Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of spreading microbial swarms and films

Bacterial swarming and biofilm formation are collective multicellular phenomena through which diverse microbial species colonize and spread over water-permeable tissue. During both modes of surface translocation, fluid uptake and transport play a key role in shaping the overall morphology and spreading dynamics. Here, using Bacillus subtilis as our model experimental system, we develop a generalized two-phase thin-film model that couples hydrodynamics, mechanics, osmotic flux and nutrient transport to describe the expansion of both highly motile bacterial swarms, and sessile bacterial biofilms. We show that swarm expansion corresponds to steady-state solutions in a nutrient-rich, capillarity dominated regime. In contrast, biofilm colony growth is described by transient solutions associated with a nutrient-limited, extracellular polymer stress driven limit. We apply our unified framework to explain a range of recent experimental observations associated with the shape, form and dynamics of Escherichia coli and Bacillus subtilis swarms and biofilms. Our results demonstrate how hydrodynamics and transport serve as key physical constraints in regulating biological organization and function in microbial communities.
Establishment of Perennial Groundcovers for Maize‐Based Bioenergy Production Systems

With increasing removal of maize (Zea mays L.) stover for cellulosic biofuels, livestock bedding, and feedstuffs, there exists a need to address natural resources-related issues such as soil erosion, nitrate leaching, and loss of organic matter content. Perennial groundcover (PGC) offers a potential solution for alleviating these problems associated with maize stover removal from conventional cropping systems. We conducted a field study to ascertain the costs of PGC establishment on the primary crop of economic interest and groundcover success under a maize or soybean (Glycine max L.) crop. To test this concept, we established either Kentucky bluegrass (KB) (Poa pratensis L.) or creeping red fescue (CF) (Festuca rubra L.) as living mulch (LM) concurrently with either maize or soybean, documenting impacts on crop maturity, stand density, leaf area index (LAI), normalized difference vegetation index (NDVI), grain yield, grain quality, yield components, and stover C and N. First-year maize and first- and second-year soybean in the no LM control yielded on average 13.00, 3.38, and 4.86 Mg ha–¹, respectively, 30, 84, and 27% greater than LM systems. However, yield did not significantly differ in the second site-year between the no LM and LM maize. Moreover, PGC treatments did not affect expected ethanol yield in the second year, averaging 5459 L ha–¹ in Year 2 over all treatments. These results indicate that further research is needed to achieve both groundcover establishment and subsequent natural resources benefits in row crop production while minimizing impact on yield.
THE INTRAMEMBRANE ASPARTYL PROTEASE SPPL3 REGULATES NATURAL KILLER CELL MATURATION

II ACKNOWLEDGEMENTS . IV TABLE OF CONTENTS . V LIST OF FIGURES . VI CHAPTER I: INTRODUCTION . 1 NATURAL KILLER CELLS . 2 INTRAMEMBRANE PROTEASES . 4 SIGNAL PEPTIDE PEPTIDASES IN THE IMMUNE SYSTEM . 6 SIGNAL PEPTIDE PEPTIDASE-3 (SPPL3) . 7 CHAPTER II: NK CELL MATURATION AND CYTOTOXICITY ARE CONTROLLED BY THE INTRAMEMBRANE ASPARTYL PROTEASE SPPL3 . 10 ABSTRACT . 11 INTRODUCTION . 12 MATERIALS AND METHODS . 15 RESULTS . 22 DISCUSSION . 33 FIGURES . 37 CHAPTER III: DISCUSSION . 58 REFERENCES . 62 BIBLIOGRAPHY . 62 CURRICULUM VITAE . 73
Public health risks associated with hepatitis E virus (HEV) as a food‐borne pathogen

