bluuebunny/crossref_metadata_2025 huggingface dataset:
Does Early-Life Exposure to Stress Shape or Impair Cognition?
Authors: Frankenhuis Willem E. , de Weerth Carolina
Published: September 2013

A predominant view in psychology is that early psychosocial adversity (e.g., abuse) impairs cognition, because children from stressful backgrounds (e.g., violent households) score lower on standard tests of intelligence, language, memory, inhibition, and other abilities. However, recent studies indicate that these people may exhibit improved detection, learning, and memory on tasks involving stimuli that are ecologically relevant to them (e.g., dangers), compared with safely nurtured peers. These findings contradict the view that cognition of stressed people is generally impaired; they suggest, rather, that these people’s minds are developmentally specialized toward local environmental conditions. Here, we review recent research supporting this hypothesis. In addition, we propose that novel studies should examine whether stressed children show not only improved detection but also improved memory and reasoning on tasks involving stimuli that are ecologically relevant to them. Finally, we discuss clinical implications of switching from conceptualizing stressed minds as “adapted” rather than “impaired.”
Beyond “to Share or Not to Share”
Authors: Shaw Alex
Published: September 2013

Fairness concerns often prompt people to share equally, but the function of such equal sharing is somewhat unclear. Some researchers have proposed that fairness functions to promote generosity and reciprocity. I will review some recent data that contradict this view: Fairness can cause people to waste resources rather than be generous and can interfere with reciprocity. On the basis of these findings, I suggest an alternative view: Fairness functions to signal the fair individual’s impartiality to others. I discuss the predictions of this account and how these predictions might be tested in future research.
Communicating Health Risks With Visual Aids
Authors: Garcia-Retamero Rocio , Cokely Edward T.
Published: September 2013

Informed decision making requires that people understand health risks. Unfortunately, many people are not risk literate and are biased by common risk communication practices. In this article, we review a collection of studies investigating the benefits of visual aids for communicating health risks to diverse vulnerable people (e.g., varying in abilities, ages, risk characteristics, and cultural backgrounds). These studies show that appropriately designed visual aids are often highly effective, transparent, and ethically desirable tools for improving decision making, changing attitudes, and reducing risky behavior. Theoretical mechanisms, open questions, and emerging applications are discussed.
The Architecture of Intelligence
Authors: Matzel Louis D. , Sauce Bruno , Wass Christopher
Published: September 2013

A person’s performance across multiple cognitive tests tends to covary. This ubiquitous observation suggests that various cognitive domains are regulated in common, and this covariance underlies the interpretation of many quantitative tests of “intelligence.” We find that, as in humans, differences in intelligence exist across genetically heterogeneous mice. Specifically, we have observed a covariance in the performance of mice across diverse tests of learning, reasoning, and attention. As in humans, the processing efficacy of working memory is both correlated with animals’ general cognitive abilities and may in some instances serve to regulate behaviors indicative of intelligence. Beyond its axiomatic significance in demonstrating the evolutionary conservation of a cognitive trait, studies of mice may provide unique opportunities to assess the molecular (e.g., brain-specific RNA expression; transgenics) and neuroanatomic substrates for intelligence. One such approach is briefly described here. Using this approach, we have determined that the signaling efficacy of the dopamine D1 receptor in the prefrontal cortex is one potential link between performance on both working-memory tasks and tests of intelligence. In combination, studies of both humans and nonhuman animals provide converging lines of evidence that might evade either approach in isolation.
Reversible bone marrow aplasia induced by pegylated interferon-α-2a therapy in a patient with primary myelofibrosis
Authors: Mainali Naba R , Bhatt Vijaya R , Kedia Shiksha , Krishnamurthy Jairam , Wake Laura M , Akhtari Mojtaba
Published: September 2013

Interferon has been widely used in the management of patients with hematological malignancies such as polycythemia vera, myelofibrosis, chronic myeloid leukemia and viral infections such as chronic hepatitis C. Hematological adverse effects such as cytopenias have been observed, particularly in patients who receive a combination of interferon-α-2a and ribavirin for hepatitis C. Mild myelosuppression can be seen with pegylated interferon; however, bone marrow aplasia in patients with myelofibrosis has not been reported. It is important to be aware of such a serious complication since persistent bone marrow aplasia can be fatal. We describe a case of pegylated interferon-induced reversible bone marrow aplasia in a patient with primary myelofibrosis.
Patterns and predictors of naturally occurring change in depressive symptoms over a 30-month period in multiple sclerosis
Authors: Ensari Ipek , Motl Robert W , McAuley Edward , Mullen Sean P , Feinstein Anthony
Published: September 2013

Background:

Depressive symptoms are common in multiple sclerosis (MS), yet there is little information about the pattern and predictors of changes in depressive symptoms over time.

Objective:

We examined changes in depressive symptoms over a 30-month period and the demographic, clinical and behavioral predictors of such changes in relapsing–remitting MS (RRMS).

Methods:

269 persons with RRMS completed the Hospital Anxiety and Depression Scale (HADS) and a demographic/clinical scale, Godin Leisure-Time Exercise Questionnaire (GLTEQ) and Patient Determined Disease Steps (PDDS) scale every 6 months over a 30-month period. Data were analyzed using latent class growth modeling (LCGM).

