FUS protein interacts with U7 snRNP and plays a role in replication-dependant histone genes expression

The U7 small nuclear ribonucleoprotein (U7 snRNP) is an essential factor mediating the unique 3’end processing of non-polyadenylated, replication-dependent histone mRNAs in metazoans. These histone genes expression and processing of their transcripts are cell cycle-regulated mechanisms that recruit a number of specific proteins as well as common factors required for expression and maturation of polyadenylated mRNAs. However, despite all the knowledge we have so far, there are still gaps in understanding of core histone RNA 3’ end processing, its coupling to transcription and regulation during cell cycle. To further elucidate this phenomena we used affinity chromatography based on tagged version of U7 snRNA molecule to identify proteins associated with U7 snRNP/U7 snRNA that could be potentially involved in core histone genes expression in human cells. Mass spectrometric analysis of affinity-purified fraction revealed, among others, multifunctional RNA/DNAbinding protein FUS/TLS (fused in sarcoma/translocated in liposarcoma) as a new factor interacting with U7 snRNA/RNP. Co-immunoprecipitation and RIP experiments confirmed the binding between FUS and the U7 RNA/snRNP. Interestingly, FUS:U7 snRNA interaction seems to be activated in S phase where the core histone genes are expressed. Moreover, FUS co-fractionates in 10-50% continuous glycerol gradient with other factors involved in histone premRNAs 3’end processing. However, this unique 3’end maturation was not disturbed upon FUS knockdown. Instead, we found that FUS depletion leads to a de-regulation of expression from selected histone promoters, suggesting that FUS is rather involved in regulation of core histone genes transcription. Thus, FUS bound to U7 snRNP can play a role in coupling between transcription and 3’end processing of replication dependant histone mRNAs.

Brief Report: How Adolescents with ASD Process Social Information in Complex Scenes. Combining Evidence from Eye Movements and Verbal Descriptions

We investigated attention, encoding and processing of social aspects of complex photographic scenes. Twenty-four high-functioning adolescents (aged 11–16) with ASD and 24 typically developing matched control participants viewed and then described a series of scenes, each containing a person. Analyses of eye movements and verbal descriptions provided converging evidence that both groups displayed general interest in the person in each scene but the salience of the person was reduced for the ASD participants. Nevertheless, the verbal descriptions revealed that participants with ASD frequently processed the observed person’s emotion or mental state without prompting. They also often mentioned eye-gaze direction, and there was evidence from eye movements and verbal descriptions that gaze was followed accurately. The combination of evidence from eye movements and verbal descriptions provides a rich insight into the way stimuli are processed overall. The merits of using these methods within the same paradigm are discussed.

Assessing the Environmental Hazard of Using Seawater for Ore Processing at the Lasail Mine Site in the Sultanate of Oman

The Lasail mining area (Sultanate of Oman) was contaminated by acid mine drainage during the exploitation and processing of local and imported copper ore and the subsequent deposition of sulphide-bearing waste material into an unsealed tailings dump. In this arid environment, the use of seawater in the initial stages of ore processing caused saline contamination of the fresh groundwater downstream of the tailings dump. After detection of the contamination in the 1980s, different source-controlled remediation activities were conducted including a seepage water collection system and, in 2005, surface sealing of the tailings dump using an HDPE-liner to prevent further infiltration of meteoric water. We have been assessing the benefits of the remediation actions undertaken so far. We present chemical and isotopic (δ18O, δ 2H, 3H) groundwater data from a long-term survey (8–16 years) of the Wadi Suq aquifer along a 28 km profile from the tailings dump to the Gulf of Oman. Over this period, most metal concentrations in the Wadi Suq groundwater decreased below detection limits. In addition, in the first boreholes downstream of the tailings pond, the salinity contamination has decreased by 30 % since 2005. This decrease appears to be related to the surface coverage of the tailings pond, which reduces flushing of the tailings by the sporadic, but commonly heavy, precipitation events. Despite generally low metal concentrations and the decreased salinity, groundwater quality still does not meet the WHO drinking water guidelines in more than 90 % of the Wadi Suq aquifer area. The observations show that under arid conditions, use of seawater for ore processing or any other industrial activity has the potential to contaminate aquifers for decades.

