Miracle-dz/UniFAR-FTUs huggingface dataset:
Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical bird diversity

Does competition influence patterns of coexistence between closely related taxa? Here we address this basic question in ecology by analyzing patterns of range overlap between related bird species (“sister pairs”) distributed along a Neotropical elevational gradient. We explicitly contrast the behavioral dimension of interspecific competition (interference competition) with similarity in resource acquisition traits (exploitative competition). We find that behavioral interactions are generally important in setting elevational range limits and preventing coexistence of closely related species. Specifically, close relatives that defend year-round territories tend to live in non-overlapping elevational distributions, while close relatives that do not defend territories tend to broadly overlap in distribution. In contrast, neither similarity in beak morphology nor evolutionary relatedness was associated with patterns of range limitation. Our main result is that interference competition can be an important driver of species ranges at the scale of entire diverse assemblages. Consequently, we suggest that behavioral dimensions of the niche should be more broadly incorporated in macroecological studies.
Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Abstract Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.
Phylogenetically distant clade of Nostoc-like taxa with the description of Minunostoc gen. nov. and Minunostoc cylindricum sp. nov

Two cyanobacterial strains morphologically identified to the genus Nostoc were isolated from a wet rocky wall in a mid-subtropical region in China, and they were taxonomically and phylogenetically characterized based on the polyphasic approach combining morphological and genetic characteristics. 16S rRNA gene sequence analysis showed that the two strains containing six clones were all >99.6% similar to each other, but had < 94.3% similarities to the existing cyanobacterial genera. The phylogenies based on 16S rRNA and rpoC1 gene sequences indicated that their sequences grouped into a unique and robust cluster with high bootstrap values. This unique cluster was separated from the clade of the 'Nostoc sensu stricto' and the respective clades formed by the morphologically similar genera Mojavia, Desmonostoc, Aliinostoc, Komarekiella and Halotia. The 16S-23S rRNA ITS secondary structure of the both strains exhibited the unique pattern of D1-D1´, Box-B and V3 helix, distinguishing it from the other heterocytous genera. Such a clear cluster leads to the establishment of Minunostoc gen. nov., with the type species as Minunostoc cylindricum sp. nov.
Investigating the consequences of climate change under different land‐use regimes: a novel experimental infrastructure

Climate change and land-use change are considered as the most important threats to ecosystems. Both factors can be expected to have interacting influences on ecosystem functions directly and indirectly via changes in biodiversity. Knowledge about these interactions is limited due to a lack of experiments which investigate climate change effects under different land-use scenarios. Among the processes involved in ecosystem responses to global change, in particular, those occurring in soils or related to biotic interactions and microevolution were underinvestigated in previous experiments. Examinations of these relationships require spatial and temporal scales which go beyond those realized in the majority of ecological field experiments. We introduce a new research facility, the Global Change Experimental Facility (GCEF), which was designed to investigate the consequences of a future climate scenario for ecosystem functioning in different land-use types on large field plots (400 m). Climate manipulation is based on projections for the period of 2070–2100 with an increased temperature and a changed precipitation pattern consisting of reduced precipitation in summer and increased precipitation in spring and autumn. We subject five different land-use types (two farming systems, three grasslands), differing in land-use intensity, to ambient and future climatic conditions. The use of automated roofs and side panels to passively increase night temperatures results in an average increase in daily mean temperature by 0.55°C accompanied by a stronger increase in minimum temperatures (up to 1.14°C in average) with longer frost-free periods and an increase in growing degree days by 5.2%. The combined use of mobile roofs and irrigation systems allows the reduction (in summer by ~20%) and increase in rainfall (in spring and autumn by ~10%) according to future scenarios superimposed on the ambient variation in precipitation. The large plot size and the technical configuration allow the establishment of realistic land-use scenarios and long-term observations of responses of ecosystem functions and community dynamics on relevant temporal and spatial scales. Thus, the GCEF provides a well-suited platform for the interdisciplinary research on the consequences of climate change under different land-use scenarios.
Community Ecology and Phylogeography of Bats in the Guianan Savannas of Northern South America