Results:

LCGM identified a two-class model for changes in HADS depression scores over time. Class 1 involved lower initial status (i.e. fewer depressive symptoms) and linear decreases in depressive symptoms over time (i.e. improving HADS scores), whereas Class 2 involved higher initial status (i.e. more depressive symptoms) and linear increases in depressive symptoms over time (i.e. worsening HADS scores). LCGM further indicated that being older (OR = 2.46; p < .05), married (OR = 2.62; p < .05), employed (OR = 4.29; p < .005) and physically active (OR = 2.71; p < .05) predicted a greater likelihood of belonging to C1 than C2.

Conclusions:

Depressive symptoms change over time in persons with RRMS, and the pattern of change can be predicted by modifiable and non-modifiable factors.
The hygroscopic properties of wood fibre, sepiolite and expanded perlite-based breathable wall for moderating the humidity environment
Authors: Wu Yi , Gong Guangcai , Yu Chuck W.F. , Fang Ping
Published: September 2013

This paper presents an evaluation of a series of novel wood fibre, sepiolite and expanded perlite (WSE)-based mortars that have been developed by Hunan University. The evaluation investigated the influence of morphology structure and the effect of different hot-humid environments on hygroscopic properties of WSE-based mortar to form breathable wall which can provide a moderation of moisture, indoor air quality and thermal insulation of building. The microstructure, thermal conductivity, mechanical properties and hygroscopic properties of WSE-based mortar specimens were assessed to characterize the relationship between performances of the material. WSE is an inorganic porous fibre-aggregate mixture. The hygroscopic properties of the mortars can be greatly improved by adding the WSE fibres-aggregates, especially under high temperature (40℃) and high relative humidity (98%) during summer. The addition of admixture can improve the properties of WSE-based mortar to meet requirements of special performances (such as compressive strength) without affecting the hygroscopic properties. The WSE-based breathable wall is a good moisture buffering controller that could improve indoor air quality. The evaluation presented in this paper should provide the design fundamental for development of breathable wall for future built environment, to allow optimizing the boundary conditions for energy saving and control of indoor humidity environment by incorporating the mortars as finishing materials.
Biodiesel effects on transient needle motion and near-exit flow characteristics of a high-pressure diesel injector
Authors: Moon Seoksu , Tsujimura Taku , Gao Yuan , Park Suhan , Wang Jin , Kurimoto Naoki , Nishijima Yoshiaki , Oguma Mitsuharu
Published: September 2013

In this study, biodiesel effects on transient needle motion and near-exit flow characteristics of a single-orifice high-pressure diesel injector were investigated in terms of needle-lift, needle speed, exit velocity and near-exit flow structure under various injection pressures. Ultrafast x-ray phase-contrast imaging technique was employed in this study to analyze the transient needle motion and near-exit flow characteristics. High-energy sub-nanosecond x-ray pulses have a potential to visualize the needle inside the nozzle and near-exit dense supersonic flow which speed reaches over 600 m/s. Transient needle motion and the structure and velocity of near-exit supersonic flows can be obtained by fabricated analysis of the x-ray images regardless of fuel, injection condition and type of injector.

High bulk modulus and viscosity of biodiesel normally slow down the needle movement and decrease the flow performance. During opening-transient, sharp increase and following overshoot in needle speed and exit velocity were observed with a concurrent increase in spray width. The biodiesel showed a slower increase in needle speed, exit velocity and spray width but a higher degree of velocity overshoot during opening-transient. At steady-state, the biodiesel showed less turbulent flow structure and smaller spray width than diesel. During closing-transient, an abrupt increase in needle speed and decrease in exit velocity were observed with a concurrent increase in spray width. The biodiesel showed the retarded start of closing-transient and longer total injection duration under same energizing pulse duration. The difference between biodiesel and diesel became insignificant at low injection pressures roughly below 100 MPa.
Macroergonomics in Health Care Quality and Patient Safety
Authors: Carayon Pascale , Karsh Ben-Tzion , Gurses Ayse P. , Holden Richard J. , Hoonakker Peter , Schoofs Hundt Ann , Montague Enid , Rodriguez A. Joy , Wetterneck Tosha B.
Published: September 2013

The U.S. Institute of Medicine and health care experts have called for new approaches to manage health care quality problems. In this chapter, we focus on macroergonomics, a branch of human factors and ergonomics that is based on the systems approach and considers the organizational and sociotechnical context of work activities and processes. Selected macroergonomic approaches to health care quality and patient safety are described, such as the SEIPS (Systems Engineering Initiative for Patient Safety) model of work system and patient safety and the model of health care professional performance. Focused reviews on job stress and burnout, workload, interruptions, patient-centered care, health information technology and medical devices, violations, and care coordination provide examples of macroergonomics contributions to health care quality and patient safety. Health care systems and processes clearly need to be systematically redesigned; examples of macroergonomic approaches, principles, and methods for health care system redesign are described. Further research linking macroergonomics and care processes/patient outcomes is needed. Other needs for macroergonomics research are highlighted, including understanding the link between worker outcomes (e.g., safety and well-being) and patient outcomes (e.g., patient safety) and macroergonomics of patient-centered care and care coordination.
Simulation Training in Health Care
Authors: Drews Frank A. , Bakdash Jonathan Z.
Published: September 2013

