bluuebunny/crossref_metadata_2025 huggingface dataset:
A modified metabolic model for mixed culture fermentation with energy conserving electron bifurcation reaction and metabolite transport energy
Authors: Zhang Fang , Zhang Yan , Chen Man , van Loosdrecht Mark C.M. , Zeng Raymond J.
Published: February 2013

A modified metabolic model for mixed culture fermentation (MCF) is proposed with the consideration of an energy conserving electron bifurcation reaction and the transport energy of metabolites. The production of H2 related to NADH/NAD+ and Fdred/Fdox is proposed to be divided in three processes in view of energy conserving electron bifurcation reaction. This assumption could fine‐tune the intracellular redox balance and regulate the distribution of metabolites. With respect to metabolite transport energy, the proton motive force is considered to be constant, while the transport rate coefficient is proposed to be proportional to the octanol–water partition coefficient. The modeling results for a glucose fermentation in a continuous stirred tank reactor show that the metabolite distribution is consistent with the literature: (1) acetate, butyrate, and ethanol are main products at acidic pH, while the production shifts to acetate and propionate at neutral and alkali pH; (2) the main products acetate, ethanol, and butyrate shift to ethanol at higher glucose concentration; (3) the changes for acetate and butyrate are following an increasing hydrogen partial pressure. The findings demonstrate that our modified model is more realistic than previous proposed model concepts. It also indicates that inclusion of an energy conserving electron bifurcation reaction and metabolite transport energy for MCF is sound in the viewpoint of biochemistry and physiology. Biotechnol. Bioeng. 2013; 110: 1884–1894. © 2013 Wiley Periodicals, Inc.
Loofa (Luffa cylindrica) sponge: Review of development of the biomatrix as a tool for biotechnological applications
Authors: Saeed Asma , Iqbal Muhammad
Published: February 2013

The review discusses the development of loofa sponge (Luffa cylindrica) as a biotechnological tool and the diversity of applications in which it has been successfully used since it was first reported as a matrix for the immobilization of microbiological cells in 1993. The fibro‐vascular reticulated structure, made up of an open network of random lattices of small cross‐sections coupled with very high porosity (79–93%), having very low density (0.02–0.04 g/cm3), and high specific pore volume (21–29 cm3/g), has the characteristics of a carrier/scaffold well‐suited for cell immobilization. This has been confirmed through the immobilization of cells of diverse types, including filamentous and microalgae, fungi, bacteria, yeasts, higher plants, and human and rat hepatocytes. The cells immobilized in loofa sponge have performed well and better than free suspended cells and those immobilized in conventionally used natural and synthetic polymeric materials for the production of ethanol, organic acids, enzymes, and secondary metabolites. The loofa‐immobilized cell systems have been efficiently used for the treatment of wastewaters containing toxic metals, dyes, and chlorinated compounds, and the technology has been used to develop biofilms for the remediation of domestic and industrial wastewaters rich in inorganic and organic matter. In addition, three‐dimensional loofa sponge scaffolds for hepatocyte culture have been suggested to have the potential for development into a bioartificial liver device. Loofa sponge is a cost‐effective, eco‐friendly, and easy to handle matrix that has been used successfully as a biotechnological tool in a variety of systems, purposes, and applications. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:573–600, 2013
A Case of in‐stent thrombosis in a patient with drug eluting stents during perioperative management with glycoprotein IIb/IIIa inhibitors
Authors: Singh Manmeet , Bolla Vema H. , Berg Ryan
Published: February 2013

The management of patients with drug eluting stents (DES) who require early surgical intervention prior to the completion of antiplatelet therapy is challenging. Available literature suggests that bridging these high risk patients with glycoprotein IIb/IIIa (g2b3a) inhibitors could be efficacious in preventing stent thrombosis (Ben Morrison et al., Catheter Cardiovasc Interv 2012;79;575–582). However, this still remains to be proven in larger prospective studies. We report a case of stent thrombosis in a patient with DES planned for neurosurgery while on bridging g2b3a inhibitors therapy in the perioperative period. © 2013 Wiley Periodicals, Inc.
Type II complex regional pain syndrome of the hand resulting from repeated arterial punctures during transradial coronary intervention
Authors: Cho Eun Jeong , Yang Jeong Hoon , Song Young Bin
Published: February 2013

Coronary catheterization using a transradial approach has become a common procedure, as the risks of local complications are low and this procedure affords relatively expeditious postprocedural patient mobilization. Access site complications—such as radial artery spasm, hematoma, and compartment syndrome—have been reported in the literature; however, cases of complex regional pain syndrome (CRPS) of the hand related to the procedure are extremely rare. We describe a case of type II CRPS affecting the hand after a transradial coronary intervention that was complicated by repeated periprocedural arterial punctures. In this case, a 55‐year‐old woman underwent a percutaneous coronary intervention for the treatment of unstable angina. After successful completion of the procedure, the patient complained of severe pain along the median and radial nerve distributions and resulting disability of the right hand. Although subsequent duplex sonography showed no abnormalities, a nerve conduction study uncovered injury to multiple nerves on the right. A diagnosis of type II CRPS was then made and the patient was treated with a nerve block as well as multiple medical modalities. This case demonstrates a very unusual complication resulting from the transradial approach to percutaneous coronary intervention.© 2013 Wiley Periodicals, Inc.
Der Gelbereich im Phasendiagramm von Klebstoffen
Authors: Simon Gerhard
Published: February 2013

