Miracle-dz/UniFAR-FTUs huggingface dataset:
Novelty by Furcation and Fusion: How tree-like is evolution?

Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study novelty phylogenetically, with a key question of whether evolution occurs by tree-like branching, or through exchange of distantly related parts in processes akin to horizontal transfer. Here, I argue that except at the lowest levels of biological organization, evolution is not usually tree-like. Perfectly vertical inheritance, an assumption of evolutionary trees, requires simultaneous co-duplication of all the parts of a duplicating or speciating (which I collectively call 'furcating') biological feature. However, simultaneous co-duplication of many parts usually requires variational processes that are rare. Therefore, instead of being perfectly tree-like, evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression and co-option are such fusion processes at different levels of organization. In addition to co-duplication, units under phylogenetic study must individuate (gaining evolutionary independence) before they can diverge. A lack of individuation erases evolutionary history, and provides another challenge to tree-like evolution. In particular, biological units in the same organism that are the products of development always share the same genome, perhaps making full individuation difficult. The ubiquity of processes that fuse distantly related parts or oppose individuation has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be violated, to the point where we may need a different metaphor, such as economic public goods, or a ‘web of life’. Secondly, we may need to expand current models. For example, even under the prevailing model of cell-type evolution, the sister-cell-type model, a lack of complete individuation and evolution by co-option will often be involved in forming new cell-types. Finally, these processes highlight a need for an expansive toolkit for studying evolutionary history. Multivariate methods are particularly critical to discover co-variation, the hallmark of an absence of complete individuation. In addition to studying phylogenetic trees, we may often need to analyze and visualize phylogenetic networks. Even though furcation - the splitting and individuation of biological features - does happen, fusion of distant events is just as critical for the evolution of novelties, and must formally be incorporated into the metaphors, models, and visualization of evolutionary history.
A Mobile Phone Application for Assessing Daily Variation in Pain Location and Pain Intensity in Patients with Urologic Chronic Pelvic Pain Syndrome: A MAPP Network Study.

Introduction We created and tested a mobile app that facilitates the ecological momentary assessment of pain intensity and pain location and identifies heterogeneous patient pain phenotypes. Methods A mobile app was created with patient, clinician and researcher input. A sample of 20 participants with urologic chronic pelvic pain syndrome were then asked to complete a 14-day pain assessment using the app. Data were analyzed to assess compliance, usability and the ability for the app to capture variation in pain intensity and pain location. Ecological momentary assessment pain data were then compared to end-of-week pain summary questions to determine construct validity. Results Mean compliance was 70±8%, higher earlier in the study period (p <0.0005) and better in older individuals (p <0.0001). During the 14-day assessment, 90% of participants reported daily variation in pelvic pain intensity (SD 0.64-3.02; out of 10), 95% reported variation in their nonpelvic pain (SD 0.17-3.63; out of 10) and 100% reported variations in number of sites with pain (SD 0.22-1.44; out of 7). Pelvic pain and nonpelvic pain intensity, as determined by cumulative app scores, were associated with patient reported end-of-week scores; worst pain (r pelvic =0.67; r nonpelvic =0.53) and average pain (r pelvic =0.78; r nonpelvic =0.73). Conclusions The easy-to-use app captured unique patterns of pain not fully captured by traditional end-of-day/week summary questions or by traditional in-office assessments. Mobile apps for assessing chronic conditions will become increasingly important as telehealth becomes more commonplace.
Kasus im Namdeutschen

Abstract This paper focusses on case marking in informal Namibian German (so called Namdeutsch). Whilst the use of nominative and accusative case is stable and similar to Standard German, there is a considerable amount of variation with regard to the dative case. This phenomenon is analysed in detail using corpus and questionnaire data. Multifactorial analyses reveal that several sociolinguistic and grammatical factors have a significant impact on the language use in this particular domain. Subsequently, the results are compared with other extraterritorial varieties of German and various similarities are found. This supports the idea that there are variety/language overarching principles at work.
Exploring the mechanisms that lead to delayed CD8+ T cell response against Salmonella Typhimurium