In this chapter, we discuss the application of human factors and ergonomics to developing effective simulation training in health care. Simulation provides a safe, effective method for training and assessing human performance. In aviation, simulation-based training and assessment has been widely used, significantly improving safety. This progress would have been impossible without the involvement of human factors and ergonomics. Although aviation and health care have similarities, there also are differences that complicate the widespread implementation of simulation in health care.
Human Factors in Critical Care Medical Environments
Authors: Drews Frank A.
Published: September 2013

The purpose of this chapter on human factors in critical care medical environments is to provide a systematic review of the human factors and ergonomics contributions that led to significant improvements in patient safety over the last five decades. The review will focus on issues that contributed to patient injury and fatalities and how human factors and ergonomics can improve performance of providers in critical care. Given the complexity of critical care delivery, a review needs to cover a wide range of subjects. In this review, I take a sociotechnical systems perspective on critical care and discuss the people, their technical and nontechnical skills, the importance of teamwork, technology, and ergonomics in this complex environment. After a description of the importance of a safety climate, the chapter will conclude with a summary on how human factors and ergonomics can improve quality in critical care delivery.
Proteomic analysis of differentially expressed proteins in vitamin C-treated AGS cells
Authors: Nagappan Arulkumar , Park Hyeon Soo , Park Kwang Il , Kim Jin A , Hong Gyeong Eun , Kang Sang Rim , Zhang Jue , Kim Eun Hee , Lee Won Sup , Won Chung Kil , Kim Gon Sup
Published: September 2013

Background

Vitamin C (ascorbic acid) is an essential nutrient of most living tissues that readily acts as a strong reducing agent, which is abundant in fruits and vegetables. Although, it inhibits cell growth in many human cancer cells in vitro, treatment in cancer is still controversial. Hence, the purpose of this study was to investigate the molecular mechanism of the inhibitory effect of vitamin C on AGS cell growth, and protein profiles in AGS cells after exposure to vitamin C treatment, by using proteomic tools.

Results

Vitamin C showed a cytotoxic effect on AGS cells (IC50 300 μg/mL) and, 20 differentially expressed proteins (spot intensities which show ≥2 fold change and statistically significant, p<0.05 between the control and vitamin-C treated group) were successfully identified by assisted laser desorption/ ionization-time of flight/mass spectrometry (MALDI-TOF/MS). Of the 20 proteins, six were up-regulated and fourteen were down-regulated. Specifically, 14-3-3σ, 14-3-3ϵ, 14-3-3δ, tropomyosin alpha-3 chain and tropomyosin alpha-4 chain were down-regulated and peroxiredoxin-4 and thioredoxin domain-containing proteins 5 were up-regulated. The identified proteins are mainly involved in cell mobility, antioxidant and detoxification, signal transduction and protein metabolism. Further, the expressions of 14-3-3 isoforms were verified with immuno-blotting analysis.

Conclusions

Our proteome results suggest that the apoptosis related proteins were involved in promoting and regulating cell death of AGS cells, and might be helpful to understand the molecular mechanism of vitamin C on AGS cell growth inhibition.
The two peptide lantibiotic lacticin 3147 acts synergistically with polymyxin to inhibit Gram negative bacteria
Authors: Draper Lorraine A , Cotter Paul D , Hill Colin , Ross R Paul
Published: September 2013

Background

The emergence of bacterial drug resistance encourages the re-evaluation of the potential of existing antimicrobials. Lantibiotics are post-translationally modified, ribosomally synthesised antimicrobial peptides with a broad spectrum antimicrobial activity. Here, we focussed on expanding the potential of lacticin 3147, one of the most studied lantibiotics and one which possesses potent activity against a wide range of Gram positive species including many nosocomial pathogens. More specifically, our aim was to investigate if lacticin 3147 activity could be enhanced when combined with a range of different clinical antibiotics.

Results

Initial screening revealed that polymyxin B and polymyxin E (colistin) exhibited synergistic activity with lacticin 3147. Checkerboard assays were performed against a number of strains, including both Gram positive and Gram negative species. The resultant fractional inhibitory concentration (FIC) index values established that, while partial synergy was detected against Gram positive targets, synergy was obvious against Gram negative species, including Cronobacter and E. coli.

