bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grazing effects on biological soil crusts and their interaction with shrubs and grasses in an arid rangeland
Authors: Tabeni Solana , Garibotti Irene A. , Pissolito Clara , Aranibar Julieta N. 
Published: June 2014

AbstractQuestionBiological soil crust (BSC) communities can be used in the identification and monitoring of degradation. A key question is how landscape‐scale livestock disturbance and other local‐scale factors influence BSC communities. We hypothesize that at the landscape scale, increased grazing pressure would lead to decreasing cover of BSC, but at the local scale biotic interactions between BSC and vascular plants would modulate the influence of grazing on BSC.MethodsSpatially explicit sampling of vegetation composition and cover was conducted using point‐sampling methods in digital images along two disturbance gradients in the central Monte Desert in Argentina.ResultsThe grazing gradient is the major determinant of changes in the structure of plant communities at the landscape scale. Approximately 1500 to 2000 m from a watering point, there is a threshold in vegetation structure associated with a nonlinear trend of the BSC, herb, grass and shrub cover. Bivariate spatial patterns show attraction between BSC and shrubs in the vicinity of settlements, and repulsion between BSC and both grasses and litter in less disturbed sites.ConclusionGrazing affects BSC directly through trampling and indirectly by altering vascular plant communities that interact with the BSC communities. Both these effects vary according to the spatial scale being considered. The results evidence that understanding of livestock impact in structuring arid ecosystems requires an integrated analysis of BSC and vascular plant communities at different spatial scales.
Expression of vasoactive proteins in gastric antral mucosa reflects vascular dysfunction in patients with cirrhosis and portal hypertension
Authors: Trebicka Jonel , Wix Cyrus , von Heydebrand Matthias , Hittatiya Kanishka , Reiberger Thomas , Klein Sabine , Schierwagen Robert , Kristiansen Glen , Peck‐Radosavljevic Markus , Fischer Hans‐Peter , Møller Søren , Bendtsen Flemming , Krag Aleksander , Sauerbruch Tilman 
Published: June 2014

AbstractBackground & AimsPatients with cirrhosis display hypocontractility of splanchnic vessels because of dysregulation of vasoactive proteins, such as decreased effect of RhoA/ROCK and increased activity of β‐Arrestin‐2 and eNOS. However, it is unknown whether the dysregulation of vasoactive proteins is displayed in other vessels. We investigated whether expression of vasoactive proteins can be evaluated in gastric mucosa vessels.MethodsBiopsies from the gastric mucosa of 111 patients with cirrhosis were collected at three different centres and from 13 controls. Forty‐nine patients had received TIPS. Portal pressure gradient was measured in 49 patients with TIPS and in 16 patients without TIPS. Biopsies from the antrum were conserved in formaldehyde for immunohistochemistry or shock‐frozen for PCR and Western blot.ResultsThe mucosal transcription of vascular markers (αSMA, CD31) was higher in cirrhotic patients than controls, which was confirmed by immunohistochemistry. On average, relative mucosal levels of RhoA and ROCK were lower, while β‐Arrestin‐2 levels were higher in cirrhotic patients compared to controls. Transcriptional levels of eNOS increased with presence of ascites and grade of oesophageal varices. Patients with TIPS showed less pronounced markers of vascular dysfunction in gastric mucosa.ConclusionThis is the first evidence that the expression of vasoactive proteins in mucosa from the gastric antrum of patients with cirrhosis reflects their vascular dysfunction and possibly changes after therapeutic interventions.
An alternative, arginase‐independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme
Authors: Romagnoli G. , Verhoeven M. D. , Mans R. , Fleury Rey Y. , Bel‐Rhlid R. , van den Broek M. , Maleki Seifar R. , Ten Pierick A. , Thompson M. , Müller V. , Wahl S. A. , Pronk J. T. , Daran J. M. 
Published: June 2014

