bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural killer T (NKT)–B-cell interactions promote prolonged antibody responses and long-term memory to pneumococcal capsular polysaccharides
Authors: Bai Li , Deng Shenglou , Reboulet Rachel , Mathew Rebecca , Teyton Luc , Savage Paul B. , Bendelac Albert
Published: September 2013

Significance

Antibodies directed against microbial polysaccharides are a critical component of protective immune responses and vaccines. We used nanoparticles coexpressing pneumococcal capsular polysaccharides and a cell wall lipid antigen analog to model NKT–B-cell interactions. Our study demonstrated CD1d-restricted cognate interactions, isotype switch, affinity maturation, and long-term memory, despite the apparent failure of NKT cells to differentiate into follicular helper cells. The findings demonstrate the importance of nonconventional sources of help for B cells responding to polysaccharide antigens.
Regulation of human hematopoietic stem cell self-renewal by the microenvironment’s control of retinoic acid signaling
Authors: Ghiaur Gabriel , Yegnasubramanian Srinivasan , Perkins Brandy , Gucwa Jessica L. , Gerber Jonathan M. , Jones Richard J.
Published: September 2013

Significance

Mechanisms that control physiologic hematopoietic stem-cell (HSC) self-renewal remain largely unknown. Inhibition of retinoic acid (RA) signaling in HSCs maintained their primitive phenotype and function, and promoted their self-renewal. Moreover, bone marrow stroma’s expression of the cytochrome P450 retinoid-inactivating enzyme, CYP26, allowed HSC self-renewal by maintaining an environment low in retinoids. Thus, HSCs appear to be intrinsically programmed to undergo RA-mediated differentiation unless prevented from doing so by bone marrow niche CYP26. Modulation of RA signaling also holds promise for clinical HSC expansion.
TLR-induced PAI-2 expression suppresses IL-1β processing via increasing autophagy and NLRP3 degradation
Authors: Chuang Shih-Yi , Yang Chih-Hsiang , Chou Chih-Chang , Chiang Yu-Ping , Chuang Tsung-Hsien , Hsu Li-Chung
Published: September 2013

The NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome, a multiprotein complex, triggers caspase-1 activation and maturation of the proinflammatory cytokines IL-1β and IL-18 upon sensing a wide range of pathogen- and damage-associated molecules. Dysregulation of NLRP3 inflammasome activity contributes to the pathogenesis of many diseases, but its regulation remains poorly defined. Here we show that depletion of plasminogen activator inhibitor type 2 (PAI-2), a serine protease inhibitor, resulted in NLRP3- and ASC (apoptosis-associated Speck-like protein containing a C-terminal caspase recruitment domain)‐dependent caspase-1 activation and IL-1β secretion in macrophages upon Toll-like receptor 2 (TLR2) and TLR4 engagement. TLR2 or TLR4 agonist induced PAI-2 expression, which subsequently stabilized the autophagic protein Beclin 1 to promote autophagy, resulting in decreases in mitochondrial reactive oxygen species, NLRP3 protein level, and pro–IL-1β processing. Likewise, overexpressing Beclin 1 in PAI-2–deficient cells rescued the suppression of NLRP3 activation in response to LPS. Together, our data identify a tier of TLR signaling in controlling NLRP3 inflammasome activation and reveal a cell-autonomous mechanism which inversely regulates TLR- or
Escherichia coli
-induced mitochondrial dysfunction, oxidative stress, and IL-1β–driven inflammation.
ABI3 controls embryo degreening through Mendel'sIlocus
Authors: Delmas Frédéric , Sankaranarayanan Subramanian , Deb Srijani , Widdup Ellen , Bournonville Céline , Bollier Norbert , Northey Julian G. B. , McCourt Peter , Samuel Marcus A.
Published: September 2013

Significance

Occurrence of mature green seeds in oil-seed crops such as canola and soybean causes severe losses in revenue. Retention of chlorophyll in seeds can be an undesirable trait as it affects seed maturation, seed oil, and meal quality. We show that the abscisic acid (ABA, plant hormone) dependent transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), confers seed degreening by regulating Mendel’s stay-green genes. This study unveils a new role for ABI3 in removal of seed chlorophyll in addition to its functions in embryo maturation and conferring desiccation tolerance. This pathway could be manipulated to tackle the cold-induced green seed problem in oil-seed crops.
Intravaginal ring eluting tenofovir disoproxil fumarate completely protects macaques from multiple vaginal simian-HIV challenges
Authors: Smith James M. , Rastogi Rachna , Teller Ryan S. , Srinivasan Priya , Mesquita Pedro M. M. , Nagaraja Umadevi , McNicholl Janet M. , Hendry R. Michael , Dinh Chuong T. , Martin Amy , Herold Betsy C. , Kiser Patrick F.
Published: September 2013