Conclusions

Combining lacticin 3147 with low levels of a polymyxin could provide a means of broadening target specificity of the lantibiotic, while also reducing polymyxin use due to the lower concentrations required as a result of synergy.
Exogenous mRNA delivery and bioavailability in gene transfer mediated by piggyBac transposition
Authors: Bire Solenne , Gosset David , Jégot Gwenhael , Midoux Patrick , Pichon Chantal , Rouleux-Bonnin Florence
Published: September 2013

Background

Up to now, the different uptake pathways and the subsequent intracellular trafficking of plasmid DNA have been largely explored. By contrast, the mode of internalization and the intracellular routing of an exogenous mRNA in transfected cells are poorly investigated and remain to be elucidated. The bioavailability of internalized mRNA depends on its intracellular routing and its potential accumulation in dynamic sorting sites for storage: stress granules and processing bodies. This question is of particular significance when a secure transposon-based system able to integrate a therapeutic transgene into the genome is used. Transposon vectors usually require two components: a plasmid DNA, carrying the gene of interest, and a source of transposase allowing the integration of the transgene. The principal drawback is the lasting presence of the transposase, which could remobilize the transgene once it has been inserted. Our study focused on the pharmacokinetics of the transposition process mediated by the piggyBac transposase mRNA transfection. Exogenous mRNA internalization and trafficking were investigated towards a better apprehension and fine control of the piggyBac transposase bioavailability.

Results

The mRNA prototype designed in this study provides a very narrow expression window of transposase, which allows high efficiency transposition with no cytotoxicity. Our data reveal that exogenous transposase mRNA enters cells by clathrin and caveolae-mediated endocytosis, before finishing in late endosomes 3 h after transfection. At this point, the mRNA is dissociated from its carrier and localized in stress granules, but not in cytoplasmic processing bodies. Some weaker signals have been observed in stress granules at 18 h and 48 h without causing prolonged production of the transposase. So, we designed an mRNA that is efficiently translated with a peak of transposase production 18 h post-transfection without additional release of the molecule. This confines the integration of the transgene in a very small time window.

Conclusion

Our results shed light on processes of exogenous mRNA trafficking, which are crucial to estimate the mRNA bioavailability, and increase the biosafety of transgene integration mediated by transposition. This approach provides a new way for limiting the transgene copy in the genome and their remobilization by mRNA engineering and trafficking.
Hypnotics and mortality in an elderly general population: a 12-year prospective study
Authors: Jaussent Isabelle , Ancelin Marie-Laure , Berr Claudine , Pérès Karine , Scali Jacqueline , Besset Alain , Ritchie Karen , Dauvilliers Yves
Published: September 2013

Background

Hypnotics are widely used by the elderly, and their impact on mortality remains controversial. The inconsistent findings could be due to methodological limitations, notably the lack of control for underlying sleep symptoms or illness associated with hypnotic use, for example, insomnia symptoms and excessive daytime sleepiness, depression and anxiety. Our objective was to examine the association between the use of hypnotics and mortality risk in a large cohort of community-dwelling elderly, taking into account a wide range of potential competing risks including sociodemographic characteristics, lifestyle, and chronic disorders as well as underlying psychiatric disorders and sleep complaints.

Methods

Analyses were carried out on 6,696 participants aged 65 years or older randomly recruited from three French cities and free of dementia at baseline. Adjusted Cox proportional hazards models with delayed entry, and age of the participants as the time scale, were used to determine the association between hypnotic use and 12-year survival.

Results

At baseline, 21.7% of the participants regularly used at least one hypnotic. During follow-up, 1,307 persons died, 480 from cancer and 344 from cardiovascular disease. Analyses adjusted for study center, age and gender showed a significantly greater risk of all-cause and cardiovascular-related mortality with hypnotics, particularly benzodiazepines, and this increased with the number of hypnotics used. None of these associations were significant in models adjusting for sociodemographic and lifestyle characteristics, chronic disorders including cardiovascular pathologies, sleep and psychiatric disorders. Results remained unchanged when duration of past hypnotic intake or persistent versus intermittent use during follow-up were taken into account.

Conclusions

When controlling for a large range of potential confounders, the risk of mortality was not significantly associated with hypnotic use regardless of the type and duration. Underlying psychiatric disorders appear to be the principal confounders of the observed association.
Novel protein isoforms of carcinoembryonic antigen are secreted from pancreatic, gastric and colorectal cancer cells
Authors: Hatakeyama Keiichi , Wakabayashi-Nakao Kanako , Ohshima Keiichi , Sakura Naoki , Yamaguchi Ken , Mochizuki Tohru
Published: September 2013

Background

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) is an oncofetal cell surface glycoprotein. Because of its high expression in cancer cells and secretion into serum, CEA has been widely used as a serum tumor marker. Although other members of CEACAM family were investigated for splice variants/variants-derived protein isoforms, few studies about the variants of CEACAM5 have been reported. In this study, we demonstrated the existence of novel CEACAM5 splice variants and splice variant-derived protein isoforms in gastrointestinal cancer cell lines.

Results

We identified two novel CEACAM5 splice variants in gastrointestinal (pancreatic, gastric, and colorectal) cancer cell lines. One of the variants possessed an alternative minor splice site that allowed generation of GC-AG intron. Furthermore, CEA protein isoforms derived from the novel splice variants were expressed in cancer cell lines and those protein isoforms were secreted into the culture medium. Although CEA protein isoforms always co-existed with the full-length protein, the secretion patterns of these isoforms did not correlate with the expression patterns.

