Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting section Compressa of Chaetoceros (Bacillariophyceae), with descriptions of C. brevispinosus sp. nov. and C. ornatus comb. nov.

ABSTRACT Recent studies have described several new species within the section Compressa of the genus Chaetoceros. To explore the diversity in the section, further studies were conducted based on monoclonal strains established from Chinese warm waters. A combination of molecular and morphological data showed the presence of a new species, Chaetoceros brevispinosus, within the section. Morphologically, C. brevispinosus is characterised mainly by the morphology of the resting spore. The primary valve is convex with numerous short spines, whereas the secondary valve has a more centrally placed vault with less developed spines and ridges. Chaetoceros brevispinosus constitutes a distinct lineage on the LSU and SSU phylogenetic trees, and forms a sister taxon to C. contortus cf. var. contortus. In the phylogenetic analyses, C. contortus var. ornatus formed a distinct lineage and did not form a sister clade to C. contortus cf. var. contortus. Nine and six different base pairs, as well as a genetic distance of 0.012 and 0.008, separated C. contortus var. ornatus and two clades of C. contortus cf. var. contortus. Morphological differences, based on vegetative cells and resting spores, are still uncertain as the morphology of C. contortus var. contortus needs to be examined based on material from the type locality. Chaetoceros contortus var. ornatus makes up the sister taxon to C. bifurcates on the LSU tree. Hence, we propose that C. contortus var. ornatus be raised to species level as C. ornatus stat. nov.
Use of plant-derived essential oil compounds , naturally-occurring apple aroma compounds and apple juice flavoring mixtures to control Escherichia coli O 157 : H 7

In recent years, there have been a number of studies looking at inhibition of microorganisms by spices, herbs or their extracts. Many of these products have been shown to have antimicrobial activity against foodborne pathogens. The purpose of this research was to evaluate the antimicrobial activity of three essential oil (EO) compounds (thymol, eugenol, and trans-cinnamaldehyde) alone and in combination with three naturally-occurring apple aroma (AA) compounds (hexanal, trans-2-hexenal and 1-hexanol) to identify the minimum inhibitory concentrations necessary to inhibit Escherichia coli O157:H7. Three commercial apple juice flavoring mixtures (natural apple cinnamon, natural apple spice and natural red apple) were additionally tested alone for antimicrobial activity against E. coli O157:H7. The standard agar dilution method (SAD) and checkerboard assay were used to evaluate the efficacy of the nine compounds, alone and in combination against E. coli O157:H7. In general, the EO compounds were significantly more effective against E. coli O157:H7 than the AA compounds (P<0.05). Cinnamaldehye, with an MIC of 0.2 mg/mL, exhibited the highest degree of activity, followed by thymol, eugenol and trans2-hexenal, which each had individual MIC values of 1.6 mg/mL. No synergism was found in the combinations of EO compounds with AA compounds.
Capital Structure, Cash Holdings and Firm Value: A Study of Brazilian Listed Firms

This study analyzed the relationship among capital structure, cash holdings and firm value for a sample of publicly traded Brazilian firms, through panel data regressions, employing the fixed-effects estimator. Initially, it was estimated regressions between capital structure (debt to total capital) and cash holdings (cash to assets), as well as between cash holdings and short and long-term debt. Next, it was applied a regression among firm value, capital structure and cash holdings. The results of this study suggested that debt, both short and long-termed, is negatively related to cash holdings, and that the level of cash holdings is also associated to a lower leverage. The study also presented indirect evidence that financially constrained firms hold more cash. Regarding to the impact of the capital structure on the firm value, short-term debt, long-term debt and the financial constraint had negative marginal effects on the firm value, suggesting a risk-averse behavior of investors in relation to debt. Cash holdings, instead, is valued as positive by investors, but up to an optimum threshold level. Further, the market capitalization is discounted with respect to cash holdings (inverted U-curve), in synergy with static trade-off theory of cash holdings.
Cutting Characteristics of Bulk Metallic Glass