Beim Hallenzusammenbruch in Bad Reichenhall im Jahr 2006, der bei Kälte unter Schneelast erfolgte, waren 15 Tote zu beklagen. Der Hallendachzusammenbruch des Supermarktes in Falkensee im Sommer 2009 erfolgte glücklicherweise erst nach Ladenschluss. Beide Hallen enthielten Brettschichtholzbinder, das sind aus Holzlatten zusammengeklebte Balken. Die beiden Vorkommnisse fordern die Klärung der Frage, ob ausgehärtete Klebefugen zu den Festkörpern zählen und wie solche zu berechnen sind; oder sind sie wie zähe Flüssigkeiten zu behandeln oder gar wie Gele?
Survey of integrated‐circuit‐oscillator phase‐noise analysis
Authors: Pankratz Erik , Sánchez‐Sinencio Edgar
Published: February 2013

This tutorial distills the salient phase‐noise analysis concepts and key equations developed over the last 75 years relevant to integrated circuit oscillators. Oscillator phase and amplitude fluctuations have been studied since at least 1938 when Berstein solved the Fokker–Planck equations for the phase/amplitude distributions of a resonant oscillator.

The principal contribution of this work is the organized, unified presentation of eclectic phase‐noise analysis techniques, facilitating their application to integrated circuit oscillator design. Furthermore, we demonstrate that all these methods boil down to obtaining three things: (1) noise modulation function; (2) noise transfer function; and (3) current‐controlled oscillator gain. For each method, this paper provides a short background explanation of the technique, a step‐by‐step procedure of how to apply the method to hand calculation/computer simulation, and a worked example to demonstrate how to analyze a practical oscillator circuit with that method.

This survey article chiefly deals with phase‐noise analysis methods, so to restrict its scope, we limit our discussion to the following: (1) analyzing integrated circuit metal–oxide–semiconductor/bipolar junction transistor‐based LC, delay, and ring oscillator topologies; (2) considering a few oscillator harmonics in our analysis; (3) analyzing thermal/flicker intrinsic device‐noise sources rather than environmental/parametric noise/wander; (4) providing mainly qualitative amplitude‐noise discussions; and (5) omitting measurement methods/phase‐noise reduction techniques. Copyright © 2013 John Wiley & Sons, Ltd.
Astrocyte‐derived adenosine modulates increased sleep pressure during inflammatory response
Authors: Nadjar Agnes , Blutstein Tamara , Aubert Agnes , Laye Sophie , Haydon Philip G.
Published: February 2013

Activation of the immune system elicits several behavioral changes collectively called sickness. Among the behavioral changes, systemic infections induce an increase in time spent in nonrapid‐eye‐movement (NREM) sleep and an increase of slow wave activity (or “sleep pressure”). Using an inducible, astrocyte‐specific transgenic dominant negative SNARE (dnSNARE) mouse line we recently demonstrated that gliotransmission plays an important role in sleep homeostasis through an adenosine receptor 1 (A1R)‐sensitive pathway. It has been hypothesized that systemic infection, mimicked by peripheral administration of lipopolysaccharide (LPS), increases sleeping behavior in part through upregulation of central adenosine levels. Moreover, as a source of immunologically relevant factors, astrocytes play a pivotal role in the central nervous system immune and inflammatory responses. However, little is known about the role of astrocytes in the CNS response to a peripheral immune challenge. We hypothesize that LPS impacts sleep homeostasis through the modulation of astrocyte‐derived adenosine accumulation. We therefore used dnSNARE mice to determine whether astrocytes contribute to the increased sleep pressure under immune challenge and whether this is a result of changes in adenosine signaling. We demonstrate that dnSNARE‐mediated gliotransmission is required for the ability of LPS to elevate sleep pressure as measured by the power of slow wave activity during NREM sleep. Moreover, in agreement with a role of astrocyte‐derived adenosine in modulating sleep homeostasis, we find that intracerebroventricular infusion of the A1R antagonist 8‐cyclopentyl‐1,3‐dimethylxanthine (CPT) mimics this dnSNARE phenotype. Taken together, our data demonstrate that astrocytic adenosine acting through A1 receptors contributes to the modulation of sleep pressure by LPS. GLIA 2013
Upper atmosphere response to stratosphere sudden warming: Local time and height dependence simulated by GAIA model
Authors: Liu Huixin , Jin Hidekatsu , Miyoshi Yasunobu , Fujiwara Hitoshi , Shinagawa Hiroyuki
Published: February 2013

The whole atmosphere model GAIA is employed to shed light on atmospheric response to the 2009 major stratosphere sudden warming (SSW) from the ground to exobase. Distinct features are revealed about SSW impacts on thermospheric temperature and density above 100 km altitude. (1) The effect is primarily quasi‐semidiurnal in tropical regions, with warming in the noon and pre‐midnight sectors and cooling in the dawn and dusk sectors. (2) This pattern exists at all altitudes above 100 km, with its phase being almost constant above 200 km, but propagates downward in the lower thermosphere between 100 and 200 km. (3) The northern polar region experiences warming in a narrow layer between 100 and 130 km, while the southern polar region experiences cooling throughout 100–400 km altitudes. (4) The global net thermal effect on the atmosphere above 100 km is a cooling of approximately −12 K. These characteristics provide us with an urgently needed global context to better connect and understand the increasing upper atmosphere observations during SSW events.
Stream temperature response to variable glacier coverage in coastal watersheds of Southeast Alaska
Authors: Fellman Jason B. , Nagorski Sonia , Pyare Sanjay , Vermilyea Andrew W. , Scott Durelle , Hood Eran
Published: February 2013

