temperature increase (increasing CTI indicates an increase in relative abundance of more southerly species), and the temporal trend of the community specialisation index (CSI) which reflects community response to land use change (declining CSI indicates an increase of generalist species). We show that the breeding bird fauna underwent distinct directional change accompanied by significant changes both in CTI and CSI which suggests a causal connection between climate and land use change and bird community change. The assemblages of particular breeding habitats neither changed at the same speed and nor were they equally affected by climate versus land use changes. In the rapidly changing farmland community, CTI and CSI both declined slightly. In contrast, CTI increased in the more slowly changing forest and heath communities, while CSI remained stable. Coastal assemblages experienced both an increase in CTI and a decline in CSI. Wetland birds experienced the fastest community change of all breeding habitat assemblages but neither CTI nor CSI showed a significant trend. Overall, our results suggest that the interaction between climate and land use changes differs between habitats, and that comparing trends in CSI and CTI may be useful in tracking the impact of each determinant.
Sub-Second Dopamine Detection in Human Striatum

Fast-scan cyclic voltammetry at carbon fiber microelectrodes allows rapid (sub-second) measurements of dopamine release in behaving animals. Herein, we report the modification of existing technology and demonstrate the feasibility of making sub-second measurements of dopamine release in the caudate nucleus of a human subject during brain surgery. First, we describe the modification of our electrodes that allow for measurements to be made in a human brain. Next, we demonstrate in vitro and in vivo, that our modified electrodes can measure stimulated dopamine release in a rat brain equivalently to previously determined rodent electrodes. Finally, we demonstrate acute measurements of dopamine release in the caudate of a human patient during DBS electrode implantation surgery. The data generated are highly amenable for future work investigating the relationship between dopamine levels and important decision variables in human decision-making tasks.
The Eastern side of the Westernmost Europeans: Insights from subclades within Y‐chromosome haplogroup J‐M304

We examined internal lineages and haplotype diversity in Portuguese samples belonging to J‐M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1‐M267 and J2‐M172.
Designing Genetic Feedback Controllers

By incorporating feedback around systems we wish to manipulate, it is possible to improve their performance and robustness properties to meet pre-specified design objectives. For decades control engineers have been successfully implementing feedback controllers for complex mechanical and electrical systems such as aircraft and sports cars. Natural biological systems use feedback extensively for regulation and adaptation but apart from the most basic designs, there is no systematic framework for designing feedback controllers in Synthetic Biology. In this paper we describe how classical approaches from linear control theory can be used to close the loop. This includes the design of genetic circuits using feedback control and the presentation of a biological phase lag controller.
Resistance-Associated Mutations and Polymorphisms among Integrase Inhibitor-Naïve HIV-1 Patients in Kuwait

Objectives: Resistance-associated mutations (RAMs) in the integrase of different HIV-1 subtypes were investigated in a cohort of patients never exposed to integrase strand transfer inhibitors (INSTIs). Methods: The viral RNA was extracted from plasma samples of 53 INSTI-naïve patients, and the integrase genetic region was sequenced and analyzed for subtype assignment and drug resistance. Results: The median viral load at sampling was 5.28 × 104 RNA copies/mL. Bayesian phylogenetic analysis showed 85% of the HIV-1 isolates were non-B subtypes, with a predominance of subtypes C (22.6%) and CRF01_AE (26.4%). A total of 52 and 110 mutations were found in the integrase region of HIV-1 B and non-B subtypes, respectively. Nonpolymorphic INSTI-RAMs were not detected in this study. However, the accessory mutation E157Q was found in 1 patient with CRF02_AG, and the polymorphic mutations L74M/I that may contribute to a reduced susceptibility to INSTIs in the presence of major mutations were observed in 6 (13.3%) patients with non-B subtypes and 1 (12.5%) patient with the B subtype. Polymorphic mutations at positions known to harbor primary and accessory RAMs were also detected in this study. Conclusion: Our results highlight the importance of monitoring the emergence of INSTI-RAMS before and after the initiation of INSTI-based therapy.
Textile sensor for heat flow measurements

