bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal Diagnosis and Postnatal Findings of Bronchogenic Cyst
Authors: Rios Livia Teresa Moreira , Araujo Júnior Edward , Nardozza Luciano Marcondes Machado , Moron Antonio Fernandes , Martins Marília da Glória
Published: May 2013

Bronchogenic cysts arise from abnormal buds from the primitive esophagus and tracheobronchial tree, which do not extend to the site where alveolar differentiation occurs. Bronchogenic cysts are typically unilocular mucus field lesions arising from posterior membranous wall of the air way. The prenatal diagnosis usually is realized by two-dimensional ultrasound showing the large unilocular cystic image in the chest fetus. The prenatal percutaneous aspiration can reduce the risk of heart compression and permit better respiratory conditions to newborn. We present a case of a primiparous pregnant 23 year-old-woman prenatal ultrasound showed a large unilocular cyst in the left hemithorax with compression of the normal left lung tissue and contralateral mediastinal shift. This cyst was percutaneously aspirated without subsequent reaccumulation of fluid. The newborn did not have respiratory distress and the computed tomography scan confirmed the finding of a fluid-filled cyst in the left chest. The chest X-ray showed the displacement of the heart and the mediastinum from the left to the right. The prenatal diagnosis of bronchogenic cyst is very important to assess the degree of the compression of the normal lung and the mediastinum shift. Furthermore, the prenatal diagnosis permits planning delivery in the tertiary hospital with multidisciplinary team because of the risk of respiratory distress.
The Limit Behavior of a Stochastic Logistic Model with Individual Time-Dependent Rates
Authors: Shang Yilun
Published: May 2013

We investigate a variant of the stochastic logistic model that allows individual variation and time-dependent infection and recovery rates. The model is described as a heterogeneous density dependent Markov chain. We show that the process can be approximated by a deterministic process defined by an integral equation as the population size grows.
Periodontal Disease: Linking the Primary Inflammation to Bone Loss
Authors: Di Benedetto Adriana , Gigante Isabella , Colucci Silvia , Grano Maria
Published: May 2013

Periodontal disease (PD), or periodontitis, is defined as a bacterially induced disease of the tooth-supporting (periodontal) tissues. It is characterized by inflammation and bone loss; therefore understanding how they are linked would help to address the most efficacious therapeutic approach. Bacterial infection is the primary etiology but is not sufficient to induce the disease initiation or progression. Indeed, bacteria-derived factors stimulate a local inflammatory reaction and activation of the innate immune system. The innate response involves the recognition of microbial components by host cells, and this event is mediated by toll-like receptors (TLRs) expressed by resident cells and leukocytes. Activation of these cells leads to the release of proinflammatory cytokines and recruitment of phagocytes and lymphocytes. Activation of T and B cells initiates the adaptive immunity with Th1 Th2 Th17 Treg response and antibodies production respectively. In this inflammatory scenario, cytokines involved in bone regulation and maintenance have considerable relevance because tissue destruction is believed to be the consequence of host inflammatory response to the bacterial challenge. In the present review, we summarize host factors including cell populations, cytokines, and mechanisms involved in the destruction of the supporting tissues of the tooth and discuss treatment perspectives based on this knowledge.
A Robust Fuzzy Sliding Mode Controller Synthesis Applied on Boost DC-DC Converter Power Supply for Electric Vehicle Propulsion System
Authors: Allaoua Boumediène , Mebarki Brahim , Laoufi Abdellah
Published: May 2013

The development of electric vehicles power electronics system control comprising of DC-AC inverters and DC-DC converters takes a great interest of researchers in the modern industry. A DC-AC inverter supplies the high power electric vehicle motors torques of the propulsion system and utility loads, whereas a DC-DC converter supplies conventional low-power, low-voltage loads. However, the need for high power bidirectional DC-DC converters in future electric vehicles has led to the development of many new topologies of DC-DC converters. Nonlinear control of power converters is an active area of research in the fields of power electronics. This paper focuses on a fuzzy sliding mode strategy (FSMS) as a control strategy for boost DC-DC converter power supply for electric vehicle. The proposed fuzzy controller specifies changes in the control signal based on the surface and the surface change knowledge to satisfy the sliding mode stability and attraction conditions. The performances of the proposed fuzzy sliding controller are compared to those obtained by a classical sliding mode controller. The satisfactory simulation results show the efficiency of the proposed control law which reduces the chattering phenomenon. Moreover, the obtained results prove the robustness of the proposed control law against variation of the load resistance and the input voltage of the studied converter.
Bilateral Paramedian Thalamic Infarction Initially Presenting as a Convulsive Seizure
Authors: Wang Jianping , Fu Xiaojie , Jiang Chao , Liu Hengfang , Zhao Yuanzheng , Han Wei
Published: May 2013

Bithalamic infarctions initially presenting as a convulsive seizure are rarely reported and, to our best knowledge, have never been reported in China. Here, we present a patient with convulsive seizure at the onset of bilateral paramedian thalamic infarction. The diffusion-weighted imaging revealed that the infarct area is supplied by Percheron artery. Associated with the relationship between seizure and centrencephalic system and reticular formation as previously reported, we suggest that seizure could be the onset symptom of paramedian thalamic infarction. Physicians should recognize this condition, because both seizure control and early ischemic stroke management are required.
Rock Art Dating and the Peopling of the Americas
Authors: Whitley David S.
Published: May 2013

