bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Oscillatory Processes Governing Cued Orienting and Allocation of Auditory Attention
Authors: Ahveninen Jyrki , Huang Samantha , Belliveau John W. , Chang Wei-Tang , Hämäläinen Matti
Published: August 2013

In everyday listening situations, we need to constantly switch between alternative sound sources and engage attention according to cues that match our goals and expectations. The exact neuronal bases of these processes are poorly understood. We investigated oscillatory brain networks controlling auditory attention using cortically constrained fMRI-weighted magnetoencephalography/EEG source estimates. During consecutive trials, participants were instructed to shift attention based on a cue, presented in the ear where a target was likely to follow. To promote audiospatial attention effects, the targets were embedded in streams of dichotically presented standard tones. Occasionally, an unexpected novel sound occurred opposite to the cued ear to trigger involuntary orienting. According to our cortical power correlation analyses, increased frontoparietal/temporal 30–100 Hz gamma activity at 200–1400 msec after cued orienting predicted fast and accurate discrimination of subsequent targets. This sustained correlation effect, possibly reflecting voluntary engagement of attention after the initial cue-driven orienting, spread from the TPJ, anterior insula, and inferior frontal cortices to the right FEFs. Engagement of attention to one ear resulted in a significantly stronger increase of 7.5–15 Hz alpha in the ipsilateral than contralateral parieto-occipital cortices 200–600 msec after the cue onset, possibly reflecting cross-modal modulation of the dorsal visual pathway during audiospatial attention. Comparisons of cortical power patterns also revealed significant increases of sustained right medial frontal cortex theta power, right dorsolateral pFC and anterior insula/inferior frontal cortex beta power, and medial parietal cortex and posterior cingulate cortex gamma activity after cued versus novelty-triggered orienting (600–1400 msec). Our results reveal sustained oscillatory patterns associated with voluntary engagement of auditory spatial attention, with the frontoparietal and temporal gamma increases being best predictors of subsequent behavioral performance.
Perceptual Learning Is Specific to the Trained Structure of Information
Authors: Cohen Yamit , Daikhin Luba , Ahissar Merav
Published: August 2013

What do we learn when we practice a simple perceptual task? Many studies have suggested that we learn to refine or better select the sensory representations of the task-relevant dimension. Here we show that learning is specific to the trained structural regularities. Specifically, when this structure is modified after training with a fixed temporal structure, performance regresses to pretraining levels, even when the trained stimuli and task are retained. This specificity raises key questions as to the importance of low-level sensory modifications in the learning process. We trained two groups of participants on a two-tone frequency discrimination task for several days. In one group, a fixed reference tone was consistently presented in the first interval (the second tone was higher or lower), and in the other group the same reference tone was consistently presented in the second interval. When following training, these temporal protocols were switched between groups, performance of both groups regressed to pretraining levels, and further training was needed to attain postlearning performance. ERP measures, taken before and after training, indicated that participants implicitly learned the temporal regularity of the protocol and formed an attentional template that matched the trained structure of information. These results are consistent with Reverse Hierarchy Theory, which posits that even the learning of simple perceptual tasks progresses in a top–down manner, hence can benefit from temporal regularities at the trial level, albeit at the potential cost that learning may be specific to these regularities.
Electrophysiological Responses to Feedback during the Application of Abstract Rules
Authors: Walsh Matthew M. , Anderson John R.
Published: August 2013

Much research focuses on how people acquire concrete stimulus–response associations from experience; however, few neuroscientific studies have examined how people learn about and select among abstract rules. To address this issue, we recorded ERPs as participants performed an abstract rule-learning task. In each trial, they viewed a sample number and two test numbers. Participants then chose a test number using one of three abstract mathematical rules they freely selected from: greater than the sample number, less than the sample number, or equal to the sample number. No one rule was always rewarded, but some rules were rewarded more frequently than others. To maximize their earnings, participants needed to learn which rules were rewarded most frequently. All participants learned to select the best rules for repeating and novel stimulus sets that obeyed the overall reward probabilities. Participants differed, however, in the extent to which they overgeneralized those rules to repeating stimulus sets that deviated from the overall reward probabilities. The feedback-related negativity (FRN), an ERP component thought to reflect reward prediction error, paralleled behavior. The FRN was sensitive to item-specific reward probabilities in participants who detected the deviant stimulus set, and the FRN was sensitive to overall reward probabilities in participants who did not. These results show that the FRN is sensitive to the utility of abstract rules and that the individual's representation of a task's states and actions shapes behavior as well as the FRN.
Spatio-temporal Patterns of Brain Activity Distinguish Strategies of Multiple-object Tracking
Authors: Merkel Christian , Stoppel Christian M. , Hillyard Steven A. , Heinze Hans-Jochen , Hopf Jens-Max , Schoenfeld Mircea Ariel
Published: August 2013

