bluuebunny/crossref_metadata_2025 huggingface dataset:
ANALYSIS OF BREAST CANCER PROFILES USING BAYESIAN NETWORK MODELING
Authors: BEN HASSEN HANEN , KALLEL IMEN , BOUCHAALA LOBNA , REBAI AHMED
Published: April 2013

Breast cancer is the leading cause of cancer-related death for women in Tunisia and the prognosis of its metastasis remains a major problem for oncologists despite advances in treatment. In this work we use Bayesian networks to develop a decision support system that is based on the modeling of relationships between key signaling proteins and clinical and pathological characteristics of breast tumors and patients. Motivated by the lack of prior information on the parameters of the problem, we use the Implicit inference for the structure and parameter learning. A dataset of 84 Tunisian breast cancer patients was used and new prognosis factors were identified. The system predicts a metastasis risk for different patients by computing a score that is the joint probability of the Bayesian network using parameters estimated on the learning database. Based on the results of the developed system we identified that overexpression of ErbB2, ErbB3, bcl2 as well as of oestrogen and progesterone receptors associated with a low level of ErbB4 was the predominant profile associated with high risk of metastasis.
Transcriptome analysis of neutrophils after endurance exercise reveals novel signaling mechanisms in the immune response to physiological stress
Authors: Neubauer Oliver , Sabapathy Surendran , Lazarus Ross , Jowett Jeremy B. M. , Desbrow Ben , Peake Jonathan M. , Cameron-Smith David , Haseler Luke J. , Wagner Karl-Heinz , Bulmer Andrew C.
Published: April 2013

Neutrophils serve as an intriguing model for the study of innate immune cellular activity induced by physiological stress. We measured changes in the transcriptome of circulating neutrophils following an experimental exercise trial (EXTRI) consisting of 1 h of intense cycling immediately followed by 1 h of intense running. Blood samples were taken at baseline, 3 h, 48 h, and 96 h post-EXTRI from eight healthy, endurance-trained, male subjects. RNA was extracted from isolated neutrophils. Differential gene expression was evaluated using Illumina microarrays and validated with quantitative PCR. Gene set enrichment analysis identified enriched molecular signatures chosen from the Molecular Signatures Database. Blood concentrations of muscle damage indexes, neutrophils, interleukin (IL)-6 and IL-10 were increased ( P < 0.05) 3 h post-EXTRI. Upregulated groups of functionally related genes 3 h post-EXTRI included gene sets associated with the recognition of tissue damage, the IL-1 receptor, and Toll-like receptor (TLR) pathways (familywise error rate, P value < 0.05). The core enrichment for these pathways included TLRs, low-affinity immunoglobulin receptors, S100 calcium binding protein A12, and negative regulators of innate immunity, e.g., IL-1 receptor antagonist, and IL-1 receptor associated kinase-3. Plasma myoglobin changes correlated with neutrophil TLR4 gene expression ( r = 0.74; P < 0.05). Neutrophils had returned to their nonactivated state 48 h post-EXTRI, indicating that their initial proinflammatory response was transient and rapidly counterregulated. This study provides novel insight into the signaling mechanisms underlying the neutrophil responses to endurance exercise, suggesting that their transcriptional activity was particularly induced by damage-associated molecule patterns, hypothetically originating from the leakage of muscle components into the circulation.
Retrospective Review of Thoracoamniotic Shunting Using a Double-Basket Catheter for Fetal Chylothorax
Authors: Miyoshi Takekazu , Katsuragi Shinji , Ikeda Tomoaki , Horiuchi Chinami , Kawasaki Kaoru , Kamiya Chizuko A. , Sasaki Yoshihito , Osato Kazuhiro , Neki Reiko , Yoshimatsu Jun
Published: April 2013

Objective: From a single-center retrospective cohort with fetal chylothorax, we evaluated the factors related to the decision to use shunting, poor prognostic factors, and reported shunting outcomes with a new double basket-catheter device. Methods: A retrospective single-center study was performed in 35 cases of fetal chylothorax. Results: There were 35 cases of chylothorax: 23 with hydrops and 12 without hydrops. Twenty-one procedures were performed on 15 fetuses (11 with hydrops) with a single shunt in 11, two shunts in 3 and four shunts in 1. All 12 nonhydropic cases survived. In 23 hydropic cases, overall survival rates with and without thoracoamniotic shunting were 46 and 33%, respectively. The mortality rates of fetal hydropic cases with and without ascites were 93 and 11%, respectively. Fetal ascites, progression of fetal hydrops, and premature delivery at <33 weeks were significant risk factors for a poor prognosis. Progression of polyhydramnios after shunting was also associated with a poor prognosis. Obstruction of the catheter was observed in 38%. There were no direct fetal deaths associated with shunting. Conclusion: Thoracoamniotic shunting should be considered for pleural effusion before development of fetal hydrops, or at least before the appearance of fetal ascites. A double-basket catheter tends to be obstructive, but may be less invasive for fetuses.
Homo Economicus and the Stories of Jacob: On the Methodological Relevance of Rational Choice Theory for Studying the Hebrew Bible
Authors: Wagner-Tsukamoto Sigmund A.
Published: April 2013

