bluuebunny/crossref_metadata_2025 huggingface dataset:
Local and landscape effects in a host–parasitoid interaction network along a forest–cropland gradient
Authors: Osorio Sergio , Arnan Xavier , Bassols Emili , Vicens Narcís , Bosch Jordi
Published: March 2015

Land‐use driven habitat modification is a major driver of biodiversity loss and impoverishment of interaction diversity. This may affect ecosystem services such as pollination and biological control. Our objective is to analyze the effects of local (nesting environment: farms vs. tree stands) and landscape (forest–cropland gradient) factors on the structure and composition of a cavity‐nesting bee–wasp (CNBW) community, their nests associates (henceforth parasitoids), and their interactions. We set up 24 nest‐trapping stations in a fragmented, extensively farmed area of ~100 km2. We obtained 2035 nests containing 7572 brood cells representing 17 bee and 18 wasp species, attacked by 20 parasitoid species. Community structure and composition, as well as network structure, were much more dependent on local than on landscape factors. Host abundance and richness were higher in farms. In addition, host abundance was positively correlated to cropland cover. We also found highly significant differences between nesting environments in host community composition. Structure and composition of the parasitoid community were conditioned by the structure and composition of the host community. Network structure was affected by nesting environment but not by landscape factors. Interactions tended to be more diverse in farms. This result was mostly explained by differences in network size (greater in farms). However, generality was significantly higher in farms even after controlling for network size, indicating that differences in species' interaction patterns associated to differences in community composition between the two nesting environments are also affecting network structure. In conclusion, open habitats associated with extensively farmed exploitations favor local CNBW diversity (especially bees) and result in more complex host–parasitoid interaction networks in comparison to forested areas. The conservation value of this kind of open habitat is important in view of the progressive abandonment of extensively cultivated farmland taking place in Europe at the expense of agricultural intensification and reforestation.
Chemically-Induced Pressure Pulse: A New Fracturing Technology for Unconventional Reservoirs
Authors: Al-Nakhli Ayman R.
Published: March 2015

The huge resources of unconventional gas worldwide along with the increasing oil demand make the contribution of unconventional gas to be critical to the world economy. However, one of the major challenges that operators face to produce from unconventional resources is commercial stimulation technique that creates sufficient stimulated reservoir volume. Unconventional reserves trapped within very low permeability formations, such as tight gas, or shale formations, exhibit little or no production, and are thus economically undesirable to develop with existing conventional recovery methods. Such reservoirs require a large fracture network with high fracture conductivity to maximize well performance.

One commonly employed technique for stimulating low productivity wells is multi-stage hydraulic fracturing, which is costly and typically involves the injection of high viscosity fluids into the well. Fracturing fluid by itself could form a damaging material for the fracture due to high capillary forces. Thus, additional needs exist for an economical method to enhance production within a tight gas formation.

This paper discusses a new stimulation method to increase stimulated reservoir volume (SRV) around wellbore and fracture area, and therefore, improve unconventional gas production. The method entails triggering an exothermic chemical reaction in-situ to generate heat, gas and localized pressure sufficient to create fractures around the wellbore. In controlled experiment, chemical reactants were separately injected into core samples with a minihole and upon mixing inside the core, an exothermic chemical reaction occurred and the resultant heat and gas pressure caused macro-fractures. NMR-porosity imaging showed significant increase in macro pores throughout the core. Additionally Large scale experiments using cement blocks with a simulated wellbore cavity were performed. Once the wellbore was filled with the chemicals and upon introducing a triggering catalyst an in-situ chemical reaction took place which generated heat and gas with sufficient pressure to cause shear fractures in the surrounding rock. These experiments showed extensive fractured and shattered pieces and also provided preliminary design requirements for a field test. The chemical reactants then incorporated into a fracturing gel to simulate creating additional fractured from the main induced hydraulic fracture. The results were very encouraging and the generated high temperature and pressure caused the gel to break thus it is concluded that this technique effectively contribute to fracture cleanup in addition to creating required SRV. The experiments were very successful in proving the new concept of generating SRV in tight gas well and the developed stimulation technique is fairly easy to implement in the field.
Optimization of Well Trajectories and Wellhead Towers' Slots Allocation Through a Collaborative Well-Planning Approach
Authors: Marir Boualem , Mandel Christian , Al Jefri Ghassan , Torres Javier , Ferdian Salman
Published: March 2015

Traditionally, geoscientists, drilling, reservoir, and facility engineers work separately on projects. The workflows between these disciplines are typically onerous, iterative, and time consuming because there is no common environment between roles. For offshore fields, the limited number of towers from which wells can be drilled make well planning a critical process for a successful development. Usually, planning is done on a well-by-well basis, which could introduce the potential for increased risks.