Human observers can readily track up to four independently moving items simultaneously, even in the presence of moving distractors. Here we combined EEG and magnetoencephalography recordings to investigate the neural processes underlying this remarkable capability. Participants were instructed to track four of eight independently moving items for 3 sec. When the movement ceased a probe stimulus consisting of four items with a higher luminance was presented. The location of the probe items could correspond fully, partly, or not at all with the tracked items. Participants reported whether the probe items fully matched the tracked items or not. About half of the participants showed slower RTs and higher error rates with increasing correspondence between tracked items and the probe. The other half, however, showed faster RTs and lower error rates when the probe fully matched the tracked items. This latter behavioral pattern was associated with enhanced probe-evoked neural activity that was localized to the lateral occipital cortex in the time range 170–210 msec. This enhanced response in the object-selective lateral occipital cortex suggested that these participants performed the tracking task by visualizing the overall shape configuration defined by the vertices of the tracked items, thereby producing a behavioral advantage on full-match trials. In a later time range (270–310 msec) probe-evoked neural activity increased monotonically as a function of decreasing target–probe correspondence in all participants. This later modulation, localized to superior parietal cortex, was proposed to reflect the degree of mismatch between the probe and the automatically formed visual STM representation of the tracked items.
The Shape of the ACC Contributes to Cognitive Control Efficiency in Preschoolers
Authors: Cachia Arnaud , Borst Grégoire , Vidal Julie , Fischer Clara , Pineau Arlette , Mangin Jean-François , Houdé Olivier
Published: August 2013

Cognitive success at school and later in life is supported by executive functions including cognitive control (CC). The pFC plays a major role in CC, particularly the dorsal part of ACC or midcingulate cortex. Genes, environment (including school curricula), and neuroplasticity affect CC. However, no study to date has investigated whether ACC sulcal pattern, a stable brain feature primarily determined in utero, influences CC efficiency in the early stages of cognitive and neural development. Using anatomical MRI and three-dimensional reconstruction of cortical folds, we investigated the effect that ACC sulcal pattern may have on the Stroop score, a classical behavioral index of CC efficiency, in 5-year-old preschoolers. We found higher CC efficiency, that is, lower Stroop interference scores for both RTs and error rates, in children with asymmetrical ACC sulcal pattern (i.e., different pattern in each hemisphere) compared with children with symmetrical pattern (i.e., same pattern in both hemispheres). Critically, ACC sulcal pattern had no effect on performance in the forward and backward digit span tasks suggesting that ACC sulcal pattern contributes to the executive ability to resolve conflicts but not to the ability to maintain and manipulate information in working memory. This finding provides the first evidence that preschoolers' CC efficiency is likely associated with ACC sulcal pattern, thereby suggesting that the brain shape could result in early constraints on human executive ability.
On some taxonomically confused species of the genus Amphiesma Duméril, Bibron & Duméril, 1854 related to Amphiesma khasiense (Boulenger, 1890) (Squamata, Natricidae)
Authors: DAVID PATRICK , VOGEL GERNOT , ROOIJEN JOHAN VAN
Published: August 2013

Three species of the genus Amphiesma Duméril, Bibron & Duméril, 1854 have long been confused in the literature, with each other and with other species of the genus. Amphiesma khasiense (Boulenger, 1890) has been considered to inhabit a large geographical region, extending from north-eastern India, east to Vietnam and southern Thailand. Amphiesma boulengeri (Gressitt, 1937) has been regarded as a species endemic to south-eastern China. Amphiesma inas (Laidlaw, 1901) has been recorded from West Malaysia, Thailand and Indonesia (Sumatra). A multivariate analysis of morphometric and meristic characters shows that these three species can be separated by combinations of characters in the scalation and pattern, the most obvious being the structure of the postocular streak. On the basis of our analysis and after comparison with name-bearing type specimens, Amphiesma khasiense is restricted to north-eastern India, Myanmar, western Yunnan Province of China, northern Laos and northern and western Thailand. Other populations from south-eastern China, Vietnam, other parts of Laos, Cambodia and central Thailand, which have been recorded in the literature as A. khasiense, A. johannis or Amphiesma modestum (Günther, 1875), should be referred to Amphiesma boulengeri. Amphiesma inas (Laidlaw, 1901) is a valid species endemic to mountain ranges of southern Peninsular Thailand and West Malaysia. The mention of Amphiesma inas in Sumatra is erroneous, being based on the second known specimen of Amphiesma kerinciense David & Das, 2003, which is here redescribed. A key to species of the Amphiesma khasiense group and other species sharing a greyish-brown background without conspicuous dark and pale stripes, is provided.
A new species of Psilorhynchus (Teleostei: Psilorhynchidae) from the Chindwin basin of Manipur, India
Authors: SHANGNINGAM BUNGDON , VISHWANATH WAIKHOM
Published: August 2013