Abstract

Economics is widely accused of being a portrayer of a dark and dismal image of human nature (i.e. its model of homo economicus as a self-interested, even selfish and opportunistic maximizer of its own gains). This article argues that the model of homo economicus is not an empirical or prescriptive image of human nature but a useful, “heuristic,” methodical instrument for economic theorizing (in our case, for the economic study of religion that connects to the Hebrew Bible). This article demonstrates that in generic, methodological perspective, the model of homo economicus compares well to similarly unrealistic, “dismal” models of human nature in other disciplines that study religion. I develop these arguments by focusing on selective stories from Genesis, especially the stories of Jacob. Implications are derived regarding the application of economic methods and concepts for research on the texts in the Hebrew Bible.
Researching the Dominant Religion: Anthropology at Home and Methodological Catholicism
Authors: Sekerdej Kinga , Pasieka Agnieszka
Published: April 2013

Abstract

The article discusses methodological problems of researching the dominant religion by native anthropologists in a majority Catholic society. By presenting both ethnographic examples and scholarly publications on religion we point at a Catholic hegemonic frame in Poland, within which religion is interpreted. Such an approach results in treating Catholicism as the taken for granted denomination, and the Roman Catholic Church as a bearer of moral authority. Engaging critically with the existing scholarship we argue that in Poland one can speak of methodological Catholicism, connected to certain implicit assumptions: treating Catholic faith as a desirable norm, describing religiosity at large with Catholic vocabulary and measuring religiosity through the prism of the Church dogmas as opposed to inquiring about the ways Catholicism is lived as a religion.
Discursive Study of Religion: Approaches, Definitions, Implications
Authors: von Stuckrad Kocku
Published: April 2013

Abstract

The article explores recent approaches to historical analysis of discourse that have been developed in disciplines such as the sociology of knowledge and historical epistemology. These approaches have only sporadically been taken seriously in the academic study of religion, although they have a great potential to establish a study of religion that is both academically rigorous and aware of its societal and historical contexts and limitations. The article defines the necessary concepts for a discursive study of religion as an hermeneutical discipline that scrutinizes and historicizes the societal organization of knowledge about religion. This discourse on religion—defined here as religion—generates, legitimizes, and maintains meaning structures and societal realities. The discourse-historical analysis of religion is not itself a method but a research perspective. Nevertheless, this perspective implies several steps in designing a research project that the article describes with concrete examples.
A Response to Kevin Schilbrack
Authors: Fitzgerald Timothy
Published: April 2013

Abstract

Kevin Schilbrack has pointed out that in my publications over a period from 1994 to 2007 there are some discrepancies in my arguments about some categories, especially “politics” and “culture.” In some earlier research on Dalits and Buddhists in Maharashtra I could not locate “religion,” so I attempted, unsuccessfully, to develop a tripartite conceptual substitution for “religion”—ritual, politics and soteriology—for purposes of description and analysis. However, though this was repeated in Ideology, I have come to realize that it contradicts a more fundamental argument which is tacit all the way through Ideology, for example in the critique of constructions of “religion-and-society.” It has become progressively clearer to me that the religion-politics binary is one of a series which rhetorically invents both domains (fundamentally religion-nonreligion) as mutually parasitic, while simultaneously transforming the nonreligious secular domains into the common sense order of things. Religion acts as the arena of “faith” and “belief ” in contrast to the supposed objective secular knowledge of the “real” world. I have pursued this latter argument most recently in Religion and Politics in International Relations: the Modern Myth, which shows how writers in that discipline have transformed “religion” into a global agent of malice threatening the benignly rational secular state.
Water Mass Transformations in the Southern Ocean Diagnosed from Observations: Contrasting Effects of Air–Sea Fluxes and Diapycnal Mixing
Authors: Badin Gualtiero , Williams Richard G. , Jing Zhao , Wu Lixin
Published: April 2013

Transformation and formation rates of water masses in the Southern Ocean are estimated in a neutral-surface framework using air–sea fluxes of heat and freshwater together with in situ estimates of diapycnal mixing. The air–sea fluxes are taken from two different climatologies and a reanalysis dataset, while the diapycnal mixing is estimated from a mixing parameterization applied to five years of Argo float data. Air–sea fluxes lead to a large transformation directed toward lighter waters, typically from −45 to −63 Sv (1 Sv ≡ 106 m3 s−1) centered at γ = 27.2, while interior diapycnal mixing leads to two weaker peaks in transformation, directed toward denser waters, 8 Sv centered at γ = 27.8, and directed toward lighter waters, −16 Sv centered at γ = 28.3. Hence, air–sea fluxes and interior diapycnal mixing are important in transforming different water masses within the Southern Ocean. The transformation of dense to lighter waters by diapycnal mixing within the Southern Ocean is slightly larger, though comparable in magnitude, to the transformation of lighter to dense waters by air–sea fluxes in the North Atlantic. However, there are significant uncertainties in the authors' estimates with errors of at least ±5 W m−2 in air–sea fluxes, a factor 4 uncertainty in diapycnal mixing and limited coverage of air–sea fluxes in the high latitudes and Argo data in the Pacific. These water mass transformations partly relate to the circulation in density space: air–sea fluxes provide a general lightening along the core of the Antarctic Circumpolar Current and diapycnal diffusivity is enhanced at middepths along the current.
Logic and the Self: After Certain Crises in Western Thought
Authors: van Fraassen Bas C
Published: April 2013

