Miracle-dz/UniFAR-FTUs huggingface dataset:
Ectopic Expression of URA3 Can Influence the Virulence Phenotypes and Proteome of Candida albicans but Can Be Overcome by Targeted Reintegration of URA3 at the RPS10 Locus

ABSTRACT Uridine auxotrophy, based on disruption of both URA3 alleles in diploid Candida albicans strain SC5314, has been widely used to select gene deletion mutants created in this fungus by “Ura-blasting” and PCR-mediated disruption. We compared wild-type URA3 expression with levels in mutant strains where URA3 was positioned either within deleted genes or at the highly expressed RPS10 locus. URA3 expression levels differed significantly and correlated with the specific activity of Ura3p, orotidine 5′-monophosphate decarboxylase. Reduced URA3 expression following integration at the GCN4 locus was associated with an attenuation of virulence. Furthermore, a comparison of the SC5314 (URA3) and CAI-4 (ura3) proteomes revealed that inactivation of URA3 caused significant changes in the levels of 14 other proteins. The protein levels of all except one were partially or fully restored by the reintegration of a single copy of URA3 at the RPS10 locus. Transcript levels of genes expressed ectopically at this locus in reconstituted heterozygous mutants also matched the levels found when the genes were expressed at their native loci. Therefore, phenotypic changes in C. albicans can be associated with the selectable marker rather than the target gene. Reintegration of URA3 at an appropriate expression locus such as RPS10 can offset most problems related to the phenotypic changes associated with gene knockout methodologies.
An Agent-oriented Conceptual Framework for Biological Systems Simulation

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. On the one hand, researchers working on Systems Biology aim at understanding how living systems perform routinely complex tasks. On the other, people involved in Pharmacogenomics strive to study how an individual’s genetic inheritance affects the body’s response to drugs. Research in all the above disciplines requires the ability to simulate particular biological processes (i.e. metabolic pathways) which characterize biological systems as cells, organs, organisms and communities. Biological processes are complex systems, i.e. a set of components that interacts with each other and with an external dynamic environment. In this work, we aim at providing an alternative way to specify complex systems based on behavioral modelling. We consider a biological process as an activity-based application performed by actors in a dynamic and sometime unpredictable environment; each actor plays his role in relation to the process it is involved, but in general they are part of a more complex system. We propose a conceptual framework to engineering an agent society which simulate the behavior of a biological process. The agents society and its social rules are described through a coordination model specified for a biological process with semiformal languages based on System Biology Modelling Languages for the static-structural and functional views and on UML-like diagrams for the dynamic (control flow) behavior.
Genetics, phosphorus availability, and herbivore-derived induction as sources of phenotypic variation of leaf volatile terpenes in a pine species

Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the α-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species.
Annexin A1 and the regulation of innate and adaptive immunity

Inflammation is the body’s way of defending itself against noxious stimuli and pathogens. Under normal circumstances, the body is able to eliminate the insult and subsequently promote the resolution of inflammation and the repair of damaged tissues. The concept of homeostasis is one that not only requires a fine balance between both pro-inflammatory mediators and pro-resolving/anti-inflammatory mediators, but also that this balance occurs in a time and space-specific manner. This review examines annexin A1, an anti-inflammatory protein that, when used as an exogenous therapeutic, has been shown to be very effective in limiting inflammation in a diverse range of experimental models, including myocardial ischemia/reperfusion injury, arthritis, stroke, multiple sclerosis, and sepsis. Notably, this glucocorticoid-inducible protein, along with another anti-inflammatory mediator, lipoxin A4, is starting to help explain and shape our understanding of the resolution phase of inflammation. In so doing, these molecules are carving the way for innovative drug discovery, based on the stimulation of endogenous pro-resolving pathways.
Heart failure management using implantable devices for ventricular resynchronization: Comparison of Medical Therapy, Pacing, and Defibrillation in Chronic Heart Failure (COMPANION) trial. COMPANION Steering Committee and COMPANION Clinical Investigators.