Significance

Topical prevention of HIV is designed to pharmacologically interrupt sexual transmission at the genital mucosa. Attempts at preventing transmission in women using vaginal gels have yielded disappointing results in part because of poor rates of adherence. Controlled topical drug delivery using intravaginal ring technology should improve efficacy and adherence by providing sustained mucosal delivery of antiretrovirals. In this paper, we describe a reservoir intravaginal ring that delivers tenofovir disoproxil fumarate (TDF) for 1 month. The ring protected pigtailed macaques from weekly vaginal simian–human immunodeficiency virus challenges for 4 mo. The sterilizing performance of this drug delivery system supports the concept that an intravaginal ring delivering TDF could be an effective tool for prevention of HIV sexual transmission in women.
Key features of σ
S
required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme
Authors: Banta Amy B. , Chumanov Robert S. , Yuan Andy H. , Lin Hueylie , Campbell Elizabeth A. , Burgess Richard R. , Gourse Richard L.
Published: September 2013

Significance

Bacteria can change the relative amounts of different sigma factors that associate with the RNA polymerase (RNAP) catalytic core enzyme, thereby altering the relative amounts of the RNAP holoenzymes and modifying gene expression globally under changing nutritional or environmental conditions. We show here that the
Escherichia coli
transcription factor Crl increases assembly of the holoenzyme containing the stress response sigma factor, sigma S. We identify the key determinants necessary for Crl to distinguish between sigma S and other sigma factors, thereby specifically promoting the sigma S transcriptional program.
Carbon substitution for oxygen in silicates in planetary interiors
Authors: Sen Sabyasachi , Widgeon Scarlett J. , Navrotsky Alexandra , Mera Gabriela , Tavakoli Amir , Ionescu Emanuel , Riedel Ralf
Published: September 2013

Significance

Carbon is an important element in the Earth and other planets, but its concentration, chemical and structural form, and dynamics throughout the crust, mantle, and core are incompletely known. Based on the thermodynamic stability of a class of synthetic materials, the polymer-derived ceramics containing Si, C, and O, and on new NMR data for such systems containing a network-modifying metal (Li), this paper suggests that the substitution of C for O (rather than C for Si) in molten, amorphous, and crystalline silicate structures may provide a hitherto hidden reservoir of carbon in planetary interiors.
Molecular decision trees realized by ultrafast electronic spectroscopy
Authors: Fresch Barbara , Hiluf Dawit , Collini Elisabetta , Levine R. D. , Remacle F.
Published: September 2013

Significance

One possible way to reduce the physical dimensions of a computing node is to instruct a molecule to evaluate a complicated logic function. This is even more so if several such functions are processed in parallel. The interaction between light and matter is a suitable route because it is bilinear, depending on both the properties of the laser and of the molecule; the outcome depends on the initial state of the molecule and there can be more than one distinct path leading to the readout signal. Two-dimensional photon spectroscopy is shown to have four paths originating from each interaction, thereby enabling, as shown in

SI Text

, quaternary logic. In the main text, we discuss the simpler case of binary logic.
A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis
Authors: Lesch Bluma J. , Dokshin Gregoriy A. , Young Richard A. , McCarrey John R. , Page David C.
Published: September 2013

Significance

Germ cells, meaning the mature sperm and egg and their developmental precursors, carry the DNA that is passed from one generation to the next. Although the sperm and egg are highly specialized, differentiated cells, they meet at fertilization to produce a totipotent zygote, a cell that can generate any other cell type. We report the finding that a set of developmentally important genes is kept in a “poised” state in the germ cells: although these genes are never expressed in the germ cells themselves, they maintain a chromatin state usually associated with the potential for rapid gene activation. We propose that maintenance of this poised state in the germ cells contributes to the generation of totipotency in the fertilized zygote.
SUMOylation is essential for sex-specific assembly and function of the
Caenorhabditis elegans
dosage compensation complex on X chromosomes
Authors: Pferdehirt Rebecca R. , Meyer Barbara J.
Published: September 2013

Significance

Dosage compensation equalizes X-chromosome transcription between nematode males (1X) and hermaphrodites (2X) via a dosage compensation complex (DCC) that binds hermaphrodite X chromosomes to repress transcription by half. We show that several DCC subunits are modified by the small ubiquitin-like modifier SUMO in response to the signal that triggers DCC assembly onto X. DCC assembly and function require SUMOylation. DCC subunit DUMPY-28 also acts in condensin complexes essential for chromosome segregation, but its SUMOylation is DCC-specific. We propose that specific signals trigger DCC protein SUMOylation, stimulating robust complex formation. SUMOylation facilitates distinct activities of proteins that function in multiple complexes.
Moving over in(to) English and French
Authors: Egan Thomas , Rawoens Gudrun
Published: September 2013

In this paper we discuss ways in which the concept that, for want of a better word, we may describe as ‘overness’ is coded in motion predications in English and French. The concept of ‘overness’ is a relational one, the basic spatial sense of which involves some sort of (elongated) superiority of a Figure (a Trajector in the terminology employed by cognitive linguists) vis-à-vis a Ground. This study compares codings in English and French of this concept as it is instantiated in translations of the same original Norwegian texts. The data for the study are taken from the Oslo Multilingual Corpus. Tokens coding motion events are analysed in detail in terms of the coding of Manner, Path, Site and Ground. The results of the study point to substantial differences between English and French in their codings of motion events, with English conforming by and large to the satellite-framed language type. The results for French are much less clear, with the picture resembling more a sort of typological hybrid than a rigid path-framed type.
Perception and reality – Portuguese adults' awareness of active lifestyle
Authors: Marques Adilson , Martins João , Ramos Madalena , Yazigi Flávia , Carreiro da Costa Francisco
Published: September 2013

