Miracle-dz/UniFAR-FTUs huggingface dataset:
Exacerbation by Positive End-Expiratory Pressure

Background: Previous experimental studies of ventilatorinduced lung injury have shown that positive end-expiratory pressure (PEEP) is protective. The authors hypothesized that the application of PEEP during volume-controlled ventilation with a moderately high tidal volume (VT) in previously healthy in vivo rats does not attenuate ventilator-induced lung injury if the peak airway pressure markedly increases during the application of PEEP. Methods: Sixty healthy, male Sprague-Dawley rats were anesthetized and randomized to be mechanically ventilated for 4 h at (1) VT of 6 ml/kg, (2) VT of 20 ml/kg, or (3) VT of 20 ml/kg plus 10 cm H2O of PEEP. Peak airway pressures, gas exchange, histologic evaluation, mortality, total lung tissue cytokine gene expression, and serum cytokine concentrations were analyzed. Results: Peak airway pressures exceeded 30 cm H2O with high VT plus PEEP. All lungs ventilated with high VT had perivascular edema and inflammatory infiltrates. In addition, those ventilated with PEEP had small hemorrhages foci. Five animals from the high VT plus PEEP group died (P 0.020). Animals ventilated with high VT (with or without PEEP) had a substantial increase in serum interleukin-6 (P 0.0002), and those ventilated with high VT plus PEEP had a 5.5-fold increase in systemic levels of tumor necrosis factor-alpha (P 0.007). Conclusions: In contrast to previous reports, PEEP exacerbated lung damage and contributed to fatal outcome in an in vivo, mild overdistension model of ventilator-induced lung injury in previously healthy rats. That is, the addition of high PEEP to a constant large VT causes injury in previously healthy animals.
Dengue virus exposure among blood donors in Ghana

Dengue is an urban arbovirus whose aetiologic agent is the flavivirus with four distinct antigen serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) that is transmitted to humans through the bite of the mosquito Aedes aegypti . Ghana is endemic for Aedes aegypti mosquitoes and probably dengue viruses. Due to limited data on dengue virus exposure among Ghanaians, we surveyed 188 healthy adult blood donors for the presence of IgG and IgM antibodies to the four serotypes of dengue. Five milliliters of peripheral blood from the blood donors were collected in plain tubes. Serum was then obtained and ELISA tests were employed to detect both dengue virus total antibodies and IgM. The samples were further tested for dengue virus RNA using RT-PCR . Dengue virus IgG was positive for 43.6% of all the 188 blood donor samples tested but all donors were negative for anti-dengue IgM antibody and dengue virus RNA. The rate of dengue virus total antibody exposure did not differ statistically between urban and rural districts. This study shows for the first time that some regions of Ghana are hyperendemic for dengue virus infection but suggests blood for transfusion is invariably dengue virus free. This report has provided a baseline data that will inform wider discussions about the impact of this dengue fever and also guide policy makers to develop effective and affordable early warning and outbreak response systems for Ghana. Journal of Medical and Biomedical Sciences (2016) 5(2), 30-35
PAX6 gene analysis in Serbian patients with aniridia

Introduction: Aniridia is a rare congenital eye anomaly associated with various ophthalmological problems. Some of the causes of this disease are mutations in the PAX6 gene or deletion of loci on the short arm of chromosome eleven, which can be complete or partial. In this study, PAX6 gene sequence was analysed in four unrelated patients. Aim: Examination of the entire coding sequence of the PAX6 gene in our patients in order to detect mutations in this gene. Material and Methods: Patients' DNA was isolated from samples of peripheral blood. All exons and flanking intronic sequences of the PAX6 gene were amplified using PCR and screened for mutation with direct DNA sequencing by Sanger method. Results: In one patient, the insertion type of mutation (c.342-2insC) was found in the second intron of the PAX6 gene. Other three patients had normal PAX6 sequence although they had phonotypical expression of aniridia. Conclusion: ttese are first results of PAX6 gene analysis in Serbia. Apart from most common mutations, deletions of various extent in coding regions of PAX6 gene, other types of mutations are also possible causes of aniridia. The insertion found in this study has not been reported before. It is also possible that mutations in other genes are associated with iris malformation, which can explain the finding of normal PAX6 gene sequence in three patients with aniridia.
Daily movement patterns and dispersal in the land snail Arianta arbustorum

