Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characteristics of Community-Associated Methicillin-resistant Staphylococcus aureus (CA- MRSA) Isolates from Clinical Specimens in Iraq

Background : Methicillin-resistant Staphylococcus aureus (MRSA) infections have been recognized for decades as hospital acquired MRSA (HA-MRSA). Nowadays, MRSA is also recognized as a worldwide emerging community-associated pathogen. Community associatedMRSA (CA-MRSA) has been shown to be more virulent with a high degree of severity of disease when compared to HA-MRSA. Objectives: The study was designed to assess the occurrence and the molecular detection of HAMRSA and CA-MRSA isolates obtained from clinical specimens in Iraq. Methods: HA-MRSA and CA-MRSA isolates were obtained from clinical specimens in three main hospitals in Hilla city/Iraq during the period, March to June 2011. MRSA isolates obtained primarily from clinical specimens of skin and soft tissue infections (SSTs) were subjected to genetic study. PCR was used for detection of genes responsible for methicillin resistance ( mec A, SCC mec type
Characteristics of alternating temperatures which stimulate loss of dormancy in seeds of Rumex obtusifolius L. and Rumex crispus L.

Abstract. Alternating temperatures stimulate the germination of Rumex crispus L. and Rumex obtusifolius L. The optimum period spent at the lower temperature in a diurnal cycle is greater than that spent at the higher temperature. Under most conditions the optimum period at the upper temperatures is about 8 h but, as the upper temperature of a cycle is increased, the optimum period at the upper temperature becomes shorter and more critical. Thus when it is 35°C the optimum period is 2.5–4 h in the light, or about 1 h in the dark. The effect of alternating temperatures is much less in the dark than in the light and in general only extreme alternations with short periods at the higher temperature are effective in the dark. In the light any temperature alternation within the range 1–35°C is effective to at least some extent, providing the temperature difference is 5°C or more and providing the alternation includes one temperature which is above approximately 15°C and one which is below approximately 25°C. The optimum temperature difference is about 15°C. In the light, 4 to 10 cycles saturate the response, but in the dark, where the effect is much less, the response may not be saturated even by 16 cycles. KNO3 at 10−3 M has little effect on the response to alternating temperatures either in the light or the dark. The response to alternating temperature regimes does not appear to vary in quality, i.e., in terms of which particular treatments are best, but it varies in magnitude with site and year of seed collection; and it increases slowly during dry storage, even when stored at a temperature as low as 1.5°C.
Growth, Yield, and Yield Component Changes among Old and New Soybean Cultivars

Soybean [Glycine max (L.) Merr. ] yield has increased at a rate of 25 to 30 kg ha -1 yr -1 due in part to improved genetic gain, and has been further advanced by the addition of resistance to soybean cyst nematode (Heterodera glycines Ichinohe; SCN) in new cultivars. The objective was to determine specific growth changes that explain the yield improvement from old to new cultivars and the further yield improvement gained from the addition of SCN resistance. Studies were conducted at three Iowa locations during 2005 and 2006. Two old and two new SCN-susceptible, and two new SCN-resistant cultivars were evaluated for total dry matter (TDM) accumulation and leaf area index (LAI) through the season along with yield and yield components at harvest. New cultivars produced yields superior to older cultivars due to increased crop growth rate (CGR) culminating in greater TDM 105 days after emergence (DAE). Yield was strongly associated with the number of seeds produced m -2 and this yield component accounted for almost all of the yield differences among cultivars. Seeds m -2 was positively related to CGR between 42 and 105 (growth stage R1-R5.5) DAE and to LAI 105 DAE. New SCN-resistant cultivars produced yields 17 to 19% greater than new susceptible cultivars across three locations. Increased TDM and CGR explained the yield response at the low-yield location, but not at the high-yield locations. Apparent harvest index (HI) was similar among all cultivars at each location. Selection for increased yield has indirectly selected for increased TDM and CGR with a similar amount partitioned to seed dry weight. Future yield gains will be made by (i) increasing the amount and the rate of dry matter (DM) and (ii) through the increased production and duration of leaf area.
Polychlorinated biphenyls in eggs and chorioallantoic membranes of American alligators (Alligator mississippiensis) from coastal South Carolina

