bluuebunny/crossref_metadata_2025 huggingface dataset:
This is Not a Chair: Complicite's Master and Margarita
Authors: Campos Liliane
Published: May 2014

In this article Liliane Campos links Complicite's Master and Margarita (2011) to the company's previous productions, from The Street of Crocodiles (1992) to Shun-Kin (2008). She develops a close analysis of The Master and Margarita as it was staged at the Avignon Festival in July 2012, arguing that the company's aesthetic is characterized by a tension between narrative fragmentation and visual connections. While Complicite's shows overflow with postmodernist multiplicity and division, the urge to connect these ‘shards of stories’ is a driving force in Simon McBurney's artistic direction. This dynamic is explored here both on a semantic level, as a consequence of Complicite's physical language, and on a narrative level, through the use of framing and frame-breaking devices. The article highlights the company's recurrent themes and the defining traits of its performance style. Liliane Campos is a Lecturer in English and Theatre studies at the Sorbonne Nouvelle University in Paris. She has published various articles on British drama and performance, and two books about the role of science in contemporary writing and devising for the theatre.
Characterizing fundamental parameter-based analysis for soil–ceramic matrices in polarized energy-dispersive X-ray fluorescence (PEDXRF) spectrometry
Authors: Abuhani Waleed Amin , Dasgupta-Schubert Nabanita , Villaseñor Cendejas Luis Manuel
Published: May 2014

Analytical polarized energy-dispersive X-ray fluorescence (PEDXRF) spectrometry (PEDXRFS) represents a substantial advancement over conventional XRF. The higher signal-to-noise commensurate with background lowering and better energy resolution, permits trace analysis for elements with Z ≥ 11. Concomitantly, improvements in analytical software based on the fundamental parameters (FP) approach have improved accuracies and precisions for standard-less analysis (SLA). Two ceramic and soil standard reference materials (SRMs), 98a-Plastic Clay and GSS-1 powders, differed in their intrinsic matrix properties of grain size, bulk, and surface monolayer densities as well as the elemental concentrations. The SRMs were analyzed as powder and as pellets compacted under the same pressure conditions to double the bulk density. Different geometries represented by the sample cup (10, 15, and 24 mm) and pellet (10, 15, and 25 mm) diameters with the same sample thickness (with differing masses and aspect ratios), as well as (for powder samples only) identical low masses (0.5 g) but with varying thicknesses, were analyzed. PEDXRFS combined with TURBOQUANT® (TQ) as SLA-FP enables good quantitative analysis for powders (Z ≥ 13) even for masses significantly lower than recommended, for soil–ceramic samples. Pellets (Z ≥ 12) yielded the best accuracy factor (AF) at high aspect ratio and thicknesses of the matrix analytical depth. Binder in pellets depreciates the AF. TQ needs to adequately quantitate matrix interferences effects, to improve accuracy in the analysis of low atomic numbers, e.g. Na and Mg.
Grundlagen von Asthma und COPD
Authors: Roth Michael
Published: May 2014

In den letzten drei Jahrzehnten nahm die Häufigkeit der chronisch entzündlichen Lungenerkrankungen (Asthma, COPD, Fibrose) weltweit zu. In der Schweiz leiden ca. 5 % der Bevölkerung an Asthma, während es in anderen Ländern bis zu 20 % sind (Maori: Neuseeland). Asthma ist der häufigste Grund für Absenzen von Bildung und Beruf, und es reduziert die Lebensqualität der Patienten und ihrer Familien. COPD, oder die Raucherlunge, ist zur Zeit die viert häufigste Todesursache weltweit und in der westlichen Gesellschaft ist der Hauptauslöser Zigarettenrauchen. In Entwicklungsländern wird die COPD durch Kochen am offenen Feuer ausgelöst und betrifft mehrheitlich Frauen. Bei Asthma und CODP können Medikamente nur die Symptome kontrollieren, eine Heilung gibt es nicht. Die dritte chronische Lungenerkrankung ist die Fibrose, deren Häufigkeit in einer alternden Gesellschaft zunimmt. Wie durch die Bezeichnung „chronisch entzündlich“ beschrieben nimmt man an, dass die Ursache der drei Erkrankungen eine anhaltende Entzündung spezifischer Lungenabschnitte ist. Diese Annahme wird seit ein paar Jahren durch neue klinische und Grundlagenstudie zunehmend in Frage gestellt. Mehrere Studien zeigten, dass sich die chronische Entzündungsreaktion der Lunge erst nach oder parallel zu Strukturveränderungen des Lungengewebes auftreten. Bisher wurden Gewebeveränderungen als Folge der Entzündungsreaktion interpretiert. Dagegen spricht, dass solche Veränderungen des Bronchialgewebes schon während der Embryogenese eingeleitet werden können und im späteren Leben eine Prädisposition für chronisch entzündliche Lungenerkrankungen darstellt. Welche Umstände zu einer solchen Prädisposition führen ist noch weitgehend unbekannt; die dazu notwendigen Untersuchungen gestalten sich schwierig und haben erst vor wenigen Jahren begonnen. Dieser Übersichtsartikel versucht die neuen Erkenntnisse der letzten zwei Jahre bezüglich Asthma und COPD zusammenzufassen.
COPD oder Asthma? Unterschiede und Gemeinsamkeiten in Abklärung und Diagnostik
Authors: Clarenbach Christian F. , Kohler Malcolm
Published: May 2014