The establishment of appropriate machining techniques for bulk metallic glasses (BMGs), which exhibit excellent mechanical, physical and chemical properties, is required to apply the BMGs. In this report, the cutting characteristics of BMGs were examined by turning with different tool materials, nose radii (Rn) and cutting speeds (V). Round bars of Zr65Cu15Ni10Al10 and Pd40Cu30Ni10P20 at% BMGs were used as the workpieces. In order to compare the cuttability of the BMGs with that of crystalline alloys, steel (JIS SGD-400D) and free-cutting brass (JIS C3604) were used. The principal cutting force (FH) and surface roughness (Ra) of the machined surfaces were measured. X-ray diffraction patterns were also obtained from the machined surfaces. The value of Ra in the BMGs exhibit the upper end of precise finishing level (i.e., Ra ¼ 0:2 mm), and was remarkably lower compared with the steel and a little lower compared with the free-cutting brass in spite of the value of V. The value became smaller with increasing values of Rn, exhibiting a very low value of 0.08 mm for an Rn value of 1.2 mm. The values of FH in both BMGs did not show a clear difference and were half that of the steel for a V value less than 40 m/min, even though the tensile strength of the BMGs was twice as large as the steel. The chip of the BMGs showed an ideal flow type with very short and regular intervals, formed by planar slip, and revealed very homogeneous, flat and featureless back surfaces. From these observations of chips, it is presumed that the reason for the excellent cuttability of BMGs is due to a slipping-off mechanism at planes of very short intervals decided only by the maximum shear stress and non-built-up edges caused by a low glass transition temperature.
Utilization of Cellulolytic Enzymes to Improve the Nutritive Value of Date Kernels and the Investigation of the Impact of Adding these Enzymes to Lactating Goat’s Diets on Rumen Fermentation and Nutrients Digestibility

Two experiments were carried out to evaluate the effects of cellulases supplementation on in vitro degradation of date kernels (the first trial) and in vivo (rumen fermentation and nutrients digestibility) by lactating Zaraibi goats (the second trial). In the in vitro experiment, dry matter and organic matter disappearance (IVDMD and IVOMD) were determined for date kernels supplemented separately with (Asperozym) and commercial cellulolytic enzyme source (Veta-Zyme Plus®) at 3 levels (15, 30 and 45 U kgG1 DM) compared with the control. The highest values (p<0.05) of IVDMD and IVOMD were observed with Asperozym supplementation level at 45 U kgG1 DM compared to control. While, Veta Zyme Plus® gave the highest (p<0.05) IVDMD and IVOMD values at 15 U kgG1 DM compared to control. In the in vivo experiment, nine lactating Zaraibi goats after 7 days of parturition were divided into three groups, three animals each, using 3×3 Latin square designs. The first group was fed 37.5% Concentrate Feed Mixture (CFM), 12.5% date kernel and 50% berseem hay (control diet). The second group was fed control diet supplemented with Veta-Zyme Plus® at level 15 U kgG1 DM (T1). The third group was fed control diet supplemented with Asperozyme at level 45 U kgG1 DM (T2). The results indicated that Asperozym and Veta-Zyme Plus® supplementation significantly (p<0.05) increased nutrients digestibility, nutritive values, ruminal Total Volatile Fatty Acids (TVFA's) and ruminal ammonia nitrogen (NH3-N) for treated groups compared with the control group.
Carbono almacenado en estrato arbóreo de sistemas ganaderos y naturales del municipio de Albania, Caquetá, Colombia