This paper describes the concept of creating and testing of a textile heat flow sensor in order to determine the amount of heat exchanged between the human body and its environment. The main advantage of this sensor is the permeability to moisture, which allows taking into account the evaporation phenomenon, contrary to the traditional heat flow sensors. Another property related to this new sensor is its flexibility conferred by the textile substrate, which allows it to be applied on deformable surfaces.
Multi-Atlas-based Segmentation with Hierarchical Max-Flow

This study investigates a method for brain tissue segmentation from 3D T1 weighted (T1w) MR images via convex relaxation with a hierarchical ordering constraint. It employs a multi-atlas-based initialization from 5 training images and is tested on 12 T1w MR images provided by the MICCAI 2013 MRBrainS segmentation challenge. The registered atlas images, fully segmented into eight different brain structures, are used to formulate shape and intensity priors for a Maximum A-Posteriori (MAP) energy that is subsequently minimized with a dual hierarchical max-flow computation. The algorithm makes use of a hierarchical label ordering constraint to regularize label families individually and its inherently globally optimal results guarantee robust segmentations. Major parts of the image processing pipeline are implemented using General-Purpose Programming on Graphics Processing Units (GPGPU) for a substantial increase in computation speed.
Stable Isotope Evidence for Dietary Overlap between Alien and Native Gastropods in Coastal Lakes of Northern KwaZulu-Natal, South Africa

Background Tarebia granifera (Lamarck, 1822) is originally from South-East Asia, but has been introduced and become invasive in many tropical and subtropical parts of the world. In South Africa, T. granifera is rapidly invading an increasing number of coastal lakes and estuaries, often reaching very high population densities and dominating shallow water benthic invertebrate assemblages. An assessment of the feeding dynamics of T. granifera has raised questions about potential ecological impacts, specifically in terms of its dietary overlap with native gastropods. Methodology/Principal Findings A stable isotope mixing model was used together with gut content analysis to estimate the diet of T. granifera and native gastropod populations in three different coastal lakes. Population density, available biomass of food and salinity were measured along transects placed over T. granifera patches. An index of isotopic (stable isotopes) dietary overlap (IDO, %) aided in interpreting interactions between gastropods. The diet of T. granifera was variable, including contributions from microphytobenthos, filamentous algae (Cladophora sp.), detritus and sedimentary organic matter. IDO was significant (>60%) between T. granifera and each of the following gastropods: Haminoea natalensis (Krauss, 1848), Bulinus natalensis (Küster, 1841) and Melanoides tuberculata (Müller, 1774). However, food did not appear to be limiting. Salinity influenced gastropod spatial overlap. Tarebia granifera may only displace native gastropods, such as Assiminea cf. ovata (Krauss, 1848), under salinity conditions below 20. Ecosystem-level impacts are also discussed. Conclusion/Significance The generalist diet of T. granifera may certainly contribute to its successful establishment. However, although competition for resources may take place under certain salinity conditions and if food is limiting, there appear to be other mechanisms at work, through which T. granifera displaces native gastropods. Complementary stable isotope and gut content analysis can provide helpful ecological insights, contributing to monitoring efforts and guiding further invasive species research.
A microtubule bestiary: structural diversity in tubulin polymers

Microtubules are long, slender polymers of αβ-tubulin found in all eukaryotic cells. Tubulins associate longitudinally to form protofilaments, and adjacent protofilaments associate laterally to form the microtubule. In the textbook view, microtubules are 1) composed of 13 protofilaments, 2) arranged in a radial array by the centrosome, and 3) built into the 9+2 axoneme. Although these canonical structures predominate in eukaryotes, microtubules with divergent protofilament numbers and higher-order microtubule assemblies have been discovered throughout the last century. Here we survey these noncanonical structures, from the 4-protofilament microtubules of Prosthecobacter to the 40-protofilament accessory microtubules of mantidfly sperm. We review the variety of protofilament numbers observed in different species, in different cells within the same species, and in different stages within the same cell. We describe the determinants of protofilament number, namely nucleation factors, tubulin isoforms, and posttranslational modifications. Finally, we speculate on the functional significance of these diverse polymers. Equipped with novel tubulin-purification tools, the field is now prepared to tackle the long-standing question of the evolutionary basis of microtubule structure.
A Self-Adaptive Deep Learning-Based System for Anomaly Detection in 5G Networks