The peopling of the Americas is both the oldest and most frequently researched question in American archaeology. Although rarely considered, early art has the potential to provide insight into questions that may be obscured by other kinds of evidence, particularly stone tools. What part did art play in the peopling of the Americas? This question is addressed starting with a reconsideration of rock varnish chronometrics as applied to Great Basin, eastern California, petroglyphs. This demonstrates, conservatively, that the petroglyph tradition began before 11,100 YBP, probably before 12,600 YBP, and potentially in the 14,000 years range. Comparison of these ages with evidence from other regions in the hemisphere demonstrates substantial artistic and stylistic variation in rock art by the Paleoindian period (circa 10,000–11,000 YBP). This suggests that, while art may have been part of the baggage of the first immigrants, regional cultural traditions had already been developed by the Terminal Pleistocene, if not earlier. The result is evidence for the development of regional cultural diversity in the Americas by Paleoindian times.
Improvement of Dispersion and Color Effect of Organic Pigments in Polymeric Films via Microencapsulation by the Miniemulsion Technique
Authors: Qi Dongming , Chen Zhijie , Yang Lei , Cao Zhihai , Wu Minghua
Published: May 2013

Three primary pigment/poly(n-butyl acrylate-co-styrene) (P(BA+St)) nanocomposites were prepared via encapsulation of the corresponding organic pigments via the miniemulsion technique. The resulting latexes of the P(BA+St)/pigment nanocomposites were filmed in a PTFE mould or printed onto cotton fabric. The morphology of the P(BA+St)/pigment nanocomposites and the dispersion of pigment particles in the latex film and on the printed fabric surface, as well as the adhesion between pigment and adhesive film, were evaluated by transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), 3D digital microscope system (3D-POM), and printing results tests. Attributing to the preprotection of adhesive polymer shell, the self-adhesive P(BA+St)/pigment nanocomposites were homogeneously and firmly dispersed both in the thin latex film and in the adhesive layer on the fiber surface. As a result, the color strength, color fastness, and handle of the fabrics printed by the P(BA+St)/pigment nanocomposites latex were significantly improved, compared to the fabrics printed by the conventional pigment blended latex.
A New Multiphase Soft Segmentation with Adaptive Variants
Authors: Wang Hongyuan , Chen Fuhua , Chen Yunmei
Published: May 2013

Soft segmentation is more flexible than hard segmentation. But the membership functions are usually sensitive to noise. In this paper, we propose a multiphase soft segmentation model for nearly piecewise constant images based on stochastic principle, where pixel intensities are modeled as random variables with mixed Gaussian distribution. The novelty of this paper lies in three aspects. First, unlike some existing models where the mean of each phase is modeled as a constant and the variances for different phases are assumed to be the same, the mean for each phase in the Gaussian distribution in this paper is modeled as a product of a constant and a bias field, and different phases are assumed to have different variances, which makes the model more flexible. Second, we develop a bidirection projected primal dual hybrid gradient (PDHG) algorithm for iterations of membership functions. Third, we also develop a novel algorithm for explicitly computing the projection fromRKto simplexΔK-1for any dimensionKusing dual theory, which is more efficient in both coding and implementation than existing projection methods.
Schistonchus molochi sp. n. and S. athertonensis sp. n. (Nematoda: Aphelenchoididae) from Ficus watkinsiana (Moraceae) in Australia
Authors: Davies Kerrie A. , Bartholomaeus Faerlie , Kanzaki Natsumi , Giblin-Davis Robin M.
Published: May 2013

Ficus watkinsiana (sub-genus Urostigma, Section Stilpnophyllum) is endemic to Australia, growing in two disjunct populations, one in north-eastern Queensland and the other in south-eastern Queensland and north-eastern New South Wales. Schistonchus molochi sp. n. is described from F. watkinsiana in Queensland, Australia, and differentiated from other species of Schistonchus by a combination of morphological characters including having the excretory pore opening near the nerve ring, a broad head, a large, strongly sclerotised, stylet, a distinct lip sector disc with raised edges, a long post-uterine sac, rose-thorn-shaped spicule, no gubernaculum, three pairs of subventral papillae on the tail (one pair pre-cloacal on the anterior lip, one pair adcloacal on the posterior lip, and one slightly posterior to mid-tail) and bluntly rounded tail tip, and apparent biogeographical range. Presence of the lip sector disc suggests that it is closest to S. macrophylla. Schistonchus athertonensis sp. n. is also described from F. watkinsiana in Queensland and is characterised by a combination of morphological characters, including having the excretory pore opening near the nerve ring, a medium length post-uterine sac, presence of vulval flap in some specimens, rose-thorn-shaped spicule, no gubernaculum, and three pairs of subventral papillae on the tail (one pair adcloacal on the posterior lip, one at three to four-fifths of the tail length and one near the tip), a narrowly rounded tail tip, and apparent biogeographical range. Morphospecies 8, originally collected from F. obliqua, was also collected from F. watkinsiana in Queensland, and S. altermacrophylla was found with it in South Australia. These collections are further evidence of host-switching within Schistonchus.
Morphological and molecular study of Californian species of the genus Aporcelaimellus Heyns, 1965 (Dorylaimida: Aporcelaimidae)
Authors: Álvarez-Ortega Sergio , Subbotin Sergei A. , Peña-Santiago Reyes
Published: May 2013