Die chronisch obstruktive Lungenerkrankung (COPD) und das Asthma bronchiale weisen Gemeinsamkeiten in der Symptomatik auf wie z. B. Husten und Atemnot. Die klinische Unterscheidung ist daher nicht immer leicht, jedoch helfen sowohl die weiterführende Anamnese als auch diagnostische Tests erheblich bei der Differenzierung. Diese ist überaus wichtig, da sich die therapeutischen Ansätze der beiden Erkrankungen unterscheiden. Die Spirometrie inklusive Bronchodilatation ist in vielen Fällen der geeignete Test für die Unterscheidung zwischen Asthma und COPD und kann auch in der Hausarztpraxis einfach durchgeführt werden. Neben der Spirometrie werden im folgenden Artikel weitere diagnostische Tests vorgestellt, mit deren Hilfe Merkmale der jeweiligen Erkrankung objektiviert werden können, die die Unterscheidung erleichtern.
Asthma und COPD am Arbeitsplatz
Authors: Miedinger David , Stöhr Susanna , Pletscher Claudia
Published: May 2014

Obstruktive Lungenerkrankungen sind in der Schweizer Bevölkerung häufig anzutreffen. Der Verlauf dieser Erkrankungen kann durch Faktoren am Arbeitsplatz beeinflusst werden. Mittels Durchführung von technischen, organisatorischen und personenbezogenen Maßnahmen am Arbeitsplatz kann dieser Einfluss jedoch begrenzt werden. Arbeitsmedizinische Vorsorgeuntersuchungen erlauben, betroffene Arbeitnehmende frühzeitig zu erkennen damit Maßnahmen eingeleitet werden können. Bei erheblicher gesundheitlicher Gefährdung durch Belastungen am Arbeitsplatz muss jedoch der Erlass einer Nichteignungsverfügung durch die Suva geprüft werden.
Therapie von Asthma und COPD
Authors: Rothe Thomas
Published: May 2014

Mindestens vier wichtige Phänotypen lassen sich je bei der COPD und beim Asthma differenzieren, für die neben allgemeinen Therapiestandards gezielte, Phänotyp-spezifische Therapieoptionen bestehen. Zur Identifikation des individuellen Phänotyps und wenn Patienten ungenügend auf die Therapie ansprechen, ist ein pneumologisches Konsil sinnvoll. Vor allem die Therapie des schweren Asthmas gehört in die Hände des Spezialisten. Mit den besseren Medikamenten ist der Status asthmaticus in Akutspitälern selten geworden. Trotzdem besteht noch ein großes Potential, die Kontrolle des Asthmas der Betroffenen in der Schweiz zu verbessern. Bezüglich COPD sind Maßnahmen zur Verbesserung der primären und sekundären Nikotinprävention nötig.
Impact von Bewegung, Sport und Rehabilitation bei Asthma und COPD
Authors: Rohrer Valérie , Schmidt-Trucksäss Arno
Published: May 2014

Patienten mit chronisch obstruktiver Lungenerkrankung (COPD) und Asthma teilen als Merkmal und Risikofaktor für die Verstärkung ihrer Symptomatik und wichtigen Marker ihres Gesundheitszustandes eine vermehrte körperliche Inaktivität die objektiv mittels Akzelerometer deutlich besser als durch Befragung quantifiziert werden kann. Die Inaktivität führt neben einer Minderung der Ausdauerleistungsfähigkeit zu einer Reduktion der Muskelkraft bei Reduktion der peripheren Muskelmasse, was die Inflammation als gemeinsame pathologische Grundsituation verstärkt. Als körperliches Training können wegen vergleichbarer Effekte auf die Ausdauerleistung Dauer- und Intervalltraining auf dem Velo und als Gehtraining gleichermaßen für Patienten mit COPD und Asthma empfohlen werden. Der potentielle Zusatznutzen des Gehtrainings in Form einer Verringerung des Sturzrisikos insbesondere bei älteren Patienten scheint greifbar, bedarf jedoch noch zusätzlicher, wissenschaftlicher Evidenz. Krafttraining ist wichtig wegen der häufig atrophierten Skelettmuskulatur, die über die frühzeitig auftretende Laktazidose die Ventilation bei Belastung übermäßig steigert und damit zur Verschärfung der Belastungsdyspnoe beiträgt. Wichtig ist die Beibehaltung der individuell angepassten Trainingsform im häuslichen Bereich nach Entlassung aus der Klinik. Die Art des Trainings sollte sich am Umfeld des Patienten orientieren (Verfügbarkeit von Trainingsgerät, Trainingsgruppen, soziales Umfeld). Die objektive Aktivitätsmessung hat das Potential, auch der Therapiesteuerung und -kontrolle zu dienen, in die wegen der häufig vorhandenen kardio-metabolischen Komorbiditäten sowohl die Belastbarkeitsuntersuchung des Patienten als auch die Ernährungsweise im Sinne einer ganzheitlichen Therapie dazugehören sollte. Eine optimierte bronchospasmolytische und anti-inflammatorische Basis-Therapie ist Voraussetzung für einen guten Trainingserfolg. Bei Patienten mit Asthma sollte das Training mit einem mindestens 15-minütiges Aufwärmen begonnen werden. Unnötige Ängste vor belastungsinduzierten Asthmaattacken sollen dadurch vermieden, gegebenenfalls ist eine zusätzliche psychologische Betreuung indiziert.
Bedeutung von Schlafstörungen, deren Abklärung und Behandlung bei Asthma und COPD
Authors: Böing Sebastian , Randerath Winfried J.
Published: May 2014