SummaryMost available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of the deletion mutant strongly increased during serial transfer in shake‐flask cultures. A combination of RNAseq‐based transcriptome analysis and 13C‐15N‐based flux analysis was used to elucidate the arginase‐independent pathway. Isotopic 13C15N‐enrichment in γ‐aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1Δ mutant of a guanidinobutyrase (EC.3.5.3.7), a key enzyme in a new pathway for arginine degradation. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi.
Obesity and mortality: are the risks declining? Evidence from multiple prospective studies in the United States
Authors: Mehta T. , Fontaine K. R. , Keith S. W. , Bangalore S. S. , de los Campos G. , Bartolucci A. , Pajewski N. M. , Allison D. B. 
Published: June 2014

SummaryWe evaluated whether the obesity‐associated years of life lost (YLL) have decreased over calendar time. We implemented a meta‐analysis including only studies with two or more serial body mass index (BMI) assessments at different calendar years. For each BMI category (normal weight: BMI 18.5 to <25 [reference]; overweight: BMI 25 to <30; grade 1 obesity: BMI 30 to <35; and grade 2–3 obesity: BMI ≥ 35), we estimated the YLL change between 1970 and 1990. Because of low sample sizes for African–American, results are reported on Caucasian. Among men aged ≤60 years YLL for grade 1 obesity increased by 0.72 years (P < 0.001) and by 1.02 years (P = 0.01) for grade 2–3 obesity. For men aged >60, YLL for grade 1 obesity decreased by 1.02 years (P < 0.001) and increased by 0.63 years for grade 2–3 obesity (P = 0.63). Among women aged ≤60, YLL for grade 1 obesity decreased by 4.21 years (P < 0.001) and by 4.97 years (P < 0.001) for grade 2–3 obesity. In women aged >60, YLL for grade 1 obesity decreased by 3.98 years (P < 0.001) and by 2.64 years (P = 0.001) for grade 2–3 obesity. Grade 1 obesity's association with decreased longevity has reduced for older Caucasian men. For Caucasian women, there is evidence of a decline in the obesity YLL association across all ages.
The mutational burden of acral melanoma revealed by whole‐genome sequencing and comparative analysis
Authors: Furney Simon J. , Turajlic Samra , Stamp Gordon , Thomas J. Meirion , Hayes Andrew , Strauss Dirk , Gavrielides Mike , Xing Wei , Gore Martin , Larkin James , Marais Richard 
Published: June 2014

SummaryAcral melanoma is a subtype of melanoma with distinct epidemiological, clinical and mutational profiles. To define the genomic alterations in acral melanoma, we conducted whole‐genome sequencing and SNP array analysis of five metastatic tumours and their matched normal genomes. We identified the somatic mutations, copy number alterations and structural variants in these tumours and combined our data with published studies to identify recurrently mutated genes likely to be the drivers of acral melanomagenesis. We compared and contrasted the genomic landscapes of acral, mucosal, uveal and common cutaneous melanoma to reveal the distinctive mutational characteristics of each subtype.
Ontogeny of bivalve immunity: assessing the potential of next‐generation sequencing techniques
Authors: Bassim Sleiman , Genard Bertrand , Gauthier‐Clerc Sophie , Moraga Dario , Tremblay Réjean 
Published: June 2014

AbstractLiving organisms are constantly evolving to secure their survival via adaptations at the molecular and cellular level. Most marine bivalves have microscopic planktonic larval stages until settlement to the benthic environment. These pelagic stages are generally more sensitive than their adult counterparts to environmental and pathogen threats. Adaptive capacities could improve survival of these early stages. Recent advancements in data mining and pipeline analysis should shed light on the currently unknown processes that occur during these first stages. Existing data on early stages are fragmented compared with the abundance of information available for adult. Exploring diversity through aquaculture and lessening the impact of common issues, for example, massive mortalities of larvae, especially within the current conditions of a changing climate, ultimately rests on our knowledge of the molecular processes responsible for phenotypic plasticity. Although it is somewhat difficult to assess immune mechanisms by tracking circulating immunocytes in larvae, studies on the development of immune processes are now feasible at the transcript level. Next‐generation techniques offer outstanding solutions for wide‐range transcriptome analysis. We present a short review of the early ontogeny of the immune system in marine bivalves, with particular focus on next‐generation sequencing applications. Like all reviews of this nature, there is a trade‐off between the depth of the coverage and the number of subjects discussed. We will thus restrict the scope to bivalve immunity and focus on the central concepts across a wide range of topics, that is, the ontogeny of immunity and advancements in molecular studies.
A combined study of radar facies, lithofacies and three‐dimensional architecture of an alpine alluvial fan (Illgraben fan, Switzerland)
Authors: Franke Daniel , Hornung Jens , Hinderer Matthias 
Published: June 2014