Several species of Aporcelaimellus collected in natural areas in California, USA, are characterised on the basis of morphological, morphometric and molecular data. Two new species are identified and described here. Aporcelaimellus californicus sp. n. is characterised by its body length of 2.46-3.42 mm, lip region offset by constriction and 24-26 μm broad, odontostyle 23-24 μm long, neck 611-765 μm long, pharyngeal expansion occupying 50-52% of total neck length, a dorsal cellular mass present at level of cardia, uterus simple and 246-408 μm long, V = 53-58, short conoid tail (43-50 μm, c = 56-71, c′ = 0.8-1.0) with a large hyaline portion occupying more than half of its total length, spicules 98 μm long, and 8-9 spaced ventromedian supplements. Aporcelaimellus salicinus sp. n. is distinguished by its body length of 1.45-1.94 mm, lip region offset by deep constriction and 16-18 μm broad, odontostyle 18-20 μm long, neck 393-521 μm long, pharyngeal expansion occupying 45-51% of total neck length, presence of a dorsal cellular mass at level of cardia, uterus simple and 21-45 μm long, V = 51-57, tail conical to conoid (31-38 μm, c = 39-59, c′ = 1.0-1.4), and male unknown. Measurements, sequences and taxonomic comments are provided for the other three Aporcelaimellus species. Californian Aporcelaimellus display a notable morphological homogeneity but a remarkable molecular diversity, putting into question the monophyly of this group.
Schistonchus fistulosus n. sp. (Nematoda: Aphelenchoididae) associated with Ficus fistulosa in China
Authors: Zeng Yongsan , Ye Weimin , Wang Xinrong , Du Zhijian , Giblin-Davis Robin M.
Published: May 2013

A new nematode species was recovered from syconia of Ficus fistulosa from the South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China, during a survey of nematode biodiversity from 2007 to 2012. It is described herein as Schistonchus fistulosus n. sp. and is typologically characterised by possessing the combined characters of a long post-uterine sac, excretory pore located near the metacorpus, amoeboid sperm, three pairs of subventral papillae on the male tail, a mucron on the male tail tip, absence of a gubernaculum and possession of ox-horn-shaped spicules without a terminal cucullus and with a short, broad and bluntly rounded rostrum. Schistonchus fistulosus n. sp. was easily differentiated from other sequenced species by the partial small subunit rRNA gene (SSU) and D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with partial SSU sequences suggests that S. fistulosus n. sp. has a closer relationship with S. guangzhouensis and S. baculum in the same highly supported monophyletic clade than to the other sequenced Schistonchus species. Based upon inferences using LSU D3 sequence data, it is also in a well-supported monophyletic clade with S. guangzhouensis and S. baculum.
Bursaphelenchus masseyi sp. n. (Nematoda: Parasitaphelenchinae) – a nematode associate of the bark beetle, Trypophloeus populi Hopkins (Coleoptera: Curculionidae: Scolytinae), in aspen, Populus tremuloides Michx. affected by sudden aspen decline in Colorado
Authors: Tomalak Marek , Worrall James , Filipiak Anna
Published: May 2013

Bursaphelenchus masseyi sp. n. is described from trunks of unhealthy trembling aspen, Populus tremuloides, affected by sudden aspen decline (SAD) in Colorado, USA. All propagative stages of the nematode were present in larval galleries of a bark beetle, Trypophloeus populi. The dauer juveniles occupy the haemocoel of older larvae, pupae and adult beetles. The characteristic morphology of the male spicules with small but distinct cucullus, extended anterior vulval lip in female, lateral fields with four incisures, and number and arrangement of male caudal papillae, indicate that B. masseyi sp. n. is closely related to the xylophilus group. This relation has been confirmed by DNA sequencing and phylogenetic analysis of the 28S rDNA region. The new species is characterised by the body length of 958 (765-1203) μm in female and 874 (691-1122) μm in male, moderately slender body (a = 38.2 (33.5-41.1) and 38.0 (33.1-44.1) in female and male, respectively), and spicules 29.2 (26.2-34.7) μm long with a small cucullus (1.3-1.5 μm in diam.) at their tips. Bursaphelenchus masseyi sp. n. can be separated from other species in the xylophilus group by the morphology of spicules which have a short capitulum and unique rostrum that is pointed somewhat anteriorly, relatively thick vulval flap, which is straight, parallel to the body long axis and bent towards the body wall at its distal end, and other morphological and morphometric characters. The new species most closely resembles B. trypophloei, but differs by the morphology of spicules (short but distinct condylus vs condylus in a continuous line with dorsal lamina, and smaller cucullus). The taxonomic separation of the new species is also confirmed by the unique molecular profile of the ITS region (ITS-RFLP). Diallelic cross-breeding in vitro revealed also that B. masseyi sp. n. and B. trypophloei are reproductively incompatible. The new species showed poor ability to develop and reproduce on Botrytis cinerea cultures, although it grew vigorously on laboratory cultures of Polish and Colorado isolates of Cytospora chrysosperma, the fungus naturally associated with galleries of the nematode vector, T. populi.
Rain and Water Symbolism in Southern African Religious Systems: Continuity and Change
Authors: Müller Retief , Kruger Frans
Published: May 2013