Salmonella Typhimurium (ST) infection of murine hosts results in a critical delay in CD8 T cell expansion, and survival is therefore solely dependent on the alternate, innate immune system. A compromised innate immune system is therefore catastrophic for the host. The mechanism of delayed CD8 T cell response was therefore explored. Results indicate that the delay in CD8 T cell activation is related to the inefficient interaction of antigen-presenting cells with ST: ST is not readily taken up by antigen-presenting cells, a significant fraction of ST escapes into the extracellular niches to avoid detection, and within the infected cell ST resides within phagosomes which does not lead to antigen-processing through the direct antigenprocessing pathway. All these mechanisms lead to activation of CD8 T cells by the alternate, cross-presentation pathway, which does not operate efficiently in all the strains of mice.
Distinct Growth Rates of the Two ENSO Types

El Niño‐Southern Oscillation (ENSO) events can be grouped into two types based on their sea surface temperature anomaly spatial patterns, that is, eastern Pacific (EP) and central Pacific (CP) types. In this study, we propose a new method to empirically diagnose linear growth rates of the EP and CP ENSO types due to a limitation of applying the traditional Bjerknes stability index method simply to these two types. We spatially project the peak‐time symmetric component of the mixed‐layer oceanic heat budget terms onto the ENSO‐related sea surface temperature anomaly patterns to estimate the ENSO grow rate. After validating the method by comparing it with the Bjerknes stability index, we show that the growth rate is positive for the CP ENSO type and weakly negative for the EP ENSO type, contributed by different feedback terms. The Coupled Model Intercomparison Project Phase 5‐based multimodel ensemble mean shows similar characteristics as the reanalysis for the EP ENSO type rather than the CP ENSO type.
Aflatoxin M2 concentrations in raw milk of different dairy animal species in Egypt

Previously we reported aflatoxin M1 (AFM1) concentrations in dairy milk of different animal species. Yet, there are no reports of aflatoxin M2 (AFM2) concentrations in raw milk and milk products of dfferent animal species. Aflatoxin M2 levels are usually very low or un-detectable using ELISA or chromatography techniques. The reasons of low concentrations of AFM2 in milk and milk products still remain obscure and controversial. In this study, variable AFM2 concentrations are being reported in milk of different animal species with the highest levels reported in goats milk.
Chemical Composition, Nutritional Value, Safety, and Acceptability of Egyptian Red Sea Coast Fresh and Dried Spider Conch (Lambis Lambis) Meats

Interest in marine mollusks consumption has increased in coastal areas as a good source of protein, minerals, and vitamins (Periyasamy et al., 2011). Mollusks are an invertebrate with soft bodies. Mollusks meat composition and safety are affected by several factors such as species, sex, maturity, feeding regime, and seasonal conditions (Periyasamy, et al., 2011). It includes bivalves, cephalopods, and gastropods group ARTICLE INFO ABSTRACT Article History: Received: June 26, 2020 Accepted: Aug. 29, 2020 Online: Sept. 6, 2020 _______________
F2PNet: font-to-painting translation by adversarial learning

: For Chinese font images, when all their strokes are replaced by pattern elements such as flowers and birds, they become flower–bird character paintings, which are traditional Chinese art treasures. The generation of flower–bird painting requires professional painters’ great efforts. How to automatically generate these paintings from font images? There is a huge gap between the font domain and the painting domain. Although many image-to-image translation frameworks have been proposed, they are unable to handle this situation effectively. In this study, a novel method called font-to-painting network (F2PNet) is proposed for font-to-painting translation. Specifically, an encoder equipped with dilated convolutions extracts features of the font image, and then the features are fed into the domain translation module for mapping the font feature space to the painting feature space. The acquired features are further adjusted by the refinement module and utilised by the decoder to obtain the target painting. The authors apply adversarial loss and cycle-consistency loss to F2PNet and further propose a loss term, which is called recognisability loss and makes the generated painting have font-level recognisability. It is proved by experiments that F2PNet is effective and can be used as an unsupervised image-to-image translation framework to solve more image translation tasks.
In Vitro Micropropagation of Carum copticum L.