Conclusions

This is the first study to identify the expression of CEA isoforms derived from the novel splice variants processed on the unique splice site. In addition, we also revealed the secretion of those isoforms from gastrointestinal cancer cell lines. Our findings suggested that discrimination between the full-length and identified protein isoforms may improve the clinical utility of CEA as a tumor marker.
Comparison of BEAM vs. LEAM regimen in autologous transplant for lymphoma at AIIMS
Authors: Sharma Atul , Kayal Smita , Iqbal Sobuhi , Malik Prabhat Singh , Raina Vinod
Published: September 2013

BEAM (BCNU, etoposide, cytarabine, melphalan) is the most widely used high dose chemotherapy regimen for autologous transplant in lymphoid malignancies. We report our early experience with an alternative regimen LEAM where BCNU was replaced with the oral analogue CCNU (lomustine) to tide over the non-availability of BCNU. Fifty one patients of relapsed or refractory lymphoma who received BEAM (n= 34) and LEAM (n= 17) from September 2001 to February 2012 were analyzed. From October 2009 onwards LEAM was used as the conditioning regimen instead of conventional BEAM. Patients in the LEAM group had more chemorefractory disease (35% vs 9%, p = 0.045) and high risk comorbidity score (24% vs 0%, p = 0.019). Grade 3 and 4 oral mucositis (67.6% vs. 64.7%, p = 0.834) and diarrhea (47% vs. 41.1%, p = 0.691) were similar. No difference was noted between the two groups in terms of engraftment, documented infections, antibiotic use, cumulative toxicity risk, length of hospital stay and 100 day transplant related mortality. The estimated 2 year overall survival (61.7% vs. 62.7%, p = 0.928) and event free survival (44.6% vs. 41.1%, p = 0.510) of the regimens BEAM and LEAM respectively were comparable. Thus LEAM appeared equivalent to BEAM in terms of toxicity and efficacy and can be used as an alternative to BEAM.
Th17 and Th22 cells in psoriatic arthritis and psoriasis
Authors: Benham Helen , Norris Paul , Goodall Jane , Wechalekar Mihir D , FitzGerald Oliver , Szentpetery Agnes , Smith Malcolm , Thomas Ranjeny , Gaston Hill
Published: September 2013

Introduction

The aim of this study was to characterize interleukin 17 (IL-17) and interleukin 22 (IL-22) producing cells in peripheral blood (PB), skin, synovial fluid (SF) and synovial tissue (ST) in patients with psoriasis (Ps) and psoriatic arthritis (PsA).

Methods

Flow cytometry was used to enumerate cells making IL-22 and IL-17, in skin and/or SF and PB from 11 patients with Ps and 12 patients with PsA; skin and PB of 15 healthy controls and SF from rheumatoid arthritis (RA) patients were used as controls. Expression of the interleukin 23 receptor (IL-23R) and chemokine receptors CCR4 and CCR6 was examined. Secretion of IL-17 and IL-22 was measured by ELISA. ST was analysed by immunohistochemical staining of IL-17 and IL-22.

Results

Increased frequencies of IL-17+ and IL-22+ CD4+ T cells were seen in PB of patients with PsA and Ps. IL-17 secretion was significantly elevated in both PsA and Ps, whilst IL-22 secretion was higher in PsA compared to Ps and healthy controls. A higher proportion of the CD4+ cells making IL-17 or IL-22 expressed IL-23R and frequencies of IL-17+, CCR6+ and CCR4+ T cells were elevated in patients with Ps and those with PsA. In patients with PsA, CCR6+ and IL-23R + T cells numbers were elevated in SF compared to PB. Increased frequencies of IL-17+ and IL-22+ CD4+ T cells were demonstrated in Ps skin lesions. In contrast, whilst elevated frequencies of CD4+ IL-17+ cells were seen in PsA SF compared to PB, frequencies of CD4+ IL-22+ T cells were lower. Whereas IL-17 expression was equivalent in PsA, osteoarthritis (OA) and RA ST, IL-22 expression was higher in RA than either OA or PsA ST, in which IL-22 was strikingly absent.

Conclusions

Elevated frequencies of IL-17 and IL-22 producing CD4+ T cells were a feature of both Ps and PsA. However their differing distribution at disease sites, including lower frequencies of IL-22+ CD4+ T cells in SF compared to skin and PB, and lack of IL-22 expression in ST suggests that Th17 and Th22 cells have common, as well as divergent roles in the pathogenesis of Ps and PsA.
Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Authors: Frantz Laurent AF , Schraiber Joshua G , Madsen Ole , Megens Hendrik-Jan , Bosse Mirte , Paudel Yogesh , Semiadi Gono , Meijaard Erik , Li Ning , Crooijmans Richard PMA , Archibald Alan L , Slatkin Montgomery , Schook Lawrence B , Larson Greger , Groenen Martien AM
Published: September 2013

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
A timely and necessary antidote to indirect methods and so-called P-wave FWI
Authors: Weglein Arthur B.
Published: September 2013

A central purpose of this article is to bring an alternative voice, perspective, and understanding to the latest geophysical stampede, technical bubble, and self-proclaimed seismic cure-all, the so-called “full-waveform inversion” or FWI. If you think this is exaggerated, I refer to the advertisement/announcement of the 2013 SEG Workshop on FWI whose opening line is, “Full-waveform inversion has emerged as the final and ultimate solution to the Earth resolution and imaging objective.”
Steam-injection monitoring in South Oman—from single-pattern to field-scale surveillance
Authors: Kiyashchenko Denis , Lopez Jorge , Berlang Wilfred , Birch Bill , Zwaan Marcel , Adawi Rashid , Rocco Guillermo , Ghafri Salah
Published: September 2013