ADMA-OPCO has begun developing an offshore green field through drilling about 90 wells (duals and singles) from eight wellhead towers. The development scheme for this field is optimized per reservoir, five-spot water injection, natural depletion, and gas injection. For each tower, slots (injector vs. producers) and allocations have to be defined with high confidence and be communicated to surface project teams to start the design and engineering process. This exercise requires working all well trajectories (drillable wells that meet the statements of requirements). Early in the field-development process, the common practice is to do the well-profile work on a well-by-well basis, which takes a minimum of three to five days per well depending on well type and complexity.

This paper addresses a different approach that is used by ADMA-OPCO, which allowed for accelerating the planning process by integrating all stakeholders for the objective of reducing the working hours while optimizing the trajectories and taking into account all criteria and safety guidelines executed within a 3-D static-model environment.

As an outcome, more than 100 horizontal drains were successfully optimized, and slot allocations were defined for all towers within 20 working days (minimum of 380 days would be required if done on a well-by-well basis). A drilling footage of more than 20, 000 ft was saved after optimization. Additionally, the real collaborative value was seen in the integrated working sessions, resulting in an improved deliverable.
Global Optimization Strategies For Well Tests In Dual Porosity Reservoirs
Authors: Al-Nemer A.A. , Issaka M.B. , Awotunde A.A. , Al-Hashem H.S.
Published: March 2015

This study presents an investigation of the performance of multiple stochastic optimization algorithms in performing automatic type-curve matching for pressure transient well test analysis. The pressure transient responses of a vertical well in a dual porosity reservoir were generated. A synthetic reservoir model that shows all flow regimes for the model was created. Gaussian White Noise data was added to the typical response to imitate measured data. In addition to the Levenberg-Marquardt algorithm, four stochastic algorithms were used to estimate the reservoir model from the noisy data. These algorithms are Deferential Evolution, Particle Swarm Optimization, Local Unimodal Sampling and Many Optimizing Liaisons. Behavioral parameters of each algorithm were investigated by comparing the performance of recommended values in the literature. Each algorithm was run for 25 realizations. The results of the runs were ordered in terms of the best achieved result. The performance was compared by comparing the best 1st, 7th, 19th and 25th results of each algorithm.

The result showed that the algorithms performance is affected by the model and the unknowns. Differential Evolution algorithm showed the best performance in Dual Porosity Reservoir when Øm, λ, ω, skin, re & kf are the unknowns. All the other stochastic algorithms performed better than Levenberg-Marquardt optimization algorithm.
Impact of Perforation Tunnel Orientation and Length in Horizontal Wellbores on Fracture Initiation Pressure in Maximum Tensile Stress Criterion Model for Tight Gas Fields in the Sultanate of Oman
Authors: Briner Andreas , Chavez Juan Carlos , Nadezhdin Sergey , Alekseenko Olga , Gurmen Nihat , Cherny Sergey , Kuranakov Dmitry , Lapin Vasily
Published: March 2015

The goal of the present work is to simulate the effects of perforation misalignment on fracture initiation pressure (FIP). A 3D numerical model of the fracture initiation from a perforated wellbore in linear elastic rock is used to model FIP. This model is based on the boundary element method (BEM) and maximum tensile stress (MTS) criterion. Simulations enable studying FIP sensitivity to perforation orientation and finding the orientation that corresponds to the lowest FIP as well as the FIP change along the length and the circumference of the perforation tunnel. The data used were from different zones and blocks of a tight gas-bearing sandstone field in the Sultanate of Oman. Some practical applications of the study include the decisions on the type of perforation technique (i.e. abrasive jetting or explosive perforations), which greatly impact the economics of the fracturing treatments.
The Impact of Gas Adsorption and Composition on Unconventional Shale Permeability Measurement
Authors: Jin Guodong , Pérez Héctor González , Agrawal Gaurav , Khodja Mohamed R. , Ali Abdulwahab Zaki , Hussaini Syed Rizwanullah , Jangda Zaid Zaffar
Published: March 2015

Permeability determination of organic-rich shales is still a major challenge. Uncertainty in this estimate involves several factors. Two significant ones are the occurrence of gas adsorption which can severely limit gas transport in the pores and understanding the physical chemistry issues of the pore's surface area estimation when using various gases. In this study, we reported our experimental results of permeability measurement on several unconventional shale samples, and investigated the effect of gas type, pore pressure, effective stress and sample orientation on the measured permeabilities.