An efficient clonal propagation protocol has been established from seedling explants of Carum copticum. Best seed germination frequency (100%) was observed on both Murashige and Skoog (MS) medium and Nitsch and Nitsch (NN) medium supplemented with 1.0 mg l-1 and 0.5 mg l-1 GA3 respectively. Shoot multiplication was initiated from hypocotyl and radical explants cultured on MS and NN media supplemented with various concentration and combination of N6-benzyladenine (BA), kinetin (Kn) and gibberellic acid (GA3). The highest shoot induction (96.66%) was observed from hypocotyl explants on NN medium supplemented with 1.5 mg l-1 BA whereas 93.33% shoot induction was observed on MS medium supplemented with 1.5 mg l-1 BA. The maximum of 11.5 shoots per hypocotyl explant with an average length of 6.68 cm was observed on MS medium supplemented with 1.5 mg l-1 BA whereas 10.83 shoots per hypocotyl explant with an average shoot length of 5.53 cm was observed on NN medium containing same level of BA concentration. Rooting of shoots was achieved on MS and NN media supplemented with various concentrations of indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and napthaleneacetic acid (NAA). The highest root regeneration frequency (96.66%) was observed either on MS supplemented with 0.25 mg l-1 NAA or on NN medium with 0.25 mg l-1 IAA. The maximum number of 7.83 roots per shoot with an average root length of 3.98 cm was observed on MS medium supplemented with 0.25 mg l-1 NAA whereas 7.33 roots per shoot with an average root length of 4.13 cm was observed on NN medium supplemented with same level of NAA. Plantlets were acclimatized in garden soil and transferred to field. The method described here can be successfully employed for large scale production of sterile plants for pharmaceutical use and genetic transformation studies.
A review on the relaxation dynamics analysis of unentangled polymers with different structures

ABSTRACT Relaxation dynamics of unentangled polymer melts (with a chain length below N = 100 for polyethylene) can be studied by performing either Rouse mode or relaxation mode analysis, such as proper orthogonal decomposition. The former mode analysis can be derived analytically from the linear equation of motion of polymers with the inclusion of inertia term, whereas the latter is designed for the case when the numerical solution to a highly nonlinear equation of motion is known, such as MD simulation data. This article presents a summary of both approaches and their applications in the evaluation of zero-shear viscosity of polymer melts.
Molecular typing of Indian isolates of Pasteurella multocida serotype B:2 by ERIC- PCR

Hemorrhagic septicemia is an important disease of livestock in Asian continent. The present study was undertaken to assess the presence of Pasteurella multocida serotype B:2 in various species of animals and to assess the genetic variation among the field isolates of Pasteurella multocida targeting Enterobacterial intergenic consensus sequence (ERIC). Samples were collected from dead and live (suspected for HS) animals and organism was isolated and were molecular typedby ERIC-PCR. Pasteurella multocida serotype B:2 was isolated from cattle, buffalo, sheep, goat, pig and wild animals ( loin and tiger). Isolates (42) were differentiated into 22 different profiles. Study indicate high genetic diversity, no geographic or host specificity among field isolates of Pasteurella multocida serotype B:2 . Vaccine strain P52 used for preparation of killed vaccine in India require reevaluation since it was found to be distantly related to field isolates.
Analysis of Spatial Point Pattern Shows No Desertion of Breeding Mute Swan Areas by the Other Waterbirds Within Fishpond