Torque efficiency of different archwires in 0.018- and 0.022-inch conventional brackets.

OBJECTIVE To compare the archwires inserted during the final stages of the orthodontic treatment with the generated moments at 0.018- and 0.022-inch brackets. MATERIALS AND METHODS The same bracket type, in terms of prescription, was evaluated in both slot dimensions. The brackets were bonded on two identical maxillary acrylic resin models, and each model was mounted on the orthodontic measurement and simulation system. Ten 0.017 × 0.025-inch TMA and ten 0.017 × 0.025-inch stainless steel archwires were evaluated in the 0.018-inch brackets. In the 0.022-inch brackets, ten 0.019 × 0.025-inch TMA and ten 0.019 × 0.025-inch stainless steel archwires were measured. A 15° buccal root torque (+15°) and then a 15° palatal root torque (-15°) were gradually applied to the right central incisor bracket, and the moments were recorded at these positions. A t-test was conducted to compare the generated moments between wires within the 0.018- and 0.022-inch bracket groups separately. RESULTS The 0.017 × 0.025-inch archwire in the 0.018-inch brackets generated mean moments of 9.25 Nmm and 14.2 Nmm for the TMA and stainless steel archwires, respectively. The measured moments in the 0.022-inch brackets with the 0.019 × 0.025-inch TMA and stainless steel archwires were 6.6 Nmm and 9.3 Nmm, respectively. CONCLUSION The 0.017 × 0.025-inch stainless steel and β-Ti archwires in the 0.018-inch slot generated higher moments than the 0.019 × 0.025-inch archwires because of lower torque play. This difference is exaggerated in steel archwires, in comparison with the β-Ti, because of differences in stiffness. The differences of maximum moments between the archwires of the same cross-section but different alloys were statistically significant at both slot dimensions.

X-ray image calibration and its application to clinical orthopedics.

X-ray imaging is one of the most commonly used medical imaging modality. Albeit X-ray radiographs provide important clinical information for diagnosis, planning and post-operative follow-up, the challenging interpretation due to its 2D projection characteristics and the unknown magnification factor constrain the full benefit of X-ray imaging. In order to overcome these drawbacks, we proposed here an easy-to-use X-ray calibration object and developed an optimization method to robustly find correspondences between the 3D fiducials of the calibration object and their 2D projections. In this work we present all the details of this outlined concept. Moreover, we demonstrate the potential of using such a method to precisely extract information from calibrated X-ray radiographs for two different orthopedic applications: post-operative acetabular cup implant orientation measurement and 3D vertebral body displacement measurement during preoperative traction tests. In the first application, we have achieved a clinically acceptable accuracy of below 1° for both anteversion and inclination angles, where in the second application an average displacement of 8.06±3.71 mm was measured. The results of both applications indicate the importance of using X-ray calibration in the clinical routine.

Intraoperative Mechanical Measurement of Bone Quality With the DensiProbe.

Reduced bone stock can result in fractures that mostly occur in the spine, distal radius, and proximal femur. In case of operative treatment, osteoporosis is associated with an increased failure rate. To estimate implant anchorage, mechanical methods seem to be promising to measure bone strength intraoperatively. It has been shown that the mechanical peak torque correlates with the local bone mineral density and screw failure load in hip, hindfoot, humerus, and spine in vitro. One device to measure mechanical peak torque is the DensiProbe (AO Research Institute, Davos, Switzerland). The device has shown its effectiveness in mechanical peak torque measurement in mechanical testing setups for the use in hip, hindfoot, and spine. In all studies, the correlation of mechanical torque measurement and local bone mineral density and screw failure load could be shown. It allows the surgeon to judge local bone strength intraoperatively directly at the region of interest and gives valuable information if additional augmentation is needed. We summarize methods of this new technique, its advantages and limitations, and give an overview of actual and possible future applications.

Uptake efficiency of surface modified gold nanoparticles does not correlate with functional changes and cytokine secretion in human dendritic cells in vitro.