Psilorhynchus chakpiensis, new species, is described from the Chakpi River, Chindwin basin in Manipur, India.  It is distinguished from its congeners by a combination of characters: a dome-shaped rostral cap with horizontally arranged pointed tubercles, 1–2 rows of prominent globular papillae behind the upper lip, three unbranched and nine branched dorsal-fin rays, 30–31 lateral-line scales, head width 74–83% HL, and characteristic colour bands on the dorsal and caudal fins. It is distinguished from all congeners in having a caudal-fin pattern consisting of two black bars, one incomplete bar near the base of the upper lobe, and a complete bar across the centre of the fin, traversing from the upper to the lower margin of the fin.
Japan’s Dual Security Identity: A Non-combat Military Role as an Enabler of Coexistence
Authors: Miyaoka Isao
Published: August 2013

Since the end of the Cold War, Japan’s acceptance and institutionalization of a non-combat military role to aid the US has led to its new identity as a US ally and has transformed the content of its ‘peace state’ identity. It is this role that has made these two identities more compatible. This article first attempts to measure the long-term shift in Japan’s two identities by conducting a content analysis of Japan’s Defence White Papers and then seeks to trace the formation process of Japan’s dual security identity through which it accepted and institutionalized a non-combat military role. For this analysis, the process is divided into three stages: the Cold War period when its two identities as a ‘peace state’ and a US ally were considered incompatible, the period of the 1990s when Japan started to accept and institutionalized a non-combat military role, and the period after 11 September 2001 when Japan’s dual security identity gradually got established. In the final section, the article discusses the source of a security identity shift in Japan and draws some implications for the future of its security policy.
Area Studies: Trajectories of Disciplinary Discourse
Authors: Batabyal Rakesh
Published: August 2013

Area studies in India have evolved as a discipline within public institutions, reflecting the plurality of discourses that define the profile of institutions in the country. Many Area studies experts share the policy narratives of the state, but there are many who do not subscribe to them and still some others even challenge them. In that sense, the discipline has maintained a large measure of intellectual autonomy. It is this autonomy that quite often irritates those who want to see a very homogenous and monolithic discourse emanating generally from ‘world class institutions’.
Erēmos Aporos as the Paradigmatic Figure of Western (Thanato) Political Subject
Authors: Ojakangas Mika
Published: August 2013

The originary figure of the Western political subject is neither the Aristotelian zōon politikon nor the Agambenian homo sacer but the Socratic erēmos aporos. Like the Agambenian homo sacer, the Socratic erēmos aporos is abandoned by his fellow citizens, not outside the polis but in the polis, being a refugee in his own city. He lives, as Callicles says of Socrates in Gorgias (486c), “in his city as an absolute outcast.” Moreover, like the Agambenian homo sacer, the Socratic erēmos aporos also lives in a state close to death—“in a state as close to death as possible,” as Socrates says of himself in Phaedo (67d). However, there is a decisive difference between the Agambenian homo sacer and the Socratic erēmos aporos. Unlike homo sacer, the Socratic political subject is not abandoned by the sovereign but by himself through his own traumatic self-accusation. Furthermore, although erēmos aporos is also a “living corpse,” he is not thereby at mercy of the sovereign. On the contrary, it is he who has become sovereign, not because he has somehow managed to sublate his condition as abandoned and forlorn subject, but because this condition is the condition of sovereign freedom. In other words, it is neither his biological life in the order of nature ( zoē) nor his form of life in the symbolic order of the polis ( bios), not even his exposure to the threat of imminent death (homo sacer), but his symbolic suicide that renders him a sovereign individual subjected to no one. By removing the subject from his proper place in the symbolic order of the polis, such a suicide not only discloses subject’s unlimited responsibility but also renders him capable of transcending his limited position as a living being and becoming a thanatopolitical subject of his own biological death. Although such a subject also affirms life, life that is affirmed here is not mere life but sovereign life in the shade of the instinct of death.
Social sciences in the field of power – the case of Danish social science
Authors: Kropp Kristoffer
Published: August 2013

The social science disciplines are strongly differentiated both on an epistemological level and in problem choice. It can be argued that they are characterized by a number of different epistemological ways of position-taking or ways of legitimizing social scientific knowledge production. Furthermore, different scientific problems and social institutions are allocated as research objects to different social science disciplines. This article looks into how these different epistemological styles and choice of scientific problems not only are internal principles of differentiation but also constitute important relations to other powerful social interests and institutions in the field of power. I argue that we can understand the social sciences as a field of force and struggle, where different disciplines compete in producing legitimate representations of the social that also represent specific societal interests. Using the language of Bourdieu, I construct a space of social scientific epistemological position-taking using Multiple Correspondence Analysis (MCA). Into this space I project a number of supplementary variables representing social science disciplines, position-taking towards non-academic institutions, interests and research subjects, and thus show how different epistemological position-taking is connected to specific societal interests, problems and institutions. The article draws on data from a survey conducted among Danish social scientists in autumn 2009.
Soy extracts suppressed iodine uptake and stimulated the production of autoimmunogen in rat thyrocytes
Authors: Tran Lisa , Hammuda Mariam , Wood Carla , Xiao Chao Wu
Published: August 2013