This study aims to assess awareness of physical activity levels among adults and to investigate the variables associated with different types of awareness. The participants were 1042 men and 1316 women aged 31–60 years old (43.3 ± 6.1). Data were collected on physical activity behaviour, physical activity awareness, perceptions and psychological factors. Awareness was assessed by comparing self‐rated physical activity with achieving physical activity guidelines. Chi‐square and logistic regression analyses were applied to the results. About 32.4% were considered active. Moreover, 61% accurately reported their physical activity (38.3% realistic inactive and 22.7% realistic active), 29.2% overestimated their physical activity (overestimators) and 9.7% incorrectly described themselves as inactive (underestimators). Perception of an excellent health status (odds ratio, OR = 4.07, 95% confidence interval, CI: 2.07–8.00, p < 0.001) was the strongest positive association with being realistic active, followed by having a high socio‐economic status (SES) (OR = 1.53, 95% CI: 1.10–2.12, p < 0.05). Overestimator participants were more likely to have an excellent perception of health (OR = 2.58, 95% CI: 1.47–4.52, p < 0.01) and had a good experience in physical education (OR = 1.46, 95% CI:1.03–2.08, p < 0.05). Almost half of these participants erroneously perceived themselves as physically active. Gender, body mass index (BMI) and the quality of physical education at school were associated with those who misperceived their physical activity.
Component Processes in Voluntary Task Switching
Authors: Demanet Jelle , Liefooghe Baptist
Published: September 2013

The present study investigated the involvement of bottom-up and top-down control in task-switching situations in which tasks are selected on a voluntary basis. We tested for indices of both types of control in the reduction in switch cost that is observed when more time is available before executing a task. Participants had to indicate their task choice overtly prior to the actual task execution, and two time intervals were manipulated: the interval between the task-execution response of the previous trial and task-indication response of the current trial and the interval between task-indication response and task-execution response of a particular trial. In Experiment 1, the length of these intervals was manipulated orthogonally, and indices for top-down and bottom-up control were observed. Concerned with the validity of these results, Experiments 2–3 additionally discouraged participants from preparing the upcoming task before their task-indication response. Indices for bottom-up control remained, but not for top-down control. The characteristics of top-down and bottom-up control in voluntary task switching and task switching in general are discussed.
Tuning voltage-gated channel activity and cellular excitability with a sphingomyelinase
Authors: Combs David J. , Shin Hyeon-Gyu , Xu Yanping , Ramu Yajamana , Lu Zhe
Published: September 2013

Voltage-gated ion channels generate action potentials in excitable cells and help set the resting membrane potential in nonexcitable cells like lymphocytes. It has been difficult to investigate what kinds of phospholipids interact with these membrane proteins in their native environments and what functional impacts such interactions create. This problem might be circumvented if we could modify specific lipid types in situ. Using certain voltage-gated K+ (KV) channels heterologously expressed in Xenopus laevis oocytes as a model, our group has shown previously that sphingomyelinase (SMase) D may serve this purpose. SMase D is known to remove the choline group from sphingomyelin, a phospholipid primarily present in the outer leaflet of plasma membranes. This SMase D action lowers the energy required for voltage sensors of a KV channel to enter the activated state, causing a hyperpolarizing shift of the Q-V and G-V curves and thus activating them at more hyperpolarized potentials. Here, we find that this SMase D effect vanishes after removing most of the voltage-sensor paddle sequence, a finding supporting the notion that SMase D modification of sphingomyelin molecules alters these lipids’ interactions with voltage sensors. Then, using SMase D to probe lipid–channel interactions, we find that SMase D not only similarly stimulates voltage-gated Na+ (NaV) and Ca2+ channels but also markedly slows NaV channel inactivation. However, the latter effect is not observed in tested mammalian cells, an observation highlighting the profound impact of the membrane environment on channel function. Finally, we directly demonstrate that SMase D stimulates both native KV1.3 in nonexcitable human T lymphocytes at their typical resting membrane potential and native NaV channels in excitable cells, such that it shifts the action potential threshold in the hyperpolarized direction. These proof-of-concept studies illustrate that the voltage-gated channel activity in both excitable and nonexcitable cells can be tuned by enzymatically modifying lipid head groups.
Cetacean–fishery interactions in Galicia (NW Spain): results and management implications of a face-to-face interview survey of local fishers
Authors: Goetz Sabine , Read Fiona L. , Santos M. Begoña , Pita C. , Pierce Graham J.
Published: September 2013