Abstract

This article presents a diachronic perspective on rain and water rituals in southern Africa. The authors claim that contemporary rituals can only be properly understood when cognisance has been taken of their deep roots into the past. The authors indicate how water and rain rituals show signs of continuity between past and present, in spite of the dramatic upheavals created by the arrival of colonialism and missionary Christianity. The authors furthermore argue that such rituals are not only of ‘religious’ importance, but also indicative of the material concerns concerning the environment in the communal consciousness of ordinary people. The popular interest in these types of rituals may indeed be understood as the refusal by ordinary people to submit to a dominant globalisation paradigm which has a vested interest in casting them in the role of permanently helpless victims.
Two new species of genus Apsilochorema Ulmer (Trichoptera: Hydrobiosidae) from India
Authors: SAINI MALKIAT S. , K. LAKHWINDER , PANDHER MANPREET S. , PAREY SAJAD H.
Published: May 2013

Two new species of Apsilochorema (Trichoptera: Hydrobiosidae) from India are described, Apsilochorema (Archichore-ma) kashmirensis sp. nov. and Apsilochorema (Archichorema) meyi sp. nov., bringing to 12 the number of species in the genus known from the country.
A new species of Pseudoleptochelia Lang, 1973 (Crustacea: Peracarida: Tanaidacea: Leptocheliidae) from the Northwest Atlantic with observations on the status of the genus
Authors: MORALES-NÚÑEZ ANDRÉS G. , HEARD RICHARD W. , ALFARO MÓNICA
Published: May 2013

Pseudoleptochelia juliae n. sp. is described from Puerto Rican waters in depths from 1 to 28 m. The new species and P. fairgo from western Australia are the only members of the genus as defined in this revision that have a distinct process on the posterior margin of the cheliped carpus. The male of P. juliae is distinguished from that of P. fairgo by this process being sub-acute and having a distinctly narrower propodus. Lang’s generic diagnosis for the female of Pseudoleptochelia is incorrect, which has led to confusion. Based in examination of Mediterranean specimens attributed to the type species P. anomala (Sars), Pseudoleptochelia is rediagnosed to contain seven species; P. anomala; P. fairgo; P. juliae; P. magna; P. mortenseni; P. occiporta; and P. straddi., The genus is reviewed and discussed and the taxonomic status for the remain-ing nine species previously assigned to the genus is re-evaluated. Pseudoleptochelia shares similarities with the more re-cently described Pacific genera Konarus and Parakonarus and to a lesser extent to the highly derived genus Makraleptochelia.
Upscale Effects of Deep Convection during the North American Monsoon
Authors: Stensrud David J.
Published: May 2013

The ability of deep monsoon convection to influence the larger-scale circulation over North America is investigated for a 6-day-long case study during the 2006 North American monsoon. Results from Rossby wave ray tracing and numerical simulations using the Advanced Research Weather Research and Forecasting model indicate that North American monsoon convection provides a source region for stationary Rossby waves. Two wave trains are seen in the numerical model simulations, with behaviors that agree well with expectations from theory and ray tracing. The shorter and faster-moving wave train moves eastward from the source region in Mexico and reaches the western Atlantic within 4 days. The longer and slower-moving wave train travels northeastward and reaches the coastal New England region within 6 days. An upstream tail of anticyclonic vorticity extends westward from the source region into the central Pacific Ocean.

The monsoon convection appears to help cut off the low-level anticyclonic flow by developing low-level southerly flow in the Gulf of Mexico and northerly flow in the eastern Pacific, as suggested in earlier global model studies. However, the stationary Rossby wave trains further alter the location and intensity of deep convection in locations remote from the monsoon. These results suggest that unless a numerical model can correctly predict monsoon convection, the ability of the model to produce accurate forecasts of the large-scale pattern and associated convective activity beyond a few days is in question. This result may be important for global climate modeling, since an inaccurate prediction of monsoon convection would lead to an inaccurate Rossby wave response.
Airborne Observations of a Catalina Eddy
Authors: Parish Thomas R. , Rahn David A. , Leon Dave
Published: May 2013