Abstract. Mute Swan Cygnus olor numbers have recently increased in a dramatic fashion in Western Europe and in North America, suggesting there could be potential consequences for the rest of the waterbird community. Breeding Mute Swan pairs may behave territorially towards other waterbirds, taking advantage of their larger size, and hence cause concern regarding their potential effects on waterbird communities. We studied how the within-site distributions of breeding Mute Swans and other waterbirds were related to each other, in order to assess if there is support to the assertion that breeding Mute Swans may affect the distribution of the other waterfowl within waterbodies. We mapped waterbird and swan distribution within fishponds during the Mute Swan breeding period. Relying on spatial point pattern analysis, our first finding is that breeding Mute Swans were located in the vicinity of the other waterbirds, using the same area within fishpond. Waterbirds do not completely desert the area used by breeding swan pairs within a waterbody, hence not supporting the claim that Mute Swans dislodge the other species. If an exclusion process by Mute Swan breeding pairs towards waterbirds exists, it is not strong enough to generate deserted areas by waterbirds around breeding Mute Swans. Our second finding is that breeding Mute Swans were not located where the density probability function for waterbird presence was the greatest within a fishpond, i.e. breeding Mute Swans were not located in the centre of groups formed by other waterbirds within each fishponds. This may indicate slightly different micro-habitat preferences or use within fishponds, or could indicate the potential occurrence of interactions. In conclusion, these results question whether the increasing Mute Swan populations actually directly threaten the other waterbird communities in such habitats, and require population control as is often claimed.
Biosynthesis and transport of terpenes

Terpenoids are the largest class of natural product that are produced by plants, with functions that range from a role in plant development to direct defence against pathogens and indirect defence against insects through the attraction of natural enemies. While terpene biosynthesis genes have been well studied, there is still only limited knowledge on how terpenes are transported within the cell and from the cell to the apoplast. In this thesis, different aspects of transport of terpenes in plants were addressed. Firstly, the issue of intermediate transport between enzymes was studied, focussing on the regulation of intermediate flux between two different biosynthesis enzymes (CYP71AV1 and DBR2) that determines the resulting Artemisia annua, low or high artemisinin, chemotype. We also investigated the role of Lipid Transfer Proteins and vesicles in the transport of terpenes. Some LTP mutants were indeed shown to emit lower terpene levels, but the exact mechanism could not be resolved. Inhibition of vesicle transport increased terpene levels, most likely due to an effect on protein stability. I conclude that there are multiple transport mechanisms involved in terpene transport which complicates the analysis of a single transport pathway.
Kernel-based curve-fitting method with spatial regularization for generation of parametric images in dynamic PET

Due to high levels of noise in pixel-wise time-activity curves, the indirect method that generates kinetic parametric images from dynamic positron emission tomography (PET) images often results in poor parametric image quality. We have demonstrated that the quality of parametric images can be improved by denoising dynamic PET images, using gradient-free curve-fitting and applying a kernel-based post-filtering to parametric images. However, many gradient-free curve-fitting methods are time-consuming. Moreover, some parameter estimates (e.g. k2 and k3) have large variability. To provide high-quality PET parametric images with low computational cost, we propose a curve-fitting method that incorporates the kernel-based denoising method and the highly constrained backprojection technique into the Levenberg-Marquardt (LM) algorithm. We conducted a simulation study to evaluate the performance of the proposed curve-fitting method. Dynamic PET images were reconstructed using the expectation-maximization (EM) algorithm and were denoised before parameter estimation. Compared to the LM algorithm with and without the kernel-based post-filtering, the proposed method achieved superior performance, offering a decrease in both bias and coefficient of variation (CV) on all parametric images. Overall, the proposed method exhibited lower bias and slightly higher CV than the gradient-free pattern search method with the kernel-based post-filtering (PatS-K). Moreover, the computation time of the proposed method was about 18 times lower than that of the PatS-K method. Finally, we show that the proposed method can further improve the quality of parametric images when dynamic PET images are reconstructed using the kernel-based EM algorithm.
Analysis and Experimentation of Modular Differential Inverter Utilizing SEPIC Modules and SIC Devices for Grid Connected Applications