Galicia (NW Spain) is an important fishing region with a high potential for cetacean–fishery interactions. Cetacean depredation on catch and damage to fishing gear can potentially lead to substantial economic loss for fishers, while cetacean bycatch raises conservation concerns. With the aim of gathering information on the types and scale of interactions and of suggesting possible management strategies, we conducted face-to-face interviews with fishers in local fishing harbours, in particular to identify specific problematic interactions and to quantify the level of economic loss and bycatch rates associated with these interactions. We found that cetacean–fishery interactions are frequent, although damage to catch and fishing gear by cetaceans was mostly reported as small. Nevertheless, substantial economic loss can result from common bottlenose dolphins (Tursiops truncatus) damaging coastal gillnets and from short-beaked common dolphins (Delphinus delphis) scattering fish in purse-seine fisheries. Cetacean bycatch mortality was reported to be highest for trawls and set gillnets, and probably exceeds sustainable levels for local common and bottlenose dolphin populations. Although interview data may be biased due to the perceptions of interviewees, and therefore should be interpreted with care, the methodology allowed us to cover multiple sites and fisheries within a reasonable time frame. Minimizing cetacean–fishery interactions requires the implementation of case-specific management strategies with the active participation of fishers. For set gillnet and purse-seine fisheries, the use of acoustic deterrent devices (pingers) may prevent cetaceans from approaching and getting trapped in the nets. For trawl fisheries, where bycatch appears to be particularly high at night in water depths of 100–300 m, possible solutions include the implementation of time/area closures and the relocation of some fishing effort to deeper waters.
Migratory connectivity of two Baltic Sea salmon populations: retrospective analysis using stable isotopes of scales
Authors: Torniainen Jyrki , Vuorinen Pekka J. , Jones Roger I. , Keinänen Marja , Palm Stefan , Vuori Kristiina A. M. , Kiljunen Mikko
Published: September 2013

Torniainen, J., Vuorinen, P. J., Jones, R. I., Keinänen, M., Palm, S., Vuori, K. A. M., and Kiljunen, M. 2014. Migratory connectivity of two Baltic Sea salmon populations: retrospective analysis using stable isotopes of scales. – ICES Journal of Marine Science, 71: 336–344.

Migratory connectivity refers to the extent to which individuals of a migratory population behave in unison, and has significant consequences for the ecology, evolution and conservation of migratory animals. We made a retrospective assessment of the migratory connectivity of River Simojoki and River Kymijoki populations of Atlantic salmon Salmo salar L. by using stable isotope analysis of archived scales to identify the final feeding areas used before ascending rivers for spawning. We also tested differences in migratory connectivity between wild and hatchery-reared salmon and compared Carlin-tag recoveries with salmon scale stable isotope analysis as methods for studying salmon migrations. Stable isotope (δ13C, δ15N) values from the last growth region of scales from salmon caught ascending their natal rivers were compared via discriminant analysis with those from scales of salmon caught in different Baltic Sea areas during 1989–2011. Most River Simojoki salmon had likely fed in the Baltic Proper (mean ± SD for ascending fish probability 0.59 ± 0.32) with secondary likely feeding areas in the Bothnian Sea (0.21 ± 0.26) and the Gulf of Finland (0.20 ± 0.27). Most River Kymijoki salmon had likely fed in the Gulf of Finland (0.71 ± 0.42) with the Baltic Proper (0.29 ± 0.41) a secondary feeding area. The results did not indicate the Bothnian Sea to be an important feeding area. The two salmon populations showed weak migratory connectivity and rather fixed areal preference throughout the record irrespective of wild or stocked origin. Although the results from the scale stable isotope analyses were broadly consistent with previously reported Carlin-tag recoveries, we argue that the stable isotope approach offers several important advantages in the study of salmon migratory behaviour.
A Novel Nonsense Mutation in the EpCAM Gene in a Patient With Congenital Tufting Enteropathy
Authors: Thoeni Cornelia , Amir Achiya , Guo Conghui , Zhang S. , Avitzur Yaron , Heng Y.M. , Cutz Ernest , Muise Aleixo M.
Published: September 2013

Objectives:

Tufting enteropathy (TE) is a classical congenital disorder of the intestinal mucosa causing protracted diarrhea in infancy as a result of a dysfunctional epithelial cell barrier, which is mainly caused by mutations in the EpCAM gene and expression of a nonfunctional epithelial cell adhesion molecule in the intestine. We report here a novel nonsense mutation in a patient suspected of having TE, resulting in a complete absence of EpCAM in duodenal enterocytes.

Methods:

A patient presenting with congenital diarrhea and suspected of having TE was screened for EpCAM mutations, and duodenal biopsies were stained for EpCAM using immunohistochemistry analysis.

Results:

We identified a novel homozygous nonsense mutation in the EpCAM gene in a patient suspected of having TE, causing a complete loss of EpCAM expression in duodenal enterocytes.

Conclusions:

With screening analysis for EpCAM mutations and immunohistochemistry for EpCAM expression in duodenal enterocytes, we found a novel homozygous mutation in a patient with classical protracted diarrhea in infancy finally diagnosed as TE, which results in a complete absence of EpCAM and in dysfunctional barrier formation in duodenal enterocytes.
Bitterness of Glucose/Galactose
Authors: Pode‐Shakked Ben , Reish Orit , Aktuglu‐Zeybek Cigdem , Kesselman Dafna , Dekel Benjamin , Bujanover Yoram , Anikster Yair
Published: September 2013