Permeability of shale samples is measured using the complex pressure transient technique. Three different gases, argon, nitrogen, and carbon dioxide, are used as permeating fluid through the samples. Experiments are conducted isothermally at various pore and confining pressures that maintain a constant net effective stress. Generally, samples have higher measured permeabilities when using nitrogen as pore fluid rather than using argon. The discrepancy was attributed to different adsorption potentials between argon and nitrogen: Argon has a similar sorption potential to methane while nitrogen's sorption potential is relatively weak. As expected, the measured permeability of all samples decreases when the pore pressure increases reflecting the reduction in the gas slippage effect. Samples from the same whole core display permeability anisotropy: Horizontal plugs cut parallel to bedding have a higher measured permeability, which is in the range of microdarcy, while the permeability of vertical plugs cut perpendicular to bedding is in the range of nanodarcy. This anisotropy behavior is believed to be caused by the fractures contained within the horizontal samples. The measured permeability is observed to decease with increasing effective stress acting on the samples. This reduction behaves differently: Permeability decreases very slowly when the increasing effective stress is resulted from the decrease of the pore pressure. The enhanced Klinkenberg effect due to the decreasing pore pressure compensates at least partly the permeability reduction resulting from increasing effective stress. However, permeability reduces dramatically when the effective stress increases because of the increasing confining pressure. In this case, the flow channels may be reduced or even closed, thus blocking the flow of gas.
A Comprehensive Approach in Diagnosing the Polycystic Ovary Syndrome
Authors: Pasquali Renato , Gambineri Alessandra
Published: March 2015

The polycystic ovary syndrome is the commonest hyperandrogenic and dysmetabolic disorder in women that, by definition, may present with different phenotypes, including the classic forms and those with a milder presentation. Its diagnosis is mainly based on careful clinical judgment, although it may require additional investigation by blood testing or imaging techniques in the differential diagnosis of androgen excess. This article summarizes the most important aspects of the diagnostic procedure and suggests how to apply them in clinical practice.
Glacier dynamics near the calving front of Bowdoin Glacier, northwestern Greenland
Authors: Sugiyama Shin , Sakakibara Daiki , Tsutaki Shun , Maruyama Mihiro , Sawagaki Takanobu
Published: March 2015

To better understand recent rapid recession of marine-terminating glaciers in Greenland, we performed satellite and field observations near the calving front of Bowdoin Glacier, a 3 km wide outlet glacier in northwestern Greenland. Satellite data revealed a clear transition to a rapidly retreating phase in 2008 from a relatively stable glacier condition that lasted for >20 years. Ice radar measurements showed that the glacier front is grounded, but very close to the floating condition. These results, in combination with the results of ocean depth soundings, suggest bed geometry in front of the glacier is the primary control on the rate and pattern of recent rapid retreat. Presumably, glacier thinning due to atmospheric and/or ocean warming triggered the initial retreat. In situ measurements showed complex short-term ice speed variations, which were correlated with air temperature, precipitation and ocean tides. Ice speed quickly responded to temperature rise and a heavy rain event, indicating rapid drainage of surface water to the bed. Semi-diurnal speed peaks coincided with low tides, suggesting the major role of the hydrostatic pressure acting on the calving face in the force balance. These observations demonstrate that the dynamics of Bowdoin Glacier are sensitive to small perturbations occurring near the calving front.
Improving the outcome for children with cancer: Development of targeted new agents
Authors: Adamson Peter C.
Published: March 2015

The outcome for children with cancer has improved significantly over the past 60 years, with greater than 80% of patients today becoming 5‐year survivors. Despite this progress, cancer remains the leading cause of death from disease in children in the United States, and significant short‐term and long‐term treatment toxicities continue to impact the majority of children with cancer. The development of targeted new agents offers the prospect of potentially more effective and less toxic treatment for children. More than a decade since imatinib mesylate was introduced into the treatment of children with Philadelphia chromosome‐positive acute lymphoblastic leukemia, transforming its outcome, a range of targeted agents has undergone study in pediatric cancer patients. Early lessons learned from these studies include a better understanding of the adverse event profile of these drugs in children, the challenge of developing pediatric‐specific formulations, and the continued reliance on successful development for adult cancer indications on pediatric drug development. The collaborative research infrastructure for children with cancer in the United States is well positioned to advance novel treatments into clinical investigations for a spectrum of rare and ultra‐rare childhood cancers. A greater investment of resources in target discovery and validation can help drive much needed development of new, more effective treatments for children with cancer. CA Cancer J Clin 2015;65: 212–220. © 2015 American Cancer Society.
She reads, he reads: gender differences and learning through self-help books
Authors: Kapell Brandi , McLean Scott
Published: March 2015

Despite considerable scholarly attention given to self-help literature, there has been a lack of research about the experience of self-help reading. In this article, we explore gender differences in self-help reading. We argue that men and women read self-help books for different reasons and with different levels of engagement, and that they experience different outcomes from reading. We provide evidence from in-depth interviews with 89 women and 45 men. Women are more likely to seek out books of their own volition, to engage in learning strategies beyond reading, and to take action as a result of reading. Men are more likely to read books relating to careers, while women are more likely to read books about interpersonal relationships. We argue that these gender differences reflect profound political-economic and cultural changes, and that such changes also help explain the gendered evolution of adult, continuing, and higher education in recent decades.
Effects of Aerosol on Cloud Liquid Water Path: Statistical Method a Potential Source for Divergence in Past Observation Based Correlative Studies
Authors: Savane Ousmane , Vant-Hull Brian , Mahani Shayesteh , Khanbilvardi Reza
Published: March 2015