Soy consumption is associated with thyroid disorders such as hypothyroidism, goiter, and autoimmune thyroid disease (ATD) as well as increased iodine requirement in certain cases. However, the anti-thyroid component(s) in soy are yet to be identified and the molecular mechanism(s) involved remain unclear. This study examined the effects of soy isoflavones (ISF) on iodide uptake and expression of thyroglobulin (Tg) and sodium/iodide symporter (NIS) in thyrocytes. Fischer rat thyroid cells (FRTL) were treated with Novasoy (a soy alcohol extract containing 30% ISF) or major ISF aglycones or glycosides for 24 h. Iodide uptake was measured by a colorimetric assay. The protein level of Tg and NIS was measured by Western blotting. Cytotoxicity of tested compounds was determined by the MTT cell proliferation assay. Iodide uptake in FRTL cells was dose-dependently suppressed by Novasoy added into the cell culture (10, 25, or 50 µg/mL, P < 0.05). However, neither the major ISF aglycones nor glycosides alone or in combination had similar effects. Novasoy (up to 200 µg/mL) had no cytotoxic effect. Novasoy (1, 10, and 50 µg/mL) and genistein (1 and 10 µM) markedly increased the protein content of a 40 kDa Tg fragment (P40, a known autoimmunogen) and non-glycosylated NIS in the FRTL cells ( P < 0.05). Overall, this study demonstrated that the alcohol soluble component(s) other than the major ISF in soy remarkably inhibited iodide uptake in the FRTL cells. Soy ISF, particularly genistein, induced the production of P40, which might be responsible for the higher incidence of ATD reported in soy infant formula-fed children.
CTLA4-Ig (abatacept) therapy modulates T cell effector functions in autoantibody-positive rheumatoid arthritis patients
Authors: Pieper Jennifer , Herrath Jessica , Raghavan Sukanya , Muhammad Khalid , Vollenhoven Ronald van , Malmström Vivianne
Published: August 2013

Background

Rheumatoid arthritis is a chronic inflammatory disease with a strong MHC class II component and where many patients develop characteristic autoantibodies towards the noncoding amino acid citrulline. Such anti-citrullinated protein antibodies (ACPA) have recently been put forward as an independent predictive factor for treatment response by co-stimulation blockade by CTLA4-Ig (abatacept). We have performed a mechanism of action study to dissect T cell functionality in RA patients with long-standing disease undergoing abatacept treatment and the influence of ACPA status.

Results

Peripheral blood samples were collected from RA patients as they started CTLA4-Ig treatment and 3 and 6 months later. A general decrease of regulatory T cell subsets was observed in the cohort. Additionally within the ACPA-positive group significant down-regulation of all key T cell effector subsets including Th1, Th2, and Th17 was observed by analyzing cytokines by intracellular flow cytometry and in cell culture supernatants.

RA synovial fluid samples were cultured in vitro in the presence or absence of CTLA4-Ig (abatacept). T cell cytokine production was diminished, but without increasing the functional capacity of CD4+CD25hi regulatory T cells as previously demonstrated in the context of TNF-blockade and anti-IL6R therapy.

Conclusions

Our immunological study of T cell functionality in RA patients, both ACPA-positive and ACPA-negative, starting biological therapy with the co-stimulation blockade abatacept (CTLA4-Ig) supports the recently published registry study implicating ACPA seropositivity as an independent predictive factor to treatment response as we observed the most striking effect on T cell subset modulation in ACPA-positive patients. These data further support the notion of RA as a disease with several sub-entities, where the ACPA-positive fraction represents a classical HLA-associated autoimmune disorder while ACPA-negative patients may have other driving forces apart from classical adaptive immune responses.
BAP1 deficiency causes loss of melanocytic cell identity in uveal melanoma
Authors: Matatall Katie A , Agapova Olga A , Onken Michael D , Worley Lori A , Bowcock Anne M , Harbour J William
Published: August 2013

Background

Uveal melanoma is a highly aggressive cancer with a strong propensity for metastasis, yet little is known about the biological mechanisms underlying this metastatic potential. We recently showed that most metastasizing uveal melanomas, which exhibit a class 2 gene expression profile, contain inactivating mutations in the tumor suppressor BAP1. The aim of this study was to investigate the role of BAP1 in uveal melanoma progression.

Methods

Uveal melanoma cells were studied following RNAi-mediated depletion of BAP1 using proliferation, BrdU incorporation, flow cytometry, migration, invasion, differentiation and clonogenic assays, as well as in vivo tumorigenicity experiments in NOD-SCID-Gamma mice.

Results

Depletion of BAP1 in uveal melanoma cells resulted in a loss of differentiation and gain of stem-like properties, including expression of stem cell markers, increased capacity for self-replication, and enhanced ability to grow in stem cell conditions. BAP1 depletion did not result in increased proliferation, migration, invasion or tumorigenicity.

