Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduced species dominate different responses of grassland communities to climate change on serpentine and nonserpentine soils

Introduced species are a common feature of modern plant communities and experience environmental challenges alongside native species. Changes to the environment may reveal distinct species-environment relationships for native and introduced components of plant communities. Extreme environmental change, such as drought, is predicted to result in declines in native species and increased opportunities for invasion, but empirical support for these ideas remains mixed. We tested for differences in the response of native and invaded species to environmental changes by analyzing a longterm dataset of species abundance in California grasslands collected during a period of severe drought. Sampling sites included a combination of stressful serpentine soils, which are resilient against invasion and maintain diverse native species assemblages, and more benign nonserpentine soils, which are heavily invaded and harbor low levels of native species cover. We found a significant correlation between sampling year and species composition for nonserpentine sites, but not for serpentine sites. These patterns were repeated when only introduced species were included in the analysis but no pattern of change was found for native species. The species most strongly associated with directional change on nonserpentine soils were three invasive Eurasian grasses, Bromus hordaceus, Taeniatherium caput-medusae, and Avena fatua. Differences in species composition on both serpentine and nonserpentine soils were significantly correlated with specific leaf area, a trait which has been linked to drought tolerance in these communities, although changes in abundance for the three Eurasian grasses most strongly associated with change did not consistently follow this pattern. Our analyses indicate relatively stable native community composition and strong directional change in introduced species composition, contradicting predictions for how native and introduced species will respond to environmental shifts, but supporting the hypothesis that native and invading species groups have important functional differences that shape their relationships to the environment.
Mechanisms of interference and exploitation competition in a guild of encrusting algae along a South African rocky shore

Within the marine benthos, space is considered an absolute requirement that is often in limited supply. The often-low availability of this essential resource causes species to interact competitively through mechanisms of interference and exploitation. Species of encrusting algae, in particular, use overgrowth as a mechanism for interference competition, and variable growth rates have regularly been argued as a mechanism for exploitation competition. This study examined overgrowth interactions as a proxy for interference competition, and cover abundance as an indirect proxy for exploitation competition, to understand how encrusting algal species coexist. Cover abundance was shown to be tightly correlated with marginal growth rates (r = 0.99, p < 0.023), although data existed for only three of the six species examined, so it was not possible to use growth rate per se as a proxy for exploitation competition. The results additionally indicated a strong competitive hierarchy for both overgrowth competition and for cover abundance, and an inverse relationship between the two proxies (overgrowth vs cover abundance) of competition (upper mid-eulittoral zone, r = −0.81; lower mid-eulittoral zone, r = −1.00). Although postulated, none of the species that are seemingly subordinate in terms of overgrowth are excluded from their respective habitats. The reason for the coexistence between subordinate and superior overgrowth competitors can be argued through the interplay between interference and exploitation competition mechanisms, in which species that are typically always overgrown (poor interference competitors) maintain their existence largely because they are better at exploiting the limited available space because their faster growth rates result in higher cover abundances.
Modulation of promoter occupancy dictates the transcriptional response to graded BMP signalling levels in the Drosophila embryo

Morphogen gradients specify cell fates during development, with a classic example being the BMP gradient’s conserved role in embryonic dorsal-ventral axis patterning. Here we use quantitative imaging and computational modelling to determine how the BMP gradient is interpreted at single-cell resolution in the Drosophila embryo. We show that BMP signalling levels are decoded by modulating promoter occupancy, the time the promoter is active, predominantly through regulating the promoter activation rate. As a result, graded mRNA numbers are detected for BMP target genes in cells across their expression domains. Introducing a heterologous promoter into a BMP target gene changes burst amplitude but not promoter occupancy suggesting that, while the promoter sequence controls amplitude, occupancy depends on the amount of BMP signal decoded by the enhancer. We provide evidence that graded mRNA output is a general feature of morphogen gradient interpretation and discuss how this can impact on cell fate decisions.
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules

The confident high-throughput identification of small molecules remains one of the most challenging tasks in mass spectrometry-based metabolomics. SIRIUS has become a powerful tool for the interpretation of tandem mass spectra, and shows outstanding performance for identifying the molecular formula of a query compound, being the first step of structure identification. Nevertheless, the identification of both molecular formulas for large compounds above 500 Daltons and novel molecular formulas remains highly challenging. Here, we present ZODIAC, a network-based algorithm for the de novo estimation of molecular formulas. ZODIAC reranks SIRIUS’ molecular formula candidates, combining fragmentation tree computation with Bayesian statistics using Gibbs sampling. Through careful algorithm engineering, ZODIAC’s Gibbs sampling is very swift in practice. ZODIAC decreases incorrect annotations 16.2-fold on a challenging plant extract dataset with most compounds above 700 Dalton; we then show improvements on four additional, diverse datasets. Our analysis led to the discovery of compounds with novel molecular formulas such as C24H47BrNO8P which, as of today, is not present in any publicly available molecular structure databases.
The P Value of Likely Extreme Events

Objective: Sometimes there are circumstances where it is necessary to calculate the P Value of extremely events xt like p(xt) = 1 while reliable methods are rare. Methods: A systematic approach to the problem of the P Values of extremely events is provided. Results: New theorems for calculating P Values of extremely likely events are developed. Conclusions: It is possible to calculate the P Values even of extreme events. E-mail: Barukcic@t-online.de Keywords: P Value, likely events, cause, effect, causal relationship.
Disparity of Risk Factors Stunting on Toddlers in the Coast and the Mountain Areas of Sinjai, South Sulawesi

Stunting is a form of malnutrition is characterized by short stature in children. The prevalence of toddler stunting in 2017 in South Sulawesi is 34%, while in Sinjai Regency in 2016 is 34.6%, 2017 is 43.7%, and 2018 is 35.8%. The purpose of this study was to analyze the disparity of stunting risk factors in toddlers on the coast and mountain areas. This study used a case-control design. The sampling techniques are Fixed Disease Sampling and Stratified Proportional Random Sampling. The population consists of the entire toddler in Sinjai, whereas consists of 60 toddler stunting age 9-59 months and 60 normal toddler on the coast and mountain areas. The instrument used the Food Frequency Questionnaire (FFQ) sheet. The data were analyzed by univariate bivariate, Chi Square and multivariate with logistic regression. The Chi square test results showed that the risk factors stunting on the coast is energy intake (p = 0.03; OR = 2.99) and Fe (p = 0.03; OR = 2.99), while in the mountain is the protein intake (p = 0.01; OR = 6.5), Fe (p = 0.01; OR = 4) and Zn (p = 0.00; OR = 5.4). The logistic regression results indicate that stunting dominant risk factors in the coast area is the intake of proteins and in the mountain area is the intake of Fe. There is a disparity between the risk factors of stunting toddler in the coast and mountain area. Poor nutritional intake increases the risk of stunting so it is necesary to increase the consumption of food sources of nutrients for toddlers. Stunting merupakan bentuk dari kurang gizi. Tahun 2017, stunting di Provinsi Sulawesi Selatan masih tinggi (34%) dan Kabupaten Sinjai tahun 2016 (34,6%), 2017 (43,7%), dan 2018 (35,8%). Tujuan penelitian untuk menganalisis disparitas faktor risiko stunting balita di wilayah pesisir pantai dan pegunungan. Penelitian ini merupakan penelitian kuantitatif menggunakan desain case control. Teknik sampling yaitu Fixed Desease Sampling dan Stratified Proportional Random Sampling . Populasi adalah seluruh balita di Sinjai dan sampel yaitu balita stunting usia 9-59 bulan dan minimal sampel sebanyak 60 balita stunting di wilayah pesisir pantai dan pegunungan serta 60 balita normal di wilayah pesisir pantai dan pegunungan. Instrumen menggunakan lembar FFQ Semikuantitatif. Data dianalisis univariat, bivariat dengan uji Chi Square dan multivariat dengan regresi logistik . Hasil uji Chi Square menunjukkan faktor risiko stunting di wilayah pesisir pantai yaitu asupan energi dengan nilai p =0.03 OR=2.99 dan Fe dengan nilai p =0.03 OR=2.99 sedangkan di pegunungan yaitu asupan protein dengan nilai p =0.01 OR 6.5, Fe dengan nilai p =0.01 OR=4, dan Zn dengan nilai p =0.00 OR=5.4. Hasil regresi logistik menunjukkan faktor risiko stunting yang dominan di wilayah pesisir pantai yaitu asupan protein dan di wilayah pegunungan yaitu asupan Fe. Terdapat disparitas faktor risiko stunting pada balita antara wilayah pesisir pantai dan pegunungan.
Sonographic measurement of lateral parapharyngeal wall thickness and severity of childhood obstructive sleep apnoea