We measured stream temperature continuously during the 2011 summer run‐off season (May through October) in nine watersheds of Southeast Alaska that provide spawning habitat for Pacific salmon. The nine watersheds have glacier coverage ranging from 0% to 63%. Our goal was to determine how air temperature and watershed land cover, particularly glacier coverage, influence stream temperature across the seasonal glacial meltwater hydrograph. Multiple linear regression models identified mean watershed elevation (related to glacier extent) and watershed lake coverage (%) as the strongest landscape controls on mean monthly stream temperature, with the weakest (May) and strongest (July) models explaining 86% and 97% of the temperature variability, respectively. Mean weekly stream temperature was significantly correlated with mean weekly air temperature in seven streams; however, the relationships were weak to non‐significant in the streams influenced by glacial run‐off. Streams with >30% glacier coverage showed decreasing stream temperatures with rising summer air temperatures, whereas those with <30% glacier coverage exhibited summertime warming. Glaciers also had a cooling effect on monthly mean stream temperature during the summer (July through September) equivalent to a decrease of 1.1 °C for each 10% increase in glacier coverage. The maximum weekly average temperature (an index of thermal suitability for salmon) in the six glacial streams was substantially below the lower threshold for optimum salmon growth. This finding suggests that although glaciers are important for moderating summer stream temperatures, future reductions in glacier run‐off may actually improve the thermal suitability of some glacially dominated streams in Southeast Alaska for salmon. Copyright © 2013 John Wiley & Sons, Ltd.
On quantifying hydraulic conductance at the soil–root interface
Authors: Li Yan , Pan Li‐Ping , Xu Gui‐Qing
Published: February 2013

This study sought to test a widely used hypothesis in water transport from soil to root: the soil textural effect on soil–root interfacial conductance can be quantified by the degree of soil water saturation. This hypothesis is inferred from basic soil physics and is commonly used in modelling root water uptake. However, it has never been subjected to rigorous experimental test. In the current study, the soil texture effect on the interfacial hydraulic conductance was evaluated on well‐watered pot‐grown cotton plants, with soil particle size ranges of 0–0.05, 0.05–0.1, 0.1–0.2, 0.2–0.3, 0.3–0.45, 0.45–0.6 and 0.6–1 mm in seven treatments, in addition to hydroponics. However, our experimental results showed that the volumetric soil water content, not degree of saturation, is the best explanatory variable for quantifying the interfacial effect on hydraulic conductance. Further analysis indicated that if temporal change of this interfacial effect on hydraulic conductance is the subject of concern, degree of saturation may still be a valid option. If soil textural or spatial variation in root water uptake is the subject of concern, volumetric soil water content is best suited to quantifying the interfacial effect on hydraulic conductance. Copyright © 2013 John Wiley & Sons, Ltd.
Crystal structures of nitric oxide reductases provide key insights into functional conversion of respiratory enzymes
Authors: Tosha Takehiko , Shiro Yoshitsugu
Published: February 2013

Summary: Respiration is an essential biological process to get bioenergy, ATP, for all kingdoms of life. Cytochrome c oxidase (COX) plays central role in aerobic respiration, catalyzing the reduction of O2 coupled with pumping proton across the biological membrane. Nitric oxide reductase (NOR) involved in anaerobic nitrate respiration is suggested to be evolutionary related to COX and share the same progenitor with COX, on the basis of the amino acid sequence homology. Contrary to COX, NOR catalyzes the reduction of nitric oxide and shows no proton pumping ability. Thus, the respiratory enzyme acquires (or loses) proton pumping ability in addition to the conversion of the catalytic property along with the environmental change on earth. Recently, we solved the structures of two types of NORs, which provides novel insights into the functional conversion of the respiratory enzymes. In this review, we focus on the structural similarities and differences between COXs and NORs and discuss possible mechanism for the functional conversion of these enzymes during molecular evolution. © 2013 IUBMB Life, 65(3):217–226, 2013
Regolith production and transport in the Susquehanna Shale Hills Critical Zone Observatory, Part 1: Insights from U‐series isotopes
Authors: Ma Lin , Chabaux Francois , West Nikki , Kirby Eric , Jin Lixin , Brantley Susan
Published: February 2013