Summertime low-level winds over the ocean adjacent to the California coast are typically from the north, roughly parallel to the coastline. Past Point Conception the flow often turns eastward, thereby generating cyclonic vorticity in the California Bight. Clouds are frequently present when the cyclonic motion is well developed and at such times the circulation is referred to as a Catalina eddy. Onshore flow south of the California Bight associated with the eddy circulation can result in a thickening of the low-level marine stratus adjacent to the coast. During nighttime hours the marine stratus typically expands over a larger area and moves northward along the coast with the cyclonic circulation. A Catalina eddy was captured during the Precision Atmospheric Marine Boundary Layer Experiment in June of 2012. Measurements were made of the cloud structure in the marine layer and the horizontal pressure field associated with the cyclonic circulation using the University of Wyoming King Air research aircraft. Airborne measurements show that the coastal mountains to the south of Los Angeles block the flow, resulting in enhanced marine stratus heights and a local pressure maximum near the coast. The horizontal pressure field also supports a south–north movement of marine stratus. Little evidence of leeside troughing south of Santa Barbara, California, was observed for this case, implying that the horizontal pressure field is forced primarily through topographic blocking by the coastal terrain south of Los Angeles, California, and the ambient large-scale circulation associated with the mean flow.
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing
Authors: Morin Ryan D. , Mungall Karen , Pleasance Erin , Mungall Andrew J. , Goya Rodrigo , Huff Ryan D. , Scott David W. , Ding Jiarui , Roth Andrew , Chiu Readman , Corbett Richard D. , Chan Fong Chun , Mendez-Lago Maria , Trinh Diane L. , Bolger-Munro Madison , Taylor Greg , Hadj Khodabakhshi Alireza , Ben-Neriah Susana , Pon Julia , Meissner Barbara , Woolcock Bruce , Farnoud Noushin , Rogic Sanja , Lim Emilia L. , Johnson Nathalie A. , Shah Sohrab , Jones Steven , Steidl Christian , Holt Robert , Birol Inanc , Moore Richard , Connors Joseph M. , Gascoyne Randy D. , Marra Marco A.
Published: May 2013

Key Points

Complete genome sequence analysis of 40 DLBCL tumors and 13 cell lines reveals novel somatic point mutations, rearrangements, and fusions. Recurrence of mutations in genes involved in B-cell homing were identified in germinal center B-cell DLBCLs.
Identification of thyroid hormone receptor binding sites in developing mouse cerebellum
Authors: Gagne Remi , Green James R , Dong Hongyan , Wade Mike G , Yauk Carole L
Published: May 2013

Background

Thyroid hormones play an essential role in early vertebrate development as well as other key processes. One of its modes of action is to bind to the thyroid hormone receptor (TR) which, in turn, binds to thyroid response elements (TREs) in promoter regions of target genes. The sequence motif for TREs remains largely undefined as does the precise chromosomal location of the TR binding sites. A chromatin immunoprecipitation on microarray (ChIP-chip) experiment was conducted using mouse cerebellum post natal day (PND) 4 and PND15 for the thyroid hormone receptor (TR) beta 1 to map its binding sites on over 5000 gene promoter regions. We have performed a detailed computational analysis of these data.

Results

By analysing a recent spike-in study, the optimal normalization and peak identification approaches were determined for our dataset. Application of these techniques led to the identification of 211 ChIP-chip peaks enriched for TR binding in cerebellum samples. ChIP-PCR validation of 25 peaks led to the identification of 16 true positive TREs. Following a detailed literature review to identify all known mouse TREs, a position weight matrix (PWM) was created representing the classic TRE sequence motif. Various classes of promoter regions were investigated for the presence of this PWM, including permuted sequences, randomly selected promoter sequences, and genes known to be regulated by TH. We found that while the occurrence of the TRE motif is strongly correlated with gene regulation by TH for some genes, other TH-regulated genes do not exhibit an increased density of TRE half-site motifs. Furthermore, we demonstrate that an increase in the rate of occurrence of the half-site motifs does not always indicate the specific location of the TRE within the promoter region. To account for the fact that TR often operates as a dimer, we introduce a novel dual-threshold PWM scanning approach for identifying TREs with a true positive rate of 0.73 and a false positive rate of 0.2. Application of this approach to ChIP-chip peak regions revealed the presence of 85 putative TREs suitable for further in vitro validation.

Conclusions

This study further elucidates TRβ gene regulation in mouse cerebellum, with 211 promoter regions identified to bind to TR. While we have identified 85 putative TREs within these regions, future work will study other mechanisms of action that may mediate the remaining observed TR-binding activity.
Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies
Authors: Yutin Natalya , Raoult Didier , Koonin Eugene V
Published: May 2013

Background

Recent advances of genomics and metagenomics reveal remarkable diversity of viruses and other selfish genetic elements. In particular, giant viruses have been shown to possess their own mobilomes that include virophages, small viruses that parasitize on giant viruses of the Mimiviridae family, and transpovirons, distinct linear plasmids. One of the virophages known as the Mavirus, a parasite of the giant Cafeteria roenbergensis virus, shares several genes with large eukaryotic self-replicating transposon of the Polinton (Maverick) family, and it has been proposed that the polintons evolved from a Mavirus-like ancestor.

Results

We performed a comprehensive phylogenomic analysis of the available genomes of virophages and traced the evolutionary connections between the virophages and other selfish genetic elements. The comparison of the gene composition and genome organization of the virophages reveals 6 conserved, core genes that are organized in partially conserved arrays. Phylogenetic analysis of those core virophage genes, for which a sufficient diversity of homologs outside the virophages was detected, including the maturation protease and the packaging ATPase, supports the monophyly of the virophages. The results of this analysis appear incompatible with the origin of polintons from a Mavirus-like agent but rather suggest that Mavirus evolved through recombination between a polinton and an unknownvirus. Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements.