BACKGROUND Although pharmacological therapy has ameliorated symptoms and improved the survival of patients with chronic heart failure (CHF), this chronic syndrome remains a progressive disease causing incremental morbidity and early mortality. A new therapy for the treatment of CHF should ideally decrease mortality, alleviate symptoms, and improve functional capacity. A growing body of evidence suggests that the use of implantable devices to resynchronize ventricular contraction may be a beneficial adjunct in the treatment of CHF. METHODS The Comparison of Medical Therapy, Pacing, and Defibrillation in Chronic Heart Failure (COMPANION) trial is a randomized, open-label, 3-arm study of patients in New York Heart Association class III or IV with an ejection fraction of 35% or less and a QRS duration of 120 milliseconds or less. The COMPANION study objectives are to determine whether optimal pharmacological therapy used with (1) ventricular resynchronization therapy alone or (2) ventricular resynchronization therapy combined with cardioverter-defibrillator capability is superior to optimal pharmacological therapy alone in reducing combined all-cause mortality and hospitalizations; reducing cardiac morbidity; improving functional capacity, cardiac performance, and quality of life; and increasing total survival.
Large historical changes of fossil‐fuel black carbon aerosols

Anthropogenic emissions of fine black carbon (BC) particles, the principal light‐absorbing atmospheric aerosol, have varied during the past century in response to changes of fossil‐fuel utilization, technology developments, and emission controls. We estimate historical trends of fossil‐fuel BC emissions in six regions that represent about two‐thirds of present day emissions and extrapolate these to global emissions from 1875 onward. Qualitative features in these trends show rapid increase in the latter part of the 1800s, the leveling off in the first half of the 1900s, and the re‐acceleration in the past 50 years as China and India developed. We find that historical changes of fuel utilization have caused large temporal change in aerosol absorption, and thus substantial change of aerosol single scatter albedo in some regions, which suggests that BC may have contributed to global temperature changes in the past century. This implies that the BC history needs to be represented realistically in climate change assessments.
North American Eocene Sea Cows (Mammalia: Sirenia)

Domning, Daryl P., Gary S. Morgan, and Clayton E. Ray. North American Eocene Sea Cows (Mammalia: Sirenia). Smithsonian Contributions to Paleobiology, number 52, 69 pages, 34 figures, 4 tables, 1982. —The record of Eocene sea cows in North America is reviewed in detail, and that of the world is summarized. The North American record includes some 20 localities, mostly yielding fragments identifiable only as sirenian. Of these, the most extensive materials are a partial skeleton from the Cook Mountain Formation of Texas, numerous isolated elements from the Avon Park Formation of Florida, and a partial skeleton and other specimens from the Castle Hayne Formation of North Carolina. The materials from North Carolina and Florida are middle Eocene in age and are referred to Protosiren species. These specimens provide further confirmation of the fact that Eocene sirenians had a 3.1. 5.3 dental formula and were the latest eutherians known to exhibit five premolars. The implications of this for the higher classification of mammals are discussed. The distribution of sirenians suggests a homogeneous middle Eocene Tethyan fauna and also seems to be a more useful guide to the former distribution of seagrasses than are the distributions of Foraminifera. Eocene sirenians have potential value in intercontinental biostratigraphic correlation. Official publication date is handstamped in a limited number of initial copies and is recorded in the Institution’s annual report, Smithsonian Year. Series cover design: The trilobite Phacops rana Green. Library of Congress Cataloging in Publication Data Domning, Daryl Paul North American Eocene sea cows (Mammalia: Sirenia) (Smithsonian contributions to paleobiology ; no. 52) Bibliography: p. 1. Sirenia, Fossil. 2. Paleontology—Eocene. 3. Paleontology—North America. I. Morgan, Gary Scott. II. Ray, Clayton Edward. III. Title. IV. Series. QE701.S56 no. 52 [QE882.S6] 560s 82-3252 [569'. 5] AACR2
Molecular Characterization of msp2/p44 of Anaplasma phagocytophilum Isolated from Infected Patients and Haemaphysalis longicornis in Laizhou Bay, Shandong Province, China

Molecular characterization of the MSP2/P44 protein of Anaplasma phagocytophilum may determine not only if the bacterium is capable of invading hosts but also whether it generates antigenic variation for the purpose of escaping the host immune response, resulting in various pathologic injuries and serious clinical outcomes. Chinese anaplasmosis patients usually present with serious manifestations, and the fatality rate is as high as 26.5%. In this study, we amplified, cloned and sequenced the msp2/p44 genes of three Chinese A. phagocytophilum isolates from Laizhou Bay, Shandong Province, where human granulocytic anaplasmosis (HGA) patients present severe clinical manifestations, and analyzed their genetic characterization and structural features. We also compared them with the HZ and Webster A. phagocytophilum strains. The sequences for both strains are available in GenBank. Analyses indicated that Chinese A. phagocytophilum isolates were significantly different from the HZ and Webster strains in terms of nucleotide sequences, amino acid sequences and protein secondary and tertiary structures. Moreover, the number of immunologic B-cell epitopes (19) of the MSP2 protein of the Chinese isolates was higher than that of the A. phagocytophilum strains HZ (16) and Webster (9). This genetic diversity of the MSP2/P44 protein of Chinese A. phagocytophilum isolates might be relevant and might have serious clinical outcomes. This observation could provide a clue to further understand the pathogenesis of Chinese A. phagocytophilum.
Adaptive communication algorithms for distributed heterogeneous systems