Conclusions

BAP1 appears to function in the uveal melanocyte lineage primarily as a regulator of differentiation, with cells deficient for BAP1 exhibiting stem-like qualities. It will be important to elucidate how this effect of BAP1 loss promotes metastasis and how to reverse this effect therapeutically.
Use of statins in lower extremity artery disease: a review
Authors: Gargiulo Giuseppe , Giugliano Giuseppe , Brevetti Linda , Sannino Anna , Schiattarella Gabriele Giacomo , Serino Federica , Carbone Andreina , Scudiero Fernando , Ferrone Marco , Corrado Roberto , Izzo Raffaele , Chiariotti Lorenzo , Perrino Cinzia , Amato Bruno , Trimarco Bruno , Esposito Giovanni
Published: August 2013

Background

Lower extremity artery disease (LE-PAD) is one of the most common manifestations of atherosclerosis, particularly in elderly patients, and it is related to a high cardiovascular risk.

Description

It is well established that statin therapy is characterized by crucial benefits on cardiovascular system by limiting atherosclerotic progression and reducing cardiovascular events and mortality. A growing body of evidence support efficacy of statins in LE-PAD due to the ability of both reducing cardiovascular risk and improving walking distance and, hence, quality of life. Consequently, statin therapy should be considered in all LE-PAD patients and new LDL-cholesterol targets should be reached.

Conclusions

Our opinion is that statin therapy remains still underutilized or with inadequate dosage, so therapy of LE-PAD patients should be improved to obtain all the demonstrated benefits of statins.
Rectosigmoid stump washout as an alternative to permanent mucous fistula in patients undergoing subtotal colectomy for ulcerative colitis in emergency settings
Authors: Pellino Gianluca , Sciaudone Guido , Candilio Giuseppe , Canonico Silvestro , Selvaggi Francesco
Published: August 2013

Background

Restorative proctocolectomy with ileopouch-anal anastomosis (IPAA) is the treatment of choice for intractable or complicated ulcerative colitis(UC). Elderly patients often present with acute colitis requiring emergent subtotal colectomy(SC). Frail patients are at risk of developing septic complications related to the closed rectosigmoidal stump, often requiring formation of a second stoma to be reversed at the time of completion proctectomy. This carries nuisance to such exhausted patients. We propose a simple and inexpensive trick to avoid the need for creating a mucous fistula.

Methods

IPAA was performed as a 3-stage procedure in emergency settings. The rectosigmoidal stump was closed and placed subcutaneously; skin was closed over it. After SC, if patients showed signs of stump-related pelvic sepsis, a lavage of the rectal stump with povidone iodine solution and with saline was carried out as a rescue treatment aiming to avoid the need of opening the rectal stump to drain sepsis.

Results

Thirty-five patients underwent SC for UC between 1987 and 2012. The skin was closed over the closed stump in the 20. Seven patients out of these 20 experienced early stump-related septic complication. In five cases, we were able to avoid opening of the rectal stump, and a second stoma was unnecessary. After opening the closed stump in the remaining ones, a prompt improving of symptoms was observed.

Conclusions

Rectal washout was well tolerated and avoided a second stoma in five out of seven patients, with better quality of life and body perception after IPAA surgery. This is relevant when dealing with geriatric patients, needing to completely recover before undergoing completion proctectomy.
BOSS: context-enhanced search for biomedical objects
Authors: Choi Jaehoon , Kim Donghyeon , Kim Seongsoon , Lee Sunwon , Lee Kyubum , Kang Jaewoo
Published: August 2013

Background

There exist many academic search solutions and most of them can be put on either ends of spectrum: general-purpose search and domain-specific "deep" search systems. The general-purpose search systems, such as PubMed, offer flexible query interface, but churn out a list of matching documents that users have to go through the results in order to find the answers to their queries. On the other hand, the "deep" search systems, such as PPI Finder and iHOP, return the precompiled results in a structured way. Their results, however, are often found only within some predefined contexts. In order to alleviate these problems, we introduce a new search engine, BOSS, Biomedical Object Search System.

Methods

Unlike the conventional search systems, BOSS indexes segments, rather than documents. A segment refers to a Maximal Coherent Semantic Unit (MCSU) such as phrase, clause or sentence that is semantically coherent in the given context (e.g., biomedical objects or their relations). For a user query, BOSS finds all matching segments, identifies the objects appearing in those segments, and aggregates the segments for each object. Finally, it returns the ranked list of the objects along with their matching segments.

Results

The working prototype of BOSS is available at http://boss.korea.ac.kr. The current version of BOSS has indexed abstracts of more than 20 million articles published during last 16 years from 1996 to 2011 across all science disciplines.

Conclusion

BOSS fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good scalability, just as with conventional document search engines, because it is designed to use a standard document-indexing model with minimal modifications. Considering the features, BOSS notches up the technological level of traditional solutions for search on biomedical information.
Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)
Authors: Derelle Romain , Kondrashov Fyodor A , Arkhipov Vladimir Y , Corbel Hélène , Frantz Adrien , Gasparini Julien , Jacquin Lisa , Jacob Gwenaël , Thibault Sophie , Baudry Emmanuelle
Published: August 2013

Background

Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons.