Introduction: Sonographic measurement of lateral parapharyngeal wall (LPW) thickness was found to be associated with severity of obstructive sleep apnoea (OSA) in an adult study. (Liu, K.H. et al. Sleep 2007; 30:1503-8) Whether it is independently associated with severity of OSA in paediatric population has not been investigated. Aims: To investigate the association between LPW thickness and obstructive apnoea hypopnoea index (OAHI) in children. We hypothesised that LPW thickness is associated with obstructive apnoea hypopnoea index (OAHI) in multivariate model adjusted for other correlates. Methods: This is a cross-sectional study. Children aged between 6 and 18 years who attended our sleep disorder clinic with symptoms suggestive of OSA were invited to participate. Children with no OSA symptoms were also recruited from aconcurrent population-based epidemiological study. All subjects underwent anthropometric measurements, nocturnal polysomnography, lateral x-ray cephalometry, tonsil size estimation and sonographic measurement of LPW thickness. Results: A total of 129 children [mean (SD) age = 10.2 (2.4), 72 boys] were included in the analysis. Their OAHI ranged from 0 to 46.9/h with a median (IQR) of 0.8 (0.2 to 3.9). Multivariate linear regression analysis revealed that larger tonsils ( p p p Conclusion: LPW thickness may be an independent risk factor for childhood OSA.
Impact of Guidelines on Use of Helicobacter pylori Testing and Treatment in Hospitalized Patients with Bleeding Ulcers: A Community-Based Study

treatment. • Design: Retrospective review of medical records. • Setting and patients: 562 adults with bleeding peptic ulcers treated in 13 Cleveland-area hospitals in 1994. • Methods: Data collected included demographic data, nonsteroidal anti-inflammatory drug (NSAID) use, endoscopic findings, use of biopsy and/or serology for H. pylori testing, and treatment with antimicrobials. • Results: H. pylori testing was performed in 159 (28%) patients. Although use of testing and treatment increased over the 1-year study period, testing and treatment rates in the 4th quarter were only 34% and 15.6%, respectively. H. pylori testing was associated with younger patient age and endoscopic gastritis. A total of 70 patients (12.5%) were treated for H. pylori. Rates of treatment were higher in younger age groups, men, patients with duodenal ulcers, patients with no history of NSAID use, and in major teaching hospitals. • Conclusion: Despite the release of authoritative published guidelines, use of H. pylori testing and treatment remains low. Further studies should elicit reasons for low adherence.
The Genome of the Charophyte Alga Penium margaritaceum Bears Footprints of the Evolutionary Origins of Land Plants

The colonization of land by plants was a pivotal event in the history of the biosphere, and yet the underlying evolutionary features and innovations of the first land plant ancestors are not well understood. Here we present the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The P. margaritaceum genome has a high proportion of repeat sequences, which are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with earlier diverging plant lineages, P. margaritaceum has uniquely expanded repertoires of gene families, signaling networks and adaptive responses, supporting its phylogenetic placement and highlighting the evolutionary trajectory towards terrestrialization. These encompass a broad range of physiological processes and cellular structures, such as large families of extracellular polymer biosynthetic and modifying enzymes involved in cell wall assembly and remodeling. Transcriptome profiling of cells exposed to conditions that are common in terrestrial habitats, namely high light and desiccation, further elucidated key adaptations to the semi-aquatic ecosystems that are home to the Zygnematophyceae. Such habitats, in which a simpler body plan would be advantageous, likely provided the evolutionary crucible in which selective pressures shaped the transition to land. Earlier diverging charophyte lineages that are characterized by more complex land plant-like anatomies have either remained exclusively aquatic, or developed alternative life styles that allow periods of desiccation.
Effect of GA3 on fruit set and yield of young southern highbush blueberry plants.