Studies show a divergence in correlation between aerosol and cloud proxies, which has been thought of in the past as the results of varying physical mechanisms. Though modeling studies have supported this idea, from an observational standpoint it is difficult to attribute with confidence the correlations to specific physical mechanisms. We explore a methodology to assess the correlation between cloud water path and aerosol optical depth using Moderate-resolution Imaging Spectroradiometer (MODIS) Aqua retrieved aerosol and cloud properties for absorbing and non-absorbing aerosol types over land and over the Atlantic Ocean for various meteorological conditions. The data covers a three-month period, June through August, during which different aerosol types are predominant in specific regions. Our approach eliminates outliers; sorts the data into aerosol bins; and the mean Aerosol Optical Depth (AOD) value for each bin and the corresponding mean Cloud Water Path (CWP) value are determined. The mean CWP is plotted against the mean AOD. The response curve for all aerosol types shows a peak CWP value corresponding to an aerosol loading value AODpeak. The peak is used to divide the total range of aerosol loading into two sub ranges. For AOD value below AODpeak, mean CWP and mean AOD are positively correlated. The correlation between mean CWP and mean AOD is negative for aerosol loading above AODpeak. Irrespective of aerosol type, atmospheric water vapor content and lower tropospheric static stability, the peak observed for each aerosol type seems to describe a universal feature that calls for further investigation. It has been observed for a variety of geographical locations and different seasons.
Projective Synchronization for a Class of Fractional-Order Chaotic Systems with Fractional-Order in the (1, 2) Interval
Authors: Zhou Ping , Bai Rongji , Zheng Jiming
Published: March 2015

In this paper, a projective synchronization approach for a class of fractional-order chaotic systems with fractional-order 1 < q < 2 is demonstrated. The projective synchronization approach is established through precise theorization. To illustrate the effectiveness of the proposed scheme, we discuss two examples: (1) the fractional-order Lorenz chaotic system with fractional-order q = 1.1; (2) the fractional-order modified Chua’s chaotic system with fractional-order q = 1.02. The numerical simulations show the validity and feasibility of the proposed scheme.
Centile Curves and Reference Values for Height, Body Mass, Body Mass Index and Waist Circumference of Peruvian Children and Adolescents
Authors: Bustamante Alcibíades , Freitas Duarte , Pan Huiqi , Katzmarzyk Peter , Maia José
Published: March 2015

This study aimed to provide height, body mass, BMI and waist circumference (WC) growth centile charts for school-children, aged 4–17 years, from central Peru, and to compare Peruvian data with North-American and Argentinean references. The sample consisted of 8753 children and adolescents (4130 boys and 4623 girls) aged 4 to 17 years, from four Peruvian cities: Barranco, La Merced, San Ramón and Junín. Height, body mass and WC were measured according to standardized techniques. Centile curves for height, body mass, BMI and WC were obtained separately for boys and girls using the LMS method. Student t-tests were used to compare mean values. Overall boys have higher median heights than girls, and the 50th percentile for body mass increases curvilinearly from 4 years of age onwards. In boys, the BMI and WC 50th percentiles increase linearly and in girls, the increase presents a curvilinear pattern. Peruvian children are shorter, lighter and have higher BMI than their counterparts in the U.S. and Argentina; in contrast, age and sex-specific WC values are lower. Height, body mass and WC of Peruvian children increased with age and variability was higher at older ages. The growth patterns for height, body mass, BMI and WC among Peruvian children were similar to those observed in North-American and Argentinean peers.
Optimized Arrangement of Constant Ambient Air Monitoring Stations in the Kanto Region of Japan
Authors: Shirato Shintaro , Iizuka Atsushi , Mizukoshi Atsushi , Noguchi Miyuki , Yamasaki Akihiro , Yanagisawa Yukio
Published: March 2015

Continuous ambient air monitoring systems have been introduced worldwide. However, such monitoring forces autonomous communities to bear a significant financial burden. Thus, it is important to identify pollutant-monitoring stations that are less efficient, while minimizing loss of data quality and mitigating effects on the determination of spatiotemporal trends of pollutants. This study describes a procedure for optimizing a constant ambient air monitoring system in the Kanto region of Japan. Constant ambient air monitoring stations in the area were topologically classified into four groups by cluster analysis and principle component analysis. Then, air pollution characteristics in each area were reviewed using concentration contour maps and average pollution concentrations. We then introduced three simple criteria to reduce the number of monitoring stations: (1) retain the monitoring station if there were similarities between its data and average data of the group to which it belongs; (2) retain the station if its data showed higher concentrations; and (3) retain the station if the monitored concentration levels had an increasing trend. With this procedure, the total number of air monitoring stations in suburban and urban areas was reduced by 36.5%. The introduction of three new types of monitoring stations is proposed, namely, mobile, for local non-methane hydrocarbon pollution, and Ox-prioritized.
A Perilipin Gene from Clonostachys rosea f. Catenulata HL-1-1 Is Related to Sclerotial Parasitism
Authors: Sun Zhan-Bin , Li Shi-Dong , Zhong Zeng-Ming , Sun Man-Hong
Published: March 2015