Schlafstörungen stellen bei Patienten mit Asthma bronchiale und chronisch obstruktiver Lungenerkrankung (COPD) ein häufiges Problem dar, das sich negativ auf Lebensqualität und Krankheitsverlauf auswirken kann. Als Ursache der Schlafstörungen kommen multiple Faktoren wie beispielweise respiratorische Symptome und Komorbiditäten in Betracht. Gleichzeitig lässt auch Schlaf selber eine Interaktion mit beiden obstruktiven Atemwegserkrankungen erkennen. Sie begünstigt respiratorische Symptome und kann bei fortgeschrittener Erkrankung in schlafbezogenen Hypoxämien und Hyperkapnien resultieren. Das obstruktive Schlafapnoe-Syndrom ist eine häufige und wichtige Begleiterkrankung bei Asthma und COPD. Es führt zu vermehrten respiratorischen Symptomen bei beiden Erkrankungen und ging in Studien bei der COPD mit einer gesteigerten Mortalität einher. Aufgrund der Heterogenität von Schlafstörungen bei Asthma und COPD stellt die Anamnese das wichtigste Instrument zur Abklärung dar und ist gleichzeitig Weichensteller für eine weitere apparative Diagnostik. Therapeutische Ziele zur Reduktion von Schlafstörungen sind die optimale medikamentöse Einstellung und die Behandlung relevanter Komorbiditäten. Weitere Therapiesäulen sind bei entsprechender Indikation die Verfahren der Positivdruckatmung, die Sauerstofftherapie und die pneumologische Rehabilitation.
An order parameter for impurity systems at quantum criticality
Authors: Bayat Abolfazl , Johannesson Henrik , Bose Sougato , Sodano Pasquale
Published: May 2014

A quantum phase transition may occur in the ground state of a system at zero temperature when a controlling field or interaction is varied. The resulting quantum fluctuations which trigger the transition produce scaling behaviour of various observables, governed by universal critical exponents. A particularly interesting class of such transitions appear in systems with quantum impurities where a non-extensive term in the free energy becomes singular at the critical point. Curiously, the notion of a conventional order parameter that exhibits scaling at the critical point is generically missing in these systems. Here we explore the possibility to use the Schmidt gap, which is an observable obtained from the entanglement spectrum, as an order parameter. A case study of the two-impurity Kondo model confirms that the Schmidt gap faithfully captures the scaling behaviour by correctly predicting the critical exponent of the dynamically generated length scale at the critical point.
Mesoporous alumina as a solid phase extraction adsorbent for the determination of abamectin and ivermectin in vegetables by liquid chromatography-tandem mass spectrometry
Authors: Hu Yeqin , Li Xianliang , Zhang Lei , Zhou Ming , Wang Guomin , Zhang Yunhuai , Xi Cunxian , Cao Shurui
Published: May 2014

We report the synthesis of mesoporous alumina and used it as a new solid phase extraction adsorbent for analysis of abamectin and ivermectin by LC-MS/MS.
Dimensionality changes in the solid phase at room temperature: 2D → 1D → 3D evolution induced by ammonia sorption–desorption on zinc phosphates
Authors: Amghouz Zakariae , Ramajo Beatriz , Khainakov Sergei A. , da Silva Iván , Castro Germán R. , García José R. , García-Granda Santiago
Published: May 2014

2D → 1D → 3D dimensionality changes on zinc phosphates induced by ammonia sorption–desorption in the solid phase at room temperature.
A novel method for photolithographic polymer shadow masking: toward high-resolution high-performance top-contact organic field effect transistors
Authors: Ji Deyang , Jiang Longfeng , Jiang Lang , Fu Xiaolong , Dong Huanli , Yu Junsheng , Hu Wenping
Published: May 2014

The present work shows a novel method to prepare polymer-based masks called photolithographic polymer shadow masking and its application in the process of fabricating top-contact high-resolution OFETs.
Dimeric pyrrole–imidazole alkaloids: synthetic approaches and biosynthetic hypotheses
Authors: Wang Xiao , Ma Zhiqiang , Wang Xiaolei , De Saptarshi , Ma Yuyong , Chen Chuo
Published: May 2014

An overview of the total syntheses and biosynthetic hypotheses of the dimeric pyrrole–imidazole alkaloids.
A one-pot hypoiodite catalysed oxidative cycloetherification approach to benzoxazoles
Authors: Boominathan Siva Senthil Kumar , Hu Wan-Ping , Senadi Gopal Chandru , Vandavasi Jaya Kishore , Wang Jeh-Jeng
Published: May 2014

A TBAI/TBHP catalysed one-pot approach to α-ketobenzoxazoles was developed in high yields with a wide substrate scope.
Synthesis and biological evaluation of novel bivalent β-carbolines as potential antitumor agents
Authors: Wu Qifeng , Bai Zhushuang , Ma Qin , Fan Wenxi , Guo Liang , Zhang Guoxian , Qiu Liqin , Yu Huijuan , Shao Guang , Cao Rihui
Published: May 2014