AbstractAlluvial fans serve as useful archives that record the history of depositional and erosional processes in mountainous regions and thus can reveal the environmental controls that influenced their development. Economically, they play an important role as groundwater reservoirs as well as host rocks for hydrocarbons in deeply buried systems. The interpretation of these archives and the evaluation of their reservoir architecture, however, are problematic because marked heterogeneity in the distribution of sedimentary facies makes correlation difficult. This problem is compounded because the accumulated sedimentary deposits of modern unconsolidated fan systems tend to be poorly exposed and few such systems have been the focus of investigation using high‐resolution subsurface analytical techniques. To overcome this limitation of standard outcrop–analogue studies, a geophysical survey of an alpine alluvial fan was performed using ground‐penetrating radar to devise a scaled three‐dimensional subsurface model. Radar facies were classified and calibrated to lithofacies within a fan system that provided outcropping walls and these were used to derive a three‐dimensional model of the sedimentary architecture and identify evolutionary fan stages. The Illgraben fan in the Swiss Alps was selected as a case study and a network of ca 60 km sections of ground‐penetrating radar was surveyed. Seven radar facies types could be distinguished, which were grouped into debris‐flow deposits and stream‐flow deposits. Assemblages of these radar facies types show three depositional units, which are separated by continuous, fan‐wide reflectors; they were interpreted as palaeo‐surfaces corresponding to episodes of sediment starvation that affected the entire fan. An overall upward decline in the proportion of debris‐flow deposits from ca 50% to 15% and a corresponding increase in stream‐flow deposits were identified. The uppermost depositional unit is bounded at its base by a significant incision surface up to 700 m wide, which was subsequently filled up mostly by stream‐flow deposits. The pronounced palaeo‐surfaces and depositional trends suggest that allocyclic controls governed the evolution of the Illgraben fan, making this fan a valuable archive from which to reconstruct past sediment fluxes and environmental change in the Alps. The results of the integrated outcrop–geophysical approach encourage similar future studies on fans to retrieve their depositional history as well as their potential reservoir properties.
Experimental design and parameter estimation for threshold models in seed germination
Authors: Onofri A , Mesgaran M B , Neve P , Cousens R D 
Published: June 2014

SummaryHydrotime threshold models are used to describe the dynamics of seed germination in response to reduced water availability. Although these models provide several biologically relevant parameters, it is unclear which statistical technique is best suited to their estimation. Most commonly, these models are fitted to the observed cumulative proportions of germinated seeds, using nonlinear regression. However, this approach has been questioned, due to its inability to account for some characteristics of data sets obtained from germination assays, such as interval censoring and correlated observations. We used Monte Carlo simulations to determine the bias and precision of nonlinear regression estimators for a wide range of experimental designs and hypothetical plant species. Results showed that point estimates of model parameters were almost unbiased, while standard errors obtained from nonlinear regression were on average 3–4 times smaller than the Monte Carlo precision. Standard errors obtained by nonparametric resampling methods were comparable to Monte Carlo precision and provided good coverage (very close to the nominal 95% value), with at least 4–8 treatments by four replicates and 50 seeds per Petri dish. With 10 seeds per Petri dish, a higher number of replicates were necessary to achieve good coverage. In particular, good results were obtained with the grouped jackknife (delete‐a‐Petri‐dish), which accounts for repeated observations on the same Petri dish. It is suggested that nonlinear regression may be used to fit the hydrotime model, in association with resampling methods, particularly when the purpose is to compare ‘hydrotime’ parameters across treatments or plant species.
Evaluation of a Fluorescence-Based Method for Antibabesial Drug Screening
Authors: Guswanto Azirwan , Sivakumar Thillaiampalam , Rizk Mohamed Abdo , Elsayed Shimaa Abd Elsalam , Youssef Mohamed Ahmed , ElSaid ElSaid El Shirbini , Yokoyama Naoaki , Igarashi Ikuo 
Published: June 2014