Delivered on the occasion of the 2009 “Giulio Preti Prize”, this lecture examines and questions the contrast between the sense of intellectual crisis in the scientific world of the first decades of the 20th century and the absence of any such sense of crisis in current philosophy. Starting in the 19the century, we were confronted with changes in perspective that affected our relation to the universe we live in as well as to our own language and logic. Not only how we see ourselves but the tools by means of which we think about ourselves came into question. How would it be possible to rationally assess conceptual change that affects the very form of reasoning by which we assess

such changes? Such are the paradoxes to which philosophers and scientists, in the throes of crisis in the first half of the 20th century, tried to respond. Philosophers today may seemingly have overcome those aporias that vexed their recent predecessors, in denial of the existence of a crisis that should actually be a fecund source for reflection.
Long-term prevention of chronic allograft rejection by regulatory T-cell immunotherapy involves host Foxp3-expressing T cells
Authors: Pasquet Lise , Douet Jean-Yves , Sparwasser Tim , Romagnoli Paola , van Meerwijk Joost P. M.
Published: April 2013

Key Points

Administration of donor-specific regulatory T cells prevents chronic rejection of BM and skin allografts in the mouse. Injected regulatory T cells induce the emergence of host regulatory T cells with similar specificity thus ensuring persistence of tolerance.
Downregulation of FOXP1 is required during germinal center B-cell function
Authors: Sagardoy Ainara , Martinez-Ferrandis Jose I. , Roa Sergio , Bunting Karen L. , Aznar María Angela , Elemento Olivier , Shaknovich Rita , Fontán Lorena , Fresquet Vicente , Perez-Roger Ignacio , Robles Eloy F. , De Smedt Linde , Sagaert Xavier , Melnick Ari , Martinez-Climent Jose A.
Published: April 2013

Key Points

FOXP1 is downregulated in germinal centers, inversely to BCL6, whereby it regulates a network of genes, half of which are also BCL6 targets. In transgenic mice, constitutive FOXP1 expression impairs GC formation and function, which might contribute to B-cell lymphomagenesis.
Identification and characterization of lysine-rich proteins and starch biosynthesis genes in the opaque2mutant by transcriptional and proteomic analysis
Authors: Jia Mo , Wu Hao , Clay Kasi L , Jung Rudolf , Larkins Brian A , Gibbon Bryan C
Published: April 2013

Background

Theopaque2mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary.

Results

In this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered byopaque2in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content ofopaque2endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly byopaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch.

Conclusions

The results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of theopaque2mutation. Alteration of amylopectin branching patterns inopaque2starch could contribute to generation of the soft, starchy endosperm.
Best proximity point theorems for rational proximal contractions
Authors: Nashine Hemant Kumar , Kumam Poom , Vetro Calogero
Published: April 2013

We provide sufficient conditions which warrant the existence and uniqueness of the best proximity point for two new types of contractions in the setting of metric spaces. The presented results extend, generalize and improve some known results from best proximity point theory and fixed-point theory. We also give some examples to illustrate and validate our definitions and results.

MSC:41A65, 46B20, 47H10.
Clinical and molecular characterization of 40 patients with classic Ehlers–Danlos syndrome: identification of 18 COL5A1 and 2 COL5A2 novel mutations
Authors: Ritelli Marco , Dordoni Chiara , Venturini Marina , Chiarelli Nicola , Quinzani Stefano , Traversa Michele , Zoppi Nicoletta , Vascellaro Annalisa , Wischmeijer Anita , Manfredini Emanuela , Garavelli Livia , Calzavara-Pinton Piergiacomo , Colombi Marina
Published: April 2013

Background

Classic Ehlers–Danlos syndrome (cEDS) is a rare autosomal dominant connective tissue disorder that is primarily characterized by skin hyperextensibility, abnormal wound healing/atrophic scars, and joint hypermobility. A recent study demonstrated that more than 90% of patients who satisfy all of these major criteria harbor a type V collagen (COLLV) defect.

Methods

This cohort included 40 patients with cEDS who were clinically diagnosed according to the Villefranche nosology. The flowchart that was adopted for mutation detection consisted of sequencing the COL5A1 gene and, if no mutation was detected, COL5A2 analysis. In the negative patients the presence of large genomic rearrangements in COL5A1 was investigated using MLPA, and positive results were confirmed via SNP-array analysis.

Results

We report the clinical and molecular characterization of 40 patients from 28 families, consisting of 14 pediatric patients and 26 adults. A family history of cEDS was present in 9 patients. The majority of the patients fulfilled all the major diagnostic criteria for cEDS; atrophic scars were absent in 2 females, skin hyperextensibility was not detected in a male and joint hypermobility was negative in 8 patients (20% of the entire cohort). Wide inter- and intra-familial phenotypic heterogeneity was observed. We identified causal mutations with a detection rate of approximately 93%. In 25/28 probands, COL5A1 or COL5A2 mutations were detected. Twenty-one mutations were in the COL5A1 gene, 18 of which were novel (2 recurrent). Of these, 16 mutations led to nonsense-mediated mRNA decay (NMD) and to COLLV haploinsufficiency and 5 mutations were structural. Two novel COL5A2 splice mutations were detected in patients with the most severe phenotypes. The known p. (Arg312Cys) mutation in the COL1A1 gene was identified in one patient with vascular-like cEDS.

Conclusions

Our findings highlight that the three major criteria for cEDS are useful and sufficient for cEDS clinical diagnosis in the large majority of the patients. The borderline patients for whom these criteria fail can be diagnosed when minor signs of connective tissue diseases and family history are present and when genetic testing reveals a defect in COLLV. Our data also confirm that COL5A1 and COL5A2 are the major, if not the only, genes involved in cEDS.
Age differences in treatment response to a collaborative care intervention for anxiety disorders
Authors: Wetherell Julie Loebach , Petkus Andrew J. , Thorp Steven R. , Stein Murray B. , Chavira Denise A. , Campbell-Sills Laura , Craske Michelle G. , Sherbourne Cathy , Bystritsky Alexander , Sullivan Greer , Roy-Byrne Peter
Published: April 2013

Background

Some data suggest that older adults with anxiety disorders do not respond as well to treatment as do younger adults.