A series of bivalent β-carbolines with a spacer between the 3-carboxyl oxygens was synthesized and their cytotoxic activities in vitro and antitumor efficacies in vivo were evaluated. Compound 22 exhibited potent antitumor activity against Lewis lung cancer in mice with a tumor inhibition rate of 64.2%.
DNA molecular recognition of intercalators affects aggregation of a thermoresponsive polymer
Authors: Sugawara Yuuki , Tamaki Takanori , Yamaguchi Takeo
Published: May 2014

Binding of intercalators to dsDNA switches the aggregation phenomena of the DNA-thermoresponsive polymer. The molecular recognition of a DNA–intercalator can induce dramatic aggregation.
Nanophase CuInS2 nanosheets/CuS composite grown by the SILAR method leads to high performance as a counter electrode in dye sensitized solar cells
Authors: Bhosale Reshma K. , Agarkar Shruti A. , Agrawal Ishita , Naphade Rounak A. , Ogale Satishchandra
Published: May 2014

CuInS2 nanosheets are synthesized by SILAR followed by annealing at 500 °C, whereas at 250 °C a composite of CIS and CuS is obtained. This composite yields an efficiency of 6.3% as counter electrode for DSSC.
Sandwich-like titania thin films with one/three-dimensional nanostructures for photocatalytic applications
Authors: Tang Ming-Zao , Wu Jin-Ming
Published: May 2014

Appropriate layer-by-layer alignment of titania thin films with one/three-dimensional nanostructures resulted in enhanced photocatalytic activity.
Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications
Authors: Kłos J. W. , Krawczyk M. , Dadoenkova Yu. S. , Dadoenkova N. N. , Lyubchanskii I. L.
Published: May 2014

We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO2 and SiO2 layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceived by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO2/SiO2 stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.
Germination of mucilaginous seeds of Plantago albicans (Plantaginaceae): effects of temperature, light, pre-sowing treatments, osmotic stress and salinity
Authors: Veiga-Barbosa L. , Pérez-García F.
Published: May 2014

Plantago albicans L. (Plantaginaceae) is a perennial herbaceous plant widely distributed throughout the Mediterranean region. The germination requirements (under different controlled conditions of light and temperature, and after two pre-sowing treatments) and tolerance to osmotic stress (polyethylene glycol, PEG 6000) and salinity (NaCl) of P. albicans seeds were studied. Seeds were germinated under constant temperatures (5°C, 10°C, 15°C, 20°C, 25°C and 30°C) and alternating temperature regimes of 20/10°C and 25/15°C with a 16 h/8 h light/dark photoperiod. The outer layer of seeds become mucilaginous when wetted and the presence of mucilage on seeds significantly increased germination percentages at all temperatures tested. P. albicans seeds were non-dormant and temperature significantly affected germination percentages and germination rate (germination velocity expressed as mean germination time, MGT). The final germination percentages ranged from 34% to 89% for intact seeds (seeds with mucilage) and from 9% to 62% for demucilaged seeds, depending on the temperature. Temperatures of 25°C and 25/15°C gave the highest germination percentages. Light did not affect seed germination at both temperature regimes assayed (25°C and 25/15°C). Germination percentages of seeds soaked for 24 h in distilled water or in a gibberellic acid (GA3) solution were not significantly higher than that of untreated seeds. In general, both the final germination percentage and germination rate were reduced by increasing salinity and PEG concentration. Seeds germinated in up to 35% PEG and 300 mmol·L–1 NaCl. Recovery of germination for seeds when transferred to distilled water after being in PEG or salinity treatments for 15 days was quite high, suggesting that P. albicans seeds are tolerant to osmotic and salt stresses.
Evaluation of Antiradical Activity and Reducing Capacity of Synthesised Bispyridinium Dibromides Obtained by Quaternisation of 4-Pyridyl-1,4-dihydropyridines with Propargyl Bromide
Authors: Rucins Martins , Gosteva Marina , Belyakov Sergey , Sobolev Arkadij , Pajuste Karlis , Plotniece Mara , Cekavicus Brigita , Tirzite Dace , Plotniece Aiva
Published: May 2014

New bispyridinium dibromides based on the 1,4-dihydropyridine (1,4-DHP) cycle were synthesised in the reaction between 4-pyridyl-1,4-DHP derivatives and propargyl bromide. It has been shown that variation of the substituent position on the pyridine as well as small changes in the electronic nature of the 1,4-DHP cycle as a result of the substituent nature at the 3 and 5 positions do not affect the course of the reaction and in all cases the corresponding bispyridinium dibromides 4a–e were formed. The antiradical activity, using 1,1-diphenyl-2-picrylhydrazine as a free radical scavenger, and the reducing capacity using phosphomolybdenum complexes have been evaluated for the newly synthesised compounds 4a–e. It has been shown that all tested 1,4-DHP bispyridinium dibromides 4a–e possess reducing capacity and antiradical properties. Moreover, the reducing capacity results could be explained by the influence of the electronic nature of the substituent at the 3 and 5 positions of the 1,4-DHP cycle.
The value of native, warm-season perennial grasses grown for pasture or biofuel in the southern Great Plains, USA
Authors: Rogers James K. , Nichols Bryan , Biermacher Jon T. , Mosali Jagadeesh
Published: May 2014