Conclusions

The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements.
A multi-site single blind clinical study to compare the effects of prolonged exposure, eye movement desensitization and reprocessing and waiting list on patients with a current diagnosis of psychosis and co morbid post traumatic stress disorder: study protocol for the randomized controlled trial Treating Trauma in Psychosis
Authors: de Bont Paul AJM , van den Berg David PG , van der Vleugel Berber M , de Roos Carlijn , Mulder Cornelis L , Becker Eni S , de Jongh Ad , van der Gaag Mark , van Minnen Agnes
Published: May 2013

Background

Trauma contributes to psychosis and in psychotic disorders post-traumatic stress disorder (PTSD) is often a comorbid disorder. A problem is that PTSD is underdiagnosed and undertreated in people with psychotic disorders. This study’s primary goal is to examine the efficacy and safety of prolonged exposure and eye movement desensitization and reprocessing (EMDR) for PTSD in patients with both psychotic disorders and PTSD, as compared to a waiting list. Secondly, the effects of both treatments are determined on (a) symptoms of psychosis, in particular verbal hallucinations, (b) depression and social performance, and (c) economic costs. Thirdly, goals concern links between trauma exposure and psychotic symptomatology and the prevalence of exposure to traumatic events, and of PTSD. Fourthly predictors, moderators, and mediators for treatment success will be explored. These include cognitions and experiences concerning treatment harm, credibility and burden in both participants and therapists.

Methods/Design

A short PTSD-screener assesses the possible presence of PTSD in adult patients (21- to 65- years old) with psychotic disorders, while the Clinician Administered PTSD Scale interview will be used for the diagnosis of current PTSD. The M.I.N.I. Plus interview will be used for diagnosing lifetime psychotic disorders and mood disorders with psychotic features. The purpose is to include consenting participants (N = 240) in a multi-site single blind randomized clinical trial. Patients will be allocated to one of three treatment conditions (N = 80 each): prolonged exposure or EMDR (both consisting of eight weekly sessions of 90 minutes each) or a six-month waiting list. All participants are subjected to blind assessments at pre-treatment, twomonths post treatment, and six monthspost treatment. In addition, participants in the experimental conditions will have assessments at mid treatment and at 12 months follow-up.

Discussion

The results from the post treatment measurement can be considered strong empirical indicators of the safety and effectiveness of prolonged exposure and EMDR. The six-month and twelve-month follow-up data have the potential of reliably providing documentation of the long-term effects of both treatments on the various outcome variables. Data from pre-treatment and midtreatment can be used to reveal possible pathways of change.

Trial registration

Trial registration:ISRCTN79584912
Photocatalytic effect of TiO2and the effect of dopants on degradation of brilliant green
Authors: Munusamy Shamalah , Aparna Rangabhatla sai laxmi , Prasad Rangabhatla gunneswara subramanya v
Published: May 2013

Photocatalysis speeds up the photoreaction in the presence of a catalyst. TiO2 has low toxicity, less resistance and less corrosion and has semiconductor properties. Its strong oxidative potential of the positive holes oxidizes water to create hydroxyl radicals. Moreover, TiO2 has been proven to be a tremendous photocatalyst compound by which many organic substrates have been shown to be oxidatively degraded under UV irradiation. In this research the photocatalytic effect of TiO2 on degradation of Brilliant Green (BG) was studied. In conjunction the effect of dopants such as Zn and Cu on photocatalysis of TiO2 were also studied. Structural and morphological properties of TiO2 were characterized by SEM and XRD. From this research the initial concentration of sample, pH of samples, chemical structure of dyes and catalyst loading were most valuable parameters for dye degradation. TiO2 showed excellent result on degradation of BG compared with doped TiO2. 99% degradation was obtained in presence of TiO2, followed by TiO2/Zn for 87% and TiO2/Cu for 46%. TiO2 doped with transition metals can increase or decrease photocatalytic degradation of dyes.
From Ancients and Moderns to Geography and Anthropology: The Meaning of History in the Thought of Adam Smith, Karl Marx, and Alfred Marshall
Authors: Cook Simon J.
Published: May 2013

Developments internal to the study of history have played a significant if overlooked role in the changing status of history within political economy. This article illustrates that claim by way of a survey of the place of history in the writings of Adam Smith, Karl Marx, and Alfred Marshall. It identifies a sea change in historical thought after the French Revolution, such that Smith's basic contrast of modern with ancient society was replaced in the thought of both Marx and Marshall by a contrast between the modern and the traditional, where the latter consisted of agrarian societies of one sort or another, distinguished according to their particular form of social bond and land ownership. But the discovery of human prehistory in the second half of the nineteenth century undermined the historical presuppositions shared by Marx and Marshall, leading both to revise not only their earlier historical accounts but also their conceptions of the relationship between the historical and the economic. While the discovery of prehistory can be seen as returning Smith's ``primitives'' to the historiographical stage, it also played an important part in fostering the twentieth-century separation of economics from history.
Recovery of DNA Synthesis from Inhibition by Ultraviolet Light in Mammalian Cells
Authors: Ventura Armando M. , Ortega J. Miguel , Schumacher R. Ivan , Meneghini Rogerio
Published: May 2013