Abstract Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10‐fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is not notifiable in all Member States, and surveillance differs between countries, the number of reported cases is not comparable and the true number of cases would probably be higher. Food‐borne transmission of HEV appears to be a major route in Europe; pigs and wild boars are the main source of HEV. Outbreaks and sporadic cases have been identified in immune‐competent persons as well as in recognised risk groups such as those with pre‐existing liver damage, immunosuppressive illness or receiving immunosuppressive treatments. The opinion reviews current methods for the detection, identification, characterisation and tracing of HEV in food‐producing animals and foods, reviews literature on HEV reservoirs and food‐borne pathways, examines information on the epidemiology of HEV and its occurrence and persistence in foods, and investigates possible control measures along the food chain. Presently, the only efficient control option for HEV infection from consumption of meat, liver and products derived from animal reservoirs is sufficient heat treatment. The development of validated quantitative and qualitative detection methods, including infectivity assays and consensus molecular typing protocols, is required for the development of quantitative microbial risk assessments and efficient control measures. More research on the epidemiology and control of HEV in pig herds is required in order to minimise the proportion of pigs that remain viraemic or carry high levels of virus in intestinal contents at the time of slaughter. Consumption of raw pig, wild boar and deer meat products should be avoided.
Phytoseiid mites of the tribe Typhlodromini (Acari: Phytoseiidae) from sub-Saharan Africa

This is the ninth publication in a series on the taxonomy of phytoseiid mites of sub-Saharan Africa. Sixty-five phytoseiid species of the tribe Typhlodromini Wainstein, all of which are in the genus Typhlodromus Scheuten are reported in this paper (62 in the subgenus Anthoseius DeLeon and 3 in the subgenus Typhlodromus Scheuten). They refer to all species of this tribe known to occur in sub-Saharan Africa. Fifteen new species are described and 41 species are redescribed. Most of the reported species were collected in various habitats in southern Africa and in cassava habitats in tropical Africa. A key is included for the separation of these species.
Litterfall and nutrient dynamics shift in tropical forest restoration sites after a decade of recovery

Multi‐year studies comparing changes in litterfall biomass and nutrient inputs in sites under different restoration practices are lacking. We evaluated litterfall dynamics and nutrient inputs at 5 yr and after a decade of recovery in four treatments (natural regeneration—no planting, plantation—entire area planted, tree islands—planting in patches, and reference forest) at multiple sites in an agricultural landscape in southern Costa Rica. We inter‐planted two native species (Terminalia amazonia and Vochysia guatemalensis) and two naturalized N‐fixing species (Inga edulis and Erythrina poeppigiana) in plantation and island treatments. Although litterfall N was higher in plantations in the first sampling period, litter production and overall inputs of C, N, Ca, Mg, P, Cu, Mn, and Fe did not differ between island, plantation, or reference forest after a decade; however, all were greater than in natural regeneration. Potassium inputs were lower in the natural regeneration, intermediate in island and plantation, and greater in reference forest. The percentage of litterfall comprised by the N‐fixing planted species declined by nearly two‐thirds in both plantations and islands between sampling periods, while the percentage of V. guatemalensis more than doubled, and the percentage from naturally regenerated species increased from 27 to 47 percent in islands. Island and plantation treatments were equally effective at restoring litterfall and nutrient inputs to levels similar to the reference system. The nutrient input changed substantially over the 7‐yr interval between measurements, reflecting shifts in vegetation composition and demonstrating how rapidly nutrient cycling dynamics can change in recovering forests.
The association of primary biliary cholangitis with platelet-derived growth factor and tumor necrosis factor-α

Objective: This study was designed to observe the expression of platelet-derived growth factor (PDGF) and tumor necrosis factor-α (TNF-α) in 32 patients with primary biliary cholangitis (PBC) and 22 healthy controls. The correlation between these two (PDGF and TNF-α) and PBC was analyzed. Methods: The expression of PDGF and TNF-α in the serum of PBC patients and healthy controls was detected by ELISA, and a correlation analysis was conducted. Results: The PDGF serum levels of PDGF was 4.21 ± 2.91 ng/L in the control group, and 1.09 ± 0.43 ng/L in the PBC groups, respectively, and the difference was highly statistically significant (p < 0.001). Furthermore, serum TNF-α level was 126.53 ± 67.79 pg/mL in the control group and 46.13 ± 17.05 pg/mL in the PBC groups, respectively, and the difference was extremely statistically significant (p < 0.001). These variables were compared between the two groups by independent sample t-test. p < 0.05 was considered statistically significant. Conclusions: The expression of PDGF and TNF-α significantly decreased in the PBC group. PDGF and TNF-α may be important expression regulators in PBC. Correspondence to: Chun-Hai Xu, Department of Infectious Diseases, The Second Affiliated Hospital of Harbin Medical University, Harbin, China, Tel: +86 138 0455 0718, Fax: +86 0470832212, E-mail: chunhaixu_dr@163.com
Pollination and fruit set for 'Kordia' and 'Regina' sweet cherry trees in the south of Chile