Engineering nanoparticles (NPs) for immune modulation require a thorough understanding of their interaction(s) with cells. Gold NPs (AuNPs) were coated with polyethylene glycol (PEG), polyvinyl alcohol (PVA) or a mixture of both with either positive or negative surface charge to investigate uptake and cell response in monocyte-derived dendritic cells (MDDCs). Inductively coupled plasma optical emission spectrometry and transmission electron microscopy were used to confirm the presence of Au inside MDDCs. Cell viability, (pro-)inflammatory responses, MDDC phenotype, activation markers, antigen uptake and processing were analyzed. Cell death was only observed for PVA-NH2 AuNPs at the highest concentration. MDDCs internalize AuNPs, however, surface modification influenced uptake. Though limited uptake was observed for PEG-COOH AuNPs, a significant tumor necrosis factor-alpha release was induced. In contrast, (PEG+PVA)-NH2 and PVA-NH2 AuNPs were internalized to a higher extent and caused interleukin-1beta secretion. None of the AuNPs caused changes in MDDC phenotype, activation or immunological properties.

Computable Diagonalizations and Turing’s Cardinality Paradox

A. N. Turing’s 1936 concept of computability, computing machines, and computable binary digital sequences, is subject to Turing’s Cardinality Paradox. The paradox conjoins two opposed but comparably powerful lines of argument, supporting the propositions that the cardinality of dedicated Turing machines outputting all and only the computable binary digital sequences can only be denumerable, and yet must also be nondenumerable. Turing’s objections to a similar kind of diagonalization are answered, and the implications of the paradox for the concept of a Turing machine, computability, computable sequences, and Turing’s effort to prove the unsolvability of the Entscheidungsproblem, are explained in light of the paradox. A solution to Turing’s Cardinality Paradox is proposed, positing a higher geometrical dimensionality of machine symbol-editing information processing and storage media than is available to canonical Turing machine tapes. The suggestion is to add volume to Turing’s discrete two-dimensional machine tape squares, considering them instead as similarly ideally connected massive three-dimensional machine information cells. Three-dimensional computing machine symbol-editing information processing cells, as opposed to Turing’s two-dimensional machine tape squares, can take advantage of a denumerably infinite potential for parallel digital sequence computing, by which to accommodate denumerably infinitely many computable diagonalizations. A three-dimensional model of machine information storage and processing cells is recommended on independent grounds as better representing the biological realities of digital information processing isomorphisms in the three-dimensional neural networks of living computers.

Volumetric analysis of lung nodules in computed tomography (CT): comparison of two different segmentation algorithm softwares and two different reconstruction filters on automated volume calculation.

BACKGROUND A precise detection of volume change allows for better estimating the biological behavior of the lung nodules. Postprocessing tools with automated detection, segmentation, and volumetric analysis of lung nodules may expedite radiological processes and give additional confidence to the radiologists. PURPOSE To compare two different postprocessing software algorithms (LMS Lung, Median Technologies; LungCARE®, Siemens) in CT volumetric measurement and to analyze the effect of soft (B30) and hard reconstruction filter (B70) on automated volume measurement. MATERIAL AND METHODS Between January 2010 and April 2010, 45 patients with a total of 113 pulmonary nodules were included. The CT exam was performed on a 64-row multidetector CT scanner (Somatom Sensation, Siemens, Erlangen, Germany) with the following parameters: collimation, 24x1.2 mm; pitch, 1.15; voltage, 120 kVp; reference tube current-time, 100 mAs. Automated volumetric measurement of each lung nodule was performed with the two different postprocessing algorithms based on two reconstruction filters (B30 and B70). The average relative volume measurement difference (VME%) and the limits of agreement between two methods were used for comparison. RESULTS At soft reconstruction filters the LMS system produced mean nodule volumes that were 34.1% (P < 0.0001) larger than those by LungCARE® system. The VME% was 42.2% with a limit of agreement between -53.9% and 138.4%.The volume measurement with soft filters (B30) was significantly larger than with hard filters (B70); 11.2% for LMS and 1.6% for LungCARE®, respectively (both with P < 0.05). LMS measured greater volumes with both filters, 13.6% for soft and 3.8% for hard filters, respectively (P < 0.01 and P > 0.05). CONCLUSION There is a substantial inter-software (LMS/LungCARE®) as well as intra-software variability (B30/B70) in lung nodule volume measurement; therefore, it is mandatory to use the same equipment with the same reconstruction filter for the follow-up of lung nodule volume.