Aims

We examined age differences in outcomes from the Coordinated Anxiety Learning and Management (CALM) study, an effectiveness trial comparing usual care to a computer-assisted collaborative care intervention for primary care patients with panic disorder, generalised anxiety disorder, post-traumatic stress disorder (PTSD), and/or social anxiety disorder. This is the first study to examine the efficacy of a collaborative care intervention in a sample that included both younger and older adults with anxiety disorders. We hypothesised that older adults would show a poorer response to the intervention than younger adults.

Method

We examined findings for the overall sample, as well as within each diagnostic category (clinicaltrials.govidentifier: NCT00347269).

Results

The CALM intervention was more effective than usual care among younger adults overall and for those with generalised anxiety disorder, panic disorder and social anxiety disorder. Among older adults, the intervention was effective overall and for those with social anxiety disorder and PTSD but not for those with panic disorder or generalised anxiety disorder. The effects of the intervention also appeared to erode by the 18-month follow-up, and there were no significant effects on remission among the older adults.

Conclusions

These results are consistent with the findings of other investigators suggesting that medications and psychotherapy for anxiety disorders may not be as effective for older individuals as they are for younger people.
Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function
Authors: Turchi Luana , Carabelli Monica , Ruzza Valentino , Possenti Marco , Sassi Massimiliano , Peñalosa Andrés , Sessa Giovanna , Salvi Sergio , Forte Valentina , Morelli Giorgio , Ruberti Ida
Published: April 2013

The Arabidopsis genome encodes ten Homeodomain-Leucine zipper (HD-Zip) II proteins. ARABIDOPSIS THALIANA HOMEOBOX 2 (ATHB2), HOMEOBOX ARABIDOPSIS THALIANA 1 (HAT1), HAT2, HAT3 and ATHB4 are regulated by changes in the red/far red light ratio that induce shade avoidance in most of the angiosperms. Here, we show that progressive loss of HAT3, ATHB4 and ATHB2 activity causes developmental defects from embryogenesis onwards in white light. Cotyledon development and number are altered in hat3 athb4 embryos, and these defects correlate with changes in auxin distribution and response. athb2 gain-of-function mutation and ATHB2 expression driven by its promoter in hat3 athb4 result in significant attenuation of phenotypes, thus demonstrating that ATHB2 is functionally redundant to HAT3 and ATHB4. In analogy to loss-of-function mutations in HD-Zip III genes, loss of HAT3 and ATHB4 results in organ polarity defects, whereas triple hat3 athb4 athb2 mutants develop one or two radialized cotyledons and lack an active shoot apical meristem (SAM). Consistent with overlapping expression pattern of HD-Zip II and HD-Zip III gene family members, bilateral symmetry and SAM defects are enhanced when hat3 athb4 is combined with mutations in PHABULOSA (PHB), PHAVOLUTA (PHV) or REVOLUTA (REV). Finally, we show that ATHB2 is part of a complex regulatory circuit directly involving both HD-Zip II and HD-Zip III proteins. Taken together, our study provides evidence that a genetic system consisting of HD-Zip II and HD-Zip III genes cooperates in establishing bilateral symmetry and patterning along the adaxial-abaxial axis in the embryo as well as in controlling SAM activity.
Organ-specific gene expression: the bHLH protein Sage provides tissue specificity toDrosophilaFoxA
Authors: Fox Rebecca M. , Vaishnavi Aria , Maruyama Rika , Andrew Deborah J.
Published: April 2013

FoxA transcription factors play major roles in organ-specific gene expression, regulating, for example, glucagon expression in the pancreas, GLUT2 expression in the liver, and tyrosine hydroxylase expression in dopaminergic neurons. Organ-specific gene regulation by FoxA proteins is achieved through cooperative regulation with a broad array of transcription factors with more limited expression domains. Fork head (Fkh), the sole Drosophila FoxA family member, is required for the development of multiple distinct organs, yet little is known regarding how Fkh regulates tissue-specific gene expression. Here, we characterize Sage, a bHLH transcription factor expressed exclusively in the Drosophila salivary gland (SG). We show that Sage is required for late SG survival and normal tube morphology. We find that many Sage targets, identified by microarray analysis, encode SG-specific secreted cargo, transmembrane proteins, and the enzymes that modify these proteins. We show that both Sage and Fkh are required for the expression of Sage target genes, and that co-expression of Sage and Fkh is sufficient to drive target gene expression in multiple cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage-Fkh targets, and Sage, Fkh and Sens colocalize on SG chromosomes. Importantly, expression of Sage-Fkh target genes appears to simply add to the tissue-specific gene expression programs already established in other cell types, and Sage and Fkh cannot alter the fate of most embryonic cell types even when expressed early and continuously.
Mouse primordial germ cells produce cysts that partially fragment prior to meiosis
Authors: Lei Lei , Spradling Allan C.
Published: April 2013