Kordia’ and ‘Regina’are partially self-compatible cultivars and usually their fruit set and crop load are low in the southern Chile. Insufficient pollen availability due to lack of flowering synchronisation with pollinisers are one of the problems in some seasons, also excessive fruitlets drops have been reported. Different trials were carried out over three seasons in order to understand the phenomenon and to improve fruit set. The main objective of this study was to determine appropriate polliniser cultivars and the effective pollination period (EPP) for ‘Kordia’ and ‘Regina’. The research was carried out in commercial orchards in the Central South region. Eight experiments were performed to determine the intensity of fruit set, using pollen from the following compatible cultivars: ‘Sam’, ‘Schneider’, ‘Staccato’, ‘Sunburst’, ‘Summit’, ‘Sandra Rose’, ‘Sylvia’, ‘Alex’, ‘Katalin’ and ‘Karina’. To assess the EPP six trials were conducted using pollen from different cultivars, ‘Sam’ and ‘Sunburst’ for ‘Kordia’ and ‘Stacatto’ and ‘Schneider’ for ‘Regina’. In the third season, one orchard, planted with ‘Regina’ on rootstock ‘Santa Lucia 64’, was chosen to sample branches and study the EPP under controlled conditions of light and temperature; ‘Kordia’ and ‘Katalin’ were used to pollinate ‘Regina’. The advance of pollen tube was observed under fluorescence microscope. In every season the flowering period was monitored. ‘Regina’ blossom coincided only with the second half of ‘Kordia’ flowering period. ‘Sunburst’, ‘Summit’ and ‘Schneider’ appear as better polliniser for ‘Kordia’ with fruit set of 12-30%. For ‘Regina’, ‘Katalin’ and ‘Schneider’ gave the best fruit set (30-40%). Considering the flowering period and 10% as minimum fruit set, ‘Sunburst’ is good polliniser for ‘Kordia’; and ‘Schneider’, ‘Summit’ and ‘Katalin’ for ‘Regina’. The EPP was about 5 to 6 days for ‘Regina’ and ‘Kordia’, highly influenced by temperature.
Effects of organic, inorganic and organo-mineral fertilizer on the growth, yield and nutrient composition of Corchorus Olitorious (L)

Corchorus olitorius (L.) is an important leafy vegetable known for its rich source of several nutrients and dietary fibre in Africa, Asia and some parts of America. One major limitation of cultivating Corchorus olitorius in the tropics is inadequate soil fertility. Fertilizer application is an integral part of the vegetable cultivation due to low soil productivity. The study therefore aims at evaluating the effects of organic, inorganic and organo-min­eral fertilizer at different concertation on the growth, yield and nutrient composition of Corchorus olitorious. The experimental setup followed a complete randomized block design with three replicates. Treatments include control, 1,000 kgha-1 sole poultry manure (PM), 2,000 kgha-1 sole PM, 200 kgha-1 sole NPK, 400 kgha-1 sole NPK, 600 kgha-1 sole NPK, 1,000 kgha-1 PM+200 kgha-1 NPK, 1,000 kgha-1 PM+400 kgha-1 NPK, 1,000 kgha-1 PM+600 kgha-1 NPK, 2,000 kgha-1 PM+200 kg/ha NPK, 2,000 kgha-1 PM+400 kgha-1 NPK and 2,000 kgha-1 PM+600 kgha-1 NPK fertilizer combinations. The growth, yield and nutrient compo­sition of C. olitorious plants were significantly enhanced in all fertilizer treated plots in comparison to the control. Significantly (p<0.05) higher growth parameters, yield and nutrient composi­tion were recorded in the plots treated with combined application of both fertilizers at 2,000 kgha-1 PM+400 kgha-1 NPK and 2,000 kgha-1 PM+600 kgha-1 NPK when compared to other application combinations. This study affirms that the combined application of organic and inorganic fertilizer as a soil amendment could en­hance growth, yield, and nutrient composition of C. olitorious in comparison with sole application of either fertilizers.
Punishment and Crime in Scandinavia, 1750–2008

