Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a Species Level Phylogeny of Symphoricarpos (Caprifoliaceae), Based on Nuclear and Chloroplast DNA

Abstract Although recent molecular phylogenetic studies of Dipsacales support a Caprifolieae clade containing Leycesteria, Triosteum, Symphoricarpos, and Lonicera, relationships among these taxa remain uncertain. Likewise, phylogenetic studies sampling more than just a handful of the species of Symphoricarpos has not been pursued. Here I present evidence based on both chloroplast and nuclear DNA to help resolve the phylogenetic relationships of both the Caprifolieae, as well as Symphoricarpos. For nuclear markers, I sequenced the ITS region in addition to the geranylgeranyl reductase (Chlp) gene, which appears to be present in only a single copy in Caprifolieae. Although Chlp does not provide a great deal of resolution by itself, it does provide additional phylogenetically informative characters. From these data, there appears to be strong congruence between both the genomes with respect to the relationships within Symphoricarpos, however, statistical support for any given hypothesis is weak. These additional data do not further support or clarify our understanding about the relationships among members of the Caprifolieae, showing conflicting results between the chloroplast and nuclear genomes.
Population density, growth and reproduction of arapaima in an Amazonian river‐floodplain

Compensatory density effects are key features of fish population dynamics that remain poorly understood in tropical river- floodplains. We investigated possible compensatory growth and reproductive processes for a river-floodplain population of Arapaima sp. , an extinction-prone fish species of South America. Body growth was studied through analysis of ring patterns on the scales, and size and age at sexual maturity was studied through analysis of female gonads. Growth and maturity were compared for unmanaged conditions with relatively low population density (in 1990s) versus managed conditions with markedly higher density (in 2005-2006); between 1999 and 2005-2006, abundance increased 7.3 fold. Results contradict theoretical expectations for slower growth and delayed reproduction at higher population density. Total lengths of arapaima at low population density were significantly shorter for age classes 1-5 compared with lengths of those age classes at high population density (ancova, P < 0.0001 for both slopes and intercepts). Total length at 50% maturity (L50) only declined about 4% with increasing density (e.g., 164 cm at low density vs. 157 cm at high density). Apparent faster growth at high density and only a slight change in size at maturity resulted in fishes spawning at an earlier age with high density conditions (age 3 vs. age 4-5). We hypothesise that these patterns reflect compliance with minimum size limits of catch during the high density (managed) situation, where there was no harvest of immature fishes. Compliance with minimum size limits, thus, may have led to faster average body growth rate and earlier reproduction, which has greatly promoted population recovery.
Three New Species of Leaf-Mining Gelechiidae (Lepidoptera) from Canada and Northeastern United States

ABSTRACT. Three new species of leaf-mining Gelechiidae are described: Xenolechia ceanothiae Priest, whose larvae feed on Ceanothus americanus L. (Rhamnaceae); Gnorimoschema shepherdiae Priest, on Shepherdia canadensis (L.) Nutt. (Elaeagnaceae); and Scrobipalpula manierreorum Priest, on Eurybia (Aster) macrophylla (L.) Cassini (Asteraceae). Their leaf mines were initially discovered in the understory in Michigan forests. Barcoding revealed additional records for two of these species from several regions of Canada. Photographs of the imagos and illustrations of the male and female genitalia, larval and pupal chaetotaxal maps are provided. Scanning electron micrographs of selected features of the larva for each species supplement illustrations. Comparative diagnoses of adult morphological characters are presented to distinguish the new species from other North American congeners. Photographs of the leaf-mines for each species are also included. DNA barcodes for each species are shown to be distinct from related North American congeners. The first occurrence of Gnorimoschema vibeiWolff in North America is confirmed by barcoded specimens from Kuujjuarapik in northern Quebec, Canada.
Calculating reference points for anthropogenic mortality of marine turtles