El objetivo del presente estudio fue estimar la capacidad de almacenamiento de carbono en el componente arbóreo de cinco usos de suelo tanto en sistemas ganaderos como naturales: a) pasturas tradicionales con árboles dispersos en baja densidad (PT), b) pasturas mejoradas con árboles dispersos en baja densidad (PM), c) sistemas silvopastoriles en alta densidad (SSP), d) bosque (Bo) y e) regeneración natural (RN). Se realizaron tres repeticiones por cada uso del suelo y se registró cada árbol dentro del inventario florístico; para PT, PM y SSP se hicieron parcelas de 1000 m2; para Bo, parcelas de 2000 m2, y para RN, parcelas de 1000 m2 para identificación de fustales, latizales y brinzales. Los datos fueron examinados mediante análisis de varianza y comparados mediante la prueba DGC con un nivel de significación del 95 %. El bosque presentó diferencias significativas con valores de 249,04 Mg ha-1 en biomasa y 124,52 Mg ha-1 en carbono, respecto a los demás usos del suelo; la variable diámetro a la altura del pecho (DAP) mostró diferencias significativas (p<0,05), donde la RN obtuvo los DAP más bajos y Bo los más altos con 4,93 y 18,52 cm, respectivamente. El número de individuos (árboles ha.1) no fue notablemente diferente entre Bo (525) y RN (930), pero estos dos mostraron diferencias considerables respecto a los tres agroecosistemas de pasturas, con valores de 17, 47 y 207 individuos ha-1 para PM, PT y SSP respectivamente. En conclusión, se observó que la cobertura con mayor capacidad de producción de biomasa y almacenamiento de carbono fue el bosque y la de menor fueron las pasturas mejoradas con especies de Brachiaria sp. ; asimismo, la mayor densidad de árboles se presentó en las coberturas de regeneración natural, que tienen un alto potencial para el incremento de la capacidad de captura de carbono.
Industrial Clusters, Innovation and Universities - The Role of the University in a Textile Cluster

The main purpose of this paper is to contribute to the discussion about the role played by universities in the traditional industrial clusters, as a result of the changing situation of the competitive environment. To achieve this objective, our work makes a study of an industrial cluster for a so-called traditional sector with serious problems of competitiveness. The study results show how the cluster has changed the redeployment of its relational capital, becoming more important the relationship between the companies of the cluster and the University. This is caused by the search of a greater product differentiation, through processes of innovation and product improvement in which the University plays an important role.
Comparison of Navier‐Stokes and DSMC Gas Flow Models in Semiconductor Process Chambers

Validated, fast turnaround simulations of flows in the transition regime are of significant use as computer‐aided design tools for the design of vacuum systems in low‐pressure semiconductor processing equipment. This work compares a generic Navier‐Stokes flow solution (CFD) using slip boundary conditions to previous simulations from a DSMC code and data taken in an instrumented vacuum test cell typical of semiconductor equipment chambers. The CFD solution matched up as well or better than the previous DSMC simulations at pressures and flows between 1 and 5 millitorr and 100 and 500 SCCM of nitrogen, respectively. This good agreement is seen because even though the mean free path at the lowest pressure is about 5 centimeters, the local Knudsen number is smaller than 0.1 in the flow, which is a generally accepted upper limit for applicability of CFD solutions with slip boundary conditions. Since CFD solutions can be obtained an order of magnitude or more faster than corresponding DSMC solutions, the CFD app.
Comparison of experimental and modelling results of thermal properties in Cu-AlN composite materials

Copper-based composites could be widely used in automotive, electronic or electrical industry due to their very promising thermal properties. In the present paper, Cu-AlN metal matrix composites with ceramic volume fractions between 0.1 and 0.4 were fabricated by hot pressing method in vacuum. Dependence of the coefficient of thermal expansion (CTE) and the thermal conductivity (TC) on the chemical composition of composites has been investigated. The measured values of the thermal expansion coefficient have been compared with the analytical models' predictions. A numerical model based on FEAP 7.5 in 3D space has been used to evaluate the influence of the porosity on the thermal properties (thermal conductivity) of the composite. A fairly good correlation between the FEM results and the experimental measurements has been obtained.
Discussion Paper 1406 HETEROGENEITY IN PREFERENCES TOWARDS