The Renewable Fuel Standard under the Energy Independence and Security Act of 2007 mandated the production of 60.5 GL (1 GL = 1 × 109 L) of cellulosic biofuel by 2022. Switchgrass (Panicum virgatum) has been identified as a primary feedstock because it is a perennial adapted to a wide environmental range and produces high yields. Development of the cellulosic biofuel industry has been slow, one reason being a lack of available feedstock driven by lack of a developed market. Rather than considering it only as a dedicated biofuel feedstock, we examined switchgrass potential for both grazing and biofuel feedstock. In a series of experiments testing dry matter yield, grazing preference and animal bodyweight gain, switchgrass (cv. Alamo) was found to produce greater total yield (17.7 kg ha–1) than 15 other warm-season perennial grasses, was the most preferred by stocker cattle in a grazing preference study, and produced good average daily gains in a grazing study (0.84–1.05 kg head–1). These results demonstrate the potential of switchgrass for both grazing and biofuel feedstock. However, the feedstock price would need to increase above US$83 Mg–1 before the economics of dedicated switchgrass feedstock production would surpass that of a combination of switchgrass grazing and feedstock production.
Optimising an integrated pest-management strategy for a spatially structured population of common carp (Cyprinus carpio) using meta-population modelling
Authors: Brown Paul , Gilligan Dean
Published: May 2014

To evaluate strategies within a carp-control plan, we developed a meta-population model of the geographic arrangement, biological connections and ‘unfished’ stock structure of the pest population of common carp (Cyprinus carpio) in a large river catchment. The model was tuned to recent observations of biomass. Published data were used to estimate sampling biases and yield from available carp-control tools. We simulated proposed carp-removal activities and also the potential effects of biological-control options; cyprinid herpesvirus-3 (CHV-3) and daughterless-carp gene technology. Outputs compared the population abundance before carp control (before 2009) and after a ~70-year period of sustained management. Models suggest that the proposed levels of carp removal may reduce biomass by ~50%. Although substantial, this control level may not be sufficient to reduce carp biomass densities below thresholds associated with ecological damage. In contrast, a CHV-3 bio-control program has potential to reduce carp biomass densities to, or exceeding, target levels, if mortality rates exceed 30% and broad-scale outbreaks occur in at least 40% of years, despite the likely development of resistance. A synergistic bio-control program using CHV-3, followed by a gene technology-based sex-ratio distortion program, is potentially the most effective strategy for reducing carp biomass by over 90% in the long term.
On commuting and semi-commuting positive operators
Authors: Gao Niushan
Published: May 2014

Let

K
K

be a positive compact operator on a Banach lattice. We prove that if either

[
K
⟩

[K\rangle

or

⟨
K
]

\langle K]

is ideal irreducible, then

[
K
⟩
=
⟨
K
]
=

L
+

(
X
)
∩
{
K

}
′

[K\rangle =\langle K]=L_+(X)\cap \{K\}’

. We also establish the Perron-Frobenius Theorem for such operators

K
K

. Finally, we apply our results to answer questions posed by Abramovich and Aliprantis (2002) and Bračič et al. (2010).
Encouraging Reductions in Nonpoint Source Pollution through Point‐nonpoint Trading: The Roles of Baseline Choice and Practice Subsidies
Authors: Ribaudo Marc , Savage Jeffrey , Talberth John
Published: May 2014

Water quality regulations in the United States apply almost exclusively to point sources. In impaired watersheds where both point and nonpoint sources contribute to pollution, the U.S. Environmental Protection Agency (EPA) is encouraging the use of point‐nonpoint trading to reduce the cost of point sources to meet their permit requirement, and to encourage nonpoint sources to voluntarily contribute more towards meeting overall water quality goals. The EPA guidance encourages trading programs to set a nonpoint source eligibility baseline that extracts some “extra” abatement from nonpoint sources. Research has shown that setting an eligibility baseline that is substantially more stringent than current management could discourage nonpoint source participation and significantly hinder trading. In this paper we examine how choosing the eligibility baseline for agricultural sources affects the efficiency goal of trading (reducing costs to point sources), as well as how it affects the EPA goal of encouraging nonpoint abatement. Using data from the Chesapeake Bay Watershed we find that eligibility baselines set to encourage additional nonpoint source abatement reduce the supply of credits in a market; the more stringent the baseline, the fewer the trades and the smaller the overall abatement from nonpoint sources. A subsidy to farmers for reducing the cost of meeting a baseline encourages greater nonpoint source abatement, but may not benefit the trading market.
The Effects of Agricultural Technological Progress on Deforestation: What Do We Really Know?
Authors: Villoria Nelson B. , Byerlee Derek , Stevenson James
Published: May 2014

Increasing agricultural yields seem an obvious way to satisfy increasing demands for food and fuel while minimizing expansion of agriculture into forest areas; however, an influential literature worries that promoting agricultural innovation could enhance agriculture's profitability thereby encouraging deforestation. Clarifying the effects of agricultural technological progress on deforestation is therefore crucial for designing effective policy responses to the challenges faced by global agriculture. In this article we review the empirical evidence on these effects and synthesize estimates of future global cropland expansion. Our main insights are that: (i) the empirical evidence on a positive link between regional technological progress and deforestation is much weaker than what seems generally accepted; (ii) at a global level, most analysts expect broad based technological progress to be land saving; however, composition effects are important as low‐yield, land‐abundant regions are likely to experience further land expansion. Toward the future, empirical work understanding how localized technological progress in agriculture transmits through international trade and commodity markets will help to bridge the gap between the findings of local, econometric, studies on the one hand and global, model based, studies on the other.
Estimating the Impact of Education on Household Fruit and Vegetable Purchases
Authors: Berning Joshua , Hogan John J.
Published: May 2014