Glucose galactose malabsorption (GGM) is a rare autosomal recessive disorder characterized by life‐threatening osmotic diarrhea at infancy. When the intake of the offending sugars (namely, glucose, galactose and lactose) is ceased, the diarrhea promptly stops. Mutations in the SLC5A1 gene, encoding the sodium‐glucose co‐transporter located in the brush border of enterocytes, have been shown to cause the disease. More than 300 subjects of diverse origin have been reported worldwide, most of whom are a result of a consanguineous union. We examined 6 patients from 4 families presenting with complaints consistent with GGM and responsive to the appropriate fructose‐based diet. Genomic DNA of the patients was polymerase chain reaction amplified for each of the 15 exons of the SLC5A1 gene and analyzed by nucleotide sequencing. The analysis lead to the identification of 2 novel mutations: a 1915 del C mutation, a frameshift mutation leading to a premature stop at codon 645; and a substitution missense mutation of T to C on nucleotide 947 (exon 9) causing a L316P substitution. In addition, G426R and C255W mutations previously described were identified; in both cases, the patients were shown to be homozygous and their parents heterozygous for the mutation. Of note, additional patients who underwent a similar evaluation at our center for suspected GGM did not show mutations in the SLC5A1 gene. Because the latter did not previously undergo a diagnostic algorithm in full, for instance, one that may consist of a glucose breath hydrogen test and an empiric attempt of a dietary switch to galactomin, we suggest that molecular genotyping of such patients should only follow such appropriate clinical evaluation.
ERCP Can Be Safely and Effectively Performed by a Pediatric Gastroenterologist for Choledocholithiasis in a Pediatric Facility
Authors: Troendle David M. , Barth Bradley A.
Published: September 2013

Objective:

The aim of this study was to demonstrate that an appropriately trained pediatric gastroenterologist can perform endoscopic retrograde cholangiopancreatography (ERCP) for suspected choledocholithiasis both safely and effectively.

Methods:

Retrospective analysis of ERCP experience from November 2006 to May 2012. Only ERCPs performed by a pediatric gastroenterologist on pediatric patients for the indication of suspected choledocholithiasis were included for formal chart review. Patient characteristics, procedural success, and adverse events were recorded, and subsequently compared with quality standards as defined by the American Society for Gastrointestinal Endoscopy Quality Task Force.

Results:

A total of 154 ERCPs were performed, of which 65 (42%) were performed on unique patients for the indication of suspected choledocholithiasis. The median age was 15.2 years (range 1 month–18.4 years). The median weight was 65 kg (range 4—127 kg). Biliary cannulation was achieved in 65 (100%). All 65 patients underwent sphincterotomy. Ductal clearance was achieved in 64 (98%) patients during the initial ERCP session. Adverse events included 3 (5%) episodes of mild pancreatitis, 1 episode of moderate bleeding, and 1 episode of sphincterotomy clot causing obstruction and need for repeat ERCP within 1 week. Overall, 5 (8%) unique patients experienced a complication.

Conclusions:

Therapeutic ERCP for the indication of choledocholithiasis can be performed by an appropriately trained pediatric gastroenterologist at a pediatric facility with acceptable cannulation rates, stone extraction rates, and adverse event rates as defined by the American Society for Gastrointestinal Endoscopy Quality Task Force.
Warm climates of the past—a lesson for the future?
Authors: Lunt D. J. , Elderfield H. , Pancost R. , Ridgwell A. , Foster G. L. , Haywood A. , Kiehl J. , Sagoo N. , Shields C. , Stone E. J. , Valdes P.
Published: September 2013

This Discussion Meeting Issue of the
Philosophical Transactions A
had its genesis in a Discussion Meeting of the Royal Society which took place on 10–11 October 2011. The Discussion Meeting, entitled ‘Warm climates of the past: a lesson for the future?’, brought together 16 eminent international speakers from the field of palaeoclimate, and was attended by over 280 scientists and members of the public. Many of the speakers have contributed to the papers compiled in this Discussion Meeting Issue. The papers summarize the talks at the meeting, and present further or related work. This Discussion Meeting Issue asks to what extent information gleaned from the study of past climates can aid our understanding of future climate change. Climate change is currently an issue at the forefront of environmental science, and also has important sociological and political implications. Most future predictions are carried out by complex numerical models; however, these models cannot be rigorously tested for scenarios outside of the modern, without making use of past climate data. Furthermore, past climate data can inform our understanding of how the Earth system operates, and can provide important contextual information related to environmental change. All past time periods can be useful in this context; here, we focus on past climates that were warmer than the modern climate, as these are likely to be the most similar to the future. This introductory paper is not meant as a comprehensive overview of all work in this field. Instead, it gives an introduction to the important issues therein, using the papers in this Discussion Meeting Issue, and other works from all the Discussion Meeting speakers, as exemplars of the various ways in which past climates can inform projections of future climate. Furthermore, we present new work that uses a palaeo constraint to quantitatively inform projections of future equilibrium ice sheet change.
Two-dimensional indirect Fourier transformation for evaluation of small-angle scattering data of oriented samples
Authors: Fritz-Popovski Gerhard
Published: September 2013