The relationship between daily movements of individuals and their dispersal over longer periods was studied in two natural populations of the land snail Arianta arbustorum in Switzerland. In a forest clearing, daily movements of individually marked snails ranged from 0 to 4.44 m (median 0.58 m); the frequency distribution of the distances traveled fitted a function with exponential decay. The snails showed no preference in direction of movement. Further, the directions chosen by an individual on consecutive days were independent from each other. These findings agree with the assumptions of a random movement model. In a 1-m wide belt of tall grass and forbs along a ditch, daily movements of A. arbustorum were exponentially distributed and ranged from 0 to 1.57 m (median 0.40 m)
The suprabenthic crustacean fauna of the infralittoral fine sand community from the bay of Seine (Eastern English Channel): composition, swimming activity and diurnal variation

La faune suprabenthique d'une station situee au debouche en mer de la Seine (Manche orientale) a ete echantillonnee avec un traineau suprabenthique Macer-GIROQ modifie. Trente-huit echantillons horaires ont ete recoltes en deux series de prelevements; ils permettent de decrire pour la premiere fois la faune suprabenthique de cette region. La composition faunistique, les activites natatoires, et les migrations nyctemerales des principales especes sont decrites. Un total de 46 especes de crustaces a ete identifie. Les especes dominantes de la communaute sont Schistomysis kervillei, Mesodopsis slabberi, Diastylis bradyi et Pseudocuma longicornis. Toutes les especes presentent une migration verticale nocturne
HELMINTH PARASITIC FAUNA OF AQUATIC BIRDS IN BAHR AL-NAJAF DEPRESSION, MID IRAQ

For two years, from January 1995 till December 1996, a survey on helminth parasites of aquatic birds of Bahr Al-Najaf depression, mid Iraq, was achieved. A total of 663 birds, belonging to 11 species, were captured and examined for helminth parasites. These birds were infected with seven trematodes (Notocotylus gibbus, Cyclocoelum mutabile, Echinostoma chloropodis, Patagifer parvispinosus, Psilochasmus oxyurus, Diplostomum spathaceum and Apharyngostrigea cornu), seven cestodes (Paricterotaenia porosa, Dicranotaenia tsengi, Diorchis brevis, D. inflatus, Tatria acanthorhyncha, T. decacantha and Diplophallus polymorphus) and four nematodes (Capillaria sp., Eustrongylides tubifex, Contracaecum sp. and Tetrameres sp.). Five bird species were recorded as new hosts in Iraq for four helminths of the present investigation. INTRODUCTION The middle and southern parts of Iraq are good habitats for many aquatic birds (both residential and migratory) where they share adequate food and slightly warm water. Aquatic plants there provide a suitable shelter for such birds (Al-Hadithi, 1971). Bahr Al-Najaf depression attracts a large number of aquatic birds. Al-Awadi (1997) listed 53 bird species, belonging to 21 families, in that depression. Like other animals, aquatic birds are vulnerable to many parasitic infections which may cause considerable mechanical and chemical damages to host vital organs and may decrease host weight and its egg production (Soulsby, 1968). Some aquatic birds act as final hosts for some helminths which use fishes as intermediate hosts (Mhaisen, 1983). Some aquatic birds may transmit some pathogenic viruses to fishes (Peters and Neukirch, 1986). The aquatic birds of Iraq received little attention from Iraqi helminthologists. Among literature concerning helminthological surveys of aquatic birds of Iraq are those of Al-Aloosi (1985), Abdullah (1988), Mahmoud and Mohamad (1989), Al-Mayah (1990), Mhaisen et al. (1990), Al-Hadithi and Abdullah, (1991), Al-Hadithi and Mustafa (1991), Al-Hadithi (1992), Mhaisen and Abul-Eis (1992), Abdullah (1993), Abdullah and Al-Mayah (1993), Al-Mayah (1994), Awad et al. (1994), Al-Daraji et al. (1998), Al-Mayah (1999), Mahmoud (2001), Mizhir (2002), Abed (2005) and Ali (2008).
Influence of surface and subsurface soil properties on atrazine sorption and degradation