Assessing chemical exposure in threatened or endangered wildlife species presents unique analytical problems. Chorioallantoic membranes (CAMs) have been proposed as surrogate tissues for evaluation of polychlorinated biphenyl (PCB) exposure in oviparous species. Research was undertaken to determine the extent of PCB accumulation in alligators (Alligator mississippiensis) at sites along the coast of South Carolina and to evaluate the utility of CAMs as surrogate tissues for determining PCB concentrations in whole alligator eggs. Polychlorinated biphenyls were found in eggs and CAMs of alligators from both sites examined. Concentrations of PCBs were higher in CAMs (p = 0.02) and eggs (p = 0.001) from sites known to contain chlorinated hydrocarbons than from more pristine sites. Total PCBs partitioned predictably (r2 > 0.59; p < 0.02) between egg and CAM tissues indicating the utility of CAMs to serve as surrogate tissues when comparing total PCB concentrations in whole eggs. Tetrachloro through octachloro biphenyl homologues and total PCBs in CAMs from reference areas were correlated with concentrations of these homologues in eggs. At contaminated sites, total PCB concentrations in CAMs were correlated with total PCB concentrations in eggs.
Incidence and patterns of surgical site infections in a teaching hospital in central India

Background: Surgical site infections (SSI) are one of the most common infections among the health care-associated infections. However, there is a scarcity of data on SSI from India. The present study was aimed to determine the incidences of SSI and to evaluate the associated factors at a hospital in Nagpur, central India region. Methods: Surgical sites were considered to be infected according to the set of clinical criteria recommended by the CDC’s NNIS system. The wounds were classified using the wound contamination class system, proposed by the American Centers for Disease Control (CDC) for use in SSI surveillance-1999, into Clean, Clean contaminated, Contaminated and Dirty wounds. Results: Among 2083 cases, 314 (15.1%) were suspected to be clinically infected, among them 250 (12%) were confirmed to have SSI. Among 2083 cases, 1214 (58.3%) operations included clean wound category and 869 cases (41.7%) were clean contaminated. From clean wounds 58 cases (4.8%) were found to be SSI and in clean contaminated wounds 192 (22.09%) cases were found to be SSI. Among the clean wounds, 103 (8.5%) were infected; about 58 cases (56.3%) were culture positive and 45 (43.7%) were culture negative. From the clean contaminated wounds, 211 (24.3%), 192 (91%) and 19 (9%) were found to be infected, culture positive and culture negative respectively. The studies of surgeries suggested that among clean surgeries Mastectomy was most common (14%), whereas Pyelolithotomy (8%) was the most common among the clean-contaminated surgeries. The prevalence of SSI was highest in Radical cystectomies (66.6%) and the least with lipoma excisions (6.4%). Conclusion: The incidences of SSIs in postsurgical infections were low in addition to this only small numbers of cases were confirmed to be SSIs. Though the reported cases are higher than the countries with high income, a well-planned strategy is required to decrease the incidences of SSI for improving the quality of health care system in present hospital and similar centers elsewhere.
Nine newly designed polymorphic microsatellite loci for the Japanese paper wasp, Polistes chinensis antennalis (Hymenoptera: Vespidae)

The paper wasp Polistes chinensis antennalis is characterized by a high incidence of worker oviposition, even in the presence of their original queen. To analyze the fine-scale genetic structure within colonies, we isolated nine novel microsatellite loci for this species, for which 13 microsatellite loci were reported. No linkage disequilibrium was detected among all 22 loci. The primer pairs described here are useful in analyzing the colony and population genetic structures of this species.
Allometric relationships for biomass and leaf area of beech (Fagus sylvatica L.).

Les objectifs de l'etude etaient i) l'etablissement de relations allometriques entre la dimension du tronc, la dimension de la couronne, la biomasse, et la surface foliaire, ii) le calcul de la distribution de la biomasse aerienne entre differents organes, iii) la quantification des relations entre la surface foliaire et la section du tronc, iv) l'etablissement du gradient vertical de la surface foliaire specifique (SLA), et v) l'estimation de biomasse aerienne et de l'indice foliaire (LAI). Au total, 38 individus ont ete echantillonnes, dont l'âge variait entre 8 et 59 ans. En general, la biomasse augmente avec le diametre du tronc a 1,30 m. Des modeles non-lineaires du diametre expliquent plus de 90 % de la variation de la biomasse. Les regressions etaient ameliorees dans les cas ou le diametre et la hauteur etaient tout deux inclus. La dimension de la couronne augmente avec le diametre du tronc. La surface et la hauteur de la couronne augmentent avec le diametre du tronc. La surface de la projection de la couronne est liee de facon non-lineaire avec la surface foliaire et la masse de la couronne. Les proportions des materiaux secs des branches augmente avec la biomasse. La proportion entre la biomasse des feuilles et la biomasse des branches diminue avec l'augmentation de la hauteur de l'arbre. La relation entre la biomasse des feuilles et la SLA est constante et a une moyenne de 172 cm 2 g -1 . SLA croit du sommet de la couronne vers la base de la couronne. Cette relation ne changeait pas entre les arbres dans la parcelle etudiee. La vitesse de variation de SLA diminue dans des conditions plus ouvertes. La relation lineaire entre la surface des feuilles et la surface d'aubier est influencee par la hauteur de la base de la couronne. La biomasse aerienne varie entre 6 et 167 t ha -1 , et croit de facon lineaire avec l'âge de la parcelle. LAI etait entre 3 et 7 : maximum LAI etait liee avec mortalite naturelle.
Application of near-infrared spectroscopy for the detection of internal insect infestation in Picea abies seed lots