An extension of the indirect Fourier transformation method for two-dimensional small-angle scattering patterns is presented. This allows for a model-free investigation of real-space functions of oriented structures. The real-space function is built from two-dimensional basis functions. The Fourier transformed basis functions are approximated to the scattering pattern. The solution to this problem in reciprocal space can be used to compute the corresponding real-space functions. These real-space functions contain information on size, shape, internal structure and orientation of the structures studied. Information on structures that are oriented in different distinct directions can be partly separated. The applicability of the technique is demonstrated on simulated data of oriented cuboids and on two experimental data sets based on the nanostructure of spruce normal wood.
Tuning the growth properties of Ge quantum dot lattices in amorphous oxides by matrix type
Authors: Buljan M. , Jerčinović M. , Siketić Z. , Bogdanović-Radović I. , Delač Marion I. , Kralj M. , Ivanda M. , Turković A. , Dražić G. , Bernstorff S. , Radić N.
Published: September 2013

Self-assembled growth of Ge quantum dot lattices in oxide matrices prepared by the quite simple magnetron sputtering deposition method allows the preparation of a variety of structures tunable by their shape, size and arrangement. The driving mechanism for the self-assembly was attributed to the surface morphology features originating from the quantum dots' growth. Here it is shown specifically that the matrix type is another critical factor that enables the control of the self-assembly process and the tuning of the ordering type and degree of regularity of quantum dot systems. The effectiveness of the matrix factor is demonstrated through the analysis of quantum dot arrangements in amorphous silica, alumina and mullite matrices. Using the same deposition conditions, different ordering types and degrees of disorder were found in the quantum dot systems based on different matrices. The matrix factor is shown to be driven by different matrix tendencies to smooth the surface during the growth of the films. The obtained results are relevant for understanding and tailoring of the self-assembled growth of quantum dot lattices in amorphous systems.
A multi-length-scale USAXS/SAXS facility: 10–50 keV small-angle X-ray scattering instrument
Authors: Freelon Byron , Suthar Kamlesh , Ilavsky Jan
Published: September 2013

Coupling small-angle X-ray scattering (SAXS) and ultra-small-angle X-ray scattering (USAXS) provides a powerful system of techniques for determining the structural organization of nanostructured materials that exhibit a wide range of characteristic length scales. A new facility that combines high-energy (HE) SAXS and USAXS has been developed at the Advanced Photon Source (APS). The application of X-rays across a range of energies, from 10 to 50 keV, offers opportunities to probe structural behavior at the nano- and microscale. An X-ray setup that can characterize both soft matter or hard matter and high-Zsamples in the solid or solution forms is described. Recent upgrades to the Sector 15ID beamline allow an extension of the X-ray energy range and improved beam intensity. The function and performance of the dedicated USAXS/HE-SAXS ChemMatCARS-APS facility is described.
Complete elliptical ring geometry provides energy and instrument calibration for synchrotron-based two-dimensional X-ray diffraction
Authors: Hart Michael L. , Drakopoulos Michael , Reinhard Christina , Connolley Thomas
Published: September 2013

A complete calibration method to characterize a static planar two-dimensional detector for use in X-ray diffraction at an arbitrary wavelength is described. This method is based upon geometry describing the point of intersection between a cone's axis and its elliptical conic section. This point of intersection is neither the ellipse centre nor one of the ellipse focal points, but some other point which lies in between. The presented solution is closed form, algebraic and non-iterative in its application, and gives values for the X-ray beam energy, the sample-to-detector distance, the location of the beam centre on the detector surface and the detector tilt relative to the incident beam. Previous techniques have tended to require prior knowledge of either the X-ray beam energy or the sample-to-detector distance, whilst other techniques have been iterative. The new calibration procedure is performed by collecting diffraction data, in the form of diffraction rings from a powder standard, at known displacements of the detector along the beam path.
Inner retinal inhibition shapes the receptive field of retinal ganglion cells in primate
Authors: Protti D. A. , Di Marco S. , Huang J. Y. , Vonhoff C. R. , Nguyen V. , Solomon S. G.
Published: September 2013

Key points

The receptive field of most retinal ganglion cells consists of an excitatory centre and an inhibitory surround.

In retinal ganglion cells of non‐primates the receptive field surround is provided by lateral inhibition in both the outer and the inner retinal synaptic layers.

We use whole cell recording methods to establish the spatial organisation of excitatory and inhibitory synaptic inputs onto ganglion cells in primate retina.

We confirm centre–surround organisation in the excitatory inputs to ganglion cells, and show further that inhibitory inputs can also show centre–surround organisation.

We show that lateral inhibition in the inner retina shapes the spatial profile of both excitatory and inhibitory synaptic inputs onto ganglion cells.

Dynamic clamp experiments provide evidence that reduction of inner retinal inhibition reduces spatial tuning in ganglion cell output.

These results show that lateral inhibition in the inner retina of primate shapes the analysis of spatial form and contrast.