Mammalian germ cells divide mitotically and form nests of associated cells just prior to entering meiosis. At least some nests contain germline cysts that arise by synchronous, incomplete mitotic divisions, but others may form by aggregation. To systematically investigate early murine germ cell development, we lineage marked the progeny of individual, newly arrived primordial germ cells in the E10.5 gonad. All the marked germ cells initially develop into clones containing two, four or eight cells, indicating cyst formation. Surprisingly, growing cysts in both sexes partially fragment into smaller cysts prior to completion and associate with cysts from unrelated progenitors. At the time divisions cease, female clones comprise five cysts on average that eventually give rise to about six primordial follicles. Male cyst cells break apart and probably become spermatogonial stem cells. Thus, cysts are invariant units of mouse germ cell development and cyst fragmentation provides insight into the amplification of spermatogonial stem cells and the origin of primordial follicles.
Very low force-generating ability and unusually high temperature-dependency in hummingbird flight muscle fibers
Authors: Reiser Peter J. , Welch Kenneth C. , Suarez Raul K. , Altshuler Douglas L.
Published: April 2013

Hummingbird flight muscle is estimated to have among the highest mass-specific power output among vertebrates, based on aerodynamic models. However, little is known about fundamental contractile properties of their remarkable flight muscles. We hypothesized that hummingbird pectoralis fibers generate relatively low force when activated in a tradeoff for high shortening speeds associated with the characteristic high wing beat frequencies that are required for sustained hovering. Our objective was to measure maximal force-generating ability (maximal force/cross-sectional area, Po/CSA) in single, skinned fibers from the pectoralis and supracoracoideus muscles, which power the wing downstroke and upstroke, respectively, in hummingbirds (Calypte anna) and in another similarly-sized species, zebra finch (Taeniopygia guttata), which also has a very high wingbeat frequency during flight but does not perform a sustained hover. Mean Po/CSA in hummingbird pectoralis fibers was very low - 1.6, 6.1 and 12.2 kN/m2, at 10, 15 and 20oC, respectively. Po/CSA in finch pectoralis fibers was also very low (for both species, ~5% of the reported Po/CSA of chicken pectoralis fast fibers at 15oC). Force generated at 20oC/force generated at 10oC ('Q10-force' value) was very high for hummingbird and finch pectoralis fibers (mean = 15.3 and 11.5, respectively), compared to rat slow and fast fibers (1.8 and 1.9, respectively). Po/CSA in hummingbird leg fibers was much higher than in pectoralis fibers, at each temperature, and the mean Q10-force was much lower. Thus, hummingbird and finch pectoralis fibers have an extremely low force-generating ability, compared to other bird and mammalian limb fibers, and an extremely high temperature-dependence of force generation. The extrapolated maximum force-generating ability of hummingbird pectoralis fibers in vivo (~48 kN/m2) is, however, substantially higher than the estimated requirements for hovering flight of C. anna. The unusually low Po/CSA of hummingbird and zebra finch pectoralis fibers may reflect a constraint imposed by a need for extremely high contraction frequencies, especially during hummingbird hovering.
A SLC6 transporter of the novel B0,- system aids in absorption and detection of nutrient amino acids in Caenorhabditis elegans
Authors: Metzler Ryan , Meleshkevitch Ella A. , Fox Jeffrey , Kim Hongkyun , Boudko Dmitri Y.
Published: April 2013

Nutrient Amino acid Transporters (NATs) of SoLute Carrier family 6 (SLC6) mediate uptake of essential amino acids in mammals and insects. Phylogenomic analysis of the Caenorhabditis elegans (Ce) SLC6 family identifies 5 genes paralogous to an insect-specific NAT subfamily. Here we cloned and characterized the first representative of the identified nematode-specific transporters, SNF-5. SNF-5 mediates broad spectrum cation-coupled transport of neutral amino acids with submillimolar affinities and stoichiometry of 1AA:1Na+, except for 1L-Pro:2 Na+. Unexpectedly, it transports acidic L-Glu- and L-Asp- (AA -1:3Na+), revealing it to be the first member of a new B0,- system among characterized SLC6 transporters. This activity correlates with a unique positively charged His+ 377 in the substrate-binding pocket. snf-5 promoter-driven EGFP labels intestinal cells INT1-9 and three pairs of amphid sensory neurons: ASI, ADF, and ASK. These cells are intimately involved in control of dauer diapause, development, metabolism, and longevity. The snf-5 deletion mutants do not show apparent morphological disorders, but increase dauer formation while reducing dauer maintenance upon starvation. Overall, our studies characterized the first nematode-specific NAT and revealed important structural and functional aspects of this transporter. In addition to the predictable role in alimentary amino acid absorption, our results indicate possible neuronal roles of SNF-5 as an amino acid provider to specific neuronal functions, including sensing of amino acid availability.
Development of the navigational system in homing pigeons: increase in complexity of the navigational map
Authors: Schiffner Ingo , Wiltschko Roswitha
Published: April 2013

The present study analyzes GPS-recorded tracks from pigeons of different age from 11 sites between 3.6 and 22.1 km from the home loft, which reveals changes in the navigational system as the birds grew older and became more experienced. The efficiency of juveniles in their 1st year of life, with only 0.27, was rather low, indicating that the young birds covered more than three times the direct distance home. In the second year, after a standard training program, the efficiency of the same birds increased up to 0.80 and was no longer different from that of older pigeons. The short-term correlation dimension, a variable that reflects the number of factors involved in the navigational process, also increased with age. In juveniles, it is markedly lower than in the other two groups, but even in yearlings, it is still significantly lower than that of old pigeons, indicating that the navigational map of the yearlings is developing further. Our results indicate that the map system, although functional in the first year of life, continues to be become more complex: - older pigeons seem to either consider more navigational factors than younger ones or at least weigh the same factors differently.
The Supervised Normalized Cut Method for Detecting, Classifying, and Identifying Special Nuclear Materials
Authors: Yang Yan T. , Fishbain Barak , Hochbaum Dorit S. , Norman Eric B. , Swanberg Erik
Published: April 2013

