Sequence features responsible for intron retention in human

Abstract Background One of the least common types of alternative splicing is the complete retention of an intron in a mature transcript. Intron retention (IR) is believed to be the result of intron, rather than exon, definition associated with failure of the recognition of weak splice sites flanking short introns. Although studies on individual retained introns have been published, few systematic surveys of large amounts of data have been conducted on the mechanisms that lead to IR. Results TTo understand how sequence features are associated with or control IR, and to produce a generalized model that could reveal previously unknown signals that regulate this type of alternative splicing, we partitioned intron retention events observed in human cDNAs into two groups based on the relative abundance of both isoforms and compared relevant features. We found that a higher frequency of IR in human is associated with individual introns that have weaker splice sites, genes with shorter intron lengths, higher expression levels and lower density of both a set of exon splicing silencers (ESSs) and the intronic splicing enhancer GGG. Both groups of retained introns presented events conserved in mouse, in which the retained introns were also short and presented weaker splice sites. Conclusion Although our results confirmed that weaker splice sites are associated with IR, they showed that this feature alone cannot explain a non-negligible fraction of events. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating IR and also reveals previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of IR.

Sexually transmitted infections in HIV-infected people in Switzerland: cross-sectional study.

Sexually transmitted infections (STI) in HIV-infected people are of increasing concern. We estimated STI prevalence and sexual healthcare seeking behaviour in 224 sexually active HIV-infected people, including men who have sex with men (MSM, n = 112), heterosexual men (n = 65) and women (n = 47). Laboratory-diagnosed bacterial STI were more common in MSM (Chlamydia trachomatis 10.7%; 95% CI 6.2, 18.0%, lymphogranuloma venereum 0.9%; 95% CI 0.1, 6.2%, Neisseria gonorrhoeae 2.7%; 95% CI 0.9, 8.0%, syphilis seroconversion 5.4%; 95% CI 2.0, 11.3%) than heterosexual men (gonorrhoea 1.5%; 95% CI 0.2, 10.3%) or women (no acute infections). Combined rates of laboratory-diagnosed and self-reported bacterial STI in the year before the study were: MSM (27.7%; 95% CI 21.1, 36.7%); heterosexual men (1.5%; 95% CI 0.2, 10.3%); and women (6.4%; 95% CI 2.1, 21.0%). Antibodies to hepatitis C virus were least common in MSM. Antibodies to herpes simplex type 2 virus were least common in heterosexual men. Most MSM, but not heterosexual men or women, agreed that STI testing should be offered every year. In this study, combined rates of bacterial STI in MSM were high; a regular assessment of sexual health would allow those at risk of STI to be offered testing, treatment and partner management.

A Time-based Passive Source Localization System for Narrow-band Signal

Time-based indoor localization has been investigated for several years but the accuracy of existing solutions is limited by several factors, e.g., imperfect synchronization, signal bandwidth and indoor environment. In this paper, we compare two time-based localization algorithms for narrow-band signals, i.e., multilateration and fingerprinting. First, we develop a new Linear Least Square (LLS) algorithm for Differential Time Difference Of Arrival (DTDOA). Second, fingerprinting is among the most successful approaches used for indoor localization and typically relies on the collection of measurements on signal strength over the area of interest. We propose an alternative by constructing fingerprints of fine-grained time information of the radio signal. We offer comprehensive analytical discussions on the feasibility of the approaches, which are backed up by evaluations in a software defined radio based IEEE 802.15.4 testbed. Our work contributes to research on localization with narrow-band signals. The results show that our proposed DTDOA-based LLS algorithm obviously improves the localization accuracy compared to traditional TDOA-based LLS algorithm but the accuracy is still limited because of the complex indoor environment. Furthermore, we show that time-based fingerprinting is a promising alternative to power-based fingerprinting.