Clonostachys rosea f. catenulata is a promising biocontrol agent against many fungal plant pathogens. To identify mycoparasitism-related genes from C. rosea f. catenulata, a suppression subtractive hybridization (SSH) cDNA library of C. rosea f. catenulata HL-1-1 that parasitizes the sclerotia of S. sclerotiorum was constructed. 502 clones were sequenced randomly, and thereby 472 expressed sequence tags (ESTs) were identified. Forty-three unigenes were annotated and exhibited similarity to a wide diversity of genes. Quantitative real -time PCR showed that a perilipin-like protein encoding gene, Per3, was up-regulated by 6.6-fold over the control at 96 h under the induction of sclerotia. The full-length sequence of Per3 was obtained via 5' and 3' rapid identification of cDNA ends. Overexpression of Per3 in HL-1-1 significantly enhanced the parasitic ability on sclerotia. The results indicated that Per3 might be involved in the mycoparasitism of C. rosea f. catenulata HL-1-1. This is the first report of a perilipin as a potential biocontrol gene in mycoparasites. The study provides usefu l insights into the interaction between C. rosea f. catenulata and fungal plant pathogens.
SOCS3 Silencing Attenuates Eosinophil Functions in Asthma Patients
Authors: Zafra Mª , Cañas Jose , Mazzeo Carla , Gámez Cristina , Sanz Veronica , Fernández-Nieto Mar , Quirce Santiago , Barranco Pilar , Ruiz-Hornillos Javier , Sastre Joaquín , Del Pozo Victoria
Published: March 2015

Eosinophils are one of the key inflammatory cells in asthma. Eosinophils can exert a wide variety of actions through expression and secretion of multiple molecules. Previously, we have demonstrated that eosinophils purified from peripheral blood from asthma patients express high levels of suppressor of cytokine signaling 3 (SOCS3). In this article, SOCS3 gene silencing in eosinophils from asthmatics has been carried out to achieve a better understanding of the suppressor function in eosinophils. SOCS3 siRNA treatment drastically reduced SOCS3 expression in eosinophils, leading to an inhibition of the regulatory transcription factors GATA-3 and FoxP3, also interleukin (IL)-10; in turn, an increased STAT3 phosphorilation was observed. Moreover, SOCS3 abrogation in eosinophils produced impaired migration, adhesion and degranulation. Therefore, SOCS3 might be regarded as an important regulator implicated in eosinophil mobilization from the bone marrow to the lungs during the asthmatic process.
A Polymorphism at the Translation Start Site of the Vitamin D Receptor Gene Is Associated with the Response to Anti-Osteoporotic Therapy in Postmenopausal Women from Southern Italy
Authors: Conti Valeria , Russomanno Giusy , Corbi Graziamaria , Toro Giuseppe , Simeon Vittorio , Filippelli Walter , Ferrara Nicola , Grimaldi Michela , D'Argenio Valeria , Maffulli Nicola , Filippelli Amelia
Published: March 2015

The present study investigated the effect of two single nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) gene, rs1544410 A/G and rs2228570 C/T, in modulating bone mineral density (BMD) and the response to treatment with bisphosphonates or strontium ranelate in postmenopausal osteoporosis (PMO). Four hundred eighteen postmenopausal women from Southern Italy treated with bisphosphonates or strontium ranelate for three years were enrolled and stratified according to their genotype. Changes in BMD were expressed as the delta t-score (Δt-score). Allelic frequencies for rs1544410 A/GSNP were 11.2% AA, 50.0% GA and 38.8% GG; for rs2228570 C/TSNP were 54.8% CC, 39.5% TC and 5.7% TT. TT carriers showed a lower t-score than TC and CC (both p < 0.02) genotypes and were more responsive to the therapy when compared to both TC (p < 0.02) and CC (p < 0.05) carriers. Specifically, TT carriers receiving alendronate demonstrated a significant improvement of the Δt-score compared to TC and CC (both p < 0.0001) carriers. After adjustment for confounders, the Δt-score showed evidence of a statistically significant positive association with TT in all treatments considered. Therapy response was independent of rs1544410 A/G SNP; instead, rs2228570 C/TSNP was associated with a better response to antiresorptive treatment, thus suggesting that the therapy for PMO should be personalized.
Helper T Lymphocyte Response in the Peripheral Blood of Patients with Intraepithelial Neoplasia Submitted to Immunotherapy with Pegylated Interferon-α
Authors: Michelin Márcia , Montes Letícia , Nomelini Rosekeila , Trovó Marco , Murta Eddie
Published: March 2015