To investigate the timescales of regolith formation on hillslopes with contrasting topographic aspect, we measured U‐series isotopes in regolith profiles from two hillslopes (north facing versus south facing) within the east‐west trending Shale Hills catchment in Pennsylvania. This catchment is developed entirely on the Fe‐rich, Silurian Rose Hill gray shale. Hillslopes exhibit a topographic asymmetry: The north‐facing hillslope has an average slope gradient of ~20°, slightly steeper than the south‐facing hillslope (~15°). The regolith samples display significant U‐series disequilibrium resulting from shale weathering. Based on the U‐series data, the rates of regolith production on the two ridgetops are indistinguishable (40 ± 22 versus 45 ± 12 m/Ma). However, when downslope positions are compared, the regolith profiles on the south‐facing hillslope are characterized by faster regolith production rates (50 ± 15 to 52 ± 15 m/Ma) and shorter durations of chemical weathering (12 ± 3 to 16 ± 5 ka) than those on the north‐facing hillslope (17 ± 14 to 18 ± 13 m/Ma and 39 ± 20 to 43 ± 20 ka). The south‐facing hillslope is also characterized by faster chemical weathering rates inferred from major element chemistry, despite lower extents of chemical depletion. These results are consistent with the influence of aspect on regolith formation at Shale Hills; we hypothesize that aspect affects such variables as temperature, moisture content, and evapotranspiration in the regolith zone, causing faster chemical weathering and regolith formation rates on the south‐facing side of the catchment. The difference in microclimate between these two hillslopes is inferred to have been especially significant during the periglacial period that occurred at Shale Hills at least ~15 ka before present. At that time, the erosion rates may also have been different from those observed today, perhaps denuding the south‐facing hillslope of regolith but not quite stripping the north‐facing hillslope. An analysis of hillslope evolution and response timescales with a linear mass transport model shows that the current landscape at Shale Hills is not in geomorphologic steady state (i.e., so‐called dynamic equilibrium) but rather is likely still responding to the climate shift from the Holocene periglacial to the modern, temperate conditions.
Influence of glycation on microencapsulating properties of soy protein isolate–lactose blends
Authors: Li Xin‐Rong , Tang Chuan‐He
Published: February 2013

Background

There is increasing interest in developing encapsulating materials from vegetable proteins as an abundant alternative for animal proteins or petroleum‐derived polymers. Relationships between emulsifying and microencapsulating properties of soy protein isolate or blends with carbohydrates have not been well characterised. The influence of glycation between soy protein isolate and lactose prior to emulsification on the emulsifying and microencapsulation properties of their blends was investigated in this work.

Results

Analysis of the emulsion characteristics indicated that the glycation resulted in a decreased size of emulsion droplets, enhanced emulsion stability, and decreased apparent viscosity, suggesting improvement of emulsifying properties. In the spray‐dried emulsions, the treatment with increasing degree of glycation from 0 to 13% progressively increased the retention efficiency from 96.4 to 98.3%. The glycation with an appropriate degree of glycation significantly decreased mean droplet size of the reconstituted emulsions, and increased the dissolution rate and capacity. However, the storage stability of the powders at 75% relative humidity was decreased by the glycation, though to a limited extent.

Conclusion

Glycation improves the encapsulation efficiency, redispersion and dissolution properties of soy protein isolate–lactose blends, but slightly accelerated the storage instability of the spray‐dried emulsions. The improvement of microencapsulation properties has been related to that of the emulsifying properties. © 2013 Society of Chemical Industry
Margin mapping in transoral surgery for head and neck cancer
Authors: Hinni Michael L. , Zarka Matthew A. , Hoxworth Joseph M.
Published: February 2013

Objectives/Hypothesis

To evaluate the results of patients treated by transoral laser microsurgery and margin mapping with attention to deep margin dimensions in the lateral pharyngeal wall.

Study Design

A microscopic margin analysis of multiblock surgical specimens applied to a prospectively accrued case series of squamous cell carcinoma of the palatine tonsils.

Methods

There were 128 tonsil cancers analyzed that were removed transorally, using microscopic margin mapping by surgeon and pathologist. The closest deep and peripheral margins were assessed. The results were then related to a study of the normal dimensions of the lateral pharyngeal wall in 20 healthy patients using magnetic resonance imaging. Outcome measures included number of positive margins, narrowest margin, local control, and disease‐free and overall survival.

Results

The average closest margin was 1.98 mm (range, 0.30–6.50 mm) deep and 2.82 mm (range, 1.00–5.00 mm) peripheral. There was one positive margin encountered in the previously untreated group (1%), and one local recurrence ultimately developed. Radiographic measures revealed a mean minimal thickness of the lateral pharyngeal wall musculature of 2.4 mm. With mean follow‐up of 4.3 years (range, 2–14 years), the 5‐year estimate for local control is 99%, disease‐free survival is 94.5%, and overall survival is 76%.

Conclusions

Margin mapping achieves a low rate of positive margins and is associated with good local control. Based on lateral pharyngeal wall anatomy, wide margins are often unobtainable and may be unnecessary so long as the final inked margin is clear.

Level of Evidence

4.
A Serum‐Resistant Low‐Generation Polyamidoamine with PEI 423 Outer Layer for Gene Delivery Vector
Authors: Pan Shirong , Cao Duanwen , Huang Huan , Yi Wu , Qin Linhao , Feng Min
Published: February 2013

A new derivative of polyamidoamine and polyethylenimine, G2.5‐PEI 423 or G1.5‐PEI 423, is prepared by an amidation reaction of PAMAM G2.5 or PAMAM G1.5 using PEI 423. The polycations show a great ability to combine with pDNA to form complexes, which protect the pDNA from nuclease degradation. The polymers display stronger buffer capacity and lower cytotoxicity. The complexes have particle sizes of 120–180 nm and zeta potentials of 20–40 mV. The G2.5‐PEI 423 complexes display much higher transfection efficiencies than PAMAM G5 and Lipo‐2k, and the G1.5‐PEI 423 complexes display higher transfection efficiencies than PAMAM G4 and PEI‐25k. The complexes possess better serum‐resistant capacity. The G2.5‐PEI 423 has a great potential to be used as a serum‐resistant gene vector.

