Synergistic effects of Tb doping in long-persistent luminescence in Ca3Ga4O9: xBi3+, yZn2+ phosphors: Implications for novel phosphorescent materials

Long afterglow phosphors constitute an emerging class of compounds with wide application in several fields, from photonic to dosimetry, solar energy storage and photocatalysis. In this study, we synthesized and thoroughly characterized a new class of persistent emitting materials, Ca3Ga4O9: xBi3+, yZn2+, zTb3+. Through the utilization of X-ray and Raman spectroscopy, as well as optical measurements including static and time-resolved luminescence, thermoluminescence, and phosphorescence, the effects of the Tb concentration on the optical and structural properties of the material has been deeply studied. A suitable mechanism was proposed to account for the long afterglow emission, wherein Tb3+ and Bi3+ ions occupying the Ca2+ sites serve as recombination centers, facilitating the generation of oxygen defects. Zn2+ in the Ga3+ sites, contribute to the charge balance and generates hole traps in the matrix. The enduring phosphorescence persists for over 3 h following the cessation of UV irradiation, discernible to the naked eye in low-light conditions.

Unveiling Hidden Prints: Optically stimulated luminescence for latent fingerprint detection

Fluorescent lighting and optical techniques have been widely utilized to enhance the detection of latent fingerprints. However, the development of new techniques is imperative to expand the range of surfaces from which latent fingerprints can be detected. When relying on traditional methods, fingerprint evidence can remain undetected or even disregarded due to insufficient detection and limited detail, especially when dealing with a luminescent background. In this study, we propose the utilization of optically stimulated luminescence (OSL) applied to a Ba2SiO4 matrix, co-doped with Eu2+ and Dy3+, as a powerful method for visualizing latent fingerprints on various surfaces, including thin plastic bags, rigid duct tape, thin aluminum foil, and glass slices. This technique effectively eliminates any luminescent background and significantly enhances optical imaging. This represents the first successful application of OSL in the development of latent fingerprints, thus paving the way for more efficient and effective forensic techniques in the future.

Lung aeration estimated by chest electrical impedance tomography and lung ultrasound during extubation

BACKGROUND

This study hypothesized that patients with extubation failure exhibit a loss of lung aeration and heterogeneity in air distribution, which could be monitored by chest EIT and lung ultrasound. Patients at risk of extubation failure were included after a successful spontaneous breathing trial. Lung ultrasound [with calculation of lung ultrasound score (LUS)] and chest EIT [with calculation of the global inhomogeneity index, frontback center of ventilation (CoV), regional ventilation delay (RVD) and surface available for ventilation] were performed before extubation during pressure support ventilation (H0) and two hours after extubation during spontaneous breathing (H2). EIT was then repeated 6 h (H6) after extubation. EIT derived indices and LUS were compared between patients successfully extubated and patients with extubation failure.

RESULTS

40 patients were included, of whom 12 (30%) failed extubation. Before extubation, when compared with patients with successful extubation, patients who failed extubation had a higher LUS (19 vs 10, p = 0.003) and a smaller surface available for ventilation (352 vs 406 pixels, p = 0.042). After extubation, GI index and LUS were higher in the extubation failure group, whereas the surface available for ventilation was lower. The RVD and the CoV were not different between groups.

CONCLUSION

Before extubation, a loss of lung aeration was observed in patients who developed extubation failure afterwards. After extubation, this loss of lung aeration persisted and was associated with regional lung ventilation heterogeneity. Trial registration Clinical trials, NCT04180410, Registered 27 November 2019-prospectively registered, https://clinicaltrials.gov/ct2/show/NCT04180410 .

Optimizing the Mechanoluminescent Properties of CaZnOS:Tb via Microwave-Assisted Synthesis: A Comparative Study with Conventional Thermal Methods

Recent developments in lighting and display technologies have led to an increased focus on materials and phosphors with high efficiency, chemical stability, and eco-friendliness. Mechanoluminescence (ML) is a promising technology for new lighting devices, specifically in pressure sensors and displays. CaZnOS has been identified as an efficient ML material, with potential applications as a stress sensor. This study focuses on optimizing the mechanoluminescent properties of CaZnOS:Tb through microwave-assisted synthesis. We successfully synthesized CaZnOS doped with Tb3+ using this method and compared it with samples obtained through conventional solid-state methods. We analyzed the material's characteristics using various techniques to investigate their structural, morphological, and optical properties. We then studied the material's mechanoluminescent properties through single impacts with varying energies. Our results show that materials synthesized through microwave methods exhibit similar optical and, primarily, mechanoluminescent properties, making them suitable for use in photonics applications. The comparison of the microwave and conventional solid-state synthesis methods highlights the potential of microwave-assisted methods to optimize the properties of mechanoluminescent materials for practical applications.