Heterogeneous network-based systems are emerging as attractive computing platforms for HPC applications. We discuss fundamental research issues that must be addressed to enable network-aware communication at the application level. We present a uniform framework for developing adaptive communication schedules for various collective communication patterns. Schedules are developed at run-time, based on network performance information obtained from a directory service. We illustrate our framework by developing communication schedules for total exchange. Our first algorithm develops a schedule by computing a series of matchings in a bipartite graph. We also present a O(P/sup 3/) heuristic algorithm, whose completion time is within twice the optimal. This algorithm is based on the open shop scheduling problem. Simulation results show performance improvements of a factor of 5 over well known homogeneous scheduling techniques.
Preliminary Studies on the Etiology of Keratoconjunctivitis in Reindeer (Rangifer tarandus tarandus) Calves in Alaska

Keratoconjunctivitis outbreaks occur each summer in reindeer (Rangifer tarandus tarandus) herds in western Alaska, USA. This condition has not been well characterized nor has a definitive primary etiologic agent been identified. We evaluated the eyes of 660 calves near Nome, Alaska, between 29 June and 14 July 2005. Clinical signs of keratoconjunctivitis were observed in 26/660 calves (3.9%). Samples were collected from the conjunctival sac of both affected (n=22) and unaffected (n=24) animals for bacterial culture, enzyme-linked immunosorbent assay testing for Chlamydophila psittaci, and for polymerase chain reaction assays for Mycoplasma and Moraxella spp. No primary bacterial or viral etiologic agent(s) were isolated or identified. The cause of keratoconjunctivitis among reindeer calves was not determined, but it could involve an anaerobic bacteria, a difficult-to-isolate viral agent, stress associated with repeated handling, ocular foreign bodies, exposure to corral dust or arthropods, or a combination.
Antibiotic resistance genes, integrons and multiple antibiotic resistance in thirty-five serotypes of Salmonella enterica isolated from humans and animals in the UK.

OBJECTIVES To examine 397 strains of Salmonella enterica of human and animal origin comprising 35 serotypes for the presence of aadB, aphAI-IAB, aadA1, aadA2, bla(Carb(2)) or pse1, bla(Tem), cat1, cat2, dhfr1, floR, strA, sul1, sul2, tetA(A), tetA(B) and tetA(G) genes, the presence of class 1 integrons and the relationship of resistance genes to integrons and antibiotic resistance. RESULTS Some strains were resistant to ampicillin (91), chloramphenicol (85), gentamicin (2), kanamycin (14), spectinomycin (81), streptomycin (119), sulfadiazine (127), tetracycline (108) and trimethoprim (45); 219 strains were susceptible to all antibiotics. bla(Carb(2)), floR and tetA(G) genes were found in S. Typhimurium isolates and one strain of S. Emek only. Class 1 integrons were found in S. Emek, Haifa, Heidelberg, Mbandaka, Newport, Ohio, Stanley, Virchow and in Typhimurium, mainly phage types DT104 and U302. These strains were generally multi-resistant to up to seven antibiotics. Resistance to between three and six antibiotics was also associated with class 1 integron-negative strains of S. Binza, Dublin, Enteritidis, Hadar, Manhattan, Mbandaka, Montevideo, Newport, Typhimurium DT193 and Virchow. CONCLUSION The results illustrate specificity of some resistance genes to S. Typhimurium or non- S. Typhimurium serotypes and the involvement of both class 1 integron and non-class 1 integron associated multi-resistance in several serotypes. These data also indicate that the bla(Carb(2)), floR and tetA(G) genes reported in the SG1 region of S. Typhimurium DT104, U302 and some other serotypes are still predominantly limited to S. Typhimurium strains.
Cadherin-20 expression by motor neurons is regulated by Sonic hedgehog during spinal cord development