Immunotherapy in cancer patients is a very promising treatment and the development of new protocols and the study of the mechanisms of regression is imperative. The objective of this study was to evaluate the production of cytokines in helper T (CD4+) lymphocytes during immunotherapy with pegylated IFN-α in patients with cervical intraepithelial neoplasia (CIN). We conducted a prospective study with 17 patients with CIN II-III using immunotherapy with pegylated IFN-α subcutaneouly weekly, and using flow cytometry we evaluated the peripheric CD4+ T lymphocytes. The results show that in the regression group the patients presented a significant increase in the amount of IFN-γ during the entire immunotherapy, compared with the group without a response. The amount of CD4+ T lymphocytes positive for IL-2, IL-4, IL-10 and TGF-β is significantly lower in patients with good clinical response. The results also demonstrate that patients with regression have a higher amount of intracellular TNF-α in CD4+ T lymphocytes before the start of treatment. Analyzing these data sets, it can be concluded that immunotherapy is a viable clinical treatment for patients with high-grade CIN and that the regression is dependent on the change in the immune response to a Th1 pattern.
CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity
Authors: Garrett Roger , Shah Shiraz , Erdmann Susanne , Liu Guannan , Mousaei Marzieh , León-Sobrino Carlos , Peng Wenfang , Gudbergsdottir Soley , Deng Ling , Vestergaard Gisle , Peng Xu , She Qunxin
Published: March 2015

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.
Gelatin Tight-Coated Poly(lactide-co-glycolide) Scaffold Incorporating rhBMP-2 for Bone Tissue Engineering
Authors: Wang Juan , Li Dongsong , Li Tianyi , Ding Jianxun , Liu Jianguo , Li Baosheng , Chen Xuesi
Published: March 2015

Surface coating is the simplest surface modification. However, bioactive molecules can not spread well on the commonly used polylactone-type skeletons; thus, the surface coatings of biomolecules are typically unstable due to the weak interaction between the polymer and the bioactive molecules. In this study, a special type of poly(lactide-co-glycolide) (PLGA)-based scaffold with a loosened skeleton was fabricated by phase separation, which allowed gelatin molecules to more readily diffuse throughout the structure. In this application, gelatin modified both the internal substrate and external surface. After cross-linking with glutaraldehyde, the surface layer gelatin was tightly bound to the diffused gelatin, thereby preventing the surface layer gelatin coating from falling off within 14 days. After gelatin modification, PLGA scaffold demonstrated enhanced hydrophilicity and improved mechanical properties (i.e., increased compression strength and elastic modulus) in dry and wet states. Furthermore, a sustained release profile of recombinant human bone morphogenetic protein-2 (rhBMP-2) was achieved in the coated scaffold. The coated scaffold also supported the in vitro attachment, proliferation, and osteogenesis of rabbit bone mesenchymal stem cells (BMSCs), indicating the bioactivity of rhBMP-2. These results collectively demonstrate that the cross-linked-gelatin-coated porous PLGA scaffold incorporating bioactive molecules is a promising candidate for bone tissue regeneration.
Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway
Authors: Nayak Dipti , Marx Christopher
Published: March 2015

Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy source for 150 generations neither fitness nor growth rate improved. These results suggest that the NMG pathway permits slow growth on methylamine and is widely distributed in methylotrophs; however, rapid growth on methylamine can be achieved quite readily through acquisition of the mau cluster by HGT.
The Effect of Number and Position of P=O/P=S Bridging Units on Cavitand Selectivity toward Methyl Ammonium Salts
Authors: Menozzi Daniela , Pinalli Roberta , Massera Chiara , Maffei Francesca , Dalcanale Enrico
Published: March 2015

The present work reports the synthesis and complexation properties of five mixed bridge P=O/P=S cavitands toward N,N-methyl butyl ammonium chloride (1) as prototype guest. The influence of number and position of P=O and P=S groups on the affinity of phosphonate cavitands toward 1 is assessed via ITC titrations in DCE as solvent. Comparison of the resulting Kass values, the enthalpic and entropic contributions to the overall binding with those of the parent tetraphosphonate Tiiii and tetrathiophosphonate TSiiii cavitands allows one to single out the simultaneous dual H-bond between the cavitand and the salt as the major player in complexation.
Two New Phenolic Glucosides from Lagerstroemia speciosa
Authors: Choi Janggyoo , Cho Jae , Choi Soo , Jeon Heejin , Kim Young , Htwe Khin , Chin Young , Lee Woo , Kim Jinwoong , Yoon Kee
Published: March 2015