Human-caused mortality threatens many marine turtle populations worldwide, with fisheries interactions being a primary cause for population declines. National and international management of fisheries interactions with marine turtles are rarely tied to turtle population biology. Quantitative tools tied to population-based objectives can provide insight into the effectiveness and urgency of bycatch mitigation. A management approach is proposed based on a bycatch control rule called Reproductive Value Loss Limit (RVLL), generalized from the Potential Biological Removal management model for marine mammal populations. For RVLL, population size is scaled by reproductive value to account for strongly age-structured population dynamics and age-dependent fisheries mortality rates in marine turtle populations. RVLL is an estimate of maximum sustainable mortality for a population, calculated from estimates of maximum population growth rate, total reproductive value in the population, and an uncertainty factor. RVLL estimates correspond to specified management goals and risk tolerances. For demonstration, simultaneous goals of maintaining populations above the maximum net productivity level (analogous to the population size that produces maximum sustainable yield) and preventing a decrease in adults are assumed, both with 95% probability. A management-strategy-evaluation-like process was used to explore parameterization of the RVLL equation for robust performance over a range of plausible life history characteristics and uncertainties in abundance and bycatch mortality estimates for marine turtle populations. The RVLL-based management approach presented here proved robust to several important sources of uncertainty and to violation of several key underlying assumptions, and can be adapted to account for important sources of bias. The architecture presented, including tailored management strategy evaluation, provides a useful basis for further development of reference-point-based management of human-added mortality in populations that experience large changes with age in reproductive value and human-caused mortality rates, as is the case for marine turtles. Copyright © 2013 John Wiley & Sons, Ltd.
LIFE CYCLE OF THE CYST FORMING NEMATODE CACTODERA TORREYANAECID DEL PRADO AND SUBBOTIN, 2014 AND ITS RELATIONSHIP WITH ITS HOST SUAEDA EDULISFLORES OLV. & NOGUEZ

The goal of this study was to examine the biology of Cactodera torreyanaeand its interaction with Suaeda edulis. Both pathogen and host are recently described organisms, but little is known about either of them, although they appear to be well-adapted to soils with a very high salinity and pH. The anatomical changes that C. torreyanaeincited in its host roots were studied. Cactodera torreyanaeinduced multinucleate syncytia to form in parenchymatous cells located in the vascular tissue of the primary phloem of the Suaeda edulisroot. The syncytia were irregular in shape and size: perimeter 0.427 - 1.748 (0.784 ± 0.43) mm; area 0.012 - 0.105 (0.032 ± 0.03) mm2. The nematode completed its life cycle in 25 days after 447-degree days, at a base temperature of 20oC. None of the post-embryonic stages completely penetrated the host roots to complete its life cycle, so C. torreyanae can be considered to be a sedentary ecto-parasite.
Digitizing Community Building and Reconciliation in Post-Conflict Communities: A Case of #Let’sTalkUganda in Northern Uganda

This research examines the use of information and communication technologies (ICTs; social media) as a tool that fosters community building and reconciliation in post-conflict regions, in particular Northern Uganda. Using Twitter data collected over 27 months (12 June 2016–9 September 2018), we found that information technology (IT) increased social actors’ (Justice and Reconciliation Project [JRP]-Uganda) advocacy for transitional justice in post-conflict communities. Interview findings evidenced the effectiveness of using social media (SM) to connect post-conflict communities to share and discuss reconciliatory ideas. This study connotes that well-thought-out SM use by social actors to share information used in resolving conflict results in socio-political stability and harmonious coexistence.
Priority Primate Areas in Tanzania

Abstract Priority Primate Areas are identified in Tanzania, mainland Africa's most important country for conservation of primates, on the basis of occupancy by globally rare, Red-Listed and range-restricted primate species and subspecies. We provide a comprehensive list and regional assessment of Tanzania's primate taxa, using IUCN Red List criteria, as well as the first national inventory of primates for 62 sites. The Priority Primate Areas, encompassing 102,513 km2, include nine national parks, one conservation area, seven game reserves, six nature reserves, 34 forest reserves and five areas with no official protection status. Primate species were evaluated and ranked on the basis of irreplaceability and vulnerability, using a combination of established and original criteria, resulting in a primate Taxon Conservation Score. Sites were ranked on the basis of summed primate scores. The majority (71%) of Priority Primate Areas are also Important Bird Areas (IBAs), or part of an IBA. Critical subsets of sites were derived through complementarity analyses. Adequate protection of just nine sites, including six national parks (Kilimanjaro, Kitulo, Mahale, Saadani, Udzungwa and Jozani-Chwaka Bay), one nature reserve (Kilombero) and two forest reserves (Minziro and Mgambo), totalling 8,679 km2, would protect all 27 of Tanzania's primate species. The addition of three forest reserves (Rondo, Kilulu Hill and Ngezi) and two game reserves (Grumeti and Biharamulo), results in a list of 14 Priority Primate Areas covering 10,561 km2 (1.1% of Tanzania's total land area), whose conservation would ensure the protection of all 43 of Tanzania's species and subspecies of primates.
Physico-chemical Properties and Antioxidant Activities of Dietary Fiber Derived from Defatted Rice Bran