Studies to predict pesticide fate often lack measurements of model input parameters. Using independent data sets and understanding how soil properties affect herbicide retention and degradation may result in more accurate prediction of herbicide fate. We conducted laboratory studies to determine the influence of soil properties on atrazine adsorption and degradation. These data will be used in a separate study involving a pesticide fate model. Atrazine adsorption and desorption isotherms were constructed for six soil depths of a Hastings silty clay loam (fine, montmorillonitic, mesic Udic Argiustoll) using batch equilibration. The Freundlich adsorption constants (log Kf ) ranged from 0.38 (60 to 90 cm) to 2.91 (0 to 30 cm). Adsorption was higher in the low pH, high organic matter-containing surface soil compared to the lower soil depths. Multiple regression of the adsorption constants against selected soil properties indicated that organic matter content was the best single predictor of atrazine adsorption (R 2 = 0.98) followed by soil pH (R 2 = 0.82). Combining organic matter and cation exchange capacity in the model produced the lowest Cp statistic (2.33) and highest R 2 value (0.99). We observed hysteresis in atrazine adsorption–desorption isotherms by higher adsorption slopes (1/n)ads compared to desorption slopes (1/n)des. Soils that adsorbed more atrazine also desorbed less atrazine. Desorption correlated negatively with organic matter content and positively with soil pH. Atrazine degradation after 84 d of incubation generally decreased with increasing depth. The first-order degradation rate was highest 0 to 30 cm deep (0.0187 day−1) and lowest 270 to 300 cm deep (0.0031 day−1). Atrazine degradation was faster in soil treated annually for 12 yr than in soil with no previous atrazine history (p = 0.01).
Extended Spectrum β-lactamases in Clinical Isolates of Escherichia coli and Enterobacter cloacae Collected from Nablus District - Palestine

Aim: To determine the prevalence of extended-spectrum β-lactamases (ESBLs) among clinical isolates of Escherichia coli (E. coli) and Enterobacter cloacae (E. cloacae) in Nablus district. Methodology: In this prospective study carried out at An-Najah National University, a total of 161 bacterial isolates were collected during a12-month period in Nablus district in Palestine. To detect ESBLs, the isolates were examined by combination disc method. PCR was used to detect blaCTXM, blaTEM and blaSHV genes in 32 representative ESBL-producer E. coli isolates. Results: Using combination disc method, ESBL enzymes were detected in 73 out 153 (47.7%) E. coli and in 1 out of 8 (12.5%) E. cloacae isolates. No significant association of ESBL-producer E. coli was observed with types of collected specimens, gender, hospital ward, outpatient, or medical source. Among 32 representative E. coli ESBL-positive, blaCTX-M, blaTEM and blaSHV genes were detected in 30 (93.8%), 2 (6.3%) and 1 (3.1%), respectively. Two new variants of ESBLs (PALTEM137b and PALSHV-2a') were identified. A unique E. cloacae isolate expressing inducible Short Research Article Al-Masri et al.; BMRJ, 16(3): 1-7, 2016; Article no.BMRJ. 27892 2 class C B-lactamase was also detected. Conclusions: In Nablus region, high frequencies of ESBLs were found among E. coli bacteria isolated from outpatients and inpatients. blaCTX-M is the predominant gene among ESBL producers. New variants of ESBLs were found.
Fourier analysis to detect phenological cycles using long‐term tropical field data and simulations

Changes in phenology are an inevitable result of climate change, and will have wide‐reaching impacts on species, ecosystems, human society and even feedback onto climate. Accurate understanding of phenology is important to adapt to and mitigate such changes. However, analysis of phenology globally has been constrained by lack of data, dependence on geographically limited, non‐circular indicators and lack of power in statistical analyses. To address these challenges, especially for the study of tropical phenology, we developed a flexible and robust analytical approach – using Fourier analysis with confidence intervals – to objectively and quantitatively describe long‐term observational phenology data even when data may be noisy. We then tested the power of this approach to detect regular cycles under different scenarios of data noise and length using both simulated and field data. We use Fourier analysis to quantify flowering phenology from newly available data for 856 individual plants of 70 species observed monthly since 1986 at Lopé National Park, Gabon. After applying a confidence test, we find that 59% of the individuals have regular flowering cycles, and 88% species flower annually. We find time‐series length to be a significant predictor of the likelihood of confidently detecting a regular cycle from the data. Using simulated data we find that cycle regularity has a greater impact on detecting phenology than event detectability. Power analysis of the Lopé field data shows that at least 6 years of data are needed for confident detection of the least noisy species, but this varies and is often >20 years for the most noisy species. There are now a number of large phenology datasets from the tropics, from which insights into current regional and global changes may be gained, if flexible and quantitative analytical approaches are used. However, consistent long‐term data collection is costly and requires much effort. We provide support for the importance of such research and give suggestions as to how to avoid erroneous interpretation of shorter length datasets and maximise returns from long‐term observational studies.
In vitro shoot proliferation of rosewood (Dalbergia latifolia: Fabaceae): a potent high quality timber species