We analyze lottery-choice data in a way that separately estimates the effects of risk aversion and complexity aversion, and allows both both of these to vary between individuals, and also to change with experience. The data is from an experiment in which 80 subjects engage in a sequence of 54 choices between pairs of lotteries. The lotteries always have the same expected value, but they differ in terms of variance and the level of complexity. Complexity is represented by the number of different outcomes in the lottery, and is either 1 (sure win), 3 (simple), 6 (complex) or 27 (very complex). A finite mixture random effects model is estimated which assumes that a proportion of the population are complexity neutral, and we find that around 32% of the population are complexity neutral. In those subjects who do react to complexity, there is a bias towards complexity aversion at the start of the experiment, but complexity aversion reduces with experience, to the extent that the average subject is complexity neutral by the end of the experiment. Around 23% of subjects appear complexity loving. Some of these findings are consistent with switching patterns seen in the choice data. Complexity aversion is found to increase with age, and is found to be higher for non-UK students than for UK students JEL classification codes C91, D03, D81
Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945

Cdc2-like kinases (CLKs) play a crucial role in the alternative splicing of eukaryotic pre-mRNAs through the phosphorylation of serine/arginine-rich proteins (SR proteins). Dysregulation of this processes is linked with various diseases including cancers, neurodegenerative diseases, and many genetic diseases. Thus, CLKs have been regarded to have a potential as a therapeutic target and significant efforts have been exerted to discover an effective inhibitor. In particular, the small molecule CX-4945, originally identified as an inhibitor of casein kinase 2 (CK2), was further revealed to have a strong CLK-inhibitory activity. Four isoforms of CLKs (CLK1, CLK2, CLK3, and CLK4) can be inhibited by CX-4945, with the highest inhibitory effect on CLK2. This study aimed to elucidate the structural basis of the selective inhibitory effect of CX-4945 on different isoforms of CLKs. We determined the crystal structures of CLK1, CLK2, and CLK3 in complex with CX-4945 at resolutions of 2.4 Å, 2.8 Å, and 2.6 Å, respectively. Comparative analysis revealed that CX-4945 was bound in the same active site pocket of the CLKs with similar interacting networks. Intriguingly, the active sites of CLK/CX-4945 complex structures had different sizes and electrostatic surface charge distributions. The active site of CLK1 was somewhat narrow and contained a negatively charged patch. CLK3 had a protruded Lys248 residue in the entrance of the active site pocket. In addition, Ala319, equivalent to Val324 (CLK1) and Val326 (CLK2), contributed to the weak hydrophobic interactions with the benzonaphthyridine ring of CX-4945. In contrast, the charge distribution pattern of CLK2 was the weakest, favoring its interactions with benzonaphthyridine ring. Thus, the relatively strong binding affinities of CX-4945 with CLK2 are consistent with its strong inhibitory effect defined in the previous study. These results may provide insights into structure-based drug discovery processes.
Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components

The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted to localize interactions that would favor formation of CcmK3/K4 hetero-hexamers. Attempts to crystallize these CcmK3/K4 associations conducted to the unambiguous elucidation of a CcmK4 homo-hexamer structure. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed in frame with reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
Cell culture isolation of Hepatitis E Virus Genotype 3 Strain obtained from human feces