What is missing to advance foliar fertilization using nanotechnology?

An urgent challenge within agriculture is to improve fertilizer efficiency in order to reduce the environmental footprint associated with an increased production of crops on existing farmland. Standard soil fertilization strategies are often not very efficient due to immobilization in the soil and losses of nutrients by leaching or volatilization. Foliar fertilization offers an attractive supplementary strategy as it bypasses the adverse soil processes, but implementation is often hampered by a poor penetration through leaf barriers, leaf damage, and a limited ability of nutrients to translocate. Recent advances within bionanotechnology offer a range of emerging possibilities to overcome these challenges. Here we review how nanoparticles can be tailored with smart properties to interact with plant tissue for a more efficient delivery of nutrients.

Effects of the Parent Alloy Microstructure on the Thermal Stability of Nanoporous Au

Nanoporous (NP) metals represent a unique class of materials with promising properties for a wide set of applications in advanced technology, from catalysis and sensing to lightweight structural materials. However, they typically suffer from low thermal stability, which results in a coarsening behavior not yet fully understood. In this work, we focused precisely on the coarsening process undergone by NP Au, starting from the analysis of data available in the literature and addressing specific issues with suitably designed experiments. We observe that annealing more easily induces densification in systems with short characteristic lengths. The NP Au structures obtained by dealloying of mechanically alloyed AuAg precursors exhibit lower thermal stability than several NP Au samples discussed in the literature. Similarly, NP Au samples prepared by annealing the precursor alloy before dealloying display enhanced resistance to coarsening. We suggest that the microstructure of the precursor alloy, and, in particular, the grain size of the metal phases, can significantly affect the thermal stability of the NP metal. Specifically, the smaller the grain size of the parent alloy, the lower the thermal stability.

A Low Power and Real-Time Architecture for Hough Transform Processing Integration in a Full HD-Wireless Capsule Endoscopy

We propose a new paradigm of a smart wireless endoscopic capsule (WCE) that has the ability to select suspicious images containing a polyp before sending them outside the body. To do so, we have designed an image processing system to select images with Regions Of Interest (ROI) containing a polyp. The criterion used to select an ROI is based on the polyp's shape. We use the Hough Transform (HT), a widely used shape-based algorithm for object detection and localization, to make this selection. In this paper, we present a new algorithm to compute in real-time the Hough Transform of high definition images (1920 x 1080 pixels). This algorithm has been designed to be integrated inside a WCE where there are specific constraints: a limited area and a limited amount of energy. To validate our algorithm, we have realized tests using a dataset containing synthetic images, real images, and endoscopic images with polyps. Results have shown that our algorithm is capable to detect circular shapes in synthetic and real images, but also can detect circles with an irregular contour, like that of polyps. We have implemented our architecture and validated it in a Xilinx Spartan 7 FPGA device, with an area of [Formula: see text], which is compatible with integration inside a WCE. This architecture runs at 132 MHz with an estimated power consumption of 76 mW and can work close to 10 hours. To improve the capacity of our architecture, we have also made an ASIC estimation, that let our architecture work at 125 MHz, with a power consumption of only 17.2 mW and a duration of approximately 50 hours.

Automatic Sleep Stages Classification Combining Semantic Representation and Dynamic Expert System

Interest in sleep has been growing in the last decades, considering its benefits for well-being, but also to diagnose sleep troubles. The gold standard to monitor sleep consists of recording the course of many physiological parameters during a whole night. The human interpretation of resulting curves is time consuming. We propose an automatic knowledge-based decision system to support sleep staging. This system handles temporal data, such as events, to combine and aggregate atomic data, so as to obtain high-abstraction-levels contextual decisions. The proposed system relies on a semantic reprentation of observations, and on contextual knowledge base obtained by formalizing clinical practice guidelines. Evaluated on a dataset composed of 131 full night polysomnographies, results are encouraging, but point out that further knowledge need to be integrated.