Possibilities of mass producing Dalbergia latifolia Roxb. (Fabaceae) trees towards clonal propagation through in vitro techniques have been evaluated. Shoot tips excised from elite trees maintained under plant house conditions were established on Mc Cowns Woody Plant medium fortified with BAP (1.0 mg/L) and IAA (0.5 mg/L). The highest proliferation rate (4.95 shoots/shoot tip) was achieved using 3.0 mg/L BAP, 0.5 mg/L Kin and 0.5 mg/L IAA. The best establishment medium for leaves is Murashige and Skoog medium fortified with 0.5 or 1.0 mg/L BAP with 1.0 mg/L 2, 4-D and 4.0 mg/L NAA to initiate compact, nodular and proliferative calli. Highest rate of shoot bud differentiation (17.7 shoot buds/ 1g of callus) was achieved using 5.0 mg/L BAP with 0.2, 0.5 or 0.6 mg/L NAA.
EMBRYONIC INDUCTION IN THE ASCIDIA

The Ascidia are grouped with those animals whose early development is termed mosaic. Yet, in the closely related Vertebrata, organs form as the result of interaction between those cells which become the definitive organ in question and neighboring cells, whose descendants take no part in the actual formation of the organ. The independent differentiation of organs in the Ascidia and the dependent differentiation of the same organs in the Vertebrata presents a problem. It is believed that the Ascidia and the Vertebrata are descendants of a common ancestor which contained organs similar to those now common to both groups. The nerve cord, for example, in the two groups is thought to be homologous. The common ancestor must have had a nerve cord which arose either under the influence of inductors or independently as a mosaic piece. It seems strange that in the course of evolution the vertebrate nerve cord and the ascidian nerve cord could have remained such similar embryonic structures, when their modes of origin were diverging so greatly that the one now forms under the influence of inductors and the other quite independently of inductors. Possibly this difference in mode of development between the two groups is more apparent than real. The injury experiments of Conklin (1905b) established the fact that in Styela partita surviving blastomeres do not deviate from their prospective potency by regulating to form more morphological units than they normally form as parts of a whole embryo. Conklin's work further showed that differences in protoplasmic appearance and cleavage peculiarities develop in the uninjured blastomeres just as they would were the blastomeres part of an intact embryo. These differences are numerous enough to allow a careful observer to differentiate the presumptive tissues and organs before the formation of the definitive structures. This fact, I think, is the basis for the belief that the ascidian egg is a mosaic of self-differentiating parts. The isolated parts certainly self-differentiate into what are recognizably distinct presumptive regions, but the question is whether any or all of these isolated presumptive regions are capable of further self-differentiation into embryonic organs. 216
Correlations and Interactions Between Population, Length of Worker Life and Honey Production by Honeybees in a Temperate Region

SummaryAn investigation of the factors influencing honey production was conducted using 12 colonies of honeybees (Apis mellifera), with 3 replications in time. Brood areas, colony populations and weights of honey produced were measured.On the average, adult worker populations amounted to only 40–60% of the numbers that should have emerged, based on brood-cell estimates for the preceding 42-day period. Correlation coefficients (r) between numbers of brood and resulting numbers of adult bees varied from +0·20 to +0·86, and values of r for population and length of worker life from −0·39 to +0·92. Average length of productive life of workers varied from 21 to 25 days and average number of larvae reared per worker bee from 0·8 to 1·5. Workers rearing more brood were shorter-lived (r = −0·71 to −0·94). Individual colonies produced between 4 and 26 kg honey. Production was related in varying degree to number of brood reared (r = +0·20 to +0·85) and to colony population (r = +0·38 to +0·70). Individual productivit.
Horizontal gene transfer studies in parasitic plants of the orobanchaceae