Gibberellic acid is a plant growth regulator that affects plant cell division, expansion, and other processes. Gibberellic acid (GA3) applied at flowering to highbush (Vaccinium corymbosum L) and rabbiteye blueberry plants (Vaccinium ashei Reade) increases fruit set and yield under suboptimal pollination conditions, however, this response has been insufficiently tested on southern highbush blueberries. The authors applied GA3 during 75 to 100% flowering to one-year-old ‘Emerald’ and ‘Meadowlark’ southern highbush blueberries, with six replicates of three plant plots per treatment. Treatments were either water, GA3 at 40 fl oz/acre, or, GA3 at 20 fl oz/acre applied twice, with the second treatment 14 days later. At harvest, total fruit weight per plant, fruit number, and average fruit weight were measured. Results verified that GA3 has little to no effect on fruit set in two primary southern highbush blueberry varieties.
Innate Immunity and Adenovirus Vector Immunization

iii DEDICATION. vii LIST OF FIGURES.viii GLOSSARY OF TERMS. ix CHAPTER I: INTRODUCTION. 1 Overview. 2 Adenovirus vector based vaccines. 3 Adenovirus biology. 3 Adenovirus as a vaccine vector . 4 Development of adenovirus vector based-vaccines . 5 Adenovirus vector vaccine immunology. 7 The immune cascade overview. 7 The immunological response elicited by adenovirus vectors. 12 The bridge between innate & adaptive immunity. 16 Innate immunity can regulate adaptive immune responses: a focus on NK cells . 16 Why innate immune regulation can be critical: regulation of immune-mediated pathologies. 18 Importance of understanding innate immunity in the context of vaccination . 21 References. 23 CHAPTER II: ADENOVIRUS VECTOR VACCINATION IMPACTS NK CELL RHEOSTAT FUNCTION FOLLOWING LCMV INFECTION. 38 Acknowledgements. 39 Abstract. 40. 40 Introduction. 41
Effect of Colchicine administration on the structure of the Spleen of adult male albino rat: Histological and Immunohistochemical study

Introduction: Colchicine is a natural alkaloid derived from autumn crocus; it is used in the treatment of gout and in preventing familial Mediterranean fever attacks. It accumulates in many organs such as spleen and may lead to their damage.Aim: This work aimed to study short and long duration effects of colchicine administration on the structure of the spleen of the adult male albino rat.Material and methods: Forty-five adult male albino rats were used in this study, aged from 4-6 months, weighting 150 -180 gm. Rats were equally divided into three groups: Group I: It was further equally subdivided into three subgroups: subgroup IA: Kept as a negative control, subgroup IB: received 1ml of distilled water/day orally for seven days and subgroup IC: received 1ml of distilled water/day orally for 30 days. Group II: received 3mg/Kg body weight/ day of colchicine orally for seven days. Group III: received colchicine as those of group II but for 30 days.Results: The present work revealed that administration of colchicine for short duration induced mild structural alteration of rat’s spleen in the form of reduction in lymphoid follicles size and subcapsular congestion of blood vessels, while, marked structural alteration of rat’s spleen was noticed in group III that received colchicine for long duration in the form of loss of distinction between the white and red pulps with nearly unidentifiable lymphoid follicles and marked parenchymal congested blood vessels.Conclusion: Colchicine administration induced structural alteration of rat’s spleen which was mild with short term use and extensive with long term use.
Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early development