The upcoming fifth-generation (5G) mobile technology, which includes advanced communication features, is posing new challenges on cybersecurity defense systems. Although innovative approaches have evolved in the last few years, 5G will make existing intrusion detection and defense procedures become obsolete, in case they are not adapted accordingly. In this sense, this paper proposes a novel 5G-oriented cyberdefense architecture to identify cyberthreats in 5G mobile networks efficient and quickly enough. For this, our architecture uses deep learning techniques to analyze network traffic by extracting features from network flows. Moreover, our proposal allows adapting, automatically, the configuration of the cyberdefense architecture in order to manage traffic fluctuation, aiming both to optimize the computing resources needed in each particular moment and to fine tune the behavior and the performance of analysis and detection processes. Experiments using a well-known botnet data set depict how a neural network model reaches a sufficient classification accuracy in our anomaly detection system. Extended experiments using diverse deep learning solutions analyze and determine their suitability and performance for different network traffic loads. The experimental results show how our architecture can self-adapt the anomaly detection system based on the volume of network flows gathered from 5G subscribers’ user equipments in real-time and optimizing the resource consumption.
Increasing Atherosclerosis in Streptozotocin-Induced Diabetes into Four Groups of Mice

AIM: To study the protective effect of medicines on the formation of atherosclerosis in mice, it is needed to conduct the study in mice which is not genetically diabetic mice induced by streptozotocin (STZ) to produce hyperglycemia and atherosclerosis, compared with mice treated by yolk or its combination. MATERIAL AND METHODS: Fifty-six mice, Double Deutch Webster strain, male, receive 10 weeks, 20 - 30 gr bodyweight were divided into 4 groups (n = 14) i.e. control (do not received any agents), STZ (45 mg/kg/BW was injected intraperitoneally for 5 days), yolk (0.2 cc orally daily for 6 weeks), and combination of STZ and yolk ( STZ: 45 mg/kg/BW intraperitoneally add 0.2 cc yolk orally). All animals were executed in the 42nd day. Then, the aorta of the mice’s heart tissue was histopathology examined. Blood glucose and cholesterol levels were determined every week. RESULTS: Hyperglycemia occurred in mice induced by STZ injection with the highest BGL (521.8 ± 48.2 mg/dl; 188.4%) in the 4th-week observation; after that BGL decrease. We found that, except the control, all treatment groups with STZ, egg yolk, and combination underwent atherosclerosis. CONCLUSION: The present study was able to demonstrate the occurrence of atherosclerosis in mice treated by STZ accompanied with increasing blood glucose and cholesterol level.
Cyclic Di-GMP-Regulated Periplasmic Proteolysis of a Pseudomonas aeruginosa Type Vb Secretion System Substrate

ABSTRACT We previously identified a second-messenger-regulated signaling system in the environmental bacterium Pseudomonas fluorescens which controls biofilm formation in response to levels of environmental inorganic phosphate. This system contains the transmembrane cyclic di-GMP (c-di-GMP) receptor LapD and the periplasmic protease LapG. LapD regulates LapG and controls the ability of this protease to process a large cell surface adhesin protein, LapA. While LapDG orthologs can be identified in diverse bacteria, predictions of LapG substrates are sparse. Notably, the opportunistic pathogen Pseudomonas aeruginosa harbors LapDG orthologs, but neither the substrate of LapG nor any associated secretion machinery has been identified to date. Here, we identified P. aeruginosa CdrA, a protein known to mediate cell-cell aggregation and biofilm maturation, as a substrate of LapG. We also demonstrated LapDG to be a minimal system sufficient to control CdrA localization in response to changes in the intracellular concentration of c-di-GMP. Our work establishes this biofilm signaling node as a regulator of a type Vb secretion system substrate in a clinically important pathogen. IMPORTANCE Here, the biological relevance of a conserved yet orphan signaling system in the opportunistic pathogen Pseudomonas aeruginosa is revealed. In particular, we identified the adhesin CdrA, the cargo of a two-partner secretion system, as a substrate of a periplasmic protease whose activity is controlled by intracellular c-di-GMP levels and a corresponding transmembrane receptor via an inside-out signaling mechanism. The data indicate a posttranslational control mechanism of CdrA via c-di-GMP, in addition to its established transcriptional regulation via the same second messenger.
Cytokine Responses to Acute Exercise in Healthy Older Adults: The Effect of Cardiorespiratory Fitness