We examine the effect that investments in education have on household expenditure on fruits and vegetables using a two‐stage model that accounts for differences in ability and heterogeneous returns to education. For this, we use the 2008 Consumer Expenditure Survey for the United States. We find that higher levels of education contribute to greater household expenditures on both fresh and processed fruits and vegetables. We find a nonlinear effect on fresh fruits and vegetables, indicating that education impacts the quality of purchases as well. Although nutritional education is often touted as important for a healthful diet, these results highlight how investments in human capital via formal education can potentially improve dietary quality as well.
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Authors: Choi Meena , Chang Ching-Yun , Clough Timothy , Broudy Daniel , Killeen Trevor , MacLean Brendan , Vitek Olga
Published: May 2014

Summary: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.

Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2014) and used via graphical user interface.

Contact:  ovitek@purdue.edu
Mirin: identifying microRNA regulatory modules in protein–protein interaction networks
Authors: Yang Ken-Chi , Hsu Chia-Lang , Lin Chen-Ching , Juan Hsueh-Fen , Huang Hsuan-Cheng
Published: May 2014

Summary: Exploring microRNA (miRNA) regulations and protein–protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein–protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein–protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users. Mirin has successfully uncovered oncomirs and their regulatory networks in various cancers, such as gastric and breast cancer.

Availability and implementation: Mirin is freely available at http://mirin.ym.edu.tw/.

Contact:  hsuancheng@ym.edu.tw or yukijuan@ntu.edu.tw

Supplementary information:  Supplementary Data are available at Bioinformatics online.
A comparison of algorithms for the pairwise alignment of biological networks
Authors: Clark Connor , Kalita Jugal
Published: May 2014

Motivation: As biological inquiry produces ever more network data, such as protein–protein interaction networks, gene regulatory networks and metabolic networks, many algorithms have been proposed for the purpose of pairwise network alignment—finding a mapping from the nodes of one network to the nodes of another in such a way that the mapped nodes can be considered to correspond with respect to both their place in the network topology and their biological attributes. This technique is helpful in identifying previously undiscovered homologies between proteins of different species and revealing functionally similar subnetworks. In the past few years, a wealth of different aligners has been published, but few of them have been compared with one another, and no comprehensive review of these algorithms has yet appeared.

Results: We present the problem of biological network alignment, provide a guide to existing alignment algorithms and comprehensively benchmark existing algorithms on both synthetic and real-world biological data, finding dramatic differences between existing algorithms in the quality of the alignments they produce. Additionally, we find that many of these tools are inconvenient to use in practice, and there remains a need for easy-to-use cross-platform tools for performing network alignment.

Contact:  cclark@uccs.edu, jkalita@uccs.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
Authors: Nedumpully-Govindan Praveen , Li Lin , Alexov Emil G. , Blenner Mark A. , Ding Feng
Published: May 2014

Motivation: Tyrosine sulfation is a type of post-translational modification (PTM) catalyzed by tyrosylprotein sulfotransferases (TPST). The modification plays a crucial role in mediating protein–protein interactions in many biologically important processes. There is no well-defined sequence motif for TPST sulfation, and the underlying determinants of TPST sulfation specificity remains elusive. Here, we perform molecular modeling to uncover the structural and energetic determinants of TPST sulfation specificity.

Results: We estimate the binding affinities between TPST and peptides around tyrosines of both sulfated and non-sulfated proteins to differentiate them. We find that better differentiation is achieved after including energy costs associated with local unfolding of the tyrosine-containing peptide in a host protein, which depends on both the peptide’s secondary structures and solvent accessibility. Local unfolding renders buried peptide—with ordered structures—thermodynamically available for TPST binding. Our results suggest that both thermodynamic availability of the peptide and its binding affinity to the enzyme are important for TPST sulfation specificity, and their interplay results into great variations in sequences and structures of sulfated peptides. We expect our method to be useful in predicting potential sulfation sites and transferable to other TPST variants. Our study may also shed light on other PTM systems without well-defined sequence and structural specificities.

Availability and implementation: All the data and scripts used in the work are available at http://dlab.clemson.edu/research/Sulfation.

Contact:  fding@clemson.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Bioclojure: a functional library for the manipulation of biological sequences
Authors: Plieskatt Jordan , Rinaldi Gabriel , Brindley Paul J. , Jia Xinying , Potriquet Jeremy , Bethony Jeffrey , Mulvenna Jason
Published: May 2014

Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.

Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure’s functional style and emphasize laziness and composability, so that BioClojure, and user-defined, functions can be chained into simple pipelines that are thread-safe and seamlessly integrate lazy evaluation.

Availability and implementation: BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence).