ABSTRACT

In vitro
evaluation of chemotherapeutic agents against
Babesia
and
Theileria
parasites has become routine, and the effectiveness of these chemicals is usually determined by comparing the parasitemia dynamics of untreated and treated parasites. Although microscopy is widely used to calculate parasitemia, several disadvantages are associated with this technique. The present study evaluated a fluorescence-based method using SYBR green I stain (SG I) to screen antibabesial agents in
in vitro
cultures of
Babesia bovis
. The linearity between relative fluorescence units (RFU) and parasitemia was found to be well correlated with a 0.9944 goodness-of-fit (
r
2
) value. Subsequently, 50% inhibitory concentration (IC
50
) values were calculated for 3 antiprotozoan agents, diminazene aceturate, nimbolide, and gedunin, by this method. For diminazene aceturate and nimbolide, the IC
50
s determined by the fluorescence-based method (408 nM and 8.13 μM, respectively) and microscopy (400.3 nM and 9.4 μM, respectively) were in agreement. Furthermore, the IC
50
of gedunin determined by the fluorescence-based method (19 μM) was similar to the recently described microscopy-based value (21.7 μM) for
B. bovis
. Additionally, the Z′ factor (0.80 to 0.90), signal-to-noise (S/N) ratio (44.15 to 87.64), coefficient of variation at the maximum signal (%CVmax) (0.50 to 2.85), and coefficient of variation at the minimum signal (%CVmin) (1.23 to 2.21) calculated for the fluorescence method using diminazene aceturate were comparable to those previously determined in malaria research for this assay. These findings suggest that the fluorescence-based method might be useful for antibabesial drug screening and may have potential to be developed into a high-throughput screening (HTS) assay.
Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals
Authors: Wright Meredith S. , Perez Federico , Brinkac Lauren , Jacobs Michael R. , Kaye Keith , Cober Eric , van Duin David , Marshall Steven H. , Hujer Andrea M. , Rudin Susan D. , Hujer Kristine M. , Bonomo Robert A. , Adams Mark D. 
Published: June 2014

ABSTRACT

Genome sequencing of carbapenem-resistant
Klebsiella pneumoniae
isolates from regional U.S. hospitals was used to characterize strain diversity and the
bla
KPC
genetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus (
cps
) and their plasmid contents. A strict association between clade and KPC variant was found. The
bla
KPC
gene was found on variants of two plasmid backbones. This study indicates that highly similar
K. pneumoniae
subpopulations coexist within the same hospitals over time.
Efficacy of Repeated Intravenous Administration of Peramivir against Highly Pathogenic Avian Influenza A (H5N1) Virus in Cynomolgus Macaques
Authors: Kitano Mitsutaka , Itoh Yasushi , Ishigaki Hirohito , Nakayama Misako , Ishida Hideaki , Pham Van Loi , Arikata Masahiko , Shichinohe Shintaro , Tsuchiya Hideaki , Kitagawa Naoko , Kobayashi Masanori , Yoshida Ryu , Sato Akihiko , Le Quynh Mai , Kawaoka Yoshihiro , Ogasawara Kazumasa 
Published: June 2014