The Guiana Shield of South America contains savannas within one of the largest contiguous expanses of pristine tropical rainforest remaining in the world, but biodiversity in the grasslands is poorly known. In lowland Neotropical areas, bats typically comprise the most species-rich group of mammals. We compare the bat faunal community and phylogeography in the savanna habitats of the Llanos in Venezuela, Rupununi in Guyana, and Sipaliwini in Suriname. Measures of species diversity and relative abundance from standardized field survey methodology enable comparison among these three grassland regions. Genetic variation is summarized by DNA barcoding to examine biogeographic patterns across larger forest–savanna landscapes. A total of 76 species of bats is documented, of which 18 species are reported from all 3 savannas and 30 species are reported from only 1 of the savannas. Endemism is low with 5 taxa restricted primarily to dry, open habitats. However, 7 other species have divergent phylogeographic lineages associated with savanna populations. Although bat species are usually distributed over wide regions of the Neotropics, the habitat mosaics of the Guiana Shield have different faunal assemblages. Going back into the Miocene, the contractions and expansions of forest–savanna paleoenvironments over time have contributed to speciation and the current high levels of biodiversity in South America.
Transfer Learning from Nucleus Detection to Classification in Histopathology Images

Despite significant recent success, modern computer vision techniques such as Convolutional Neural Networks (CNNs) are expensive to apply to cell-level prediction problems in histopathology images due to difficulties in providing cell-level supervision. This work explores the transferability of features learned by an object detection CNN (Faster R-CNN) to nucleus classification in histopathology images. We detect nuclei in these images using class-agnostic models trained on small annotated patches, and use the CNN representations of detected nuclei to cluster and classify them. We show that with a small training dataset, the proposed pipeline can achieve superior nucleus detection and classification performance, and generalizes well to unseen stain types.
A confirmation bias in perceptual decision-making due to hierarchical approximate inference

Human decisions are known to be systematically biased. A prominent example of such a bias occurs when integrating a sequence of sensory evidence over time. Previous empirical studies differ in the nature of the bias they observe, ranging from favoring early evidence (primacy), to favoring late evidence (recency). Here, we present a unifying framework that explains these biases and makes novel psychophysical and neurophysiological predictions. By explicitly modeling both the approximate and the hierarchical nature of inference in the brain, we show that temporal biases depend on the balance between “sensory information” and “category information” in the stimulus. Finally, we present new data from a human psychophysics task that confirms a critical prediction of our framework showing that effective temporal integration strategies can be robustly changed within each subject, and that allows us to exclude alternate explanations through quantitative model comparison.
Deconvolving the contributions of cell-type heterogeneity on cortical gene expression

Complexity of cell-type composition has created much skepticism surrounding the interpretation of brain bulk-tissue transcriptomic studies. We generated paired tissue genome-wide gene expression data and immunohistochemistry data, enabling us to assess statistical methods for modeling and estimating cellular heterogeneity in the brain. We demonstrate that several algorithms that rely on single-cell and cell-sorted data to define cell marker gene sets yield accurate relative and absolute estimates of constituent cell-type proportions.
A parallel operator splitting algorithm for solving constrained total-variation retinex

An ideal image is desirable to faithfully represent the real-world scene. However, the observed images from imaging system are typically involved in the illumination of light. As the human visual system (HVS) is capable of perceiving identical color with spatially varying illumination, retinex theory is established to probe the rationale of HVS on perceiving color. In the realm of image processing, the retinex models are devoted to diminishing illumination effects from observed images. In this paper, following the recent work by Ng and Wang (SIAM J. Imaging Sci. 4:345-356, 2011), we develop a parallel operator splitting algorithm tailored for the constrained total-variation retinex model, in which all the resulting subproblems admit closed form solutions or can be tractably solved by some subroutines without any internally nested iterations. The global convergence of the novel algorithm is analysed on the perspective of variational inequality in optimization community. Preliminary numerical simulations demonstrate the promising performance of the proposed algorithm.
CMOS High-Efficiency Wireless Battery Charging System With Global Power Control Through Backward Data Telemetry for Implantable Medical Devices