„Extra locos sepulturae“ – Review about finds of newborns inside Roman settlements in present-day Switzerland

Finds of remains of newborns inside Roman settlements are a widespread phenomenon in the Imperium Romanum, including presentday Switzerland. Since the publication of the last review article (Berger 1993) numerous new finds have been made. Therefore it seems important to summarize archaeological and anthropological parameters again, and to re-assess them collectively. During a literature review a total of 262 cases were collected. Similarities as well as differences in the funerary practices become evident. A combination of inhumation, single deposit/grave, and absence of grave goods is the least common denominator in the funerary treatment of individuals who died around the time of birth. However, methods of classical physical anthropology are limited. Histological and biochemical methods are promising and may allow further statements in the future, e.g. with regard to the differentiation between live and still births. In order to evaluate possible correlations between archaeological and anthropological parameters, findings from settlements and cemeteries that are documented in situ as well as a sustainable theoretical framework are required.

Cancer's positive flip side: posttraumatic growth after childhood cancer.

BACKGROUND Surviving childhood cancer may result in positive psychological changes called posttraumatic growth (PTG). Knowing about the possibility of positive changes may facilitate survivors' reintegration in daily life. We aimed to (1) describe PTG in Swiss childhood cancer survivors including the most and the least common PTG phenomena on the subscale and item levels and (2) determine factors associated with PTG. METHOD Within the Swiss Childhood Cancer Survivor Study (SCCSS), we sent two questionnaires to childhood cancer survivors registered in the Swiss Childhood Cancer Registry (SCCR). Eligible survivors were diagnosed after 1990 at age ≤16 years, survived ≥5 years, and were aged ≥18 years at the time the second questionnaire was sent. We included the Posttraumatic Growth Inventory (PTGI) to assess five areas of PTG. We investigated the association of PTG with socio-demographic characteristics, self-reported late effects, and psychological distress, which were assessed in the SCCSS and clinical variables extracted from the SCCR. We used descriptive statistics to describe PTG and linear regressions to investigate factors associated with PTG. RESULTS We assessed PTG in 309 childhood cancer survivors. Most individuals reported to have experienced some PTG. The most endorsed change occurred in "relation with others," the least in "spiritual change." PTG was significantly higher in survivors with older age at diagnosis (p = 0.001) and those with a longer duration of treatment (p = 0.042), while it was lower in male survivors (p = 0.003). CONCLUSIONS Supporting experiences of PTG during follow-up may help survivors successfully return to daily life.

Quantifying differences in land use emission estimates implied by definition discrepancies

The quantification of CO2 emissions from anthropogenic land use and land use change (eLUC) is essential to understand the drivers of the atmospheric CO2 increase and to inform climate change mitigation policy. Reported values in synthesis reports are commonly derived from different approaches (observation-driven bookkeeping and process-modelling) but recent work has emphasized that inconsistencies between methods may imply substantial differences in eLUC estimates. However, a consistent quantification is lacking and no concise modelling protocol for the separation of primary and secondary components of eLUC has been established. Here, we review differences of eLUC quantification methods and apply an Earth System Model (ESM) of Intermediate Complexity to quantify them. We find that the magnitude of effects due to merely conceptual differences between ESM and offline vegetation model-based quantifications is ~ 20 % for today. Under a future business-as-usual scenario, differences tend to increase further due to slowing land conversion rates and an increasing impact of altered environmental conditions on land-atmosphere fluxes. We establish how coupled Earth System Models may be applied to separate secondary component fluxes of eLUC arising from the replacement of potential C sinks/sources and the land use feedback and show that secondary fluxes derived from offline vegetation models are conceptually and quantitatively not identical to either, nor their sum. Therefore, we argue that synthesis studies should resort to the "least common denominator" of different methods, following the bookkeeping approach where only primary land use emissions are quantified under the assumption of constant environmental boundary conditions.