Mesoporous bioactive glasses for the combined application of osteosarcoma treatment and bone regeneration

In this study, mesoporous bioactive glass (MBG) sub-micro particles were prepared through sol-gel synthesis and possessed a uniform and spherical structure with particle size of 302 ± 43 nm, a pore size of 4 nm and a high surface area of 354 m² g^-1. Alendronate (AL) is often used for the treatment of bone associated diseases, in particular osteosarcoma. However, due to the low bioavailability and high toxicity at increased doses, local and sustained release would be an ideal approach to AL delivery. Here, MBGs and aminated MBGs (AMBG) were applied as carriers for AL loading. High encapsulation efficiency of 75% and 85% and loading efficiency of 60% and 63%, for MBG and AMBG, respectively, was achieved. The release profile of AL from AMBG showed a better sustained and controlled release mechanism compared to MBG. In vitro results demonstrated the non-cytotoxic nature of both MBG and AMBG following exposure to MG63 osteoblast like cell line. AL release from MBG and AMBG, even at lower concentration, provoked decreased MG63 proliferation. The osteogenic potential of MBG and AMBG following exposure to dental pulp stem cells was evaluated using alizarin red assay.

Corneal Graft Rejection after Penetrating Keratoplasty for Keratoconus in Turner's Syndrome

Purpose

To report a patient with Turner's syndrome who developed graft rejection after penetrating keratoplasty (PK) for keratoconus and to review the ophthalmic literature on the association between keratoconus and Turner's syndrome.

Methods

A woman with bilateral keratoconus and Turner's syndrome (45,XO) was referred for progressive visual loss in the right eye. Best-corrected visual acuity was 20/400 in the right eye. Slit-lamp examination revealed corneal thinning with ectatic protrusion of the central cornea and Vogt's striae in the right eye. The patient underwent PK in the right eye in January 2001. She developed graft rejection in April 2003 and visual acuity dropped to hand motion. After treatment with topical and systemic steroids and systemic cyclosporine A, visual acuity recovered to 20/80 in July 2003.

Results

The authors know of only three other reported patients (six eyes) with keratoconus in Turner's syndrome. Five eyes underwent PK with good visual rehabilitation, but one developed immunologic graft rejection 7 years after surgery. On the whole, considering the current report and the other cases described in the literature, graft rejection occurred in 2 out of 6 eyes (33.3%). The graft survival rate was 80% after 2 years and 40% after 7 years.

Conclusions

The results suggest that grafts for keratoconus in patients with Turner's syndrome might have an increased risk of immunologic rejection. Corneal grafts in Turner's syndrome need to be monitored closely. Early detection of graft rejection and aggressive treatment with topical and systemic steroids and systemic cyclosporine A can save the graft and restore useful vision.

High frame rate medical quality video compression for tele-EEG

More and more, exams require medical images as a tool to diagnose pathologies. Thus, the transfer and storage of the exam data becomes a critical issue. To address this issue, an image compression algorithm called Waaves has been developed and certified for medical imaging. Our work in this paper deals with a scenario of EEG exams where video of the patient is also recorded in order to correctly diagnose myoclonus pathologies. To achieve this goal, the video needs to be of high quality and at frame rate of at least 100 frames per second. This high data rate cannot be compressed on the fly by Waaves codec. In this paper, we present a novel codec based on the Waaves compression algorithm that fits the requirements of tele-video-EEG. We have used the characteristics of the input sequence and the analysis of the original codec, to improve the compression speed. The proposed video codec has shown a speed-up of around 3.4 times compared to the original algorithm. In addition, we have been able to improve the compression ratio while retaining necessary quality to identify myoclonus.

Epileptic seizure detection based on expected activity measurement and Neural Network classification

Epilepsy is known as the second reason to visit a neurophysiologist after migraine. In this paper, we propose a new approach to automatically detect crises of epilepsy in an Electroencephalogram (EEG). Our algorithm is based on image transformation, Wavelet Decomposition (DWT) and taking advantage of the correlation between wavelet coefficients in each sub-band. Therefore, an Expected Activity Measurement (EAM) is calculated for each coefficient as a feature extraction method. These features are fed into back propagation Neural Network (ANN) and the periods with epileptic seizures and non-seizures are classified. Our approach is validated using a public dataset and the results are very promising, reaching accuracy up to 99.44% for detection epileptic seizures.