The objective of the study is to study the Physico-chemical properties and antioxidant activities of total, soluble and insoluble dietary fibers from defatted rice bran. Enzymatic-gravimetric method was used to obtain Total, Soluble and Insoluble fraction of dietary fiber from defatted rice bran. The fractions were used to study their structure (SEM), physical properties (color, density, porosity and oil or fat adsorption capacity), hydration properties (water holding, water binding and swelling emulsifying capacity), and antioxidant capacity (DPPH-scavenging activity, metal chelating and reducing power capacity). The physical properties except FBC of SDF were significantly higher than IDF and TDF; however hydration properties were lower than IDF and TDF (p<0.05). Compared to SDF, IDF showed the highest CEC, while its GDRI value was lowest (p<0.05). All dietary fiber fractions at high concentration (5% or 50 mg/mL) showed a high antioxidant activity.
Mycobacterium moriokaense sp. nov., a Rapidly Growing, Nonphotochromogenic Mycobacterium

A new species of rapidly growing, nonphotochromogenic mycobacteria, Mycobacterium moriokaense, is described. This taxon commonly occurs in the soil and may have been erroneously identified previously as Mycobacterium fortuitum. M. moriokaense can be differentiated from all previously described species of mycobacteria. The type strain is strain ATCC 43059 (= NCH E11715).
Ionic Relations of Garden Orache, A triplex hortensis L.: Growth and Ion Distribution at Moderate Salinity and the Function of Bladder Hairs

The growth of garden orache, Atriplex hortensis was studied under conditions of mild NaCl or Na2S04 salinity. Growth, dry matter production and leaf size were substantially stimulated at 10 mM and 50 mM Na+ salts. Increased growth, however, appeared to be due to a K+-sparing effect of Na+ rather than to salinity per se. The distribution of K+ and Na+ in the plant revealed a remarkable preference for K+ in the roots and the hypocotyl. In the shoot the K/Na ratio decreased strongly with leaf age. However, the inverse changes in K+ and Na+ content with leaf age were dependent on the presence of bladder hairs, which removed almost all of the Na+ from the young leaf lamina. Measurements of net fluxes of K+ and Na+ into roots and shoots of growing Atriplex plants showed a higher K/Na selectivity of the net ion flux to the root compared to the shoot. With increasing salinity the selectivity ratio Na of net ion fluxes to the roots and to the shoots was increased. The data suggest that recirculation of K+ from leaves to roots is an important link in establishing the K/Na selectivity in A. hortensis plants. The importance of K+ recirculation and phloem transport for salt tolerance is discussed.
Prognostic Role of IL-18 in Various Human Cancers and Radiation Injuries: A Meta-Analysis

Background: In recent years, more and more studies have shown that various inflammatory factors have predictive effects on the prognosis of various human tumors. However, the prognostic role of interleukin 18 (IL-18) remains controversial. Furthermore, its role in radiation-induced injuries relating to radiotherapy (RT) is also unclear. In this study, we conducted the meta-analysis to clarify its roles in prognosis of human tumors and radiation-induced injuries relating to RT. Methods: We comprehensively searched PubMed, Embase, and Cochrane Library to identify studies published before November 2019 involving patients with cancer expressing IL-18 and which reported overall survival (OS) during the follow-up period. Results: A total of 1376 samples from 16 studies showed that high expression of IL-18 is closely related to prognosis and OS for patients with carcinoma (hazard ratio [HR]: 2.12; 95% CI: 1.81-2.49; P = .04; random-effect model). In addition, subgroup analysis proved that high expression of IL-18 was related to poor OS of hematologic tumor (HR: 2.03, 95% CI: 1.44-2.86, P < .00001), hepatocellular carcinoma (HR: 1.99, 95% CI: 1.38-2.86, P = .0002), and gastric cancer (HR: 2.00, 95% CI: 1.12-3.57, P = .02). Conclusions: High expression of IL-18 is related with poor prognosis of carcinoma.
“Model”