The detection of illicit nuclear materials is a major tool in preventing and deterring nuclear terrorism. The detection task is extremely difficult because of physical limitations of nuclear radiation detectors, shielding by intervening cargo materials, and the presence of background noise. We aim at enhancing the capabilities of detectors with algorithmic methods specifically tailored for nuclear data. This paper describes a novel graph-theory-based methodology for this task. This research considers for the first time the utilization of supervised normalized cut (SNC) for data mining and classification of measurements obtained from plastic scintillation detectors that are of particularly low resolution. Specifically, the situation considered here is for when both energy spectra and the time dependence of such data are acquired.

We present here a computational study, comparing the supervised normalized cut method with alternative classification methods based on support vector machine (SVM), specialized feature-reducing SVMs (i.e., 1-norm SVM, recursive feature elimination SVM, and Newton linear program SVM), and linear discriminant analysis (LDA). The study evaluates the performance of the suggested method in binary and multiple classification problems of nuclear data. The results demonstrate that the new approach is on par or superior in terms of accuracy and much better in computational complexity to SVM (with or without dimension or feature reduction) and LDA with principal components analysis as preprocessing. For binary and multiple classifications, the SNC method is more accurate, more robust, and is computationally more efficient by a factor of 2–80 than the SVM-based and LDA methods.
Building Energy Performance Analytics on Cloud as a Service
Authors: Lee Young M. , An Lianjun , Liu Fei , Horesh Raya , Chae Young Tae , Zhang Rui , Meliksetian Estepan , Chowdhary Pawan , Nevill Paul , Snowdon Jane L.
Published: April 2013

Reducing energy consumption, improving energy efficiency, and reducing greenhouse gas (GHG) emissions are among the most important initiatives in today's world. Occupied buildings consume a substantial amount of energy, mounting to about 40% of overall energy consumption in most countries. The majority of the world's population either lives or works in buildings; therefore, everybody can contribute in reducing energy consumption, controlling GHG emissions, and mitigating climate change and its potential impact. We developed an analytical tool that can assist building owners, facility managers, operators, and tenants of buildings in assessing, benchmarking, diagnosing, tracking, forecasting, simulating, and optimizing energy consumption in building portfolios. Furthermore, for greater dissemination, we have made this analytic service available on demand in a flexible cloud environment. Cloud is an efficient and effective medium to provide building energy analytics capability to various functions and people in a variety of roles in buildings without investing a substantial amount of money in hardware, software, and information technology infrastructure. We present results of the building energy analytics developed for K–12 public school buildings and a commercial office building complex.
830 W average power femtosecond fiber CPA system
Authors: Eidam T. , Hanf S. , Andersen T. V. , Seise E. , Wirth C. , Schreiber T. , Gabler T. , Limpert J. , Tünnermann A.
Published: April 2013

In this contribution we report on the generation of 830 W of compressed average power at 78 MHz pulse repetition frequency from an ultrashort pulse fiber chirped pulse amplification system. The pulses are as short as 640 fs.
Microjoule Pulse Energies at 1 MHz Repetition Rate from an All-Fiber Nonlinear Chirped-Pulse Amplifier
Authors: Kalaycıoğlu Hamit , Oktem Bulent , Ilday F. Ömer
Published: April 2013

We report a 1-MHz robust, all-fiber amplifier-oscillator system. Amplified pulses of 3 μJ are externally compressed to 140 fs. The highest peak power from an integrated fiber source, up to 50 kW, is obtained.
High average power, high energy fiber laser system : operation at 977 nm and frequency doubling at 488 nm
Authors: Boullet Johan , Dubrasquet Romain , Bello-Doua Ramatou , Traynor Nicholas , Cormier Eric
Published: April 2013

A pulsed fiber laser operating at 977 nm generating >0.75 mJ, 12 ns pulses at adjustable multi- 10kHz of repetition rate is reported. Generation of 16 W of blue light by frequency conversion is also demonstrated.
Passive All-fiber Transversal Mode Filter for High-Power CW Fiber Laser Applications
Authors: Jauregui C. , Stutzki F. , Thomas J. , Voigtländer C. , Nolte S. , Limpert J. , Tünnermann A.
Published: April 2013

It is shown that monolithic CW LMA-fiber lasers inherently operate in a transversally multimode regime. Accordingly, a novel all-fiber passive transversal mode filter to improve the performance of CW fiber lasers is proposed.
All-Fiber Regenerative Amplification of Low-Energy 40 ps Pulses from a Gain-Switched Laser Diode at Low Repetition Rates
Authors: Kanzelmeyer S. , Hildebrandt M. , Theeg T. , Frede M. , Neumann J. , Kracht D.
Published: April 2013

All-fiber acousto-optic modulator controlled regenerative amplification of low-energy 40 ps pulses from a gain-switched laser diode is demonstrated. Unwanted amplified spontaneous emission is suppressed effectively and gain values of more than 37 dB were achieved.
Zig-Zag Active-Mirror Laser with Cryogenic Yb:YAG
Authors: Furuse Hiroaki , Kawanaka Junji , Miyanaga Noriaki , Saiki Taku , Fujita Masayuki , Imasaki Kazuo , Takeshita Kenji , Ishii Shinya , Izawa Yasukazu
Published: April 2013