Downhole seismic monitoring has become an alternative to more conventional surface seismic in cases where the latter has low signal-to-noise ratio or poor repeatability, or when frequent monitoring of a local target is required. Downhole 3D VSP monitoring has been applied to both onshore (O'Brien et al., 2004; Kiyashchenko et al., 2011) and offshore environments (Wu et al., 2011). In onshore environments, surface seismic repeatability often suffers from surface noise and near-surface variations caused by water-table changes or surface facilities construction. For VSP surveys, the wavefield separation into downgoing and upgoing fields presents an opportunity to discriminate between near-surface and reservoir changes, thus making time-lapse applications more effective.
Switching cell fates in the developing Drosophila eye
Authors: Mavromatakis Yannis Emmanuel , Tomlinson Andrew
Published: September 2013

The developing Drosophila ommatidium is characterized by two distinct waves of pattern formation. In the first wave, a precluster of five cells is formed by a complex cellular interaction mechanism. In the second wave, cells are systematically recruited to the cluster and directed to their fates by developmental cues presented by differentiating precluster cells. These developmental cues are mediated through the receptor tyrosine kinase (RTK) and Notch (N) signaling pathways and their combined activities are crucial in specifying cell type. The transcription factor Lozenge (Lz) is expressed exclusively in second wave cells. Here, we ectopically supply Lz to precluster cells and concomitantly supply the various RTK/N codes that specify each of three second wave cell fates. We thereby reproduce molecular markers of each of the second wave cell types in precluster cells and draw three inferences. First, we confirm that Lz provides key intrinsic information to second wave cells. We can now combine this with the RTK/N signaling to provide a cell fate specification code that entails both extrinsic and intrinsic information. Second, the reproduction of each second wave cell type in the precluster confirms the accuracy of the RTK/N signaling code. Third, RTK/N signaling and Lz need only be presented to the cells for a short period of time in order to specify their fate.
Semicircular canal morphogenesis in the zebrafish inner ear requires the function ofgpr126(lauscher), an adhesion class G protein-coupled receptor gene
Authors: Geng Fan-Suo , Abbas Leila , Baxendale Sarah , Holdsworth Celia J. , Swanson A. George , Slanchev Krasimir , Hammerschmidt Matthias , Topczewski Jacek , Whitfield Tanya T.
Published: September 2013

Morphogenesis of the semicircular canal ducts in the vertebrate inner ear is a dramatic example of epithelial remodelling in the embryo, and failure of normal canal development results in vestibular dysfunction. In zebrafish and Xenopus, semicircular canal ducts develop when projections of epithelium, driven by extracellular matrix production, push into the otic vesicle and fuse to form pillars. We show that in the zebrafish, extracellular matrix gene expression is high during projection outgrowth and then rapidly downregulated after fusion. Enzymatic disruption of hyaluronan in the projections leads to their collapse and a failure to form pillars: as a result, the ears swell. We have cloned a zebrafish mutant, lauscher (lau), identified by its swollen ear phenotype. The primary defect in the ear is abnormal projection outgrowth and a failure of fusion to form the semicircular canal pillars. Otic expression of extracellular matrix components is highly disrupted: several genes fail to become downregulated and remain expressed at abnormally high levels into late larval stages. The lau mutations disrupt gpr126, an adhesion class G protein-coupled receptor gene. Expression of gpr126 is similar to that of sox10, an ear and neural crest marker, and is partially dependent on sox10 activity. Fusion of canal projections and downregulation of otic versican expression in a hypomorphic lau allele can be restored by cAMP agonists. We propose that Gpr126 acts through a cAMP-mediated pathway to control the outgrowth and adhesion of canal projections in the zebrafish ear via the regulation of extracellular matrix gene expression.
The unfolded protein response has a protective role in yeast models of classic galactosemia
Authors: De-Souza Evandro A. , Pimentel Felipe S. A. , Machado Caio M. , Martins Larissa S. , da-Silva Wagner S. , Montero-Lomelí Mónica , Masuda Claudio A.
Published: September 2013

Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast) which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to the cellular adaptation in these models of classic galactosemia.
Deletion of SHP-2 in mesenchymal stem cells causes growth retardation, limb and chest deformity, and calvarial defects in mice
Authors: Lapinski Philip E. , Meyer Melissa F. , Feng Gen-Sheng , Kamiya Nobuhiro , King Philip D.
Published: September 2013