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Copolyesters of Lactide, Isosorbide, and Terephthalic Acid‐Biobased, Biodegradable, High‐Tg Engineering Plastics
Authors: Kricheldorf Hans R. , Weidner Steffen M.
Published: February 2013

Various copolyesters of lactide, isosorbide, and terephthalic acid are prepared by a two‐step process performed in a “one‐pot” procedure, beginning with an isosorbide‐initiated oligomerization of L‐lactide followed by polycondensation with terephthaloyl chloride using SnCl2 as a catalyst for both steps. The SEC data show the formation of random copolyesters with high polydispersities as a consequence of the relatively high fraction of cyclics proved by matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). The glass‐transition temperatures (89–180 °C) obey an almost linear trend with the molar composition. The thermostability decreases with increasing lactide content. The successful incorporation of phenyl phosphate results in copolyesters of lower inflammability.
Different Wording of the Patient Global Visual Analogue Scale (PG‐VAS) Affects Rheumatoid Arthritis Patients’ Scoring and the Overall Disease Activity Score (DAS28): A Cross‐Sectional Study
Authors: French Tracy , Hewlett Sarah , Kirwan John , Sanderson Tessa
Published: February 2013

Objective

The Disease Activity Score in 28 joints (DAS28) is a key measure in clinical practice and clinical trials. There are at least five different versions of the ‘Patient Global’ Visual Analogue Scale (PG‐VAS) being used in the DAS28. The developers suggested that the PG‐VAS can be an assessment of global health or disease activity, but did not specify the wording of the question. There is no consensus on what the PG‐VAS is intended to capture, and the different words and phrases have not been evaluated. The aim of this study was to test if phrasing affects PG‐VAS scores and hence yields different results for the DAS28.

Methods

Fifty patients with rheumatoid arthritis taking biologic agents in a rheumatology outpatient department completed a self‐administered questionnaire containing five versions of the 100 mm PG‐VAS.

Results

All PG‐VAS versions correlated strongly with each other (rho = 0.67–0.87, p < 0.0001). However, individual scores for each PG‐VAS, when compared with the comparator on a Bland–Altman chart had wide limits of agreement—the largest being −42 mm to +45 mm. The five overall DAS28 scores were calculated for each patient using the five different PG‐VAS. The largest difference in DAS28 scores was 0.63.

Conclusion

Different phrasing of the PG‐VAS gives different DAS28 results. As the DAS28 is a key outcome measure, such differences have the potential to influence clinical decisions relating to eligibility for biologic agents and evaluation of new therapies. We urgently need to decide on the concept to be measured and the phrasing required to capture this. The PG‐VAS phrasing should then be standardized and validated. Copyright © 2013 John Wiley & Sons, Ltd. Copyright © 2013 John Wiley & Sons, Ltd.
Pediatric rhabdoid tumors of kidney and brain show many differences in gene expression but share dysregulation of cell cycle and epigenetic effector genes
Authors: Birks Diane K. , Donson Andrew M. , Patel Purvi R. , Sufit Alexandra , Algar Elizabeth M. , Dunham Christopher , Kleinschmidt‐DeMasters B.K. , Handler Michael H. , Vibhakar Rajeev , Foreman Nicholas K.
Published: February 2013

Background

Rhabdoid tumors (RTs) are aggressive tumors of early childhood that occur most often in brain (AT/RTs) or kidney (KRTs). Regardless of location, they are characterized by loss of functional SMARCB1 protein, a component of the SWI/SNF chromatin remodeling complex. The aim of this study was to determine genes and biological process dysregulated in common to both AT/RTs and KRTs.

Procedure

Gene expression for AT/RTs was compared to that of other brain tumors and normal brain using microarray data from our lab. Similar analysis was performed for KRTs and other kidney tumors and normal kidney using data from GEO. Dysregulated genes common to both analyses were analyzed for functional significance.

Results

Unsupervised hierarchical clustering of RTs identified three major subsets: two comprised of AT/RTs, and one of KRTs. Compared to other tumors, 1,187, 663, and 539 genes were dysregulated in each subset, respectively. Only 14 dysregulated genes were common to all three subsets. Compared to normal tissue, 5,209, 4,275, and 2,841 genes were dysregulated in each subset, with an overlap of 610 dysregulated genes. Among these genes, processes associated with cell proliferation, MYC activation, and epigenetic dysregulation were common to all three RT subsets.

Conclusions

The low overlap of dysregulated genes in AT/RTs and KRTs suggests that factors in addition to SMARCB1 loss play a role in determining subsequent gene expression. Drugs which target cell cycle or epigenetic genes may be useful in all RTs. Additionally, targeted therapies tailored to specific RT subset molecular profiles should be considered. Pediatr Blood Cancer 2013; 60: 1095–1102. © 2013 Wiley Periodicals, Inc.
Peculiarities of photoluminescence efficiency dependence on excitation intensity in GaN/Al2O3 epilayers
Authors: Lutsenko Evgenii V. , Rzheutski Mikalai V. , Zubialevich Vitalii Z. , Pavlovskii Viacheslav N. , Yablonskii Gennadii P. , Shulenkov Alexei S. , Reklaitis Ignas , Kadys Arūnas , Malinauskas Tadas , Nargelas Saulius , Jarašiūnas Kęstutis , Žukauskas Artūras
Published: February 2013