Findings

We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene.

Conclusions

Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.
Polycyclic Aromatic Hydrocarbons in drinking water of Tehran, Iran
Authors: Karyab Hamid , Yunesian Masud , Nasseri Simin , Mahvi Amir Hosein , Ahmadkhaniha Reza , Rastkari Noushin , Nabizadeh Ramin
Published: August 2013

Distribution and seasonal variation of sixteen priority polycyclic aromatic hydrocarbons (PAHs) were investigated in the drinking water of Tehran, the capital of Iran. Detected single and total PAHs concentrations were in the range of 2.01-38.96 and 32.45-733.10 ng/L, respectively, which were quite high compared to the values recorded in other areas of the world. The average occurrence of PAHs with high molecular weights was 79.55%; for example, chrysene occurred in 60.6% of the samples, with a maximum concentration of 438.96 ng/L. In addition, mean carcinogen to non-carcinogen PAHs ratio was 63.84. Although the concentration of benzo[a]pyrene, as an indicator of water pollution to PAHs, was lower than the guideline value proposed by World Health Organization (WHO) as well as that of Iranian National Drinking Water Standards for all of the samples, the obtained results indicated that carcinogen PAHs present in the drinking water of Tehran can cause threats to human health.
Wiener estimation of the Green’s function
Authors: Ziolkowski Anton
Published: August 2013

I consider the problem of finding the impulse response, or Green’s function, from a measured response including noise, given an estimate of the source time function. This process is usually known as signature deconvolution. Classical signature deconvolution provides no measure of the quality of the result and does not separate signal from noise. Recovery of the earth impulse response is here formulated as the calculation of a Wiener filter in which the estimated source signature is the input and the measured response is the desired output. Convolution of this filter with the estimated source signature is the part of the measured response that is correlated with the estimated signature. Subtraction of the correlated part from the measured response yields the estimated noise, or the uncorrelated part. The fraction of energy not contained in this uncorrelated component is defined as the quality of the filter. If the estimated source signature contains errors, the estimated earth impulse response is incomplete, and the estimated noise contains signal, recognizable as trace-to-trace correlation. The method can be applied to many types of geophysical data, including earthquake seismic data, exploration seismic data, and controlled source electromagnetic data; it is illustrated here with examples of marine seismic and marine transient electromagnetic data.
Foundation News
Authors: Berg Sandra
Published: August 2013

With a family full of geophysicists, Johannes Douma grew up “never going into geophysics.” His father worked for Shell, his uncle worked for WesternGeco, and his cousin worked for ION. However, he was always intrigued by the adventurous lifestyle. Johannes was born in the Netherlands. His family moved to Malaysia when he was four and then moved back to Holland when he was eight. At the age of 12, his family was transferred to New Orleans, and that's where his interest in physics and math began to develop into a “desire to analyze the Earth with physics.”
Advancements in satellite gravity gradient data for crustal studies
Authors: Ebbing Jörg , Bouman Johannes , Fuchs Martin , Lieb Verena , Haagmans Roger , Meekes J. A. C. , Fattah Rader Abdul
Published: August 2013

In recent years, global gravity models, both based only on satellite data and from combination with terrestrial data, are increasingly available and particularly useful to construct regional models before more local interpretations on the exploration scale are carried out. Often it is challenging to distinguish clearly between near-surface and regional or even subcrustal signals in the gravity field. Applying simple techniques like wavelength-filtering might lead to an incorrect estimate of the regional and residual field, which may significantly alter estimates of the thickness of sedimentary basins or the size of mineral deposits. An alternative is to use satellite gravity gradients to establish the regional components before studying local geology. Sampietro (2011) presented a global Mohorovicic discontinuity (Moho) depth map, which sparked a discussion about the validity of such results. Especially the question remains about whether crustal thickness estimates based on Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellite data have a higher accuracy than models based on global gravity models or terrestrial data. For example, the density contrast between crust and mantle remains a main factor of uncertainty.
Analysis and reprocessing of airborne gravity gradiometer data over the Strange Lake rare Earth deposit, Québec-Labrador
Authors: Keating Pierre , Pilkington Mark
Published: August 2013

A high-resolution airborne gravity gradiometer survey was flown in March 2012 over the Strange Lake intrusive complex, located on the border of Québec and Newfoundland and Labrador. This survey provided an opportunity to better understand the performance and limitations of this technology and also investigate potential improvements to the associated data processing. Airborne gravity gradient data low-pass-filtered at 75 m, rather than the standard 300 m, were provided by the contractor for this purpose. One flight line was reflown several times and used to assess the repeatability of the data, showing that in this particular area, the airborne gradient gravity system has a full-sine (wavelength) resolution of about 700 m. The system can therefore detect anomalies having a width of about 350 m. We also found that for gradiometer data, kriging is a better interpolator than low-pass filtering combined with minimum curvature gridding. Using kriging, line-to-line correlation (and in some cases, resolution) appears slightly improved.
Hungry for more at this year's Annual Meeting? SEG satisfies your APP-etite
Authors: Posey Chris
Published: August 2013