Two new phenolic glucosides, 1-O-benzyl-6-O-E-caffeoyl-β-d-glucopyranoside and 1-O-(7S,8R)-guaiacylglycerol-(6-O-E-caffeoyl)-β-d-glucopyranoside, were isolated from the aerial parts of Lagerstroemia speciosa, along with ten known compounds. The structures of the isolated compounds were determined based on 1D- and 2D-NMR, Q-TOF MS and optical rotation spectroscopic data. All of the compounds showed moderate inhibitory activities against nitric oxide production in lipopolysaccharide-treated RAW264.7 cells, with IC50 values of 69.5–83.3 μM.
Multigram Synthesis and in Vivo Efficacy Studies of a Novel Multitarget Anti-Alzheimer’s Compound
Authors: Sola Irene , Viayna Elisabet , Gómez Tània , Galdeano Carles , Cassina Matteo , Camps Pelayo , Romeo Margherita , Diomede Luisa , Salmona Mario , Franco Pilar , Schaeffer Mireille , Colantuono Diego , Robin David , Brunner Daniela , Taub Nicole , Hutter-Paier Birgit , Muñoz-Torrero Diego
Published: March 2015

We describe the multigram synthesis and in vivo efficacy studies of a donepezil‒huprine hybrid that has been found to display a promising in vitro multitarget profile of interest for the treatment of Alzheimer’s disease (AD). Its synthesis features as the key step a novel multigram preparative chromatographic resolution of intermediate racemic huprine Y by chiral HPLC. Administration of this compound to transgenic CL4176 and CL2006 Caenorhabditis elegans strains expressing human Aβ42, here used as simplified animal models of AD, led to a significant protection from the toxicity induced by Aβ42. However, this protective effect was not accompanied, in CL2006 worms, by a reduction of amyloid deposits. Oral administration for 3 months to transgenic APPSL mice, a well-established animal model of AD, improved short-term memory, but did not alter brain levels of Aβ peptides nor cortical and hippocampal amyloid plaque load. Despite the clear protective and cognitive effects of AVCRI104P4, the lack of Aβ lowering effect in vivo might be related to its lower in vitro potency toward Aβ aggregation and formation as compared with its higher anticholinesterase activities. Further lead optimization in this series should thus focus on improving the anti-amyloid/anticholinesterase activity ratio.
Macro- and Micronutrients Consumption and the Risk for Colorectal Cancer among Jordanians
Authors: Tayyem Reema , Bawadi Hiba , Shehadah Ihab , Abu-Mweis Suhad , Agraib Lana , Bani-Hani Kamal , Al-Jaberi Tareq , Al-Nusairr Majed , Heath Dennis
Published: March 2015

Objective: Diet and lifestyle have been reported to be important risk factors for the development of colorectal cancer (CRC). However, the association between total energy and nutrient intake and the risk of developing CRC has not been clearly explained. The aim of our study is to examine the relationship between total energy intake and other nutrients and the development of CRC in the Jordanian population. Research Methods and Procedures: Dietary data was collected from 169 subjects who were previously diagnosed with CRC, and 248 control subjects (matched by age, gender, occupation and marital status). These control subjects were healthy and disease free. Data was collected between January 2010 and December 2012, using interview-based questionnaires. Logistic regression was used to evaluate the association between quartiles of total energy, macro- and micronutrient intakes with the risk of developing CRC in our study population. Results: Total energy intake was associated with a higher risk of developing CRC (OR = 2.60 for the highest versus lowest quartile of intake; 95% CI: 1.21–5.56, p-trend = 0.03). Intakes of protein (OR = 3.62, 95% CI: 1.63–8.05, p-trend = 0.002), carbohydrates (OR = 1.41, 95% CI: 0.67–2.99, p-trend = 0.043), and percentage of energy from fat (OR = 2.10, 95% CI: 0.38–11.70, p-trend = 0.009) significantly increased the risk for the development of CRC. Saturated fat, dietary cholesterol and sodium intake showed a significant association with the risk of developing CRC (OR = 5.23, 95% CI: 2.33–11.76; OR = 2.48, 95% CI: 1.18–5.21; and OR = 3.42, 95% CI: 1.59–7.38, respectively), while vitamin E and caffeine intake were indicative of a protective effect against the development of CRC, OR = 0.002 (95% CI: 0.0003–0.011) and 0.023 (95%CI: 0.008–0.067), respectively. Conclusion: Our results suggest an increased risk for the development of CRC in subjects with high dietary intake of energy, protein, saturated fat, cholesterol, and sodium, and diets high in vitamin E and caffeine were suggestive of a protective effect against the risk of developing CRC. Impact: This is the first study in Jordan to suggest that it may be possible to reduce CRC risk by adjusting the intake of some macro-and micronutrients.
Statistical Modeling of Soil Moisture, Integrating Satellite Remote-Sensing (SAR) and Ground-Based Data
Authors: Hosseini Reza , Newlands Nathaniel , Dean Charmaine , Takemura Akimichi
Published: March 2015