Excitation‐intensity dependent photoluminescence (PL) as well as effective recombination time of a series of c‐plane GaN layers grown on sapphire substrates were measured at room temperature. It was shown that at low excitation level a high background free‐electron concentration causes an increase of radiative recombination rate in the near band edge region of GaN that results in an increase of the PL efficiency. In the investigated series, the GaN layers with lower crystal quality but having higher free‐electron concentration showed higher PL efficiency at excitation levels under ∼50 kW/cm2. At elevated excitation levels the impact of free‐carrier concentration decreases and the PL efficiency is mainly determined by nonradiative recombination time. From simulations of excitation‐intensity dependent PL efficiency, the Auger recombination coefficient in the investigated GaN samples was estimated to be much less then 10–30 cm6s–1. A drop of PL efficiency was observed at excitation levels higher than 2500 kW/cm2 when PL was registered from sample's surface. The reason of the drop was stimulated emission propagating along the in‐plane direction and causing the saturation of photogenerated carrier density. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multivariate factor analysis of heavy minerals concentrate from Athabasca oil sands tailings by X‐ray photoelectron spectroscopy
Authors: Marshall Gregory M. , Kingston David M. , Moran Kevin , Mercier Patrick H.J.
Published: February 2013

Multivariate factor analysis of X‐ray photoelectron spectroscopy data acquired from Athabasca oil sands heavy minerals concentrate was used to identify the primary mineral components and their physical associations. Using large‐area spectroscopy, a principal components analysis (PCA) and Varimax rotation of the PCA spectral loadings matrix demonstrated that the most significant factors index the mineral chemistry by virtue of the within‐factor spectral correlations. Analysis of the Varimax rotated factor scores indicated the physical character of several mineral associations. Emphasis is placed on the high‐value materials, namely, zircon and the titanium‐bearing minerals. In spectral imaging mode, Varimax rotation in the spatial domain applied to a PCA noise‐reduced data reconstruction was used to render component images illustrating the spatial distribution of selected mineral chemistries. The component images also revealed evidence of surface species consistent with pyrite weathering. Data are supported with optical microscopy and energy‐dispersive X‐ray spectroscopy. Our work demonstrates the utility of multivariate spectroscopic techniques in the analysis of complex mineral chemistry. © 2013 National Research Council Canada and John Wiley & Sons Ltd.
Der Beginn einer Erfolgsgeschichte
Authors: Henning Hinrich
Published: February 2013

Nach der weltweit aufsehenerregenden Erfindung der Molekularpumpe hat Wolfgang Gaede nur wenige Jahre später, Herbst 1913, das Prinzip der Diffusionspumpe erfunden; das Patent wurde angemeldet unter dem schlicht anmutenden Namen „Vorrichtung zum Evakuieren”︁. Und wieder wie zuvor war es ein längerer Weg, bis der neue Pumpentyp zu dem wurde, was mitte des vorigen Jahrhunderts das wichtigste Werkzeug für die Hochvakuumtechnik wurde. Zwar kündigte E.Leybold's Nachf. schon 1913 die erste Quecksilberdiffusionspumpe aus Glas in der 2. Auflage seines großen Firmenkatalogs an, die aber nur geringes Saugvermögen aufwies. Vermutlich unabhängig von Gaede gelang es Langmuir in 1916 in den USA, eine ähnliche Pumpe mit besserem Saugvermögen zu konstruieren. 1919 trat Prof. Volmer in Berlin mit einer 2stufigen Diffusionspumpe auf den Plan. Nun war kein Halten mehr: viele Glasbläserfirmen brachten derartige Pumpen auf den Markt. Aber da Gaede nicht seine Pumpe, sondern vor allem das Prinzip der Diffusionspumpe patentiert hatte, mussten alle schließlich seit den 20er‐Jahren Lizenzen von Leybold nehmen, bei Langmuir im Austausch mit einer Lizenz auf dessen Patent. Bald wurden die Diffusionspumpen nicht mehr aus Glas, sondern aus Metall hergestellt und benutzen spezielle Mineralöle als Treibmittel, um das giftige, teure Quecksilber zu vermeiden. Damit wurde die Diffusionspumpe in der Mitte des 20. Jahrhunderts das wichtigste Werkzeug für die Hochvakuumerzeugung, gebaut in allen Größen mit Saugvermögen zwischen wenigen Litern pro Sekunde bis zu einigen zehntausend L/s.
Building quantitative, three‐dimensional atlases of gene expression and morphology at cellular resolution
Authors: Knowles David W. , Biggin Mark D.
Published: February 2013

Animals comprise dynamic three‐dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy‐based approaches to establish permanent, quantitative datasets—atlases—that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. WIREs Dev Biol 2013, 2:767–779. doi: 10.1002/wdev.107

This article is categorized under:

Gene Expression and Transcriptional Hierarchies > Quantitative Methods and Models

Technologies > Analysis of Cell, Tissue, and Animal Phenotypes

Technologies > Analysis of the Transcriptome
Multiobjective optimization of water distribution systems accounting for economic cost, hydraulic reliability, and greenhouse gas emissions
Authors: Wu Wenyan , Maier Holger R. , Simpson Angus R.
Published: February 2013

Key Points

Three‐objective WDS optimization considering cost, reliability and GHGs

Shape of solution space formed by the objectives is a U‐shaped curve

Location of Pareto front in the solution space and its practical implications
Molecular mechanism of oxidation‐induced TDP‐43 RRM1 aggregation and loss of function
Authors: Chang Chung-ke , Chiang Ming-hui , Toh Elsie Khai-Woon , Chang Chi-Fon , Huang Tai-huang
Published: February 2013