Contact:  jason.mulvenna@qimrberghofer.edu.au or jason.mulvenna@qimr.edu.au
unifiedWMWqPCR: the unified Wilcoxon–Mann–Whitney test for analyzing RT-qPCR data in R
Authors: De Neve Jan , Meys Joris , Ottoy Jean–Pierre , Clement Lieven , Thas Olivier
Published: May 2014

Motivation: Recently, De Neve et al. proposed a modification of the Wilcoxon–Mann–Whitney (WMW) test for assessing differential expression based on RT-qPCR data. Their test, referred to as the unified WMW (uWMW) test, incorporates a robust and intuitive normalization and quantifies the probability that the expression from one treatment group exceeds the expression from another treatment group. However, no software package for this test was available yet.

Results: We have developed a Bioconductor package for analyzing RT-qPCR data with the uWMW test. The package also provides graphical tools for visualizing the effect sizes.

Availability and implementation: The unifiedWMWqPCR package and its user documentation can be obtained through Bioconductor.

Contact:  JanR.DeNeve@UGent.be
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
Authors: Jiao Yinming , Widschwendter Martin , Teschendorff Andrew E.
Published: May 2014

Motivation: There is a growing number of studies generating matched Illumina Infinium HumanMethylation450 and gene expression data, yet there is a corresponding shortage of statistical tools aimed at their integrative analysis. Such integrative tools are important for the discovery of epigenetically regulated gene modules or molecular pathways, which play key roles in cellular differentiation and disease.

Results: Here, we present a novel functional supervised algorithm, called Functional Epigenetic Modules (FEM), for the integrative analysis of Infinium 450k DNA methylation and matched or unmatched gene expression data. The algorithm identifies gene modules of coordinated differential methylation and differential expression in the context of a human interactome. We validate the FEM algorithm on simulated and real data, demonstrating how it successfully retrieves an epigenetically deregulated gene, previously known to drive endometrial cancer development. Importantly, in the same cancer, FEM identified a novel epigenetically deregulated hotspot, directly upstream of the well-known progesterone receptor tumour suppressor pathway. In the context of cellular differentiation, FEM successfully identifies known endothelial cell subtype-specific gene expression markers, as well as a novel gene module whose overexpression in blood endothelial cells is mediated by DNA hypomethylation. The systems-level integrative framework presented here could be used to identify novel key genes or signalling pathways, which drive cellular differentiation or disease through an underlying epigenetic mechanism.

Availability and implementation: FEM is freely available as an R-package from http://sourceforge.net/projects/funepimod.

Contact:  andrew@picb.ac.cn

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Introduction: Marine Harvesting in the Arctic
Authors: Haug Tore , Aschan Michaela , Hoel Alf Håkon , Johansen Torild , Sundet Jan H.
Published: May 2014

In a warmer Arctic, living conditions will change at all trophic levels of the marine ecosystem. Increased air and water temperatures will likely substantially reduce ice coverage. Trophic interactions might change and increased competition between resident Arctic species and invasive species seems likely. A theme session on “Marine harvesting in the Arctic” was held at the international Arctic Frontiers Conference in Tromsø, Norway, in January 2013. The theme session partitioned the topic into two sub-sessions: (i) introduced species, immigration and fate of resident species and (ii) prospective harvesting of marine biological resources in the Arctic. The four articles that follow this introduction are based on presentations made at the Arctic Frontiers theme session. These articles cover topics such as: how ice breeding seals (Pagophilus groenlandicus) can cope with ice retention in the Northwest Atlantic, how planktonic stages of the resident polar cod (Boreogadus saida) and the pole-ward expanding Pacific sand lance (Ammodytes hexapterus) may compete for food in the warming Beaufort Sea, and how the introduced red king crab (Paralithodes camtschaticus) disperse in the Barents Sea. The fourth article shows how differences in the life-history strategies of keystone zooplankton species will likely affect future productivity of commercial fisheries in polar regions.
Regulation of the gut microbiota by the mucosal immune system in mice
Authors: Hasegawa Mizuho , Inohara Naohiro
Published: May 2014

The benefits of commensal bacteria to the health of the host have been well documented, such as providing stimulation to potentiate host immune responses, generation of useful metabolites, and direct competition with pathogens. However, the ability of the host immune system to control the microbiota remains less well understood. Recent microbiota analyses in mouse models have revealed detailed structures and diversities of microbiota at different sites of the digestive tract in mouse populations. The contradictory findings of previous studies on the role of host immune responses in overall microbiota composition are likely attributable to the high β-diversity in mouse populations as well as technical limitations of the methods to analyze microbiota. The host employs multiple systems to strictly regulate their interactions with the microbiota. A spatial segregation between the host and microbiota is achieved with the mucosal epithelium, which is further fortified with a mucus layer on the luminal side and Paneth cells that produce antimicrobial peptides. When commensal bacteria or pathogens breach the epithelial barrier and translocate to peripheral tissues, the host immune system is activated to eliminate them. Defective segregation and tissue elimination of commensals result in exaggerated inflammatory responses and possibly death of the host. In this review, we discuss the current understanding of mouse microbiota, its common features with human microbiota, the technologies utilized to analyze microbiota, and finally the challenges faced to delineate the role of host immune responses in the composition of the luminal microbiota.
Starbursts triggered by intergalactic tides andinterstellar compressive turbulence
Authors: Renaud Florent , Bournaud Frédéric , Kraljic Katarina , Duc Pierre-Alain
Published: May 2014