The use of near-infrared (NIR) spectroscopy to discriminate between uninfested seeds of Picea abies (L.) Karst and seeds infested with Plemeliella abietina Seitn (Hymenoptera, Torymidae) larva is sensitive to seed origin and year of collection. Five seed lots collected during different years from Sweden, Finland, and Belarus were used in this study. Initially, seeds were classified as infested or uninfested with X-radiography, and then, NIR spectra from single seeds were collected with a NIR spectrometer from 1100 to 2498 nm with a resolution of 2 nm. Discriminant models were derived by partial least squares regression using raw and orthogonal signal corrected spectra (OSC). The resulting OSC model developed on a pooled data set was more robust than the raw model and resulted in 100% classification accuracy. Once irrelevant spectral variations were removed by using OSC pretreatment, single-lot calibration models resulted in similar classification rates for the new samples irrespective of origin and year o.
The relationship between the Rubisco reaction mechanism and models of photosynthesis

Abstract. A new model of photosynthesis published recently in this journal (H. Farazdaghi & G. E. Edwards, Plant, Cell and Environment (1988) 11, 789–798; 799–809) clams to have a more complete mechanistic basis than currently used models based on the paper of G. D. Farquhar, S. von Caemmerer & J. A. Berry (Planta (1980) 149, 78–90). In this paper, we examine the validity of the new kinetic expression for the rate of CO2 fixation by Rubisco, and the derivation of an equation for photosynthetic CO2 assimilation as a function of light intensity and CO2 concentration presented in the new model. In addition, we compare measured response curve of photosynthesis to CO2 and light with simulated curves using alternative models. We conclude that the new model is mechanistically misleading and, empirically, overestimates the extent to which light and CO2 co-limit the rate of photosynthesis under most physiological conditions.
AN ALL HUMAN 3D IN VITRO MODEL OF THE BLOOD BRAIN BARRIER IN NANOPARTICLE DELIVERY AND CANCER METASTASIS STUDIES

BACKGROUND: The blood-brain barrier (B-BB) is a dynamic functional unit consisting of endothelial cells, astrocytic endfeet and pericytes embedded in a specialized basement membrane. Most in vitro studies examine the ability of therapeutics to cross the B-BB using monolayer cultures or mixed species co-cultures and rely on Trans-Endothelial Electrical Resistance (TEER) measurements without verification of tight-junction (TJ) formation. More reliable high throughput in vitro models are therefore essential in brain tumour drug delivery and metastatic tumour behavioural studies. We are developing and testing a 3-dimensional in vitro model incorporating aspects of known B-BB in vivo characteristics. METHODS: A 3D model of the B-BB was constructed using human brain endothelial cells (hCMEC/D3), human astrocytes (SC-1800/UP010) and human brain vascular pericytes (HBVP) in mono-, co-, tri- cultures. TEER values were measured using a cell monitoring system- cellZscope®. TJ proteins (ZO-1 and occludin) were examined by Western blotting and immunocytochemistry. Effects of extracellular matrix (ECM) molecules (laminin, fibronectin, collagen type IV, agrin, perlecan) were assessed on endothelial cell proliferation, adhesion and TEER changes using an Electric Cell-Substrate Impedance Sensing (ECIS) system. Modified chitosyme nanoparticles and metastatic lung cancer cells were tested for effects on B-BB integrity. RESULTS: Co-cultures and tri-cultures resulted in significantly higher TEER values compared to endothelial cells alone (p < 0.05). TEER values for co-culture of ECs and astrocytes were 4620 Ω/cm2, and for tri-cultivation including pericytes, 4141.50 Ω/cm2 compared to single EC cultures (2244 Ω/cm2). Western blot revealed higher expression of ZO-1 and occludin in co- and tri-cultures. The individual optimal ECM concentrations for highest and longest TEER values differed depending on ECM molecule and concentration. Cell adhesion (%) correlated with TEER values. Recovery time of B-BB integrity following chitosyme nanoparticle/metastatic cell treatment, differed in mono-, co-, tri-cultures. CONCLUSIONS: Astrocytes contribute to B-BB formation in this in vitro model. Motile pericytes may positively or negatively influence barrier formation or TJ tightness. ECM has varied and profound effects on TEER values. Multiple measures are needed to confirm TJ formation in addition to TEER values as these may not reflect ‘true’ B-BB integrity. Using compounds with known low B-BB penetration and analysing TJ protein expression in combination with novel therapeutics will aid in providing meaningful data to bridge the gap between drug discovery and pre-clinical studies. In addition, our brain metastatic research group utilizes this model to test effect of CD15 knockdown in lung metastatic cells on endothelial cell adhesion and B-BB passage. SECONDARY CATEGORY: Tumor Biology.
The influence of temperature on consumption and utilization of artificial diet by Spodoptera littoralis (Boisd.) (Lepidopt., Noctuidae)