ABSTRACT

Highly pathogenic avian influenza A (H5N1) viruses cause severe and often fatal disease in humans. We evaluated the efficacy of repeated intravenous dosing of the neuraminidase inhibitor peramivir against highly pathogenic avian influenza virus A/Vietnam/UT3040/2004 (H5N1) infection in cynomolgus macaques. Repeated dosing of peramivir (30 mg/kg/day once a day for 5 days) starting immediately after infection significantly reduced viral titers in the upper respiratory tract, body weight loss, and cytokine production and resulted in a significant body temperature reduction in infected macaques compared with that of macaques administered a vehicle (
P
< 0.05). Repeated administration of peramivir starting at 24 h after infection also resulted in a reduction in viral titers and a reduction in the period of virus detection in the upper respiratory tract, although the body temperature change was not statistically significant. The macaque model used in the present study demonstrated that inhibition of viral replication at an early time point after infection by repeated intravenous treatment with peramivir is critical for reduction of the production of cytokines, i.e., interleukin-6 (IL-6), tumor necrosis factor α, gamma interferon, monocyte chemotactic protein 1, and IL-12p40, resulting in amelioration of symptoms caused by highly pathogenic avian influenza virus infection.
Glucose-6-Phosphate Dehydrogenase Status and Risk of Hemolysis in Plasmodium falciparum-Infected African Children Receiving Single-Dose Primaquine
Authors: Eziefula Alice C. , Pett Helmi , Grignard Lynn , Opus Salome , Kiggundu Moses , Kamya Moses R. , Yeung Shunmay , Staedke Sarah G. , Bousema Teun , Drakeley Chris 
Published: June 2014

ABSTRACT
Glucose-6-phosphate dehydrogenase (G6PD) enzyme function and genotype were determined in Ugandan children with uncomplicated falciparum malaria enrolled in a primaquine trial after exclusion of severe G6PD deficiency by fluorescent spot test. G6PD A− heterozygotes and hemizygotes/homozygotes experienced dose-dependent lower hemoglobin concentrations after treatment. No severe anemia was observed.
Bile Acids Repress Hypoxia-Inducible Factor 1 Signaling and Modulate the Airway Immune Response
Authors: Legendre Claire , Reen F. Jerry , Woods David F. , Mooij Marlies J. , Adams Claire , O'Gara Fergal 
Published: June 2014

ABSTRACT
Gastroesophageal reflux (GER) frequently occurs in patients with respiratory disease and is particularly prevalent in patients with cystic fibrosis. GER is a condition in which the duodenogastric contents of the stomach leak into the esophagus, in many cases resulting in aspiration into the respiratory tract. As such, the presence of GER-derived bile acids (BAs) has been confirmed in the bronchoalveolar lavage fluid and sputum of affected patients. We have recently shown that bile causes cystic fibrosis-associated bacterial pathogens to adopt a chronic lifestyle and may constitute a major host trigger underlying respiratory infection. The current study shows that BAs elicit a specific response in humans in which they repress hypoxia-inducible factor 1α (HIF-1α) protein, an emerging master regulator in response to infection and inflammation. HIF-1α repression was shown to occur through the 26S proteasome machinery via the prolyl hydroxylase domain (PHD) pathway. Further analysis of the downstream inflammatory response showed that HIF-1α repression by BAs can significantly modulate the immune response of airway epithelial cells, correlating with a decrease in interleukin-8 (IL-8) production, while IL-6 production was strongly increased. Importantly, the effects of BAs on cytokine production can also be more dominant than the bacterium-mediated effects. However, the effect of BAs on cytokine levels cannot be fully explained by their ability to repress HIF-1α, which is not surprising, given the complexity of the immune regulatory network. The suppression of HIF-1 signaling by bile acids may have a significant influence on the progression and outcome of respiratory disease, and the molecular mechanism underpinning this response warrants further investigation.
Host Response to Nontuberculous Mycobacterial Infections of Current Clinical Importance
Authors: Orme Ian M. , Ordway Diane J. 
Published: June 2014

ABSTRACTThe nontuberculous mycobacteria are a large group of acid-fast bacteria that are very widely distributed in the environment. WhileMycobacterium aviumwas once regarded as innocuous, its high frequency as a cause of disseminated disease in HIV-positive individuals illustrated its potential as a pathogen. Much more recently, there is growing evidence that the incidence ofM. aviumand related nontuberculous species is increasing in immunocompetent individuals. The same has been observed forM. abscessusinfections, which are very difficult to treat; accordingly, this review focuses primarily on these two important pathogens. Like the host response toM. tuberculosisinfections, the host response to these infections is of the TH1 type but there are some subtle and as-yet-unexplained differences.