RRM2 and RRM2 bind by molecular sieving (View Interaction: 1, 2)
Dean vortices in finite-aspect-ratio ducts
Authors: Haines Philip E. , Denier James P. , Bassom Andrew P.
Published: February 2013

We consider the development of Dean vortices in a curved channel of finite aspect ratio. Solutions to the axisymmetric Navier–Stokes equations are obtained through a finite-element analysis, allowing us to explore the complex and rich bifurcation pattern of the flow as the aspect ratio and Dean number vary. We demonstrate a new class of finite-amplitude vortices and discuss their relationship to similar structures seen in finite-length Taylor–Couette flow.
Infant neurocognitive development is independent of the use of iodised salt or iodine supplements given during pregnancy
Authors: Santiago Piedad , Velasco Inés , Muela Jose Antonio , Sánchez Baltasar , Martínez Julia , Rodriguez Alvaro , Berrio María , Gutierrez-Repiso Carolina , Carreira Mónica , Moreno Alberto , García-Fuentes Eduardo , Soriguer Federico
Published: February 2013

The benefits of iodine supplements during pregnancy remain controversial in areas with a mild-to-moderate iodine deficiency. The aim of the present study was to determine the effect of improving iodine intakes, with iodised salt (IS) or iodine supplements, in pregnant Spanish women. A total of 131 pregnant women in their first trimester were randomly assigned to three groups: (1) IS in cooking and at the table, (2) 200 μg potassium iodide (KI)/d or (3) 300 μg KI/d. No differences were found in thyroid-stimulating hormone (TSH), free thyroxine (FT4), free triiodothyronine (FT3) or thyroid volume (TV) between the three groups. Regardless of the group in which women were included, those who had been taking IS for at least 1 year before becoming pregnant had a significantly lower TV in the third trimester (P= 0·01) and a significantly higher urinary iodine in the first (173·7 (sd81·8)v. 113·8 (sd79·6) μg/l,P= 0·001) and third trimesters (206·3 (sd91·2)v. 160·4 (sd87·7) μg/l,P= 0·03). Also, no differences were seen in TSH, FT4 or FT3. Children's neurological development was not significantly associated with the consumption of IS for at least 1 year before becoming pregnant and no differences were found according to the treatment group. In conclusion, in pregnant women with insufficient iodine intake, the intake of IS before becoming pregnant was associated with a better maternal thyroid function. The form of iodide intake was not associated with maternal thyroid function or children's neurological development.
The relationship between parental education and adolescents' soft drink intake from the age of 11–13 years, and possible mediating effects of availability and accessibility
Authors: Totland Torunn H. , Lien Nanna , Bergh Ingunn H. , Bjelland Mona , Gebremariam Mekdes K. , Klepp Knut-Inge , Andersen Lene F.
Published: February 2013

The present study examined the prospective relationship between parental education and adolescents' soft drink intake over 20 months, and possible mediating effects of adolescents' availability and accessibility of soft drinks at home. A total of 866 adolescents, with data on two time points in the Norwegian HEalth In Adolescents (HEIA) cohort study (2007–9), were included in the analyses. Data on intake and determinants of soft drinks were collected from adolescents and both parents by questionnaires. Mediation analyses using linear regression investigated the total and direct effects of parental education on adolescents' soft drink intake from the age of 11–13 years. In order to investigate prospective relationships, two models were set up to measure the (1) prediction and (2) change in consumption over 20 months. Possible mediation effects of availability and perceived accessibility at home were further examined in both models. The results showed that a lower level of parental education predicted a higher intake of soft drinks among adolescents after 20 months, and that higher perceived accessibility of soft drinks reported by adolescents and mothers explained 39 % of the total effect. No relationship was observed between parental education and the change in adolescents' intake of soft drinks over 20 months. Interventions aimed at families with low parental education should target the perceived accessibility of soft drinks at home in order to diminish social differences in adolescents' soft drink consumption.
Socialism as the Extension of Democracy
Authors: Arneson Richard J.
Published: February 2013

Are socialists best regarded as those who are most truly and consistently committed to democracy, under modern industrial conditions? Is the underlying issue that divides liberals from socialists the degree of their wholeheartedness in affirming the ideal of a democratic society? On the liberal side, Friedrich Hayek has remarked: “It is possible for a dictator to govern in a liberal way. And it is also possible that a democracy governs with a total lack of liberalism. My personal preference is for a liberal dictator and not for a democratic government lacking in liberalism.” No doubt many socialists would wish to quibble with Hayek's free-market oriented conception of liberalism. But I am wondering whether the conceptual map implicit in Hayek's remark is apt. Hayek appears to assume that there are two independent lines of division, one marking greater and lesser commitment to liberal values, the other marking greater and lesser commitment to democratic procedures. According to the conception of socialism as democracy that I wish to examine, a better picture of the political landscape would show one line of division with gradations indicating greater and lesser commitment to democracy. On this continuum, socialists are located at the extreme pro-democratic end, those who favor autocracy at the other end, and liberals somewhere in the middle. The analyst who finds this latter conceptual picture the more illuminating of the two will say that Hayek reveals his rejection of socialism by being less than wholehearted in his support of democracy.
The Implied Standpoint of Kant's Religion: An Assessment of Kant's Reply to (and an English Translation of) an Early Book Review of Religion Within the Bounds of Bare Reason
Authors: Palmquist Stephen R. , Otterman Steven
Published: February 2013