The effect of controlled temperatures: 20, 25 and 30 ± 1°C on the growth, consumption and utilization of semi-artificial diet by the last larval instar of Spodoptera littoralis (Boisd.) was investigated on dry weight basis. The physiological capacity of food consumption and utilization are described by a reaction chain consisting of the steps: feeding activity ŕ digestibility ŕ assimilation activity. The results of the sequence suggested the operation of compensatory mechanisms in physiology of insect nutrition. The total reaction is represented numerically by the relative growth rate index (RGR). In order to obtain an evaluation of the actual food conversion a further index called AC is formed. The results of the index indicated that the range of 25 °C provides the optimum developmental conditions for S. littoralis. The pattern of the nutritional indices shows that at this temperature range high feeding and digesting activities are coincident with a relatively low assimilation rate and an optimum growth rate. Zusammenfassung Der Einflus der Temperatur auf die Aufnahme und Verwertung semisynthetischer Diat durch die Baumwolleule Spodoptera littoralis (Boisd.) (Lepidopt., Noctuidae) Bei Temperaturen von 20, 25 und 30°C und einer Photoperiode von 12:12 (L:D) wurden Larven von Spodoptera littoralis angezogen. Die ernahrungsphysiologischen Indices CI, AD, GR, ECI und ECD wurden auf Trockengewichtsbasis ermittelt. Die ernahrungsphysiologische Situation von S. littoralis wurde durch die kausale Reaktionskette “Frasaktivitat Verdauung Assimilation” dargestellt und durch die relative Wachstumsrate RGR = CI × AD/100 × ECD/ 100 numerisch charakterisiert. Um den aktuellen Stofftransfer aus der Nahrung in das Insekt zu erfassen, wurde ein weiterer Index AC eingefuhrt, in dem RGR - als Mas fur die ernahrungsphysiologische Kapazitat - mit der jeweils aktuell verzehrten Nahrungsmenge multipliziert wird. Die Ergebnisse zeigen, das S. littoralis im Temperaturbereich von 25°C ein ernahrungsphysiologisches Optimum besitzt, das durch hohe Fras-, Verdauungs- und Atmungsaktivitaten sowie eine relativ niedrige Assimilationsleistung gekennzeichnet ist.
THE BIOLOGY OF CANADIAN WEEDS.: 77. Echinochloa crus-galli (L.) Beauv.

Echinochloa crus-galli (L.) Beauv. , barnyard grass (pied-de-coq), is an annual grass and a cosmopolitan weed with a range from 50°N to 40°S latitude. In Canada, it extends up to 53°N latitude in the prairies and is widely distributed along roadsides and in cultivated fields of all provinces. The success of this weed may be attributed to the production of large numbers of small, easily dispersed seeds per plant, possession of seed dormancy, rapid development and ability to flower under a wide range of photoperiods, and relative resistance of mature plants to herbicide sprays. In this review a summary of biological information on E. crus-galli is presented.Key words: Barnyard grass, weed biology, Echinochloa crus-galli
Activation of Nuclear Factor of Activated T Cells by Human T-Lymphotropic Virus Type 1 Accessory Protein p12I