Cerium oxide nanoparticles (CeO2 NPs) improve the developmental competence of in vitro-matured prepubertal ovine oocytes

The present study investigated whether supplementation with different doses of cerium dioxide nanoparticles (CeO2 NPs) during in vitro maturation (IVM) of prepubertal ovine oocytes influenced their embryonic development in vitro. Cumulus–oocyte complexes derived from the ovaries of slaughtered prepubertal sheep underwent IVM with CeO2NPs (0, 44, 88 or 220 µg mL–1). Matured oocytes were fertilised in vitro and zygotes were cultured for 7 days. The results demonstrated that CeO2NPs were internalised in the cumulus cells and not in the oocyte. The treatment with CeO2NPs did not affect nuclear maturation or intracellular levels of reactive oxygen species of the oocytes. The percentage of oocytes with regular chromatin configuration and cytoskeleton structures when treated with 44 µg mL–1 CeO2NPs was similar to oocytes matured in the absence of CeO2NPs and significantly higher than those treated with 88 or 220 µg mL–1 CeO2NPs. The relative quantification of transcripts in the cumulus cells of oocytes matured with 44 µg mL–1 CeO2NPs showed a statistically lower mRNA abundance of BCL2-associated X protein (BAX), B-cell CLL/lymphoma 2 (BCL2) and superoxide dismutase 1 (SOD1) compared with the 0 µg mL–1 CeO2 NPs group. A concentration of 44 µg mL–1 CeO2NPs significantly increased the blastocyst yield and their total, inner cell mass and trophectoderm cell numbers, compared with the 0 and 220 µg mL–1 groups. A low concentration of CeO2NPs in the maturation medium enhanced in vitro embryo production of prepubertal ovine oocytes.

Liver transplantation for "very early" intrahepatic cholangiocarcinoma: International retrospective study supporting a prospective assessment

The presence of an intrahepatic cholangiocarcinoma (iCCA) in a cirrhotic liver is a contraindication for liver transplantation in most centers worldwide. Recent investigations have shown that "very early" iCCA (single tumors ≤2 cm) may have acceptable results after liver transplantation. This study further evaluates this finding in a larger international multicenter cohort. The study group was composed of those patients who were transplanted for hepatocellular carcinoma or decompensated cirrhosis and found to have an iCCA at explant pathology. Patients were divided into those with "very early" iCCA and those with "advanced" disease (single tumor >2 cm or multifocal disease). Between January 2000 and December 2013, 81 patients were found to have an iCCA at explant; 33 had separate nodules of iCCA and hepatocellular carcinoma, and 48 had only iCCA (study group). Within the study group, 15/48 (31%) constituted the "very early" iCCA group and 33/48 (69%) the "advanced" group. There were no significant differences between groups in preoperative characteristics. At explant, the median size of the largest tumor was larger in the "advanced" group (3.1 [2.5-4.4] versus 1.6 [1.5-1.8]). After a median follow-up of 35 (13.5-76.4) months, the 1-year, 3-year, and 5-year cumulative risks of recurrence were, respectively, 7%, 18%, and 18% in the very early iCCA group versus 30%, 47%, and 61% in the advanced iCCA group, P = 0.01. The 1-year, 3-year, and 5-year actuarial survival rates were, respectively, 93%, 84%, and 65% in the very early iCCA group versus 79%, 50%, and 45% in the advanced iCCA group, P = 0.02.

CONCLUSION

Patients with cirrhosis and very early iCCA may become candidates for liver transplantation; a prospective multicenter clinical trial is needed to further confirm these results. (Hepatology 2016;64:1178-1188).

Personalized sleep staging system using evolutionary algorithm and symbolic fusion

This paper presents a novel system for automatic sleep staging based on evolutionary technique and symbolic intelligence. Proposed system mimics decision making process of clinical sleep staging using Symbolic Fusion and considers personal singularity with an adaptive thresholds setting up system using Evolutionary Algorithm. It proved to be an effective and promising system in personalizing sleep staging. This system can also be integrated with other medical systems to realize remote sleep monitoring or home-care.