In the second edition Preface of Religion Within the Bounds of Bare Reason Kant responds to an anonymous review of the first edition. We present the first English translation of this obscure book review. Following our translation, we summarize the reviewer's main points and evaluate the adequacy of Kant's replies to five criticisms, including two replies that Kant provides in footnotes added in the second edition. A key issue is the reviewer's claim that Religion adopts an implied standpoint, described using transcendental terminology. Kant could have avoided much confusion surrounding Religion, had he taken this review more seriously. We therefore respond to three objections that Kant failed to address: how the Wille–Willkür distinction enables the propensity to evil to be viewed as coexisting with freedom of choice; how moral improvement is possible, even though the propensity to evil is necessary and universal; and how a ‘deed’ can be regarded as ‘noumenal’.
The Non-Conceptuality of the Content of Intuitions: A New Approach
Authors: Tolley Clinton
Published: February 2013

There has been considerable recent debate about whether Kant's account of intuitions implies that their content is conceptual. This debate, however, has failed to make significant progress because of the absence of discussion, let alone consensus, as to the meaning of ‘content’ in this context. Here I try to move things forward by focusing on the kind of content associated with Frege's notion of ‘sense (Sinn)’, understood as a mode of presentation of some object or property. I argue, first, that Kant takes intuitions to have a content in this sense, and, secondly, that Kant clearly takes the content of intuitions, so understood, to be distinct in kind from that possessed by concepts. I then show how my account can respond to the most serious objections to previous non-conceptualist interpretations.
A Method for Producing Site-Specific TEM Specimens from Low Contrast Materials with Nanometer Precision
Authors: Pettersson Henrik , Nik Samira , Weidow Jonathan , Olsson Eva
Published: February 2013

A method that enables high precision extraction of transmission electron microscope (TEM) specimens in low contrast materials has been developed. The main idea behind this work is to produce high contrast markers on both sides of and close to the area of interest. The markers are filled during the depositing of the protective layer. The marker material can be of either Pt or C depending on which one gives the highest contrast. It is thereby possible to distinguish the location of the area of interest during focused ion beam (FIB) milling and ensure that the TEM sample is extracted precisely at the desired position. This method is generally applicable and enables FIB/scanning electron microscope users to make high quality TEM specimens from small features and low contrast materials without a need for special holders. We explain the details of this method and illustrate its potential by examples from three different types of materials.
LIFE HISTORIES OFFER A CLUE TO THE FUTURE OF INFECTIOUS DISEASE ON CORAL REEFS
Authors: YAKOB L. , MUMBY P. J.
Published: February 2013

Increased frequency and severity of stressors associated with climate change are drastically altering ecosystems. Caribbean coral reefs differ markedly from just 30 years ago, with much restructuring attributable to infectious disease outbreaks. Using a classic epidemiological approach, we demonstrate how density-dependent demographic rates serve as a mechanism for intrinsic coral resilience to population perturbations arising from disturbances such as disease. We explore the impact of allowing infection status to influence demographic rates and ascertain outbreak thresholds that are corroborated by epizootic patterns observed in the field. We discuss how our threshold calculations may provide metrics of coral epizootic early warning systems. Integrating our infection model with equations describing the interspecific competition for space between coral and macroalgae, we provide new mechanistic understanding of the influence that coral life history dynamism and infectious disease have on the changing face of these threatened ecosystems.
ON A VARIATION OF A CONGRUENCE OF SUBBARAO
Authors: DUJELLA ANDREJ , LUCA FLORIAN
Published: February 2013

We study positive integers $n$ such that $n\phi (n)\equiv 2\hspace{0.167em} {\rm mod}\hspace{0.167em} \sigma (n)$, where $\phi (n)$ and $\sigma (n)$ are the Euler function and the sum of divisors function of the positive integer $n$, respectively. We give a general ineffective result showing that there are only finitely many such $n$ whose prime factors belong to a fixed finite set. When this finite set consists only of the two primes $2$ and $3$ we use continued fractions to find all such positive integers $n$.
Carl-Philipp Heisenberg: Early embryos make a big move
Authors: Sedwick Caitlin
Published: February 2013

Heisenberg is studying how cells’ physical properties drive early developmental events.
Conservative constraints on early cosmology with MONTE PYTHON
Authors: Benjamin Audren  , Julien Lesgourgues  , Karim Benabed  , Simon Prunet
Published: February 2013

Models for the latest stages of the cosmological evolution rely on a less solid theoretical and observational ground than the description of earlier stages like BBN and recombination. As suggested in a previous work by Vonlanthen et al., it is possible to tweak the analysis of CMB data in such way to avoid making assumptions on the late evolution, and obtain robust constraints on ''early cosmology parameters''. We extend this method in order to marginalise the results over CMB lensing contamination, and present updated results based on recent CMB data. Our constraints on the minimal early cosmology model are weaker than in a standard ΛCDM analysis, but do not conflict with this model. Besides, we obtain conservative bounds on the effective neutrino number and neutrino mass, showing no hints for extra relativistic degrees of freedom, and proving in a robust way that neutrinos experienced their non-relativistic transition after the time of photon decoupling. This analysis is also an occasion to describe the main features of the new parameter inference code MONTE PYTHON, that we release together with this paper. MONTE PYTHON is a user-friendly alternative to other public codes like COSMOMC, interfaced with the Boltzmann code CLASS.