This paper presents a three-phase Modular Differential Inverter (MDI) utilizing DC-DC modules that provide AC power to the utility grid with step-up voltage capability. The construction of the MDI has many advantages such as flexibility and reliability, and can be designed, optimized and scaled to any power level. Moreover, Single–Ended Primary–Inductor Converter (SEPIC) modules have been proposed to incorporate in the MDI because it has many merits that enhance the overall performance of the differential inverter. SiC devices are also integrated into the SEPIC modules for efficient operation at a high switching frequency. An in-depth mathematical model discussing the practical issues of differential inverter such as variable duty cycle, low order harmonics and circulating power is also presented. The design steps of the proposed SEPIC modules are presented in detail considering the standard grid side requirements of total harmonic distortion (THD). The MDI, which implements three parallel modules in each phase, is investigated using PSIM simulation software. A mismatch of ±20% in the SEPIC module parameters of each phase is investigated to confirm the system performance. Moreover, a laboratory prototype of the system, considering only one SEPIC module in each phase with 200 V grid-side voltage, 1.6 kW, and 50 kHz switching frequency, is carried out to verify the validity of the system.
Epitheliocystis in lake trout (Salvelinus namaycush)

EPITHELIOCYSTIS IN LAKE TROUT (SALVELINUS NAMAYCUSH ) Elena Contador Advisor: University of Guelph, 2013 Dr. John S. Lumsden Epitheliocystis is a condition that has been recognised in a wide range of freshwater and marine fish species. The infection is characterized by intracytoplasmic inclusions in gills and less commonly, skin. Since 2004, molecular evidence has shown that epitheliocystis is associated with Chlamydia-like organisms. Lake trout (Salvelinus namaycush) are raised for release by the Ontario Ministry of Natural Resources at Blue Jay Creek, Manitoulin Island, ON. This facility has experienced yearly epizootics of epitheliocystis during winter. Affected lake trout have marked gill lesions including: severe branchial epithelial cell necrosis, epithelial hyperplasia with thickening and blunting of lamellae and occasionally small to large numbers of scattered epithelial cells containing 10-30 μm bacterial inclusions. The use of PCR primers previously described to identify chlamydialike organisms has not produced consistent results with the gills of these LT with prominent intraepithelial microcolonies. The use of universal bacterial primers to 16S rDNA and laser capture microdissection in this thesis provide evidence that a novel βproteobacteria is more consistently associated with affected gills of LT and that this organism may play an important role in these epizootics of EP.
Was a Sacred Curtain (Parokhet) Depicted on Portable Shrines in the Ancient Near East?

The Parokhet, or sacred curtain, was an important item of cultic paraphernalia in the ancient Near East. It is known from the Sumerian and Akkadian texts, the biblical tradition, the Second Temple in Jerusalem, Greek temples, and synagogues of the Roman and Byzantine eras, and is still in use today. We suggest that such a sacred curtain is depicted on several of the miniature clay objects known as portable shrines. In Egypt, thanks to the dry climate, a miniature curtain of this kind has indeed been preserved in association with a portable shrine. Depictions of shrines on Egyptian sacred barks also include life-size curtains.
The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae)

Abstract Cucurbita pepo is an important economic plant cultivated widely in the world. The complete chloroplast genome sequence of C. pepo is reported here. The genome is 157,343 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,970 bp) and small (SSC, 18,167 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,603 bp). A total of 131 genes were predicted including 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. Further, phylogenetic analysis showed that C. pepo were closely related to other species in the family Cucurbitaceae. The complete chloroplast genome of C. pepo would be taken as a useful molecular tool for species discrimination, taxonomy, and phylogenetic relationships in the family Cucurbitaceae.