Denmark, Finland, Norway, and Sweden have collected criminal justice data since at least the first half of the nineteenth century. These data can be used to describe basic trends in criminal justice interventions as regards violent and property offenses. They can also be used to screen the potential effects of criminal justice interventions on crime compared with more basic structural factors such as urbanization, industrialization, migration, and control of substance use. The marginal effects of changes in criminal sanctions appear to be negligible for the development of recorded crime. These changes include use and abolition of the death penalty, the gradual replacement of imprisonment with alternative sanctions, and the shifting use of fines. The influence of urbanization and industrialization appears to be insignificant, but measures to control alcohol use have had a great effect on violence, as have changes in the opportunity structure on theft. Viewed over the long term, criminal justice interventions during the twentieth century were inefficient in controlling the development of crime and criminals in Scandinavia.
Oviposition preference of three lepidopteran species is not affected by previous aphid infestation in wild cabbage

Several studies have shown that pre‐infestation with aphids can improve plant quality for herbivorous caterpillars. This effect is often explained by the negative crosstalk between specific plant defence, signal‐transduction pathways induced by aphids and caterpillars, respectively. However, in these studies caterpillars are introduced on the plants by the researcher, whereas in nature, the adult mother often chooses the food plants for her offspring. According to the preference–performance hypothesis adult females should choose oviposition sites that result in optimal performance and survival of their offspring. In this study, we investigated whether three lepidopteran species–Pieris brassicae (L.) (Pieridae), Plutella xylostella L. (Plutellidae) and Mamestra brassicae L. (Noctuidae)–prefer aphid‐infested over clean plants. Adult females of the three species was given the choice between wild cabbage (Brassica oleracea L., Brassicaceae) plants infested with aphids, Brevicoryne brassicae (L.) (Hemiptera: Aphididae) for 3, 7, or 14 days vs. non‐infested clean plants. Pieris brassicae females was also given the choice between plants dually infested with B. brassicae aphids and P. xylostella caterpillars when the order of infestation was varied. For oviposition, adult females of all three species did not discriminate between aphid‐infested and clean plants, irrespective of the duration of aphid infestation. Also, P. brassicae females did not discriminate between sets of dually infested plants, irrespective of the order of infestation. Several mechanisms are discussed that could explain this lack of preference.
Molecular Insights into Profilin Regulation and Its Role in Breast Cancer

Dysregulation of actin-regulatory proteins is a hallmark feature of tumor malignancy. Along this line, it has been shown that actin-binding protein profilin-1 (Pfn1) is downregulated in human breast cancer. Contrary to its pro-migratory role in most physiological contexts, loss of Pfn1 promotes migration and invasion of breast cancer cells, and conversely, restoring Pfn1 expression in breast cancer cells by genetic overexpression suppresses these pro-metastatic traits. Based on these previous findings, we set out to a) determine whether Pfn1 regulates breast cancer cell motility through vascular endothelial cells (an obligatory step for intravasation and systemic dissemination of cancer cells) [Aim 1], b) identify small molecules that can elevate Pfn1 expression and suppress motility of breast cancer cells in a Pfn1-dependent manner [Aim 2], and c) gain fundamental insight into how Pfn1 expression is regulated in cells [Aim 3]. We established that loss of Pfn1 promotes transendothelial cell migration of breast cancer cells through enhancing VEGF secretion and barrier disruption of endothelial cells. Next, through a small-scale screen of small molecules, we identified several molecules that are capable of elevating Pfn1 expression including a broad-range kinase inhibitor Tyrphostin A9. The anti-migratory action of Tyrphostin A9 was further shown to be Pfn1-dependent. Finally, we identified megakaryoblastic leukemia (MKL), a transcriptional co-activator of serum response factor (SRF), to be a major co-regulator of the expression of Pfn1, and its closely related isoform Pfn2 (also implicated in breast cancer), and established a novel MKL/STAT (signal transducer and activator of transcription) signaling axis in the context of Pfn regulation.
Assessing the impact of climate change on crop management in winter wheat – a case study for Eastern Austria