Two-Dimensional Crystallisation of Membrane Proteins and Structural Assessment

Two-dimensional (2D) crystallisation of Membrane proteins reconstitutes them into their native environment, the lipid bilayer. Electron crystallography allows the structural analysis of these regular protein–lipid arrays up to atomic resolution. The crystal quality depends on the protein purity, ist stability and on the crystallisation conditions. The basics of 2D crystallisation and different recent advances are reviewed and electron crystallography approaches summarised. Progress in 2D crystallisation, sample preparation, image detectors and automation of the data acquisition and processing pipeline makes 2D electron crystallography particularly attractive for the structural analysis of membrane proteins that are too small for single-particle analyses and too unstable to form three-dimensional (3D) crystals.

Acute and Chronic Altitude-Induced Cognitive Dysfunction in Children and Adolescents.

OBJECTIVE To assess whether exposure to high altitude induces cognitive dysfunction in young healthy European children and adolescents during acute, short-term exposure to an altitude of 3450 m and in an age-matched European population permanently living at this altitude. STUDY DESIGN We tested executive function (inhibition, shifting, and working memory), memory (verbal, short-term visuospatial, and verbal episodic memory), and speed processing ability in: (1) 48 healthy nonacclimatized European children and adolescents, 24 hours after arrival at high altitude and 3 months after return to low altitude; (2) 21 matched European subjects permanently living at high altitude; and (3) a matched control group tested twice at low altitude. RESULTS Short-term hypoxia significantly impaired all but 2 (visuospatial memory and processing speed) of the neuropsychological abilities that were tested. These impairments were even more severe in the children permanently living at high altitude. Three months after return to low altitude, the neuropsychological performances significantly improved and were comparable with those observed in the control group tested only at low altitude. CONCLUSIONS Acute short-term exposure to an altitude at which major tourist destinations are located induces marked executive and memory deficits in healthy children. These deficits are equally marked or more severe in children permanently living at high altitude and are expected to impair their learning abilities.

Dish Detection and Segmentation for Dietary Assessment on Smartphones

Diet-related chronic diseases severely affect personal and global health. However, managing or treating these diseases currently requires long training and high personal involvement to succeed. Computer vision systems could assist with the assessment of diet by detecting and recognizing different foods and their portions in images. We propose novel methods for detecting a dish in an image and segmenting its contents with and without user interaction. All methods were evaluated on a database of over 1600 manually annotated images. The dish detection scored an average of 99% accuracy with a .2s/image run time, while the automatic and semi-automatic dish segmentation methods reached average accuracies of 88% and 91% respectively, with an average run time of .5s/image, outperforming competing solutions.

The CODE MGEX orbit and clock solution

The Center for Orbit Determination in Europe (CODE) is contributing as a global Analysis center to the International GNSS Service (IGS) since many years. The processing of GPS and GLONASS data is well established in CODE’s ultra-rapid, rapid, and final product lines. With the introduction of new signals for the established and new GNSS, new challenges and opportunities are arising for the GNSS data management and processing. The IGS started the Multi-GNSS-EXperiment (MGEX) in 2012 in order to gain first experience with the new data formats and to develop new strategies for making optimal use of these additional measurements. CODE has started to contribute to IGS MGEX with a consistent, rigorously combined triple-system orbit solution (GPS, GLONASS, and Galileo). SLR residuals for the computed Galileo satellite orbits are of the order of 10 cm. Furthermore CODE established a GPS and Galileo clock solution. A quality assessment shows that these experimental orbit and clock products allow even a Galileo-only precise point positioning (PPP) with accuracies on the decimeter- (static PPP) to meter-level (kinematic PPP) for selected stations.