In general mammalian cells recover from DNA synthesis inhibition by ultraviolet light (u.v.) before most of the pyrimidine dimers have been removed from the genome. This is a complex phenomenon whose biological significance has not been fully assessed. In Chinese hamster V79 cells this recovery seems to be directly coupled to an enhanced rate of double-stranded DNA elongation. The presence of the DNA polymerase it inhibitor, aphidicolin, after u.v. irradiation produces two different responses. At low concentration, sufficient to inhibit 95 % of DNA replication but having no effect on excision repair, the drug has no effect on the recovery. This shows that ongoing replicative DNA synthesis is not required for recovery. At higher concentrations of aphidicolin, sufficient to block excision repair, the recovery phenomenon was prevented. The recovery was also prevented by actinomycin D at a concentration that inhibits 60 % of RNA synthesis. In quantitative autoradiography experiments in which previously irradiated cells were fused with unirradiated cells the nuclei of the latter exhibited a higher resistance to inhibition by u.v. than nuclei from non-fused cells. These results indicate that: (1) even the low repair rate exhibited by V79 cells (relative to human cells) is important for recovery; although most of the dimers remain in the V79 genome after recovery of DNA synthesis, either the removal of lesions from some important region of chromatin or the activity of the repair process itself is important for the recovery; (2) the recovery mechanism is induced and depends on RNA synthesis and the production of specific factors.

Finally, we have observed that cells previously treated with fluorodeoxyuridine become more resistant to inhibition by u.v. After irradiation these cells replicate DNA faster than untreated cells. Since it has been shown that this drug activates unused origins of replication in Chinese hamster cells, reducing the average replicon size, we assume that the acquired resistance has to do with the operation of a larger number of smaller replicons. This may also be the mechanism whereby recovery from inhibition occurs after u.v. irradiation.
The Role of O6-Methylguanine in Human Cell Killing, Sister Chromatid Exchange Induction and Mutagenesis: A Review
Authors: Day Rufus S. , Babich Michael A. , Yarosh Daniel B. , Scudiero Dominic A.
Published: May 2013

O 1-methylguanine (O1mG) produced in DNA by such SN1 methylating agents as N-methyl-N-nitrososurea and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) has been suggested by some to be the lesion that leads to certain biological endpoints in mammalian cells: cell killing, sister chromatid exchange (SCE) production, mutagenesis and cellular transformation. Other evidence is interpreted as inconsistent with this point of view. The finding of Karran & Williams (1985) that O1mG delivered to cells in culture resulted in the depletion of the activity of the protein responsible for repair of O1mG in DNA (O1mG-DNA methyltransferase, O1MT) provided a tool for the assessment of the role of O1mG in producing biological endpoints. In this paper we review much of the literature on human cells pertinent to this question. In addition we present our survival data obtained using the depletion technique of Karran & Williams as well as data supporting a model invoking a mismatch and excision response to O1mG proposed by Sklar & Strauss (1980). Although data linking O1mG to causation are inconclusive, it is premature to conclude that O1mG is not a lesion lethal to certain cultured cells.
Cellulose microfibril assembly and orientation: recent developments
Authors: Brown R. Malcolm
Published: May 2013

A brief history of the literature dealing with cellulose microfibril assembly is presented, and a current summary of cellulose microfibril synthesizing complexes among eukaryotic cells is given. Terminal complexes not described before include the following: linear terminal complexes (TCs) with three rows in Eremosphaera, Microdictyon and Chaetomorpha’, globular terminal complexes in Ophioglossum, Psilotum, Equisetum and Gingko. Cellulose microfibril assembly in Acetobacter xylinum is described very briefly and compared with the process among eukaryotic cells. Particular emphasis on structures that may be involved in the spatial control of cellulose synthesis is given i Among these are cytoplasmic structures such as microtubules and microfilaments. Microfilament structures are shown to clearly surround individual microtubules that lie adjacent to the plasma membrane. Using freeze-fracture techniques, these labile associations have been shown for the first time. Microfibril orientation may be mediated through an interaction of cortical microtubules in association with microfilaments. A review of Mueller and Brown’s membrane flow model for microfibril orientation is presented. Cellulose terminal complex clustering and its role in gravitropic response is covered. Definitive membrane changes with TC clustering/disaggregation and intramembranous particle frequencies, occur within 12 min following gravistimulation. These differences are pronounced in the cells from upper and lower hemicylinders of rapidly frozen tissue, which was studied by the freeze-fracture method. A hypothesis for cellulose microfibril interaction in controlling the constraint of the growth axis is presented, and the supporting data for terminal complex clustering/disaggregation as well as fluorescent brightener inhibition of the gravitropic response support this hypothesis. The onset and regulation of cellulose microfibril assembly is presented for synchronized protoplasts generated by Boergesenia, using inhibitors of transcription and translation. These results suggest dynamic turnover of terminal complex subunits during the assembly of the cellulose microfibril. This study is concluded with a brief discussion of possible phylogenetic trends in the evolution of cellulose synthesis. A principal underlying theme is that the specific arrangement and consolidation of the terminal complex subunits determine to a large degree the size and shape of the microfibril, its crystallinity, as well as intramicrofibrillar associations. Three basic types of TCs appear among all eukaryotic cells studied so far: namely, the rosette, the globular and the linear complex.
Molecular dissection of the human transferrin receptor
Authors: Schneider Claudio , Williams J. G.
Published: May 2013