Abstract  The centre–surround organisation of receptive fields is a feature of most retinal ganglion cells (RGCs) and is critical for spatial discrimination and contrast detection. Although lateral inhibitory processes are known to be important in generating the receptive field surround, the contribution of each of the two synaptic layers in the primate retina remains unclear. Here we studied the spatial organisation of excitatory and inhibitory synaptic inputs onto ON and OFF ganglion cells in the primate retina. All RGCs showed an increase in excitation in response to stimulus of preferred polarity. Inhibition onto RGCs comprised two types of responses to preferred polarity: some RGCs showed an increase in inhibition whilst others showed removal of tonic inhibition. Excitatory inputs were strongly spatially tuned but inhibitory inputs showed more variable organisation: in some neurons they were as strongly tuned as excitation, and in others inhibitory inputs showed no spatial tuning. We targeted one source of inner retinal inhibition by functionally ablating spiking amacrine cells with bath application of tetrodotoxin (TTX). TTX significantly reduced the spatial tuning of excitatory inputs. In addition, TTX reduced inhibition onto those RGCs where a stimulus of preferred polarity increased inhibition. Reconstruction of the spatial tuning properties by somatic injection of excitatory and inhibitory synaptic conductances verified that TTX‐mediated inhibition onto bipolar cells increases the strength of the surround in RGC spiking output. These results indicate that in the primate retina inhibitory mechanisms in the inner plexiform layer sharpen the spatial tuning of ganglion cells.
Extrusion Process Modeling for Aqueous-Based Ceramic Pastes—Part 2: Experimental Verification
Authors: Li Mingyang , Tang Lie , Landers Robert G. , Leu Ming C.
Published: September 2013

In the Part 1 paper, a constitutive law for the extrusion process of aqueous-based ceramic pastes was created. In the study described herein, a capillary rheometer was used to calibrate the viscosity of an alumina paste, and a single extruder system was used to conduct extrusion experiments to validate the constitutive model. It is shown that the extrusion response time and its change both depend on the amount of air in the extruder and the magnitude of the extrusion force. When the extrusion force is small, the rapid change of extrusion response time gives the extrusion dynamic an apparent quadratic response. When the extrusion force is large, the extrusion response time changes slowly, and is dominated by a first-order response. Air bubble release was observed in some of the experiments. A series of simulation and experimental studies were conducted to validate the predictive capabilities of the constitutive model for both steady-state and transient extrusion force behaviors. Good agreements between the simulation and experimental results were obtained. The experimental results demonstrate that the constitutive model is capable of capturing the characteristics of the highly nonlinear response at low extrusion forces and the air bubble release phenomenon. The numerical studies show that the decrease in the extrusion force during an air bubble release depends on the volume of the air bubble.
Progress of the 40 MW-Class Advanced Humid Air Turbine Tests
Authors: Yagi Manabu , Araki Hidefumi , Tagawa Hisato , Koganezawa Tomomi , Myoren Chihiro , Takeda Takuya
Published: September 2013

A 40 MW-class test facility has been constructed to verify practicability of applying the advanced humid air turbine (AHAT) system to a heavy-duty gas turbine. Verification tests have been carried out from January 2012, and interaction effects between the key components were established. First, water atomization cooling (WAC) was confirmed to contribute to both increased mass flow rate and pressure ratio for the axial-flow compressor. The good agreement between measured and calculated temperatures at the compressor discharge was also confirmed. These results demonstrated the accuracy of the developed prediction model for the WAC. Second, a control method that realized both flame stability and low nitrogen oxides (NOx) emissions was verified. Although the power output and air humidity were lower than the rated values, NOx concentration was about 10 ppm. Finally, a hybrid nozzle cooling system, which utilized both compressor discharged air and humid air, was developed and tested. The metal surface temperatures of the first stage nozzles were measured, and they were kept under the permissible metal temperature. The measured temperatures on the metal surface reasonably corresponded with calculation results.
Capacitive Film Thickness Measurements in a Ventless Aero-Engine Bearing Chamber—Influence of Operating Conditions and Offtake Design
Authors: Kurz Wolfram , Dullenkopf Klaus , Bauer Hans-Jörg
Published: September 2013

The paper presents results from film thickness measurements in a bearing chamber test rig. The measurements were performed at different operating conditions and with two offtake designs. A discussion of the measurement technique using in situ calibrated capacitive sensors shows good accuracy and repeatability. The film thickness results are first compared to measurements with the same chamber in a vented configuration. The analysis of the measurements at various operating conditions shows a strong influence of the shaft speed, the chamber pressure, and the offtake design. In contrast to that, flow rate and scavenge ratio have only minor influence. Furthermore, the momentum flux of the core air flow is proposed as a suitable parameter with which the influence of shaft speed and pressure can be correlated to the film thickness distribution.
On the Failure of a Gas Foil Bearing: High Temperature Operation Without Cooling Flow
Authors: Ryu Keun , San Andrés Luis
Published: September 2013