School screening for tuberculosis in high risk areas of Texas

Screening for latent tuberculosis infection (LTBI) is an integral component of an effective tuberculosis control strategy, but one that is often relegated to the lowest priority. In a state with higher than national average rates of tuberculosis, due consideration should be given to LTBI screening. Recent large scale contact investigations in the middle school of Del Rio, Texas, raised questions about the status of school screening for LTBI. An evidence based approach was used to evaluate school screening in high risk areas of Texas. A review of the literature revealed that the current recommendations for LTBI screening in children is based on administration of a risk factor questionnaire that should be based on the four main risk factors for LTBI in children that have been identified. Six representative areas in Texas were identified for evaluation of the occurrence of contact investigations in schools for the period of 2006 to 2009 and any use of school screening programs. Of the five reporting areas that responded, only one utilized a school screening program; this reporting area had the lowest percentage of contact investigations occurring in schools. Contact investigations were most common in middle schools and least common in elementary schools. In metropolitan areas, colleges represented up to 42.9% of contact investigations. The number of contact investigations has increased from 2006 to 2008. This report represents a small sample, and further research into the frequency, distribution and risk for contact investigations in schools and the efficacy of screening programs should be done. ^

Geochemistry of volcanic rocks of ODP Holes 126-792E and 126-793B

The Izu-Bonin forearc basement volcanic rocks recovered from Holes 792E and 793B show the same phenocrystic assemblage (i.e., plagioclase, two pyroxenes, and Fe-Ti oxides ±olivine), but they differ in the crystallization sequence and their phenocryst chemistry. All the igneous rocks have suffered low-grade hydrothermal alteration caused by interaction with seawater. As a result, only clinopyroxenes, plagioclases, and oxides have preserved their primary igneous compositions. The Neogene olivine-clinopyroxene diabasic intrusion (Unit II) recovered from Hole 793B differs from the basement basaltic andesites because it lacks Cr-spinels and contains abundant titanomagnetites (Usp38.5-46.4) and uncommon FeO-rich (FeO = 29%) spinels. It displays petrological and geochemical similarities to the Izu Arc volcanoes and, thus, can be considered as related to Izu-Bonin Arc magmatic activity. The titanomagnetites (Usp28.5-33) in the calc-alkaline andesitic fragments of the Oligocene volcaniclastic breccia in Hole 793B (Unit VI) represent an early crystallization phase. The Plagioclase phenocrysts enclosed in these rocks show oscillatory zoning and are less Ca-rich (An78.6-67.8) than the plagioclase phenocrysts of the diabase sill and the basement basaltic andesites. Their clinopyroxenes are Fe-rich augites (Fs ? 19.4; FeO = 12%) and thus, differ significantly from the clinopyroxenes of the Hole 793B arc-tholeiitic igneous rocks. The 30-32 Ma porphyritic, two-pyroxene andesites recovered from Hole 792E are very similar to the andesitic clasts of the Neogene breccia recovered in Hole 793B (Unit VI). Both rocks have the same crystallization sequence, and similar chemistry of the Fe-Ti oxides, clinopyroxenes, and plagioclases: that is, Ti-rich (Usp25.5-30.4) magnetites, Fe-rich augites, and intensely oscillatory zoned plagioclases with bytownitic cores (An86-63) and labradorite rims (An73-68). They display a calc-alkaline differentiation trend (Taylor et al., this volume). So, the basement highly porphyritic andesites recovered at Hole 792E, and the Hole 793B andesitic clasts of Unit VI show the same petrological and geochemical characteristics, which are that of calc-alkaline suites. These Oligocene volcanic rocks represent likely the remnants of the Izu-Bonin normal arc magmatic activity, before the forearc rifting and extension. The crystallization sequence in the basaltic andesites recovered from Hole 793B is olivine-orthopyroxene-clinopyroxene-plagioclase-Fe-Ti oxides, indicating a tholeiitic differentiation trend for these volcanic rocks. Type i is an olivine-and Cr-spinel bearing basaltic andesite whereas Type ii is a porphyritic pyroxene-rich basaltic andesite. The porphyritic plagioclase-rich basaltic andesite (Type iii) is similar, in most respects, to Type ii lavas but contains plagioclase phenocrysts. The last, and least common lava is an aphyric to sparsely phyric andesite (Type iv). Cr-spinels, included either in the olivine pseudomorphs of Type i lavas or in the groundmass of Type ii lavas, are Cr-rich and Mg-rich. In contrast, Cr-spinels included in clinopyroxenes and orthopyroxenes (Types i and ii lavas) show lower Cr* and Mg* ratios and higher aluminium contents. Orthopyroxenes from all rock types are Mg-rich enstatites. Clinopyroxenes display endiopsidic to augitic compositions and are TiO2 and Al2O3 depleted. All the crystals exhibit strong zoning patterns, usually normal, although, reverse zoning patterns are not uncommon. The plagioclases show compositions within the range of An90-64. The Fe-Ti oxides of the groundmass are TiO2-poor (Usp16-17). The Hole 793B basaltic andesites show, like the Site 458 bronzites from the Mariana forearc, intermediate features between arc tholeiites and boninites: (1) Cr-spinel in olivine, (2) presence of Mg-rich bronzite, Ca-Mg-rich clinopyroxenes, and Ca-plagioclase phenocrysts, and (3) transitional trace element depletion and epsioln-Nd ratios between arc tholeiites and boninites. Thus, the forearc magmatism of the Izu-Bonin and Mariana arcs, linked to rifting and extension, is represented by a depleted tholeiitic suite that displays boninitic affinities.