Markers of chronic inflammation increase with aging, and are associated with cardiovascular disease prevalence and mortality. Increases in fitness with exercise training have been associated with lower circulating concentrations of cytokines known to have pro-inflammatory actions (such as interleukin-6 [IL-6]) and higher circulating concentrations of anti-inflammatory cytokines (interleukin-10 [IL-10]). However, the effect of cardiorespiratory fitness on acute cytokine responses to a single bout of exercise in healthy older individuals is unknown. We compared the response of plasma cytokines IL-6, tumor necrosis factor-alpha (TNF-α) and IL-10 to a bout of moderate-intensity continuous and higher-intensity interval exercise between older individuals with higher and lower levels of cardiorespiratory fitness. Sixteen lower-fit (VO2peak: 22.6±2.8 mL.kg−1.min−1) and fourteen higher-fit participants (VO2peak: 37.4±5.9 mL.kg−1.min−1) completed three 24 min experimental protocols in a randomized order: (1) moderate-intensity continuous exercise (40% of peak power output [PPO]); (2) higher-intensity interval exercise (12 × 1 min intervals at 70% PPO separated by 1 min periods at 10% PPO); or (3) non-exercise control. Plasma cytokines were measured at rest, immediately after, and during 90 min of recovery following exercise or control. Plasma IL-6 concentrations at baseline were greater in the higher-fit compared to the lower-fit group (P = 0.02), with no difference in plasma IL-10 or TNF-α concentrations at baseline between groups. Plasma IL-6 and IL-10 concentrations in both groups increased immediately after all protocols (IL-6: P = 0.02, IL-10: P < 0.01). However, there was no difference in the IL-6 and IL-10 response between the exercise and non-exercise (control) protocols. After all protocols, no changes in plasma TNF-α concentrations were observed in either the higher- or lower-fit groups. In this study, basal concentrations of circulating IL-6 were elevated in older individuals with higher levels of cardiorespiratory fitness. However, changes in plasma cytokine concentrations after exercise were not different to changes after non-exercise control in both the lower- and higher-fit groups.
COUP-TFII Controls Mouse Pancreatic β-Cell Mass through GLP-1-β-Catenin Signaling Pathways

Background The control of the functional pancreatic β-cell mass serves the key homeostatic function of releasing the right amount of insulin to keep blood sugar in the normal range. It is not fully understood though how β-cell mass is determined. Methodology/Principal Findings Conditional chicken ovalbumin upstream promoter transcription factor II (COUP-TFII)-deficient mice were generated and crossed with mice expressing Cre under the control of pancreatic duodenal homeobox 1 (pdx1) gene promoter. Ablation of COUP-TFII in pancreas resulted in glucose intolerance. Beta-cell number was reduced at 1 day and 3 weeks postnatal. Together with a reduced number of insulin-containing cells in the ductal epithelium and normal β-cell proliferation and apoptosis, this suggests decreased β-cell differentiation in the neonatal period. By testing islets isolated from these mice and cultured β-cells with loss and gain of COUP-TFII function, we found that COUP-TFII induces the expression of the β-catenin gene and its target genes such as cyclin D1 and axin 2. Moreover, induction of these genes by glucagon-like peptide 1 (GLP-1) via β-catenin was impaired in absence of COUP-TFII. The expression of two other target genes of GLP-1 signaling, GLP-1R and PDX-1 was significantly lower in mutant islets compared to control islets, possibly contributing to reduced β-cell mass. Finally, we demonstrated that COUP-TFII expression was activated by the Wnt signaling-associated transcription factor TCF7L2 (T-cell factor 7-like 2) in human islets and rat β-cells providing a feedback loop. Conclusions/Significance Our findings show that COUP-TFII is a novel component of the GLP-1 signaling cascade that increases β-cell number during the neonatal period. COUP-TFII is required for GLP-1 activation of the β-catenin-dependent pathway and its expression is under the control of TCF7L2.