Navigating your way through the thousands of participants at the 2013 SEG International Exposition and 83rd Annual Meeting, as well as through the hundreds of exhibitor booths, the Continuing Education courses, technical sessions, posters, (and ePosters too!) can be a daunting task. To add to that, you'll also have to meet up with the right people, grab the right bus, and schmooze at the right receptions. Then it's back to your hotel to prepare to do it all again tomorrow. Wouldn't it simplify things if you could have all of the important Annual Meeting information you need neatly organized into a personalized schedule, all in the palm of your hand?
Intra-ER sorting of the peroxisomal membrane protein Pex3 relies on its luminal domain
Authors: Fakieh Mohammad H. , Drake Peter J. M. , Lacey Joanne , Munck Joanne M. , Motley Alison M. , Hettema Ewald H.
Published: August 2013

Pex3 is an evolutionarily conserved type III peroxisomal membrane protein required for peroxisome formation. It is inserted into the ER membrane and sorted via an ER subdomain (the peroxisomal ER, or pER) to peroxisomes. By constructing chimeras between Pex3 and the type III ER membrane protein Sec66, we have been able to separate the signals that mediate insertion of Pex3 into the ER from those that mediate sorting within the ER to the pER subdomain. The N-terminal 17-amino acid segment of Pex3 contains two signals that are each sufficient for sorting to the pER: a chimeric protein containing the N-terminal domain of Pex3 fused to the transmembrane and cytoplasmic segments of Sec66 sorts to the pER in wild type cells, and does not colocalise with peroxisomes. Subsequent transport to existing peroxisomes requires the Pex3 transmembrane segment. When expressed in Drosophila S2R+ cells, ScPex3 targeting to peroxisomes is dependent on the intra-ER sorting signals in the N-terminal segment. The N-terminal segments of both human and Drosophila Pex3 contain intra-ER sorting information and can replace that of ScPex3. Our analysis has uncovered the signals within Pex3 required for the various steps of its transport to peroxisomes. Our generation of versions of Pex3 that are blocked at each stage along its transport pathway provides a tool to dissect the mechanism, as well as the molecular machinery required at each step of the pathway.
Zebrafish rhabdomyosarcoma reflects the developmental stage of oncogene expression during myogenesis
Authors: Storer Narie Y. , White Richard M. , Uong Audrey , Price Emily , Nielsen G. Petur , Langenau David M. , Zon Leonard I.
Published: August 2013

Rhabdomyosarcoma is a pediatric malignancy thought to arise from the uncontrolled proliferation of myogenic cells. Here, we have generated models of rhabdomyosarcoma in the zebrafish by inducing oncogenic KRASG12D expression at different stages during muscle development. Several zebrafish promoters were used, including the cdh15 and rag2 promoters, which drive gene expression in early muscle progenitors, and the mylz2 promoter, which is expressed in differentiating myoblasts. The tumors that developed differed in their ability to recapitulate normal myogenesis. cdh15:KRASG12D and rag2:KRASG12D fish developed tumors that displayed an inability to complete muscle differentiation as determined by histological appearance and gene expression analyses. By contrast, mylz2:KRASG12D tumors more closely resembled mature skeletal muscle and were most similar to well-differentiated human rhabdomyosarcoma in terms of gene expression. mylz2:KRASG12D fish showed significantly improved survival compared with cdh15:KRASG12D and rag2:KRASG12D fish. Tumor-propagating activity was enriched in myf5-expressing cell populations within all of the tumor types. Our results demonstrate that oncogenic KRASG12D expression at different stages during muscle development has profound effects on the ability of tumor cells to recapitulate normal myogenesis, altering the tumorigenic capability of these cells.
The miR-310/13 cluster antagonizes β-catenin function in the regulation of germ and somatic cell differentiation in theDrosophilatestis
Authors: Pancratov Raluca , Peng Felix , Smibert Peter , Yang Jr-Shiuan , Olson Emily Ruth , Guha-Gilford Ciaran , Kapoor Amol J. , Liang Feng-Xia , Lai Eric C. , Flaherty Maria Sol , DasGupta Ramanuj
Published: August 2013

MicroRNAs (miRNAs) are regulators of global gene expression and function in a broad range of biological processes. Recent studies have suggested that miRNAs can function as tumor suppressors or oncogenes by modulating the activities of evolutionarily conserved signaling pathways that are commonly dysregulated in cancer. We report the identification of the miR-310 to miR-313 (miR-310/13) cluster as a novel antagonist of Wingless (Drosophila Wnt) pathway activity in a functional screen for Drosophila miRNAs. We demonstrate that miR-310/13 can modulate Armadillo (Arm; Drosophila β-catenin) expression and activity by directly targeting the 3′-UTRs of arm and pangolin (Drosophila TCF) in vivo. Notably, the miR-310/13-deficient flies exhibit abnormal germ and somatic cell differentiation in the male gonad, which can be rescued by reducing Arm protein levels or activity. Our results implicate a previously unrecognized function for miR-310/13 in dampening the activity of Arm in early somatic and germline progenitor cells, whereby inappropriate/sustained activation of Arm-mediated signaling or cell adhesion may impact normal differentiation in the Drosophila male gonad.
Oct transcription factors in development and stem cells: insights and mechanisms
Authors: Tantin Dean
Published: August 2013