In mice, induced global disruption of the Ptpn11 gene, which encodes the SHP-2 tyrosine phosphatase, results in severe skeletal abnormalities. To understand the extent to which skeletal abnormalities can be attributed to perturbation of SHP-2 function in bone-forming osteoblasts and chondrocytes, we generated mice in which disruption of Ptpn11 is restricted to mesenchymal stem cells (MSCs) and their progeny, which include both cell types. MSC-lineage-specific SHP-2 knockout (MSC SHP-2 KO) mice exhibited postnatal growth retardation, limb and chest deformity, and calvarial defects. These skeletal abnormalities were associated with an absence of mature osteoblasts and massive chondrodysplasia with a vast increase in the number of terminally differentiated hypertrophic chondrocytes in affected bones. Activation of mitogen activated protein kinases (MAPKs) and protein kinase B (PKB; also known as AKT) was impaired in bone-forming cells of MSC SHP-2 KO mice, which provides an explanation for the skeletal defects that developed. These findings reveal a cell-autonomous role for SHP-2 in bone-forming cells in mice in the regulation of skeletal development. The results add to our understanding of the pathophysiology of skeletal abnormalities observed in humans with germline mutations in the PTPN11 gene (e.g. Noonan syndrome and LEOPARD syndrome).
Detection of Offal Adulteration in Beefburgers Using near Infrared Reflectance Spectroscopy and Multivariate Modelling
Authors: Zhao Ming , O'Donnell Colm P. , Downey Gerard
Published: September 2013

The main aim of this study was to develop a rapid and reliable tool using near infrared (NIR) reflectance spectroscopy to confirm beefburger authenticity in the context of offal (kidney, liver, heart and lung) adulteration. An experimental design was used to develop beef burger formulations to simultaneously maximise the variable space describing offal-adulterated samples and minimise the number of experiments required. Authentic ( n = 36) and adulterated ( n = 46) beefburger samples were produced using these formulations. Classification models (partial least squares discriminant analysis, PLS1-DA) and class-modelling tools (soft independent modelling of class analogy, SIMCA), were developed using raw and pre-treated NIR reflectance spectra (850–1098nm wavelength range) to detect authentic and adulterated beefburgers in (1) fresh, (2) frozen-then-thawed and (3) fresh or frozen-then-thawed states. In the case of authentic samples, the best PLS1-DA models achieved 100% correct classification for fresh, frozen-then-thawed and fresh or frozen-then-thawed samples. SIMCA models correctly identified all the fresh samples but not all the frozen-then-thawed and fresh or frozen-then-thawed samples. For the adulterated samples, PLS1-DA models correctly classified 95.5% of fresh, 91.3% of frozen-then-thawed and 88.9% of fresh or frozen-then-thawed beefburgers. SIMCA models exhibited specificity values of 1 for both fresh and frozen-then-thawed samples, 0.99 for fresh or frozen-then-thawed samples; sensitivity values of 1, 0.88 and 0.97 were obtained for fresh, frozen-then-thawed and fresh or frozen-then-thawed products, respectively. Quantitative models (PLS1 regression) using both 850–1098nm and 1100–2498 nm wavelength ranges were developed to quantify (1) offal adulteration and (2) added fat in adulterated beefburgers, both fresh and frozen-then-thawed. Models predicted added fat in fresh samples with acceptable accuracy ( RMSECV=2.0; RPD=5.9); usefully accurate predictions of added fat in frozen-then-thawed samples were not obtained nor was prediction of total offal possible in either sample form.
Visible and Shortwave near Infrared Spectroscopy for Predicting Sugar Content of Sugarcane Based on a Cross-Sectional Scanning Method
Authors: Nawi Nazmi Mat , Chen Guangnan , Jensen Troy
Published: September 2013

The need for a reliable in-field quality measurement in the sugarcane industry is growing as the quality of sugarcane could vary significantly across the field. However, current monitoring systems in this industry only monitor crop yield and do not have the ability to measure the product quality. Thus, the potential of the visible/shortwave near infrared (vis/SW-NIR) spectroscopic technique as a low-cost alternative to predict sugar content from sugarcane stalks was investigated. Two hundred and ninety-two internode samples were extracted from three different sugarcane varieties to assess the ability of this technique. Each sample was cut into four sections and the spectra collected from the cross-sectional surface of each section were later correlated with its sugar content (°Brix). Partial least square (PLS) models were developed using calibration samples. The best model predicted samples in a prediction set had a coefficient of determination ( r2) of 0.87 and root means square error of prediction ( RMSEP) of 1.45°Brix. The value of the ratio of the standard deviation to the standard error of prediction ( RPD) was 2. The variations of °Brix and prediction accuracy along the individual internode were 8.7 and 13%, respectively. These results indicated the vis/SW-NIR spectroscopy could be applied to predict °Brix values from sugarcane stalks based on a cross-sectional scanning method.
Shortwave near Infrared Spectroscopy for Determination of Dry Rubber Content and Total Solids Content of Para Rubber (Hevea Brasiliensis) Latex
Authors: Sirisomboon Panmanas , Deeprommit Metee , Suchaiboonsiri Woradet , Lertsri Wipasiri
Published: September 2013