We report on a multiple total-reflection active-mirror laser with cryognic Yb:YAG ceramics using zigzag optical path. A 214W output power with 62% slope efficiency has been demonstrated.
Profile Analysis of a Yb:YAG Chirped-Pulse Oscillator
Authors: Uemura Sadao , Torizuka Kenji
Published: April 2013

We report a diode-pumped Yb:YAG chirped-pulse oscillator that delivers a total pulse energy of 2.1 μJ, and analyze the temporal and spectral profiles of the laser pulse using a chip parameter C, which is calculated as C = 1.50. The group-delay dispersion needed for pulse compression is also estimated to be - 2.40 (ps^2).
Milli-Joules, Kilo-Hertz Regenerative Amplifier Using Total-Reflection Active-Mirror with Cryogenic Yb:YAG
Authors: Nakanishi Takuya , Takeuchi Yasuki , Yoshida Akira , Kawanaka Junji , Yasuhara Ryo , Kawashima Toshiyuki , Kan Hirofumi
Published: April 2013

A regenerative amplifier by using total-reflection active-mirror with a cryogenic YAG/Yb:YAG composite ceramics has been demonstrated up to kHz repetition rate. A 6.5-mJ pulse energy and a 9.3% optical efficiency were obtained at 200-Hz.
Progress Towards Monolithic Microchip Lasers Incorporating Diamond
Authors: Birch Rolf B. , Millar Patricia , Zhang Yanfeng , Gu Erdan , Kemp Alan J. , Dawson Martin D. , Burns David
Published: April 2013

Microchip lasers are robust, alignment-free sources; however, output powers are limited by excessive thermal lensing and stress fracture. The bonding of gain media to diamond is discussed as a means to circumvent this drawback.
Femtosecond High Repetition Rate External Cavity Beyond The Average Power Limit for Linear Enhancement
Authors: Pupeza I. , Eidam T. , Pronin O. , Rauschenberger J. , Bernhardt B. , Ozawa A. , Udem Th. , Holzwarth R. , Limpert J. , Apolonski A. , Hänsch T. W. , Tünnermann A. , Krausz F.
Published: April 2013

We report on the cavity enhancement of a 78MHz, 200fs ytterbium-fiber laser system. Linear enhancement up to a record intra-cavity power of 18kW has been observed. In a non-linear enhancement regime 40kW have been reached.
Novel Concept for Generating High Beam Quality from High Pulse Energy Optical Parametric Oscillators
Authors: Farsund Øystein , Arisholm Gunnar , Rustad Gunnar
Published: April 2013

A new concept for generating high beam quality from high pulse energy optical parametric oscillators has been developed and experimentally demonstrated. The idea is to use two different types of crystals type 2 phase matched for the same interaction, but with orthogonal walk-off directions, in the same resonator. By adding BBO crystals to a KTA-based OPO, the astigmatism was removed from the beam and beam quality was improved from M2 ~ 2 × 9 to M2 ~ 2 × 2 without decreasing the conversion efficiency.
80-nJ multipass-cavity chirped-pulse Cr4+:forsterite laser
Authors: Cankaya Huseyin , Fujimoto James G. , Sennaroglu Alphan
Published: April 2013

By using 8.5 W of incident pump power, we obtained 80-nJ, 5.5-ps pulses at 1260 nm with a spectral width of 17 nm from a multipass-cavity, chirped-pulse Cr4+:forsterite laser operated at 4.9-MHz repetition rate.
Applications of High-Repetition Rate Diode-Pumped Solid State Lasers for Combustion Diagnostics
Authors: Meier W. , Boxx I. , Arndt C. , Carter C.D. , Stöhr M. , Steinberg A. , Frank J.H.
Published: April 2013

A high-speed measuring system based on commercially available diode-pumped solid state Nd:YLF and Nd:YAG lasers, tunable dye lasers in combination and intensified CMOS cameras is presented. The system has been used to perform simultaneous Particle Image Velocimetry and Planar Laser Induced Fluorescence of OH radicals in turbulent flames at frame rates of up to 10 kHz. Unsteady processes such as local flame extinction, a precessing vortex core, and turbulence-flame interactions were investigated.
Performance Testing of an Extended Depth of Field Digital Night Vision Device
Authors: Christopher James J. , Brandon Vaughan R. , Wood Jack W. , Bennett Gisele , Draper Russell S. , Hastings Art , Stevens James , Bryant Kyle
Published: April 2013

Performance testing of a night vision technology demonstrator incorporating wavefront coding to increase image depth of field was recently completed. Test results indicate that depth of field was increased with some loss in performance in other image quality aspects.
3-D Imaging Using Helical Point Spread Functions
Authors: Quirin Sean , Piestun Rafael
Published: April 2013

We engineer three-dimensional point spread functions to collect the information required for depth recovery and imaging. We investigate computational imaging systems using helical point spread functions for 3-D passive imaging and compare with prevailing methods. Article not available.
DARPA Imaging System Research
Authors: Horn Stuart
Published: April 2013

Article not available.
Theory of Chirped-Probe Pulse Single-Shot Femtosecond Coherent Anti-Stokes Raman Scattering Thermometry in Flames at 1000 Hz
Authors: Richardson Daniel R. , Lucht Robert P. , Kulatilaka Waruna D. , Roy Sukesh , Gord James R.
Published: April 2013