ABSTRACT Human T-lymphotropic virus type 1 (HTLV-1) is the agent of an aggressive malignancy of CD4+ T lymphocytes, called adult T-cell lymphoma/leukemia, and is associated with numerous immune-mediated diseases. To establish infection, HTLV-1 must activate targeted T cells during early stages of infection. We recently demonstrated that the HTLV-1 accessory protein p12I is critical for persistent infection in vivo and for viral infectivity in quiescent primary lymphocytes, suggesting a role for p12I in lymphocyte activation. To test whether p12I modulates signaling pathways required for T-lymphocyte activation, we examined AP-1-, NF-κB-, and nuclear factor of activated T cells (NFAT)-driven reporter gene activity in p12I-expressing Jurkat T cells compared to vector-transfected control cells. HTLV-1 p12I specifically induced NFAT-mediated transcription approximately 20-fold in synergy with the Ras/mitogen-activated protein kinase pathway, but did not influence AP-1- or NF-κB-dependent gene expression. Inhibition of calcium-dependent signals by cyclosporin A, BAPTA-AM [glycine, N,N′-1,2-ethanediylbis(oxy-2,1-phenylene)-bis-N-2-(acetyloxy)methoxy-2-oxoethyl]-[bis(acetyloxy)methyl ester], and a dominant negative mutant of NFAT2 abolished the p12I-mediated activation of NFAT-dependent transcription. In contrast, inhibition of phospholipase C-γ and LAT (linker for activation of T cells) did not affect p12I-induced NFAT activity. Importantly, p12I functionally substituted for thapsigargin, which selectively depletes intracellular calcium stores. Our data are the first to demonstrate a role for HTLV-1 p12I in calcium-dependent activation of NFAT-mediated transcription in lymphoid cells. We propose a novel mechanism by which HTLV-1, a virus associated with lymphoproliferative disease, dysregulates common T-cell activation pathways critical for the virus to establish persistent infection.
Mortality Rates of Insular Anolis Lizards: A Systematic Effect of Island Area?

Caracteristiques des sites des Anolis des Antilles et des iles du Lac Gatun, Panama. Competition avec les oiseaux. Mortalite. L'hypothese de Waide et Reagan selon laquelle l'abondance des A. est limitee par les predateurs, du moins sur les grandes iles, est rejetee
Bioenergetics of Pelagic Fish: Theoretical Change in Swimming Speed and Ration with Body Size

It is shown from hydrodynamics theory and the size composition of particles in marine food chains that there are two unique swimming speeds of importance to pelagic fish: (1) the optimal cruising speed, which maximizes the distance traveled per unit energy expenditure and (2) the optimal foraging speed, which maximizes the rate of flow of surplus energy, or production in its broadest sense. With sockeye salmon (Oncorhynchus nerka) as an example, the optimal cruising and foraging speeds were found to be proportional to the body length raised to the 0.4 power. By analogy, if pelagic fish in general tend to move at either of these speeds, their ration and growth rates relative to the body weight should be proportional to a power that varies between 0.7 and 0.8. These predictions are consistent with field growth measurements for several pelagic species. Therefore, the necessary conditions for a theory of optimal foraging exist since (1) all adaptive swimming speeds are physiologically possible and (2) there i.
Pollen morphology of Dioscorea (Dioscoreaceae) and its relation to systematics

This paper adds new data on the pollen and orbicule morphology of 61 Dioscorea L. (Dioscoreaceae) species to the survey of Schols et al. (2001). The results indicate that pollen characters may be significant in infrageneric systematics in Dioscorea. Pollen and orbicule characters are described based on observations with light microscopy, and scanning and transmission electron microscopy, and are critically evaluated and discussed in the context of existing hypotheses of systematic relationships within the genus. Pollen is mostly disulculate (sometimes monosulcate) with a perforate, microreticulate, striate, gemmate, rugulate, or cerebroid perforate sexine. The basal section Stenophora is one of the few sections with monosulcate pollen. Brachyandra, Cardiocapsa, and Seriflorae, three Malagasy sections, are characterized by striate pollen. Pollen morphology strongly supports section Enantiophyllum as a monophyletic group. The correlation between pollen size and tuber type, as suggested previously by P. Su (1987), is confirmed by our data. As found in our earlier survey, orbicules in Dioscorea are mostly spherical with a smooth or spinulose surface. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 143, 375–390.