Using parsec-resolution simulations of a typical galaxy merger, we study the triggering of starbursts by connecting the (inter-)galactic dynamics to the structure of the interstellar medium. The gravitational encounter between two galaxies enhances tidal compression over large volumes, which increases and modifies the turbulence, in particular its compressive mode with respect to the solenoidal one. This generates an excess of dense gas leading to intense star formation activity. Along the interaction, the compressive turbulence modifies the efficiency of gas-to-star conversion which, in the Schmidt–Kennicutt diagram, drives the galaxies from the sequence of discs to that of starbursts.
Dissecting the Spitzer colour–magnitude diagrams of extreme Large Magellanic Cloud asymptotic giant branch stars
Authors: Dell'Agli F. , Ventura P. , García Hernández D. A. , Schneider R. , Di Criscienzo M. , Brocato E. , D'Antona F. , Rossi C.
Published: May 2014

We trace the full evolution of low- and intermediate-mass stars (1 ≤ M ≤ 8 M⊙) during the asymptotic giant branch (AGB) phase in the Spitzer two-colour and colour–magnitude diagrams. We follow the formation and growth of dust particles in the circumstellar envelope with an isotropically expanding wind, in which gas molecules impinge upon pre-existing seed nuclei, favour their growth. These models are the first able to identify the main regions in the Spitzer data occupied by AGB stars in the Large Magellanic Cloud (LMC). The main diagonal sequence traced by LMC extreme stars in the [3.6] − [4.5] versus [5.8] − [8.0] and [3.6] − [8.0] versus [8.0] planes is nicely fit by carbon stars models; it results to be an evolutionary sequence with the reddest objects being at the final stages of their AGB evolution. The most extreme stars, with [3.6] − [4.5] > 1.5 and [3.6] − [8.0] > 3, are 2.5–3 M⊙ stars surrounded by solid carbon grains. In higher mass (>3 M⊙) models dust formation is driven by the extent of hot bottom burning (HBB) – most of the dust formed is in the form of silicates and the maximum obscuration phase by dust particles occurs when the HBB experienced is strongest, before the mass of the envelope is considerably reduced.
The incidence of cerebrovascular accidents and second brain tumors in patients with pituitary adenoma: a population-based study
Authors: Brown Paul D. , Blanchard Miran , Jethwa Krishan , Flemming Kelly D. , Brown Cerise A. , Kline Robert W. , Jacobson Debra J. , St. Sauver Jennifer , Pollock Bruce E. , Garces Yolanda I. , Stafford Scott L. , Link Michael J. , Erickson Dana , Foote Robert L. , Laack Nadia N.I.
Published: May 2014

Background

To assess the risk of cerebrovascular accidents (CVAs) and second brain tumors (SBTs) in patients with pituitary adenoma after surgery or radiotherapy.

Methods

A cohort of 143 people from Olmsted County, who were diagnosed with pituitary adenoma between 1933 and 2000, was studied. Only patients from Olmsted County were included because of the unique nature of medical care in Olmsted County, which allows the ascertainment of virtually all cases of pituitary adenoma for this community's residents and comparisons to the general population in the county. Surgical resection was performed in 76 patients, 29 patients underwent radiotherapy (with 21 undergoing both surgery and radiotherapy), 5 patients were reirradiated, and 59 patients were managed conservatively and observed.

Results

Median follow-up was 15.5 years. There was no difference in CVA-free survival between treatment groups. On univariate analysis age > 60 years (hazard ratio [HR], 11.93; 95% CI, 6.26–23.03; P < .001); male sex (HR, 3.67; 95% CI, 2.03–6.84; P < .001), and reirradiation (HR, 3.41; 95% CI, 1.05–9.68; P = .04) were associated with worse CVA-free survival. In multivariate analysis, only age > 60 years was associated with worse CVA-free survival. Compared with the general population, there was a 4-fold increase in the rate of CVAs in pituitary adenoma patients (HR, 4.2; 95% CI, 2.8–6.1). Two patients developed SBT (an irradiated patient and a surgically managed patient).

Conclusion

CVA is a significant risk for patients with pituitary tumors, but treatment does not seem to impact the risk. Even with long-term follow-up, SBTs are a rare event regardless of treatment modality.
Cancer around the brain
Authors: Grisold Wolfgang , Grisold Anna
Published: May 2014

Background

Neuro-oncologists are familiar with primary brain tumors, intracerebral metastases meningeal carcinomatosis and extracerebral intracranial tumors as meningeoma. For these conditions, and also some other rare tumor entities several treatment options exist. Cancer can also involve structures around the brain as the dura, the base of the skull, the cavities of the skull and tissue around the bony skull, the skin, the tissue of the neck. and either compress, invade or spread in the central or peripheral nervous system.

Methods

A systematic literature research was conducted determining symptoms and signs, tumor sites of nerve invasion, tumor types, diagnostic techniques, mechanisms of nerve invasion, and important differential diagnosis. Additional cases from own experience were added for illustration.

Results

The mechanisms of tumor invasion of cranial nerves is heterogenous and not only involves several types of invasion, but also spread along the cranial nerves in antero- and retrograde fashion and even spread into different nerve territories via anastomosis. In addition the concept of angiosomas may have an influence on the spread of metastases.

Conclusion

In addition to the well described tumor spread in meningeal carcinomatosis and base of the skull metastases, dural spread, lesions of the bony skull, the cavities of the skull and skin of the face and tissue of the neck region need to be considered, and have an impact on therapeutic decisions.