Proper positioning of cells is important for many aspects of embryonic development, tissue homeostasis, and regeneration. A simple mechanism by which cell positions can be specified is via orienting the cell division axis. This axis is specified at the onset of cytokinesis, but can be reoriented as cytokinesis proceeds. Rotatory actomyosin flows have been implied in specifying and reorienting the cell division axis in certain cases, but how general such reorientation events are, and how they are controlled, remains unclear. In this study, we set out to address these questions by investigating early Caenorhabditis elegans development. In particular, we determined which of the early embryonic cell divisions exhibit chiral counter-rotating actomyosin flows, and which do not. We follow the first nine divisions of the early embryo, and discover that chiral counter-rotating flows arise systematically in the early AB lineage, but not in early P/EMS lineage cell divisions. Combining our experiments with thin film active chiral fluid theory we identify specific properties of the actomyosin cortex in the symmetric AB lineage divisions that favor chiral counter-rotating actomyosin flows of the two halves of the dividing cell. Finally, we show that these counter-rotations are the driving force of both the AB lineage spindle skew and cell reorientation events. In conclusion, we here have shed light on the physical basis of lineage-specific actomyosin-based processes that drive chiral morphogenesis during development.
Larval morphology of three Afrotropical pit-building antlions of the genus Myrmeleon Linnaeus (Neuroptera, Myrmeleontidae)

The remarkable diversity of antlions in the Afrotropical region is counterbalanced by the scarce knowledge of their biology and ecology. In particular, their larval stages are largely unknown and the morphology of African pit-building species was never investigated in detail. The larvae of three pit-building species attaining a wide distribution across the whole continent, namely Myrmeleon caliginosus , M. obscurus and M. quinquemaculatus are described, illustrated and compared with congeners for the first time. Moreover, M. caliginosus is reported for the first time from Namibia, notably extending the known range of this antlion, with implications on the taxonomy and the identification of African Myrmeleon species. The larvae of these three species highlight the overall conservative morphology across the whole genus, differing in relatively minor characters such as size, proportions, pattern and chaetotaxy.
Quality of olive oils from southeastern Brazil

Bragantia, Campinas, v. 78, n. 4, p.479-489, 2019 ABSTRACT: This study aimed to characterize the volati le composition and sensory characteristics of virgin olive oils (VOOs) from eight olive cultivars grown in the southeast region of Brazil. The volatiles were extracted by Solid Phase Micro Extraction (SPME) and analyzed by Gas Chromatography coupled to Mass Spectrometry (GC-MS). The dominant sensory attributes were determined by Temporal Dominance of Sensations (TDS). C5 and C6 alcohols and C6 aldehydes were the most abundant volatiles in the investigated VOOs. E-2-hexenal was among the majority of volatiles in all investigated olive oils, mainly in VOOs from cultivars Arbequina, Arbosana and Grappolo 541, in which it had BASIC AREAS Article
Demographic and Clinical Characteristics of Multiple Sclerosis

Background and purpose: Multiple sclerosis (MS) is one the most prevalent diseases associated with neurological and non-traumatic disability in adults. This autoimmune disease affects the central nervous system (CNS) and manifests different signs and symptoms. The prevalence of disease and age of onset varies considerably across the world. This study aimed at investigating demographic, clinical characteristics, and different risk factors in patients with MS. Materials and methods: The study was performed on 152 MS patients from May 2013-July 2014. McDonald diagnostic criteria were used for disease diagnosis. Data was recorded and analyzed in SPSS V.17. Results: The mean age of patients was 31.6 ± 7.3 and females were three times more likely to be afflicted with MS. Most of the female patients were married. The majority of patients had benign disease (86.4%), and positive family history of MS was found in 21.2%. Plaque lesions in MRI were seen in 94% of the patients. Sensory loss, visual impairment and depression were observed in 45.7%, 43.8%, and 9.2%, respectively. Visual impairment was the first sign of the disease that was observed in most of the patients (41.3%). Fatigue and sexual dysfunction were significantly different between relapse-remitting, primary progressive, and secondary progressive form of MS (P= 0.05 and P= 0.02, respectively). Fatigue was associated with disease progression but other symptoms were not significantly different between three forms of the disease. Conclusion: Demographic and clinical characteristics of MS in Mazandaran province were similar to those reported from other countries. MS registry is recommended to record all MS cases in order to increase knowledge on demographic and clinical characteristics, treatment options, and patient’s response to medications. Furthermore, high familial prevalence of multiple sclerosis in Mazandaran province compared with other regions in Iran calls for further genetic analyses.