Transferrin is the major iron carrier protein in vertebrates and is required for maintenance of cell viability. To deliver iron, transferrin binds to its receptor, the complex is internalized and directed into acidic vacuoles where iron is dissociated and the ligand-receptor complex is recycled back to the plasma membrane. The transferrin receptor is a transmembrane glycoprotein, composed of two disulphide-bonded subunits (each of apparent Mr 90000). It contains three N-linked glycan units and is post-translationally modified with both phosphate and fatty-acyl groups. The primary structure of the receptor consists of 760 amino acids divided into three domains. Starting from the N-terminal residue the cytoplasmic domain consists of 62 amino acids, followed by 26 predominantly non-polar residues, which constitute the transmembrane domain, and 672 residues form the C-terminal extracellular domain. It does not contain an N-terminal cleavable signal sequence.
Synergistic signals in mitogenesis: role of ion fluxes, cyclic nucleotides and protein kinase c in swiss 3t3 cells
Authors: Rozengurt Enrique , Mendoza Stanley A.
Published: May 2013

A fundamental feature in the action of most mitogenic agents when added to quiescent cells in serum-free medium is that they exhibit striking synergistic effects when applied in specific combinations. A tenable hypothesis of growth control must provide a cogent explanation for the molecular mechanisms underlying this complex pattern of synergistic effects. To gain an understanding of the mechanisms by which these synergistic effects arise, we studied the initial cellular responses associated with the interaction of mitogenic factors and hormones with the cell, including changes in cation fluxes, cyclic nucleotides and cellular phosphoproteins. In this paper, some of our recent results on the early signals and responses elicited by multiple growth-promoting agents in quiescent cultures of Swiss 3T3 cells will be summarized. On the basis of the emerging information, we propose a framework that integrates early events and synergistic effects in a unified hypothesis of growth control.
Production of epidermal growth factor in ESCHERICHIA COLI from a synthetic gene
Authors: Allen Geoffrey , Paynter Cora A. , Winther Michael D.
Published: May 2013

Mouse epidermal growth factor (EGF) is under investigation as a defleecing agent for sheep. Substantial quantities of the pure protein are required for these studies and to supply this need a gene for the protein was synthesized and inserted into plasmid vectors to direct the expression of EGF polypeptide, or fusion proteins containing the EGF peptide sequence, in transformed Escherichia coli. Mature EGF was released by lysine specific proteolysis of a fusion protein consisting of part of theE. coli TrpE protein, a lysine linker and EGF polypeptide. The EGF was purified and characterized and was found to be biologically active.
Insulin-like growth factor receptors
Authors: Nissley S. Peter , Haskell Joyce F. , Sasaki Norio , Vroede Monique A. De , Rechler Matthew M.
Published: May 2013

There are two types of insulin-like growth factor (IGF) receptors. The type I receptor generally binds IGF-I more tightly than IGF-II and also interacts weakly with insulin. The type II receptor prefers IGF-II over IGF-I and does not recognize insulin. The type I receptor is made up of an alpha binding subunit (Mr 130000) and a beta subunit (Mr 95 000) probably organized as a heterotetramer (α2β2). The type II receptor consists of a single binding unit (Mr 250000). IGF stimulates phosphorylation of the beta subunit of the type I receptor in whole cells and solubilized receptor preparations. Tyrosine kinase activity is associated with the type I receptor, resulting in autophosphorylation of the beta subunit and phosphorylation of exogenous substrates. In contrast, phosphorylation of the type II receptor in whole cells is less IGF-dependent, solubilized receptor preparations are not phosphorylated, and purified type II receptors do not exhibit tyrosine kinase activity toward the artificial substrate poly(Glu,Tyr)4:1. There are many similarities between the type I IGF receptor and the insulin receptor; however, different ligand-binding properties, subtle differences in the size of alpha and beta subunits, and immunoreactivity toward anti-receptor antibodies allow us to distinguish between these two receptors. The presence of both IGF receptors as well as insulin receptors on most cells and cross-reactivity of ligands for binding to these receptors present difficulties in assigning a particular biological response to a specific receptor. The type I receptor is down-regulated by ligand while in several cell types the type II receptor is rapidly up-regulated by insulin; the mechanism of up-regulation appears to be a translocation of type II receptors to the cell surface. There are two classes of serum binding proteins for IGF, a Mr 150 000 species found in adult blood and a Mr 40 000 species, which predominates in foetal blood. Like the type II receptor, IGF binding proteins do not bind insulin. The binding site on the type II receptor can be distinguished from the binding protein sites by a hybrid molecule Ainsulin-BIDF-I, which recognizes the binding protein but not the type II receptor. Binding proteins produced by cells in culture may cause confusion in the interpretation of experiments that are designed to study the binding of radiolabelled IGF to cell surface receptors in monolayer culture.