Implementing gas foil bearings (GFBs) in micro gas turbine engines is a proven approach to improve system efficiency and reliability. Adequate thermal management for operation at high temperatures, such as in a gas turbine or a turbocharger, is important to control thermal growth of components and to remove efficiently mechanical energy from the rotor mainly. The paper presents a test rotor supported on GFBs operating with a heated shaft and reports components temperatures and shaft motions at an operating speed of 37 krpm. An electric cartridge heater loosely inserted in the hollow rotor warms the test system. Thermocouples and noncontact infrared thermometers record temperatures on the bearing sleeve and rotor outer diameter (OD), respectively. No forced cooling air flow streams were supplied to the bearings and rotor, in spite of the high temperature induced by the heater on the shaft outer surface. With the rotor spinning, the tests consisted of heating the rotor to a set temperature, recording the system component temperatures until reaching thermal equilibrium in  ∼ 60 min, and stepping the heater set temperature by 200 °C. The experiments proceeded without incident until the heater set temperature equaled 600 °C. Ten minutes into the test, noise became apparent and the rotor stopped abruptly. The unusual operating condition, without cooling flow and a too large increment in rotor temperature, reaching 250 °C, led to the incident which destroyed one of the foil bearings. Post-test inspection evidenced seizure of the hottest bearing (closest to the heater) with melting of the top foil at the locations where it rests on the underspring crests (bumps). Analysis reveals a notable reduction in bearing clearance as the rotor temperature increases until seizure occurs. Upon contact between the rotor and top foil, dry-friction quickly generated vast amounts of energy that melted the protective coating and metal top foil. Rather than a reliability issue with the foil bearings, the experimental results show poor operating procedure and ignorance on the system behavior (predictions). A cautionary tale and a lesson in humility follow.
Reduction of angular dip width of surface plasmon resonance sensor by coupling surface plasma waves on sensing surface and inside metal–dielectric–metal structure
Authors: Huang Bohr-Ran , Liao Chung-Chi , Lu Chun-Yi , Ke Wen-Cheng , Huang Yi-Lun , Chen Nai-Chuan
Published: September 2013

A surface plasmon resonance (SPR) scheme was developed using a metal/dielectric/metal (MDM) structure. The surface plasma wave (SPW) dispersion curves within the MDM structure can be controlled by tuning the dielectric layer thickness. Therefore, the properties of the SPWs on the sensing surface of the SPR sensor can be tuned by coupling the tunable odd SPWs in the MDM structure to the sensing SPWs. The proposed tuning procedure was based on the tendency for anticrossing formation to occur between two nonparallel dispersion curves, and the reduction in the angular dip widths of the SPR sensors using the proposed procedure was demonstrated both numerically and experimentally.
On the g/2 Acceleration of a Pulse in a Vertical Chain
Authors: Foster Theodore , van Wyngaarden Willem , Cary Arthur , Mottmann John
Published: September 2013

We have frequently enhanced our department's laboratory experiment involving standing transverse waves in a taut horizontal cord. In addition to the standard experiment, students in these labs investigate the surprising concept that the acceleration of a pulse in a chain hanging vertically is a constant and is equal to half the acceleration of gravity.
Circuits in the Sun: Solar Panel Physics
Authors: Gfroerer Tim
Published: September 2013

Typical commercial solar panels consist of approximately 60 individual photovoltaic cells connected in series. Since the usual Kirchhoff rules apply, the current is uniform throughout the circuit, while the electric potential of the individual devices is cumulative. Hence, a solar panel is a good analog of a simple resistive series circuit, except that the devices generate (rather than burn!) electrical power. For example, in order to sustain the current flow, each device must generate the requisite current. As a result, the least efficient device limits the current throughout. Photovoltaic cells also have a more complicated current-voltage (I–V) characteristic, which determines the optimal load for power extraction. These considerations, among others, make the solar panel an excellent platform for exploring the physics of electric circuits.
Tracking the Career Paths of Physics Teachers in Texas
Authors: Mount Jennifer , Marshall Jill , Fuller Edward
Published: September 2013

In Texas, and some other states, there is a documented shortage of physics teachers, in terms of both number and qualifications.1 The shortage in Texas is due as much to teachers leaving the field (attrition) as to a lack of teachers entering. There are efforts under way to prepare more and better-qualified physics teachers who will stay in the field longer,2 but increasing the overall supply and retention will not necessarily address localized teacher shortages. To investigate this issue, we obtained a database cataloging every teacher who taught science in Texas public schools from 2003 to 2008, indicating the school where they taught during each of those years, the subjects they taught, and their route to certification. This allowed us to track not only teachers entering and leaving the public school system, but also migration between schools within the system. We found that migration poses a much bigger problem than attrition for some schools. We also found patterns in the movement of physics teachers in Texas that we would not necessarily have predicted and that varied substantially depending on certification.
Computer Supported Collaborative Rocketry: Teaching students to distinguish good and bad data like expert physicists
Authors: d'Alessio Matthew , Lundquist Loraine
Published: September 2013

Each year our physical science class for pre-service elementary teachers launches water-powered rockets based on the activity from NASA.1 We analyze the rocket flight using data from frame-by-frame video analysis of the launches. Before developing the methods presented in this paper, we noticed our students were mired in calculation details while losing sight of physical concepts. Sloppy measurements and calculations (even when using spreadsheets with formulas provided) sometimes led to such poor results that physical concepts could not be reliably taught from the data, but students were unmotivated to either notice or correct their errors. We adopted a collaborative, computer supported approach using simple and easily available functions in Google Spreadsheets to pool observations, provide instant feedback, and publicly display results from all teams side-by-side in real time. These instant comparisons promote student accountability and engagement, inspiring them to think more carefully about why answers may be different and notice sloppy data or unlikely outcomes—in short, to facilitate and motivate expert thinking about data.
Little Green Man Physics
Authors: Higbie J.
Published: September 2013

We have frequently enhanced our department's laboratory experiment involving standing transverse waves in a taut horizontal cord. In addition to the standard experiment, students in these labs investigate the surprising concept that the acceleration of a pulse in a chain hanging vertically is a constant and is equal to half the acceleration of gravity.