A high-efficiency CMOS wireless battery charging system with battery voltage tracking and global power control through the proposed pulsed load-shift keying (PLSK) backward data telemetry technique is designed. The power transmitted from the adaptively controlled power transmitter (ACPT) for battery charging is automatically adjusted with the battery voltage tracking through the PLSK backward data telemetry. Therefore, the generated rectifier output voltage is only slightly larger than battery voltage and tracks with battery voltage during the charging time of linear battery charger. Experimental result shows that the average receiver efficiency with battery voltage tracking from 3.3 V to 4.2 V and global power control is 90.9% which is 14.9% higher than that without these techniques and 28.9% higher than that in the prior work. The measured power loss is 8 mW (4.44%) under the maximum output power of 180 mW and with the PLSK data rate of 211 kbps. The proposed wireless battery charging system with a single pair of coils at the resonant frequency of 13.56 MHz is suitable for the applications of implantable medical devices.
Optimization of the antifungal activity of essential oil isolated from aerial parts of Thymus kotschyanus Boiss & Hohen (Lamiaceae)

Although utilization of synthetic chemicals is inevitable for management of economically detrimental agents, numerous side-effects such as environmental contaminations and effects of non-target organisms associated with them. Plant essential oils with low/without toxicity on mammals and as bio-degradable natural materials have been considered for different pests and fungi management in the recent years. In the present study, the essential oil of Thymus kotschyanus isolated by a Clevenger apparatus and its mycelial growth inhibition was measured against two phytopathogenic fungi Botrytis cinerea and Fusarium graminearum . The best models for predicting of antifungal effects were quadratic models. The essential oil showed a prospective mycelial growth inhibition against both phytopathogenic fungi. Optimization of the antifungal effects indicated that 206.207 ppm of the essential oil caused 50% mycelial growth inhibition of B. cinerea after 89.651 h. This value was 85.600 ppm for F. graminearum within 117.194 h. Results of the present study designated a great potential of T. kotschyanus essential oil for management of pathogenic fungi B. cinerea and F. graminearum . Keywords: Essential oil, mycelial growth inhibition, response surface, Thymus kotschyanus
A NEW METHOD FOR SOLVING FUZZY TRANSPORTATION PROBLEM USING PENTAGONAL FUZZY NUMBERS

In this paper, we propose a new approach for the solution of fuzzy transportation problem under a fuzzy environment in which transportation costs are taken as fuzzy pentagonal numbers. The fuzzy numbers and fuzzy values are predominantly used in various fields such as experimental sciences, artificial intelligence, etc. because of their uncertainty. Here, we are converting fuzzy pentagonal numbers into crisp value by using range technique and then solved by the max-min method for the transportation problem.
Micropropagation of dwarf schefflera [Schefflera arboricola (Hayata) Merr.] via direct shoot regeneration

Schefflera [ Schefflera arboricola ( Hayata) Merr. ] is one of the most popular ornamental house plants conventionally propagated by seeds. Rapid multiplication of elite clones is an important driving force for the pot plant’s market. In this regard, In vitro clonal propagation of three schefflera cultivars, ‘Luseane’, ‘Charlotte’ and ‘Gold Capella’, was examined. Sterilization was done by 70% ethanol for 2 min and 1% sodium hypochlorite solution for 15 min. Shoot proliferation of the nodal segments was dependent on cytokinin supply. The greatest number of shoots was obtained when nodal explants were cultured on the MS medium with 0.5 mg l-1 TDZ for ‘Luseane’, or 8 mg l-1 BA for ‘Charlotte’ and ‘Gold Capella’. Subculture of nodal segments harvested from the in vitro derived axillary shoots on the multiplication medium enabled continuous production of healthy shoots with similar frequency. Plantlets of ‘Luseane’ and ‘Gold Capella’ demonstrated 100% rooting using 2 mg l-1 NAA, while ‘Charlotte’ showed 93.75% root induction by 1 mg l-1 NAA. Plantlets were acclimatized successfully using peat moss and sand mixture (‘Luseane’), loam soil, sand and leaf compost (‘Charlotte’) or peat moss and perlite mixture (‘Gold Capella’).
A Community-Based Participatory Research Project Involving Latino Families of Deaf and Hard-of-hearing Children

The community-based participatory research project described in this paper was designed to help Spanish-speaking families of deaf and hard-of-hearing children gain access to necessary health, education, and local resource information. The project was motivated by the need to improve communication between medical and education resource centers with Spanish-speaking families. This paper reports on the specific methods and implementation of the partnership approach, the development of the project, and lessons learned for future projects of this type.
HIV-1 evasion of restriction factors: cyclophilin A and cell fusion provide a helping hand