The objective of this research was to apply shortwave near infrared (NIR) (700–1100nm) spectroscopy to the evaluation of dry rubber content (DRC, %) and total solids content (TSC, %) in Para rubber field and concentrated latex. The spectra were obtained in transmission mode. There were 282 samples including field latex, concentrated latex and concentration adjusted concentrated latex of 171, 86 and 25 samples, respectively. The field latex had around 30% DRC and the concentrated latex had around 60% DRC. The concentration adjusted concentrated latex was in five levels which were 55%, 50%, 45%, 40% and 35% DRC. The calibration models were developed by original and pre-treated absorbance spectra using partial least square regression The pre-treatment methods were smoothing, normalisation, derivative, baseline offset, standard normal variate or multiple scatter correction. By statistical analysis, the model developed from smoothing and range normalisation pre-treated spectra in the wavelength range of 700–950 nm provided the best accuracy of prediction for DRC and the models using raw spectra in the same wavelength range gave the best results for TSC. The slope, offset, coefficient of determination ( r2), standard error of prediction ( SEP) and bias were 1.0154, −0.6286, 0.992, 1.1092% and 0.0321%, respectively, for the prediction of DRC and 1.0084, −0.2332, 0.991, 1.3611% and 0.1456%, respectively for the prediction of TSC. The best models were validated using new sets of 50 and 35 unknown samples for DRC and TSC, respectively. The models achieved an r2 of 0.988 and 0.974, SEP of 1.4296 and 2.1255, RPD of 10.0 and 6.2 and bias of −0.6191% and 0.5476% for DRC and TSC, respectively. This work showed the high accuracy of SW-NIR spectroscopy in the evaluation of TSC, the essential parameter for quality assurance and process control in the concentrated rubber latex factory. However, the accuracy for prediction of DRC was still not acceptable for the latex factory because a bias of more than 0.01% is not acceptable for it would affect the amount of money which the factory may lose or gain.
Diffuse Optical Techniques Applied to Wood Characterisation
Authors: Bargigia Ilaria , Nevin Austin , Farina Andrea , Pifferi Antonio , D'Andrea Cosimo , Karlsson Marcus , Lundin Patrik , Somesfalean Gabriel , Svanberg Sune
Published: September 2013

We propose an optical method for non-invasive characterisation of wood samples based on two optical techniques: time-resolved diffuse optical spectroscopy and gas in scattering media absorption spectroscopy. While the latter is sensitive to gases present inside wood pores, the former extracts information on the bulk material regarding light scattering and absorption. Measurements on spruce samples, cut along different wood fibre directions, are presented to show an example of the advantages of this combined approach: by applying these two non-destructive techniques together, in fact, relevant information on wood such as porosity, permeability and moisture content can be assessed. Furthermore, the chemical composition, internal structure and the anisotropy due to the wood fibres can be investigated.
Spectroscopic Characterization of Urea Aqueous Solutions: Experimental Phase Diagram of the Urea–Water Binary System
Authors: Durickovic Ivana , Thiébaud Laura , Bourson Patrice , Kauffmann Thomas , Marchetti Mario
Published: September 2013

Raman spectroscopy was used to analyze mixtures of urea and water in order to identify the influence of the urea concentration on the solution's freezing point. Our approach consisted in the analysis of urea aqueous solutions and the determination of their phase transitions at low temperatures. Hence, Raman spectra of these solutions were acquired in a −30 to 10 °C temperature range. This enabled us to build the experimental phase diagram of the urea–water binary system.
Accurate Fourier Transform Infrared (FT-IR) Spectroscopy Measurements of Nitrogen Dioxide (NO2) and Nitric Acid (HNO3) Calibrated with Synthetic Spectra
Authors: Flores Edgar , Viallon Joële , Moussay Philippe , Wielgosz Robert Ian
Published: September 2013

A novel method for determining the accuracy of laboratory-based measurements of nitrogen dioxide (NO2) and nitric acid (HNO3) mole fractions using Fourier transform infrared (FT-IR) spectroscopy 1 cm−1 resolution instruments calibrated with synthetic spectra has been developed. The traceability of these measurement results is to the reference line strength data contained within the high-resolution transmission molecular absorption (HITRAN) database. Incorporating a proper estimate of the uncertainty of this data into the measurement results will ensure that the SI traceable values are encompassed within the uncertainty of the measurement results. The major contributors to the uncertainties of the results are, in descending order of importance, the uncertainty in the line strength values (HITRAN 2004), the uncertainty attributed to the generation of reference spectra (including knowledge of the optical path length of the FT-IR gas cell), and temperature measurements of the gas. The stability of the FT-IR instrument itself is only a minor contributor to the overall uncertainty of the measurements. FT-IR measurements of NO2 mole fractions at nominal values of 10 μmol mol−1 calibrated with synthetic spectra lead to standard uncertainties of 0.34 μmol mol−1 (3.4% relative). In contrast, calibration of the FT-IR instrument with SI traceable gas standards generated by a dynamic weighing system resulted in measurements results with standard uncertainties of 0.04 μmol mol−1 (0.4% relative). When comparing the consistency of measurement results based on the synthetic calibration method against those obtained by calibrations with SI traceable gas standards, the existence of a potential bias of ∼5% was observed, although this was within the stated uncertainties of the results. The FT-IR measurements of HNO3 mole fractions at nominal values of 200 nmol mol−1 calibrated with synthetic spectra resulted in values with standard uncertainties of 23 nmol mol−1 (11% relative) with the dominating uncertainty in this case arising from the stabilization of the mole fraction value within the FT-IR gas cell.