A theoretical model and fitting routine for analyzing single-shot femtosecond coherent anti-Stokes Raman scattering (CARS) temperature measurements in flames is discussed. The model is validated in a heated gas cell and laminar H2-air flames.
Demonstration of Tomographic Imaging of Chemical Species Using THz Time-Domain Absorption Spectroscopy
Authors: Ma Lin , Zhang Sebastian B. , Cai Weiwei , Gord James R. , Roy Sukesh , Schroeder Nicholas , Ganti Satya , Smith Stanley , Deibel Jason A.
Published: April 2013

A technique has been developed to image chemical species using THz time-domain absorption spectroscopy. Preliminary demonstration on a jet flow of steam is reported.
Tm 2 µm fiber laser for LIBS of organic and biological materials
Authors: Baudelet Matthieu , Willis Christina , Shah Lawrence , Richardson Martin
Published: April 2013

This study applies a Tm-fiber laser emitting at 2 μm for LIBS analysis of organic samples and discusses the benefits of the use of this fiber laser for analytical applications towards biological samples.
Laser-Induced Breakdown Spectroscopy (LIBS) for the Rapid Field Identification and Classification of Pathogenic Bacteria
Authors: Rehse Steven J. , Mohaidat Qassem , Palchaudhuri Sunil
Published: April 2013

LIBS has been utilized to spectrally fingerprint multiple species of bacteria. Differences in the atomic composition of these bacteria allow a real-time classification and identification of unknown samples after a computerized chemometric analysis.
Detection of Surface-Bound Organophosphate Compounds with Dual-Pulse Photofragmentation / Laser-Induced Fluorescence
Authors: Headrick Jeffrey M. , Farrow Roger L. , Bisson Scott E. , Reichardt Thomas A. , Kulp Thomas J.
Published: April 2013

A dual-pulse method for detection of low-volatility organophosphate compounds is demonstrated, in which the first pulse photofragments the molecule, producing the daughter fragment phosphorus monoxide (PO), and the second pulse probes the resulting PO with laser-induced fluorescence.
Atmospheric Correction of Spectral Imagery from Sensor Systems with Changing Viewing Geometry over a Scene
Authors: Felde Gerald W. , Anderson Gail P. , Cooley Thomas W.
Published: April 2013

Simulated radiance cubes are used to gain a quantitative understanding of FLAASH reflectance retrieval errors due to viewing geometry errors. For a particular zenith view angle error, the retrieval error increases as the viewing becomes more off-nadir.
The Hyperspectral Imager for the Coastal Ocean (HICO) and Environmental Characterization of the Coastal Zone from the International Space Station
Authors: Corson Michael R. , Lucke Robert L. , Davis Curtiss O.
Published: April 2013

The Hyperspectral Imager for the Coastal Ocean (HICO), now operating on the International Space Station, is the first spaceborne hyperspectral imager optimized for environmental characterization of the coastal ocean. HICO image data is being exploited to produce maps of coastal ocean properties including bathymetry, in-water suspended and dissolved matter, and bottom characteristics, offering a new remote sensing capability for coastal types worldwide.
Multi-Source Geospatial Information Integration and Analysis for Coastal Management and Decision Making
Authors: Li Ron
Published: April 2013

This paper reviews coastal-related research being undertaken at the Mapping and GIS Laboratory, The Ohio State University, on the multi-source geospatial information integration and analysis for coastal management and decision making.
The Advanced Analyst Exploitation Environment
Authors: Clements Jake , Doody Colin , Schott John , Walli Karl
Published: April 2013

In this paper we discuss model building and data fusion through photogrammetry, advanced forms of exploitation through simple math and stats models, and the advantages of integrating these together in an interactive computer gaming environment.
Photovoltaic and Solar Thermal Improvement Factors in Fiber Optic Filtered Hybrid Systems
Authors: Shepard Scott
Published: April 2013

We define photovoltaic and hybrid system improvement factors which can characterize the utility of optical filters for solar energy applications. Comparison of two types of optical fiber filtered concentrators is then facilitated by this metric.
High Efficiency, Spectrum Splitting Solar Cell Assemblies: Design, Measurement and Analysis
Authors: Barnett Allen , Wang Xiaoting
Published: April 2013

A spectrum splitting photovoltaic architecture was proposed for high energy conversion efficiency. Assemblies of this architecture were constructed, measured and analyzed, which allow assessment of current assemblies and help identify pathways to higher efficiency.
Nanoarrays for Light Management in Thin Film Solar cells
Authors: Ji Jin , Nasr Magued B. , McCutcheon Murray W. , Herring Cy
Published: April 2013

We report the use of plasmonic and photonic nanoarray to achieve light management in thin film solar cells. Theoretical and experimental data will be presented.
Evaluation of the Quality Factor of microcrystalline thin-film solar cell
Authors: Chen Sheng-Hui , Chang Ting-Wei , Chen Yi-Chan , Chen Yu-Hung
Published: April 2013

By dividing the absorption coefficient at 1.4eV with the value at 0.9eV, we could judge the quality of μc-Si:H and predict (Voc*Isc) of solar cell when using this layer as its intrinsic layer.
Detailed Balance Solar Cell Efficiency Limits for Internal Fluorescence Yield Slightly Less Than 100%
Authors: Miller Owen , Yablonovitch Eli
Published: April 2013

The Shockley-Queisser approach to calculating solar cell efficiencies assumes 100% internal fluorescence yield. This is misleading, as even a slight drop in internal yield to 90% already causes a severe drop below the Shockley-Queisser limit.