Synchronizing physiological data and video in a telemedicine application: A multimedia approach

Several medical examinations require that multiple modalities of exams are stored in a synchronized manner. For instance, an EEG exam needs that several physiological signals along with video of the exam are acquired synchronously to aid the neurophysiologists to perform their diagnostics. Furthermore support for telemedicine for such exams have become important in recent years. The existing EDF standard that is used for physiological signals makes it difficult to provide integrated support of adding video and compressed component data, however due to widespread use of EDF standard in the domain, cross compatibility with EDF standard for physiological data is also essential. We present in this work a novel idea to solve these issues. Our approach uses standard multimedia containers in which physiological data are embedded alongside video and audio. This paper provides our analyses of the state of the art of multimedia containers EDF, AVI, ASF, MPEG and MKV and their potentials for a telemedicine application and outlines how MKV stands out as an interesting option in this regard, allowing also capability of compression of physiological data if needed.

Towards a Wireless Smart Polysomnograph Using Symbolic Fusion

Polysomnography is the gold standard test for sleep disorders among which the Sleep Apnea Syndrome (SAS) is considered a public health issue because of the increase of the cardio-and cerebro-vascular risk it is associated with. However, the reliability of this test is questioned since sleep scoring is a time-consuming task performed by medical experts with a high inter- and intra-scorers variability, and because data are collected from 15 sensors distributed over a patient's body surface area, using a wired connection which may be a source of artefacts for the patient's sleep. We have used symbolic fusion to support the automated diagnosis of SAS on the basis of the international guidelines of the AASM for the scoring of sleep events. On a sample of 70 patients, and for the Apnea-Hypopnea Index, symbolic fusion performed at the level of sleep experts (97.1% of agreement). The next step is to confirm these preliminary results and move forward to a smart wireless polysomnograph.

Decision System Integrating Preferences to Support Sleep Staging

Scoring sleep stages can be considered as a classification problem. Once the whole recording segmented into 30-seconds epochs, features, extracted from raw signals, are typically injected into machine learning algorithms in order to build a model able to assign a sleep stage, trying to mimic what experts have done on the training set. Such approaches ignore the advances in sleep medicine, in which guidelines have been published by the AASM, providing definitions and rules that should be followed to score sleep stages. In addition, these approaches are not able to solve conflict situations, in which criteria of different sleep stages are met. This work proposes a novel approach based on AASM guidelines. Rules are formalized integrating, for some of them, preferences allowing to support decision in conflict situations. Applied to a doubtful epoch, our approach has taken the appropriate decision.

Towards real-time in situ polyp detection in WCE images using a boosting-based approach

This paper presents a new embeddable method for polyp detections in Wireless Capsule Endoscopic - WCE images. this approach consists first of extracting candidate polyps within the image using geometric considerations about related shape, and second, in classifying (polyp/non-polyp) obtained candidates by a boosting-based method using texture features. The proposed approach has been designed in accordance with the hardware constraints related to FPGA implementation for integration within WCE imaging device. The classification performance of the method have been evaluated on a large dataset of 300 polyps, and 1200 non-polyps images. Experiments show interesting and promising performance: the boosting-based classification is characterized by a sensitivity of 91%, a specificity of 95% and a false detection rate of 4.8%, the detection rate of the overall processing chain being of 68%. The performance of the boosting-based classification are in accordance with the most recent reference on this particular topic using the same dataset. Building of a dedicated WCE image database should permit the improvement of the global detection rate.

Effect of vaccination against gonadotropin-releasing hormone (GnRH) in heavy male pigs for Italian typical dry-cured ham production

The aim of this study was to evaluate immunocastration (vaccination against GnRH using Improvac® vaccine), as an alternative to surgical castration in heavy male pigs (average live weight 165 ± 10 kg), used in the production of Italian typical dry-cured ham. A total of 60 Landrace × Large White male pigs were assigned to three groups of 20 units, including one group of surgically castrated (SC), and two of immunocastrated pigs, with two (IC2) or three (IC3) vaccine treatments, respectively. The groups were compared for green ham traits, processing weight losses, chemo-physical, and sensory properties of dry-cured hams. While IC3 were not different (P>0.05) from SC group, IC2 hams were found to differ (P<0.05) both from SC and IC3 groups in ham traits, final weight losses, texture and sensory boar taint in finished hams. Therefore, vaccination with three doses could be taken into account to control boar taint in the manufacturing of typical Italian dry-cured ham.