Comparing the factorial structure, invariance, and predictive validity of transtheoretical model constructs for alcohol use across restricted and unrestricted settings

With substance abuse treatment expanding in prisons and jails, understanding how behavior change interacts with a restricted setting becomes more essential. The Transtheoretical Model (TTM) has been used to understand intentional behavior change in unrestricted settings, however, evidence indicates restrictive settings can affect the measurement and structure of the TTM constructs. The present study examined data from problem drinkers at baseline and end-of-treatment from three studies: (1) Project CARE (n = 187) recruited inmates from a large county jail; (2) Project Check-In (n = 116) recruited inmates from a state prison; (3) Project MATCH, a large multi-site alcohol study had two recruitment arms, aftercare (n = 724 pre-treatment and 650 post-treatment) and outpatient (n = 912 pre-treatment and 844 post-treatment). The analyses were conducted using cross-sectional data to test for non-invariance of measures of the TTM constructs: readiness, confidence, temptation, and processes of change (Structural Equation Modeling, SEM) across restricted and unrestricted settings. Two restricted (jail and aftercare) and one unrestricted group (outpatient) entering treatment and one restricted (prison) and two unrestricted groups (aftercare and outpatient) at end-of-treatment were contrasted. In addition TTM end-of-treatment profiles were tested as predictors of 12 month drinking outcomes (Profile Analysis). Although SEM did not indicate structural differences in the overall TTM construct model across setting types, there were factor structure differences on the confidence and temptation constructs at pre-treatment and in the factor structure of the behavioral processes at the end-of-treatment. For pre-treatment temptation and confidence, differences were found in the social situations factor loadings and in the variance for the confidence and temptation latent factors. For the end-of-treatment behavioral processes, differences across the restricted and unrestricted settings were identified in the counter-conditioning and stimulus control factor loadings. The TTM end-of-treatment profiles were not predictive of drinking outcomes in the prison sample. Both pre and post-treatment differences in structure across setting types involved constructs operationalized with behaviors that are limited for those in restricted settings. These studies suggest the TTM is a viable model for explicating addictive behavior change in restricted settings but calls for modification of subscale items that refer to specific behaviors and caution in interpreting the mean differences across setting types for problem drinkers. ^

Evaluation of Polymer Gel Dosimeters for Measurements of Dose and LET in Proton Beams

This project assessed the effectiveness of polymer gel dosimeters as tools for measuring the dose deposited by and LET of a proton beam. A total of three BANG® dosimeter formulations were evaluated: BANG®-3-Pro-2 BANGkits™ for dose measurement and two BANG®-3 variants, the LET-Baseline and LET-Meter dosimeters, for LET measurement. All dosimeters were read out using an OCT scanner. The basic characteristics of the BANGkits™ were assessed in a series of photon and electron irradiations. The dose-response relationship was found to be sigmoidal with a threshold for response of approximately 15 cGy. The active region of the dosimeter, the volume in which dosimeter response is not inhibited by oxygen, was found to make up roughly one fourth of the total dosimeter volume. Delivering a dose across multiple fractions was found to yield a greater response than delivering the same dose in a single irradiation. The dosimeter was found to accurately measure a dose distribution produced by overlapping photon fields, yielding gamma pass rates of 95.4% and 93.1% from two planar gamma analyses. Proton irradiations were performed for measurements of proton dose and LET. Initial irradiations performed through the side of a dosimeter led to OCT artifacts. Gamma pass rates of 85.7% and 89.9% were observed in two planar gamma analyses. In irradiations performed through the base of a dosimeter, gel response was found to increase with height in the dosimeter, even in areas of constant dose. After a correction was applied, gamma pass rates of 94.6% and 99.3% were observed in two planar gamma analyses. Absolute dose measurements were substantially higher (33%-100%) than the delivered doses for proton irradiations. Issues encountered while calibrating the LET-Meter gel restricted analysis of the LET measurement data to the SOBP of a proton beam. LET-Meter overresponse was found to increase linearly with track-average LET across the LET range that could be investigated (1.5 keV/micron – 3.5 keV/micron).