The POU domain family of transcription factors regulates developmental processes ranging from specification of the early embryo to terminal differentiation. About half of these factors display substantial affinity for an 8 bp DNA site termed the octamer motif, and are hence known as Oct proteins. Oct4 (Pou5f1) is a well-known Oct factor, but there are other Oct proteins with varied and essential roles in development. This Primer outlines our current understanding of Oct proteins and the regulatory mechanisms that govern their role in developmental processes and concludes with the assertion that more investigation into their developmental functions is needed.
Iridophores and their interactions with other chromatophores are required for stripe formation in zebrafish
Authors: Frohnhöfer Hans Georg , Krauss Jana , Maischein Hans-Martin , Nüsslein-Volhard Christiane
Published: August 2013

Colour patterns of adult fish are produced by several types of pigment cells that distribute in the dermis during juvenile development. The zebrafish, Danio rerio, displays a striking pattern of dark stripes of melanophores interspersed by light stripes of xanthophores. Mutants lacking either cell type do not form proper stripes, indicating that interactions between these two chromatophore types are required for stripe formation. A third cell type, silvery iridophores, participates to render a shiny appearance to the pattern, but its role in stripe formation has been unclear. Mutations in rose (rse) or shady (shd) cause a lack or strong reduction of iridophores in adult fish; in addition, the melanophore number is drastically reduced and stripes are broken up into spots. We show that rse and shd are autonomously required in iridophores, as mutant melanophores form normal sized stripes when confronted with wild-type iridophores in chimeric animals. We describe stripe formation in mutants missing one or two of the three chromatophore types. None of the chromatophore types alone is able to create a pattern but residual stripe formation occurs with two cell types. Our analysis shows that iridophores promote and sustain melanophores. Furthermore, iridophores attract xanthophores, whereas xanthophores repel melanophores. We present a model for the interactions between the three chromatophore types underlying stripe formation. Stripe formation is initiated by iridophores appearing at the horizontal myoseptum, which serves as a morphological landmark for stripe orientation, but is subsequently a self-organising process.
Pain hypersensitivity mechanisms at a glance
Authors: Gangadharan Vijayan , Kuner Rohini
Published: August 2013

There are two basic categories of pain: physiological pain, which serves an important protective function, and pathological pain, which can have a major negative impact on quality of life in the context of human disease. Major progress has been made in understanding the molecular mechanisms that drive sensory transduction, amplification and conduction in peripheral pain-sensing neurons, communication of sensory inputs to spinal second-order neurons, and the eventual modulation of sensory signals by spinal and descending circuits. This poster article endeavors to provide an overview of how molecular and cellular mechanisms underlying nociception in a physiological context undergo plasticity in pathophysiological states, leading to pain hypersensitivity and chronic pain.
Innexins Ogre and Inx2 are required in glial cells for normal postembryonic development of the Drosophila central nervous system
Authors: Holcroft Catherine E. , Jackson William D. , Lin Wei-Hsiang , Bassiri Kayleigh , Baines Richard A. , Phelan Pauline
Published: August 2013

Innexins are one of two gene families that have evolved to permit neighbouring cells in multicellular systems to communicate directly. Innexins are found in prechordates and persist in small numbers in chordates as divergent sequences termed pannexins. Connexins are functionally analogous proteins exclusive to chordates. Members of these two families of proteins may form intercellular channels, assemblies of which constitute gap junctions. Each intercellular channel is a composite of two hemichannels, one from each of two apposed cells. Hemichannels dock in the extracellular space to form a complete channel with a central aqueous pore that regulates the cell-cell exchange of ions and small signalling molecules. Hemichannels may also act independently by releasing paracrine signalling molecules. optic ganglion reduced (ogre) is a member of the Drosophila innexin family, originally identified as a gene essential for postembryonic neurogenesis. Here we demonstrate, by heterologous expression in paired Xenopus oocytes, that Ogre alone does not form homotypic gap-junction channels, however, co-expression of Ogre with Innexin2 (Inx2) induces formation of functional channels, with properties distinct from Inx2 homotypic channels. In the Drosophila larval CNS, we find that Inx2 partially co-localises with Ogre in proliferative neuroepithelia and in glial cells. Downregulation of either ogre or inx2 selectively in glia, by targeted expression of RNA interference transgenes, leads to a significant reduction in the size of the larval CNS and behavioural defects in surviving adults. We conclude that these innexins are critically required in glial cells for normal postembryonic development of the CNS.