We present a flexible, integrated statistical-based modeling approach to improve the robustness of soil moisture data predictions. We apply this approach in exploring the consequence of different choices of leading predictors and covariates. Competing models, predictors, covariates and changing spatial correlation are often ignored in empirical analyses and validation studies. An optimal choice of model and predictors may, however, provide a more consistent and reliable explanation of the high environmental variability and stochasticity of soil moisture observational data. We integrate active polarimetric satellite remote-sensing data (RADARSAT-2, C-band) with ground-based in-situ data across an agricultural monitoring site in Canada. We apply a grouped step-wise algorithm to iteratively select best-performing predictors of soil moisture. Integrated modeling approaches may better account for observed uncertainty and be tuned to different applications that vary in scale and scope, while also providing greater insights into spatial scaling (upscaling and downscaling) of soil moisture variability from the field- to regional scale. We discuss several methodological extensions and data requirements to enable further statistical modeling and validation for improved agricultural decision-support.
A New Global Climatology of Annual Land Surface Temperature
Authors: Bechtel Benjamin
Published: March 2015

Land surface temperature (LST) is an important parameter in various fields including hydrology, climatology, and geophysics. Its derivation by thermal infrared remote sensing has long tradition but despite substantial progress there remain limited data availability and challenges like emissivity estimation, atmospheric correction, and cloud contamination. The annual temperature cycle (ATC) is a promising approach to ease some of them. The basic idea to fit a model to the ATC and derive annual cycle parameters (ACP) has been proposed before but so far not been tested on larger scale. In this study, a new global climatology of annual LST based on daily 1 km MODIS/Terra observations was processed and evaluated. The derived global parameters were robust and free of missing data due to clouds. They allow estimating LST patterns under largely cloud-free conditions at different scales for every day of year and further deliver a measure for its accuracy respectively variability. The parameters generally showed low redundancy and mostly reflected real surface conditions. Important influencing factors included climate, land cover, vegetation phenology, anthropogenic effects, and geology which enable numerous potential applications. The datasets will be available at the CliSAP Integrated Climate Data Center pending additional processing.
Glass vs. Plastic: Life Cycle Assessment of Extra-Virgin Olive Oil Bottles across Global Supply Chains
Authors: Accorsi Riccardo , Versari Lorenzo , Manzini Riccardo
Published: March 2015

The environmental impacts of global food supply chains are growing with the need for their measurement and management. This paper explores the operations of a global supply chain for extra-virgin olive oil (EVOO) according to a life cycle assessment (LCA) methodology. The LCA assessment methodology is applied to determine the environmental impact categories associated with the bottled EVOO life cycle, focusing on packaging decisions. The proposed analysis identifies the greatest environmental stressors of the EVOO supply chain, thereby supporting strategic and operative decisions toward more efficient and environmentally-friendly operations management and packaging choices. This paper quantifies the environmental categories of the impacts of global warming potential, ozone layer depletion, non-renewable energy use, acidification, eutrophication and photochemical smog, for the observed EVOO supply chain, given alternative packaging configurations, i.e., a glass bottle vs. a plastic bottle. The observed system includes the supply of EVOO, the EVOO processing and bottling, the supply of packaging, the distribution of final products to customers, the end-of-life (EOL) treatments regarding the management, recycling and the disposal of waste across a global supply chain. The findings from the LCA highlight the potential of PET bottles in reducing the environmental impact of EVOO supply chains and identifies hotspots of discussion for policy-makers, EVOO producers and consumers.
HPV-E7 Delivered by Engineered Exosomes Elicits a Protective CD8+ T Cell-Mediated Immune Response
Authors: Bonito Paola , Ridolfi Barbara , Columba-Cabezas Sandra , Giovannelli Andrea , Chiozzini Chiara , Manfredi Francesco , Anticoli Simona , Arenaccio Claudia , Federico Maurizio
Published: March 2015

We developed an innovative strategy to induce a cytotoxic T cell (CTL) immune response against protein antigens of choice. It relies on the production of exosomes, i.e., nanovesicles spontaneously released by all cell types. We engineered the upload of huge amounts of protein antigens upon fusion with an anchoring protein (i.e., HIV-1 Nefmut), which is an inactive protein incorporating in exosomes at high levels also when fused with foreign proteins. We compared the immunogenicity of engineered exosomes uploading human papillomavirus (HPV)-E7 with that of lentiviral virus-like particles (VLPs) incorporating equivalent amounts of the same antigen. These exosomes, whose limiting membrane was decorated with VSV-G, i.e., an envelope protein inducing pH-dependent endosomal fusion, proved to be as immunogenic as the cognate VLPs. It is noteworthy that the immunogenicity of the engineered exosomes remained unaltered in the absence of VSV-G. Most important, we provide evidence that the inoculation in mouse of exosomes uploading HPV-E7 induces production of anti-HPV E7 CTLs, blocks the growth of syngeneic tumor cells inoculated after immunization, and controls the development of tumor cells inoculated before the exosome challenge. These results represent the proof-of-concept about both feasibility and efficacy of the Nefmut-based exosome platform for the induction of CD8+ T cell immunity.