Hepatitis E virus (HEV) is considered one of the leading causes of acute viral hepatitis worldwide, and about 20 million infections and approximately 57 000 deaths occurred every year. However, little is known about the replicative virus cycle due to the absence of a consensus cell culture model. A549 cell line is considered susceptible to HEV genotype 3, however, both viral strain and cell culture conditions could affect the viral isolation in vitro. The objective of this work was to isolate in vitro an HEV-3 strain obtained from human feces. To this, a genotype 3 HEV strain previously identified by genetic characterization was inoculated in A549 monolayers, and incubated for two hours at 37 °C. Five days post-infection, cells were passaged (subcultured) for the first time, and serial passages were done on average every four days during 41 days. HEV replication was evaluated through RT-qPCR in each passage, and reinfection of the cell line with the viral progeny derived from A549 infected monolayers was assessed through immunofluorescence and RT-qPCR. Viral RNA was detected in each passage from infected monolayers, and the highest amount was found after 26 days (2 x 106 copies/μL). In reinfection assay, capsid antigen was detected perinuclearly and forming foci, and 1x104 copies/μL of viral RNA was detected after 96 hours post infection. This shows that HEV recovered from the cell lysate monolayers was infectious. This viral isolate offers a critical tool to study the unknown aspect of HEV infection.
Environmental filtering underpins the island species—area relationship in a subtropical anthropogenic archipelago

Numerous mechanisms have been proposed to explain the island species–area relationship (ISAR), including the passive sampling effect, the habitat diversity effect, ecological drift and a group of mechanisms jointly termed environmental filtering (or abiotic selection process). However, determining which of these hypotheses underpins the ISAR in a given system remains an open and controversial question, particularly with regards to the environmental filtering. The effect of environmental filtering on the ISAR for woody plants was tested on 29 islands in a subtropical land‐bridge archipelago. Island area had a significant effect on species richness, while isolation was not found to have an effect. After controlling for the passive sampling effect and habitat diversity using a systematic sampling design, we found that a positive ISAR remained. After controlling for island area and isolation, species richness was significantly affected by environmental conditions (e.g. total phosphorus, soil depth and bulk density). When a null model was used that randomly assigned individuals to islands from the regional pool, the difference between the observed and expected richness was greater for smaller islands relative to larger islands. Synthesis. Our results point to an overlooked role of environmental filtering in driving the island species–area relationship (ISAR). Consequently, our study highlights the importance of considering deterministic process in future analyses of the ISAR.
Measurement of skeletal muscle fiber contractility with high-speed traction microscopy

We describe a technique for simultaneous quantification of the contractile forces and cytosolic calcium dynamics of muscle fibers embedded in three-dimensional biopolymer gels. We derive a scaling law for linear elastic matrices such as basement membrane extract hydrogels (Matrigel) that allows us to measure contractile force from the shape of the relaxed and contracted muscle cell and the Young’s modulus of the matrix, without further knowledge of the matrix deformations surrounding the cell and without performing computationally intensive inverse force reconstruction algorithms. We apply our method to isolated mouse flexor digitorum brevis (FDB) fibers that are embedded in 10 mg/ml Matrigel. Upon electrical stimulation, individual FDB fibers show twitch forces of 0.37 µN ± 0.15 µN and tetanic forces (100 Hz stimulation frequency) of 2.38 µN ± 0.71 µN, corresponding to a tension of 0.44 kPa ± 0.25 kPa and 2.53 kPa ± 1.17 kPa, respectively. Contractile forces of FDB fibers increase in response to caffeine and the troponin-calcium-stabilizer Tirasemtiv, similar to responses measured in whole muscle. From simultaneous high-speed measurements of cell length changes and cytosolic calcium concentration using confocal line scanning at a frequency of 2048 Hz, we show that twitch and tetanic force responses to electric pulses follow the low-pass filtered calcium signal. In summary, we present a technically simple high speed and high throughput method for measuring contractile forces and cytosolic calcium dynamics of single muscle fibers. We expect that our method will help to reduce preparation time, costs, and the number of sacrificed animals needed for experiments such as drug testing. Statement of significance We describe a high speed, high throughput method for the simultaneous measurement of contractile force and cytoplasmic calcium dynamics following electrical pulse stimulation of muscle fibers embedded in a 3-dimensional biopolymer matrix. In contrast to the classical approach of attaching muscle fibers to a force-transducer, our method allows for a highly efficient, parallel analysis of large numbers of fibers under different treatment conditions.