Open Wiki community (do-ocracy) (sort of like Wikipedia but for software instead of content) Wiki Way participation in the code (500+ with full write access to the complete code base) Scheduled releases (major releases every eight months, with Long Term Support versions, similar to Ubuntu) All-in-one codebase (1,000,000 lines of code, with everything bundled. Each feature is optional.) Inherent synchronized releases (all features have to be ready at the same time). Half the code comes from other projects such as Zend Framework, jQuery, Smarty, etc. Many features, but no duplication (in a wiki, similar/related content is merged, so the same is applied to Tiki's features). Tiki is the Free/Open Source Web Application with the most built-in features. Dogfood Tiki is a community recursively developing a community management system.
Production of microbial protein from waste cellulose by Thermomonospora fusca, a thermophilic actinomycete

The growth characteristics of Thermomonospora fusca, a cellulolytic thermophilic actinomycete, are described in terms of growth on pulping fines, a cellulosic waste of the paper industry. A fermentation was developed which substantially degrades this waste, with the residual product of growth containing about 30% microbial protein. This protein, as shown by a preliminary feeding study with baby chicks and by amino acid analyses, appears to be of good nutritional quality and contains no strongly toxic materials. The extracellular cellulolytic enzymes present in the spent broth are discussed in relation to their potential recovery as a by‐product of the fermentation, as is also the possible use of the fermentation as a waste disposal system.
of the human recombination activating gene 1 (RAGl) to chromosome 11p13

The human recombination activating gene 1 (RAGl) has previously been mapped to chromosomes 14q and 11 p. Here we confirm the chromosome 11 as­ signment by two independent approaches: autoradio­ graphic and fluorescence in situ hybridization to meta­ phase spreads and analysis of human-hamster somatic cell hybrid DNA by the polymerase chain reaction (PCR) and Southern blotting. Our results unequivocally localize RAG1 to llp13.
Characterization of Aspergillus niger B-1 RNase and Its Inhibitory Effect on Pollen Germination and Pollen Tube Growth in Selected Tree Fruit

ADDITIONAL INDEX WORDS. RNase B1, Citrus reticulata, peach, pollen tube growth, Prunus persica (Peach Group), tangerine ABSTRACT. Aspergillus niger B-1 (CMI CC 324626) extracellular RNase (RNase B1) was purified to homogeneity. It was found to contain two isoforms of 32- and 40-kDa glycoproteins, sharing a 29-kDa protein moiety. Optimal RNase activity was observed at 60 °C and pH 3.5. In 'Almog' peach ( Prunus persica (L.) Batsch (Peach Group) 'Almog') and 'Murcott' tangerine (Citrus reticulata Blanco 'Murcott') the enzyme inhibited pollen germination and pollen tube growth in vitro as well as in vivo. In field experiments, spray application of the RNase caused a reduction in 'Fantasia' nectarine ( Prunus persica (L.) Batsch (Nectarine Group) 'Fantasia') fruit set and interfered with embryo development. The biological effect of the RNase may be of horticultural value, due to its potential to control fertilization. In many deciduous fruit trees, yields of commercial value depend upon massive thinning of the flowers and fruitlets. In stone fruits (peach, plum (Prunus domestica L.), etc.) the thinning process is currently performed manually. In Citrus L. trees, on the other hand, seedless fruits are desirable. Therefore, a further step in this research was to examine an effective RNase that can be produced in large amounts. Species of Aspergillus have been reported to produce extracellular RNases (Egami and Nakamura, 1969). Aspergillus niger is also used as a source for important materials and enzymes in the food industry, such as citric acid and pectinases (Kerns et al., 1987; Li and King, 1963; Rombout and Pilnik, 1978). In the present work we describe production, purification, and partial characterization of A. niger B-1 extracellular RNase (RNase B1) and its effect on in vitro and in vivo pollen germina- tion and pollen tube growth.
A Feasible Study for Virtual Intrusion Detection System (VIDS) using VMware and SNORT IDS