Cancelación activa del ruido utilizando el KIT TMS320C5515 EZDSP

El control, o cancelación activa de ruido, consiste en la atenuación del ruido presente en un entorno acústico mediante la emisión de una señal igual y en oposición de fase al ruido que se desea atenuar. La suma de ambas señales en el medio acústico produce una cancelación mutua, de forma que el nivel de ruido resultante es mucho menor al inicial. El funcionamiento de estos sistemas se basa en los principios de comportamiento de los fenómenos ondulatorios descubiertos por Augustin-Jean Fresnel, Christiaan Huygens y Thomas Young entre otros. Desde la década de 1930, se han desarrollado prototipos de sistemas de control activo de ruido, aunque estas primeras ideas eran irrealizables en la práctica o requerían de ajustes manuales cada poco tiempo que hacían inviable su uso. En la década de 1970, el investigador estadounidense Bernard Widrow desarrolla la teoría de procesado adaptativo de señales y el algoritmo de mínimos cuadrados LMS. De este modo, es posible implementar filtros digitales cuya respuesta se adapte de forma dinámica a las condiciones variables del entorno. Con la aparición de los procesadores digitales de señal en la década de 1980 y su evolución posterior, se abre la puerta para el desarrollo de sistemas de cancelación activa de ruido basados en procesado de señal digital adaptativo. Hoy en día, existen sistemas de control activo de ruido implementados en automóviles, aviones, auriculares o racks de equipamiento profesional. El control activo de ruido se basa en el algoritmo fxlms, una versión modificada del algoritmo LMS de filtrado adaptativo que permite compensar la respuesta acústica del entorno. De este modo, se puede filtrar una señal de referencia de ruido de forma dinámica para emitir la señal adecuada que produzca la cancelación. Como el espacio de cancelación acústica está limitado a unas dimensiones de la décima parte de la longitud de onda, sólo es viable la reducción de ruido en baja frecuencia. Generalmente se acepta que el límite está en torno a 500 Hz. En frecuencias medias y altas deben emplearse métodos pasivos de acondicionamiento y aislamiento, que ofrecen muy buenos resultados. Este proyecto tiene como objetivo el desarrollo de un sistema de cancelación activa de ruidos de carácter periódico, empleando para ello electrónica de consumo y un kit de desarrollo DSP basado en un procesador de muy bajo coste. Se han desarrollado una serie de módulos de código para el DSP escritos en lenguaje C, que realizan el procesado de señal adecuado a la referencia de ruido. Esta señal procesada, una vez emitida, produce la cancelación acústica. Empleando el código implementado, se han realizado pruebas que generan la señal de ruido que se desea eliminar dentro del propio DSP. Esta señal se emite mediante un altavoz que simula la fuente de ruido a cancelar, y mediante otro altavoz se emite una versión filtrada de la misma empleando el algoritmo fxlms. Se han realizado pruebas con distintas versiones del algoritmo, y se han obtenido atenuaciones de entre 20 y 35 dB medidas en márgenes de frecuencia estrechos alrededor de la frecuencia del generador, y de entre 8 y 15 dB medidas en banda ancha. ABSTRACT. Active noise control consists on attenuating the noise in an acoustic environment by emitting a signal equal but phase opposed to the undesired noise. The sum of both signals results in mutual cancellation, so that the residual noise is much lower than the original. The operation of these systems is based on the behavior principles of wave phenomena discovered by Augustin-Jean Fresnel, Christiaan Huygens and Thomas Young. Since the 1930’s, active noise control system prototypes have been developed, though these first ideas were practically unrealizable or required manual adjustments very often, therefore they were unusable. In the 1970’s, American researcher Bernard Widrow develops the adaptive signal processing theory and the Least Mean Squares algorithm (LMS). Thereby, implementing digital filters whose response adapts dynamically to the variable environment conditions, becomes possible. With the emergence of digital signal processors in the 1980’s and their later evolution, active noise cancellation systems based on adaptive signal processing are attained. Nowadays active noise control systems have been successfully implemented on automobiles, planes, headphones or racks for professional equipment. Active noise control is based on the fxlms algorithm, which is actually a modified version of the LMS adaptive filtering algorithm that allows compensation for the acoustic response of the environment. Therefore it is possible to dynamically filter a noise reference signal to obtain the appropriate cancelling signal. As the noise cancellation space is limited to approximately one tenth of the wavelength, noise attenuation is only viable for low frequencies. It is commonly accepted the limit of 500 Hz. For mid and high frequencies, conditioning and isolating passive techniques must be used, as they produce very good results. The objective of this project is to develop a noise cancellation system for periodic noise, by using consumer electronics and a DSP development kit based on a very-low-cost processor. Several C coded modules have been developed for the DSP, implementing the appropriate signal processing to the noise reference. This processed signal, once emitted, results in noise cancellation. The developed code has been tested by generating the undesired noise signal in the DSP. This signal is emitted through a speaker simulating the noise source to be removed, and another speaker emits an fxlms filtered version of the same signal. Several versions of the algorithm have been tested, obtaining attenuation levels around 20 – 35 dB measured in a tight bandwidth around the generator frequency, or around 8 – 15 dB measured in broadband.