Retroviral restriction factors are important regulators of viral infection, targeting vulnerable steps of the virus lifecycle; steps that are also targeted by antiviral drugs. It has become clear that the route of cellular infection can alter the sensitivity of HIV-1 to these agents. Using CRISPR-Cas9 edited pluripotent stem cell-derived macrophages, we have explored the potential of a modified restriction factor (human TRIMCyp) to inhibit HIV-1 replication in both cell free and cell-cell infection models. We show that the expression of TRIMCyp from the endogenous TRIM5α locus potently restricts infection by cell-free HIV-1. Our results also show the importance of the human cyclophilin A-HIV-1 capsid interaction for viral escape from restriction by native human TRIM5α, highlighting the evolutionary interplay between virus and this host restriction factor. However, when co-cultured with infected T cells, stem cell-derived macrophages are primarily infected by fusion between the cells. We have termed infected cells that result from these fusions heterocytia, and show that their formation overcomes multiple restriction factors and the reverse transcriptase inhibitor AZT. Importance As sentinels of the immune system, macrophages are relatively resistant to infection by pathogens such as HIV-1. However, infected macrophages are found in infected patients and they play key roles in the pathogenesis of the disease as well as being a component of the viral reservoir that must be targeted before treatment can become cure. In this article, we show that some of the mechanisms by which macrophages restrict HIV-1 can be overcome through a recently described cell-cell interaction leading to cell-cell fusion. We also highlight an evolutionary battle between virus and host and show how the virus has co-opted a host protein to protect it from destruction by an antiviral mechanism. These two key findings suggest potential novel treatment strategies that may reduce the viral reservoir and help our natural defences take back control from the virus.
Exploring the Nexus between Migration and Social Positions using a Mixed Methods Approach

Using a mixed methods approach, this article analyses the nexus between migration and social positions drawing on recent survey data on migrants who have arrived in Germany after 1994 from the Socio-Economic Panel (SOEP), as well as qualitative interviews with 26 respondents to the survey. Drawing on a Bourdieusian forms of capital approach (Bourdieu, 1986) and applying the method of Multiple Correspondence Analysis (MCA) to the SOEP survey data, we highlight two dimensions structuring the nexus between migration and social positions in Germany: (1) capital related to legal status and multiple migration and (2) (trans)national cultural capital. Through a cluster analysis based on the MCA results, we then identify and describe four profiles of migrants characterised by distinct configurations of cultural capital (social class background, education and linguistic skills before and after settlement), legal status (citizenship and status at migration), experiences of multiple cross-border movements and social positions: the ‘foreign working-class,’ the ‘foreign middle class,’ the ‘adapted German migrants,’ and the ‘young highly educated urbans. ’ The complementary analysis of the qualitative data allows us to go further in understanding some of the factors that may play a role in shaping migrants’ social position(ing) in the four clusters. In particular, we show that resources such as determination and perseverance can be crucial for some migrants to counter structural constraints related to their legal status in transferring or accessing cultural capital, and that linguistic skills are also used by some migrants as a marker of social distinction.
Biodegradation of RDX by Stimulating Humic Substance- and Fe(III) - Reduction

Abstract : The project demonstrated that extracellular electron shuttling compounds and Fe(III)reduction are critical microbially-mediated processes for the biodegradation of the cyclic nitramine compound RDX. Electron shuttles are compounds that promote electron transfer between cells and alternate, extracellular electron acceptors. All electron shuttles increase the rate and extent of Fe(III)reduction; however, until this study, it was unknown whether these molecules could also stimulate RDX reduction and subsequent biodegradation steps. In addition to the electron shuttling data, this study demonstrated that Fe(III) reduction and Fe(III)reducing microorganisms are most likely the dominant process and microbial community, respectively, for complete degradation of RDX in contaminated environments. The project was the first to demonstrate electron shuttle mediated RDX and HMX biodegradation and this strategy serves as the foundation for the future development of technology for the in situ or ex situ biodegradation of RDX.
PNP (Purine Nucleoside Phosphorylase)

The purine nucleoside phosphorylase gene (PNP) encodes an enzyme which reversibly catalyzes the phosphorolysis of purine nucleosides. PNP is ubiquitously expressed in mammalian cells and tissues. PNP mutations cause nucleoside phosphorylase deficiency which result in defective T cell mediated immunity but can also affect B cell immunity and antibody responses.