This report summarizes the HGT findings in the PPGP (The Parasitic Plant Genome Project) by utilizing a phylogenomic approach in identifying HGT events. Twenty-two plant genomes, two asterid EST datasets (Lactuca sativa and Helianthus annuus), and four PPGP species (Lindenbergia Philipensis, Triphysaria versicolor, Striga hermonthica, and Phelipanche aegyptiaca) were used in orthogroup classifications. The phylogenies for each orthogroup were built, and customized JAVA scripts were used to perform the initial automated HGT screening for genes in the parasite with phylogenetic positions inconsistent with the known species relationships and common gene family evolutionary processes. Secondary manual screening was carried out under stringent criteria to avoid scenarios other than HGT that could also lead to phylogenetic incongruence. Twenty-three well supported cases of putative HGT of transcribed gene sequences were identified. With each case supported by incongruent phylogenies, the expression profiles for the HGT genes, potential gene functions, evolutionary constraint analyses, and genomic evidences are discussed. The majority of the transgenes show evidence of introns, indicating that HGT transfer happened at the DNA (not transcript) level. We also identified two high confidence HGT transgenes in Striga hermonthica located adjacent to each other. This is the first time that two adjacent HGT transgenes have been reported in host plant to parasitic plant gene transfer. HGT transgenes detected from EST datasets could be just a “tip of the iceberg” of a potentially much
Stomatal characteristics and water relations of in vitro grown Quercus robur NL 100 in relation to acclimatization

Experiments were carried out to study stomatal characteristics and the % of moisture loss of in vitro grown leaves of Q. robur NL 100 in relation to acclimatization. Microscopic observations on the abaxial leaf surfaces of acclimatized and greenhouse grown plants showed elliptical stomata (16 μm to 18 μm) with narrow apertures (3 μm to 4 μm). In comparison, the stomata of leaves from in vitro showed spherical stomata (20 μm to 30 μm) with widely opened apertures (6 μm to 8 μm). Leaves from shoot multiplication and the two stages of rooting (in vitro) had higher stomatal density and index values as compared to acclimatized and greenhouse-grown plants. The % of moisture loss of in vitro grown leaves was considerably greater than that of acclimatized and greenhouse grown plants. This study will help to explain the failure of in vitro Q. robur NL 100 plants after transplanting to the greenhouse.
for neural tube closure in the tuft mouse

© 2016. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. A mutation disrupting TET1 activity alters the expression of genes critical for neural tube closure in the tuft mouse
Karyology of six cyprinid fishes from Seyhan and Ceyhan rivers in Anatolia

Abstract Karyological properties of Cyprinus carpio, Capoeta damascina, Luciobarbus pectoralis, Pseudophoxinus zekayi, Squalius seyhanensis and Alburnus adanensis from the Seyhan and Ceyhan river systems were investigated by examining metaphase chromosomes through Giemsa staining, C-banding and Ag-NOR techniques. The diploid number of chromosomes in A. adanensis, P. zekayi and S. seyhanensis were 50, in C. carpio and L. pectoralis 100, and in C. damascina 150. Sex chromosomes were not observed in any of the examined species. Several chromosomes presented C-bands in pericentromeric and/or paracentromeric position, near the centromere. Some species had centromeric and pericentromeric heterochromatic blocks. NORs were observed in one pair of submetacentric chromosomes in L. pectoralis, P. zekayi, S. seyhanensis and A. adanensis, in one pair of metacentric chromosomes in C. carpio and three pairs of chromosomes in C. damascina. The cytogenetic features of endemic fishes A. adanensis, L. pectoralis, P. zekayi and S. seyhanensis were detected for the first time in this study.
Mechanical Control of Mesenchymal Stem Cell Adipogenesis

Increased Mesenchymal Stem Cell (MSC) commitment and differentiation into adipocytes contributes to obesity. Other than dietary and biochemical factors, recent studies have begun to explore the role of mechanical signals in controlling MSC adipocytic commitment and differentiation. Several reported data suggest that by subjecting MSCs to certain mechanical stimuli, such as stretching, compression, and fluid shear, their adipogenesis could be inhibited or decreased. However, it is still very early to draw conclusions on the detailed mechanical regimens to optimally inhibit MSC adipogenesis and on the molecular pathways governing such adipogenesis-inhibitory mechanosensitive signaling. In this commentary, key data on the mechanical control of MSC adipogenesis and proposed molecular mechanisms will be highlighted and a future perspective in this new topic area will be provided.