Extreme clonal uniformity of Phoxinus eos/neogaeus gynogens (pisces: Cyprinidae) among variable habitats in northern Minnesota beaver ponds.

Genetic surveys of parthenogenetic vertebrate populations have demonstrated a common pattern of relatively high degrees of clonal variation and the coexistence of numerous clones. In striking contrast, the Phoxinus eos/Phoxinus neogaeus/hybrid gynogen complex of cyprinid fishes exhibits no clonal variation within a northern Minnesota drainage characterized by successional beaver ponds. Gynogens were sampled from three habitats in each of four different pond types in a single drainage in Voyageurs National Park, Minnesota. The abundance of gynogens relative to sexual dace varied with pond type, being least common in deep upland ponds and most common in shallow, collapsed, lowland ponds (13.4% and 48.6%, respectively). Simple-sequence multilocus DNA fingerprinting of 464 individual gynogens detected one, and only one, clone. DNA fingerprints, generated sequentially by using three oligonucleotide probes, (CAC)5, (GACA)4, and the Jeffreys' 33.15 probe, all revealed the same unprecedented lack of variation. The extreme lack of clonal diversity in these gynogens across a range of habitat types does not fit the general pattern of high clonal diversity found within populations of other vertebrate parthenogens.

Symptoms and diagnosis of borderline, early and advanced epithelial ovarian cancer