Nowadays, the majorly signature based Intrusion Detection System(IDS) are used to detect intrusions in their intranet. We have used the concept of virtualization to develop an Intrusion Detection System which will use Honeypots/Honey Clients to detect and trap the attackers. With the increasing popularity of cloud networks, serious issues around security for ubiquitous hosts will need to be addressed. In this project we focus on a virtual intrusion detection system (V-IDS). We present an architecture that uses basic principles of computer networking, virtualization, and Cyber security and apply them to intrusion detection systems, in order to protect networks characterized by a constantly changing underlying infrastructure and physical topology. Our goal is to define a process and a novel architecture that minimizes the security risk in networks, implementing the principle that network security and reliability is not a “product,” but a well-defined “process. ” On the basis of the defined architecture we have implemented a prototype Virtual IDS.
Montane outcrop vegetation of Banks Peninsula, South Island, New Zealand

Species composition patterns and vegetation-environment relationships were quantified for montane volcanic outcrops on Banks Peninsula. The flora of these habitat islands comprises 346 vascular plant species including 82 exotic species and 52 species that are nationally rare, regionally rare, or regional endemics. Both Multidimensional scaling (MDS) ordination analysis and TWINSPAN results illustrated the high compositional and environmental heterogeneity across the outcrops. MDS revealed that primary environmental factors related to community composition comprise both regional-scale gradients of altitude and outcrop-scale gradients of slope steepness, soil pH, area available to plants, maximum vegetation height, and the percentage of the surrounding vegetation that is forest. Accordingly, TWINSPAN separated four outcrop communities that occur on steeper slopes, have less fertile soils and tend not to face north from three outcrop communities that have shallower slopes, more fertile soils and tend to face north. Types in the first group are more likely to be bordered by forest or taller shrublands, whereas those in the second group occur on outcrops primarily bordered by grasslands and support more exotic species. Within these broader groups, communities differ in their altitude and the size, soil depth and shading of the outcrops on which they occur. We describe the vegetation of the seven communities; this ranges from predominance of stunted trees and taller statured species such as Podocarpus hallii and Phormium cookianum to vegetation of shrubby species such as Heliohebe lavaudiana and Hebe strictissima, to short vegetation of native woodland and grassland species such as Polystichum vestitum and Rytidosperma corinum, to exotic pasture-like vegetation of clovers and exotic grasses. The percentage of species on an outcrop face that are exotic is well modelled by site factors, with exotics increasing as the surrounding matrix becomes more disturbed, slopes become more gentle, the percentage of shade on the outcrop decreases, and soil fertility increases. In contrast, nearby disturbance has little influence on the percentage or number of species that are rare on an outcrop face; rather rare species richness is more strongly related to outcrop area and lack of shade, echoing patterns observed for rare outcrop species elsewhere in the world. These results highlight the importance of considering the high compositional heterogeneity among outcrops and the influence of disturbance to surrounding ecosystems in guiding conservation planning.
Genetic Relations related to Chemical Containing and the Efficient Barcodes by psbA- trnH Spacer and its Combinations with rbcL and matK on Gardenia Species

Gardenia species have been used worldwide for ornamentation and for traditional medicines. The Thailand species observed include eight native species, G. carinata, G. collinsae, G. elata, G. jasminoides, G. obtusifolia, G. saxatilis, G. sootepensis and G. thailandica, and three introduced species, G. gjellerupii, G. taitensis, and G. volkensii. The dendrogram constructed from RAPD banding patterns shows a monophyletic group for each species. Genetic similarity (S) values range from 0.916 to 0.997 for intraspecific level and from 0.651 to 0.816 for interspecific level. The S values are in accordance with similar phenotypic characteristics and a common ancestry of the species, genera, and major groups of chemicals contained within them, such as terpenoids and flavonoids. The standard regions in the genus that could be efficiently used as barcode markers are the trnH-psbA spacer (and combinations of itself), the rbcL, and the matK genes. Genetic distance (D) values of trnH-psbA spacer sequences are 0.005 to 0.481 in intraspecific level, and 0.014 to 0.572 for the interspecific level. The combined sequences give the intraspecific and interspecific D values of 0.004 to 0.102 and 0.008 to 0.178. Keyword: DNA barcoding, Genetic relationships, Gardenia species.