During chicken spinal cord development, cadherin-20 is expressed by motor neurons of the lateral motor column and other cells in the basal and alar plates. To investigate the regulation of cadherin-20 expression, Sonic hedgehog (Shh) signaling was altered in chicken spinal cord and hindbrain by in-vivo electroporation. Our results show that, at an early embryonic stage 12, Shh induces cadherin-20 expression by motor neurons. Later, at stage 24 when the sorting of motor neuron pools begins, cadherin-20 expression is induced in the neural progenitors of the ventricular zone but not in motor neurons. Blockage of Shh signaling inhibits cadherin-20 expression in the motor column. Therefore, cadherin-20 expression in motor neurons is regulated by Shh in a time-dependent manner.
Population-Wide Failure to Breed in the Clark’s Nutcracker (Nucifraga columbiana)

In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark’s nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark’s nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark’s nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark’s nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.
A synthetic instrument for diagnosis and performance measurement of Individuals with Visual Sequential Memory Deficit

When performing tasks such as remembering letters, numbers, objects, or shapes, a persons Visual Sequential Memory (VSM) plays a crucial role, especially when the order of the tasks is important. Lack of VSM makes the persons life more challenging, possibly leading to dyslexia and dyscalculia. As such, it is important to detect and treat Visual Sequential Memory Deficit (VSMD). But current clinical methods have a low rate of diagnosis, and also offer limited hours to persons being treated in the clinics. In this paper, we propose an Origami based Serious Game, called Memori, as a synthetic instrument for the diagnosis, performance measurement, and treatment of people with VSMD. We illustrate the rationale behind using Origami, the design process of our game, and its implementation. Our preliminarily performance evaluations with 24 adults reveal a 13% improvement of memory and 1.00 score increase in performance while a slight decrease occurred in attentiveness from 2.33 to 2.02 for people who use our tool.
Stability analysis of spectral methods for hyperbolic initial-boundary value systems

We treat a constant coefficient hyperbolic system in one space variable, with zero initial data. Dissipative boundary conditions are imposed at the two points $x = \pm 1$. This problem is discretized either by a spectral or pseudospectral approximation in space. We demonstrate sufficient conditions under which the spectral numerical solution is stable; moreover, these conditions have to be checked only for scalar equations. The stability theorems take the form of explicit bounds for the norm of the solution in terms of the boundary data. The dependence of these bounds on N, the number of points in the domain (or equivalently the degree of the polynomials involved), is investigated for a class of standard spectral methods, including Chebyshev and Legendre collocations.
Heart beat-to-beat intervals classification for epileptic seizure prediction

This work is devoted to the prediction of epileptic seizures using heart rate variability (HRV) characteristics. Several HRV features were extracted (statistical, spectral, histogram, polynomial approximation coefficients) for various durations of sliding time windows and various lengths of preictal intervals. The data from 14 subjects with generalized epileptic seizures was used. Support Vector Machine was exploited as a classifier. Leave-One-Group-Out validation, yielded the following values of classifier performance: AUC = 0.7622, sensitivity = 0.7252, specificity = 0.7252. These results indicate the possibility of seizure prediction using HRV characteristics. Our findings regarding positioning and sizing of used time windows, namely the imitations in finding optimal parameters between different subjects, could be used for further advancement of methods for epileptic seizure prediction using the heart rate variability characteristics.
A Comparison of Two Landing Styles in a Two-Foot Vertical Jump

Gutiérrez-Davila, M, Campos, J, and Navarro, E. A comparison of two landing styles in a two-foot vertical jump. J Strength Cond Res 23(1): 325-331, 2009-In team sports, such as basketball and volleyball, the players use different takeoff styles to make the vertical jump. The two-foot vertical jump styles have been classified according to the landing style and identified as hop style, when both feet touch the ground at the same time, and step-close style, when there is a slight delay between the first and second foot making contact with the ground. The aim of this research is to identify the differences between the two styles. Twenty-three subjects participated in the study, of whom 14 were volleyball players and 9 were basketball players. The jumps were video recorded and synchronized with two force platforms at 250 Hz. Two temporal periods of the takeoff were defined according to the reduction or increase in the radial distance between the center of gravity (CG) and the foot support (T - RDCG and T + RDCG, respectively). The findings produced no specific advantages when both styles were compared with respect to takeoff velocity and, consequently, to jump height, but takeoff time was significantly shorter (p < 0.001) in the hop style takeoff. However, this reduction was compensated for by the greater time employed in the last step of the approach run (p < 0.001). When the step-close style was used, the vertical velocity of CG at the beginning of the takeoff is significantly lower. Moreover, the mean vertical force developed during T − RDCG was reduced by −627.7 ± 251.1 N, thus lessening impact on landing. Horizontal velocity at the end of the takeoff is less when the step-close style is used (p < 0.005), suggesting that this style is better for jumps where it is necessary to move horizontally during the flight against an opponent.