Objective. To document symptoms associated with borderline, early and advanced ovarian cancer and identify personal characteristics associated with early versus late diagnosis. Methods. Information concerning symptoms and diagnosis history was available from 811 women with ovarian cancer who took part in an Australian case–control study in the early 1990s. Women were classified into three groups for comparison based on their diagnosis: borderline, early (stage I–II) and advanced (stage III–IV) invasive cancer. Results. Sixteen percent of women with borderline tumors, 7% with early cancer and 4% with advanced cancer experienced no symptoms before diagnosis (P < 0.0001). Among women with symptoms, abdominal pain (44%) or swelling (39%) were most frequently reported; an abdominal mass (12%) and gynecological symptoms (12%) were less common. Compared to advanced stage cancer, women with early stage cancer were more likely to report an abdominal mass or urinary symptoms but less likely to report gastrointestinal problems or general malaise. General malaise and ‘other’ symptoms were least common in borderline disease. Older women, and those with higher parity or a family history of breast or ovarian cancer, were more likely to be diagnosed at an advanced stage of disease. Conclusions. Women who experience persistent or recurrent abdominal symptoms, particularly swelling and/or pain should be encouraged to seek medical attention and physicians should be alert to the possibility of ovarian cancer even in the absence of an abdominal mass. Further information about the prevalence of these symptoms in the general population is essential to assist physicians in patient management.

Management of dry eye in UK pharmacies

Purpose - To investigate the ability of pharmacy staff in the United Kingdom (UK) to diagnose and treat dry eye. Methods - A mystery shopper technique to simulate a patient with presumed dry eye was used in 50 pharmacy practices in major towns and cities across the UK. Pharmacies were unaware of their involvement in the study. With the exception of a predetermined opening statement to initiate the consultation, no further information was volunteered. Questions asked, diagnoses given, management strategy advised and staff type was recorded immediately after the consultation. Results - The mean number of questions was 4.5 (SD 1.7; range 1–10). The most common question was the duration of symptoms (56%) and the least common was whether the patient had a history of headaches (2%). All pharmacy staff gave a diagnosis, but the majority were incorrect (58%), with only 42% correctly identifying dry eye. Treatment was advised by 92% of pharmacy staff, with the remaining 8% advising referral directly to the patient's GP or optometrist. Dry eye treatments involved topical ocular lubrication via eye drops (90%) and lipid based sprays (10%). However, only 10% gave administration advice, 10% gave dosage advice, 9% asked about contact lens wear, and none offered follow up although 15% also advised GP or optometrist referral. Conclusions - There is a need for improved ophthalmological training amongst pharmacists and pharmacy staff and establishment of cross referral relationships between pharmacies and optometry practices.

Meta-regulation approach of law : a potential legal strategy to develop socially responsible business self-regulation in least developed common law countries

In the corporate regulation landscape, 'meta-regulation' is a comparatively new legal approach. The sketchy role of state promulgated authoritative laws in pluralized society and scepticism in corporate self-regulation's role have resulted in the development of this legal approach. It has opened up possibilities to synthesize corporate governance to add social values in corporate self-regulation. The core of this approach is the fusion of responsive and reflexive legal strategies to combine regulators and regulatees for reaching a particular goal. This paper argues that it is a potential strategy that can be successfully deployed to develop a socially responsible corporate culture for the business enterprises, so that they will be able to acquire social, environmental and ethical values in their self-regulation sustainably. Taking Bangladeshi corporate laws as an instance, this paper also evaluates the scope of incorporating this approach in laws of the least developed common law countries in general.

Non-stationary signal analysis by least mean fourth (LMF) adaptive algorithm

A modified least mean fourth (LMF) adaptive algorithm applicable to non-stationary signals is presented. The performance of the proposed algorithm is studied by simulation for non-stationarities in bandwidth, centre frequency and gain of a stochastic signal. These non-stationarities are in the form of linear, sinusoidal and jump variations of the parameters. The proposed LMF adaptation is found to have better parameter tracking capability than the LMS adaptation for the same speed of convergence.

Invited paper Application of the least mean fourth (LMF) adaptive algorithm to signals associated with gaussian noise

This paper considers the applicability of the least mean fourth (LM F) power gradient adaptation criteria with 'advantage' for signals associated with gaussian noise, the associated noise power estimate not being known. The proposed method, as an adaptive spectral estimator, is found to provide superior performance than the least mean square (LMS) adaptation for the same (or even lower) speed of convergence for signals having sufficiently high signal-to-gaussian noise ratio. The results include comparison of the performance of the LMS-tapped delay line, LMF-tapped delay line, LMS-lattice and LMF-lattice algorithms, with the Burg's block data method as reference. The signals, like sinusoids with noise and stochastic signals like EEG, are considered in this study.