SUMMARY Climate change is expected to affect optimum agricultural management practices for autumn-sown wheat, especially those related to sowing date and nitrogen (N) fertilization. To assess the direction and quantity of these changes for an important production region in eastern Austria, the agricultural production systems simulator was parameterized, evaluated and subsequently used to predict yield production and grain protein content under current and future conditions. Besides a baseline climate (BL, 1981–2010), climate change scenarios for the period 2035–65 were derived from three Global Circulation Models (GCMs), namely CGMR, IPCM4 and MPEH5, with two emission scenarios, A1B and B1. Crop management scenarios included a combination of three sowing dates (20 September, 20 October, 20 November) with four N fertilizer application rates (60, 120, 160, 200 kg/ha). Each management scenario was run for 100 years of stochastically generated daily weather data. The model satisfactorily simulated productivity as well as water and N use of autumn- and spring-sown wheat crops grown under different N supply levels in the 2010/11 and 2011/12 experimental seasons. Simulated wheat yields under climate change scenarios varied substantially among the three GCMs. While wheat yields for the CGMR model increased slightly above the BL scenario, under IPCM4 projections they were reduced by 29 and 32% with low or high emissions, respectively. Wheat protein appears to increase with highest increments in the climate scenarios causing the largest reductions in grain yield (IPCM4 and MPEH-A1B). Under future climatic conditions, maximum wheat yields were predicted for early sowing (September 20) with 160 kg N/ha applied at earlier dates than the current practice.
Age and growth of bigeye kilka (Clupeonella grimmi Kessler, 1877) in Iranian waters of the Caspian Sea

Age and growth of Bigeye Kilka, Clupeonella grimmi, were studied in Iranian waters of the Caspian Sea from early May 2006 to April 2007. The sagitta otoliths were removed for each 5 mm length interval up to a total number of 262 fish. Fork length and weight ranged from 92.5 to 142.5 mm and 4.2 g to 23.4 g, respectively. The largest lengthgroups was observed from December to February and the lowest in April, which was coincided with spawning period and feeding during wintering, respectively. The overall sex ratio (male:female) was 0.33:1 which differed significantly from the expected ratio of 1:1. The length-weight regression was W= 0.0000744 FL for females and W=0.0000341FL for males, indicating the Caspian Bigeye grew isometrically for both sexes. Age determination based on otoliths readings showed that the population was composed of sixgroups from 2 to 7 years old which observed a rapidly growth during the second year. In the age compositions, the four years old specimens with a mean fork length and weight 115.5±7.8 mm and 11.9 ± 2.8 g were the most abundant age group and accounted for 40.1%. The condition factor was 0.7-0.8 which varied in difference months and coincided to the gonad development. Age-at-length data were used to determine von Bertalanffy growth parameters for this population in both sexes, indicating that K value and L∞ of females was more than that of males. The results showed that C. grimmi is a rapidly-growing species in the southern parts of the Caspian Sea.
Entitling

Convention and style manuals are largely agreed in mandating that, in references to works of art, titles require special typographic treatment. They are not always agreed, however, on what to do with such expressions as "Franz Schubert's Second Symphony" or "Vasily Kandinsky's unfinished painting of 1944," or the dozens of works called "Untitled. " It would seem to depend upon the manual or the editor. What exactly is a title? What kinds of entities are entitled to titles?
Structural view on the role of WT1’s zinc finger 1 in DNA binding

The WT1 protein is a transcription factor that controls genes involved in cell proliferation, differentiation and apoptosis. It has become increasing apparent that WT1 can act both as a tumor suppressor and oncogene in a tissue specific manner. This opposing role of WT1 is linked to its underlying transcriptional regulatory function, which involves the specific binding to its regulatory elements on gene promoters. WT1 binds DNA using it C-terminal domain made up of 4 C2H2-typ zinc fingers. This same zinc finger domain is used to bind RNA and proteins and it is still not clear how each zinc finger contributes to this promiscuous binding behavior. The molecular details of DNA binding by zinc finger 2 to 4 have been described but it remains to be determined whether or not zinc finger 1 binds DNA and if so whether it exhibits any DNA binding specificity. We present the X-ray structures of zinc finger 1 to 3 bound to a 9 bp and an 8 bp DNA. The two structures refined to 1.7 Å, show no DNA binding specificity for zinc finger 1. The only DNA interactions involving zinc finger 1 are crystal-packing interactions with a symmetry related molecule. In the structure of zinc finger 1 to 3 bound to the 9 bp DNA we observe a shift in the DNA binding positions for zinc fingers 2 and 3. These structures provide molecular detail into the WT1-DNA interaction showing that zinc finger 1 only modestly contributes to DNA binding affinity through transient interactions. The dislocation of zinc finger 2 and 3 emphasizes the importance of zinc finger 4 for maintaining gene transcriptional specificity.