Meta-analysis of the effect of preoperative breast MRI on the surgical management of ductal carcinoma in situ

Background

MRI has been used increasingly in the diagnosis and management of women with invasive breast cancer. However, its usefulness in the preoperative assessment of ductal carcinoma in situ (DCIS) remains questionable. A meta-analysis was conducted to examine the effects of MRI on surgical treatment of DCIS by analysing studies comparing preoperative MRI with conventional preoperative assessment.

Methods

Using random-effects modelling, the proportion of women with various outcomes in the MRI versus no-MRI groups was estimated, and the odds ratio (OR) and adjusted OR (adjusted for study-level median age) for each model were calculated.

Results

Nine eligible studies were identified that included 1077 women with DCIS who had preoperative MRI and 2175 who did not. MRI significantly increased the odds of having initial mastectomy (OR 1·72, P = 0·012; adjusted OR 1·76, P = 0·010). There were no significant differences in the proportion of women with positive margins following breast-conserving surgery (BCS) in the MRI and no-MRI groups (OR 0·80, P = 0·059; adjusted OR 1·10, P = 0·716), nor in the necessity of reoperation for positive margins after BCS (OR 1·06, P = 0·759; adjusted OR 1·04, P = 0·844). Overall mastectomy rates did not differ significantly according to whether or not MRI was performed (OR 1·23, P = 0·340; adjusted OR 0·97, P = 0·881).

Conclusion

Preoperative MRI in women with DCIS is not associated with improvement in surgical outcomes.

266 BIOCOMPATIBILITY OF NANOCERIA IN RAM SPERM DURING 24 HOURS OF INCUBATION

In recent years, there has been increasing interest in nanoparticles, especially those widely present in our environment. Several studies have been performed to evaluate their potential toxic effect and their possible use for biomedical applications. Among others, cerium dioxide nanoparticles (nanoceria, CeO2 ENPs) have been recently investigated for their use in biomedicine, based on their potential antioxidant function, due to the presence of oxygen vacancies and redox transformations (Ce4+/Ce3+) occurring at the surface. However, little is known about the potential toxicity of nanoceria in the reproductive system and on gametes, and no information is available with regard to its biocompatibility and potential toxicity on male gametes. The aim of the present study was to investigate effects of increasing doses of CeO2 ENPs on ram spermatozoa during 24 h storage at 4°C, based on assessment of main kinematic parameters, membranes and DNA integrity, ROS production, mitochondrial activity, and CeO2 intracellular uptake. The ejaculates of 3 rams of proven fertility were pooled and incubated with increasing doses of nanoceria (0, 22, 44, and 220 µg mL–1) up to 24 h at 4°C. The experiment was conducted in 4 replicates. At 0, 2, and 24 h of incubation, the 4 groups were submitted to the following analyses: i) main kinematic parameters (total motility and progressive motility) through CASA (computer-assisted sperm analysis); ii) acrosome and membrane integrity (propidium iodide + Pisum sativum agglutinin staining, PI+PSA); iii) flow cytometry for sperm chromatin structure assay (SCSA, acridine orange staining), mitochondrial activity (Mitotracker Orange), and ROS production (H2DCFDA). Moreover, an aliquot of semen from each group in each time step was fixed and processed for transmission electron microscopy to assess intracellular uptake of CeO2 nanoparticles by spermatozoa. Increasing concentrations of nanoceria did not affect the main kinematic parameters of ram semen; there were no differences in total and progressive motility among groups at any time point during the 24 h of incubation (P > 0.05). Integrity of the acrosome and cytoplasmic membranes, assessed through PI+PSA staining, was not affected by nanoceria in any group (P > 0.05). Moreover, exposure to nanoparticles did not increase DNA fragmentation (P > 0.05), and there was no difference in the amount of ROS produced and mitochondrial activity within the 24 h of incubation with nanoceria (P > 0.05). Absence of internalization of the nanoparticles by spermatozoa and occasional interaction between the sperm surface and nanoceria were observed by transmission electron microscopy analysis. In the present study, exposure of ram spermatozoa to increasing doses of nanoceria was not cytotoxic; furthermore, high concentrations of these nanoparticles were well tolerated. These data open new perspectives on the biomedical use of nanoceria and provide more information about their impact on male gametes.

Boosting, probing and switching-off visible light-induced photocurrents in eumelanin-porous silicon hybrids

Improved solid state polymerization of eumelanin in porous silicon and new insights into the mechanisms of photoconduction of eumelanin films.

Orione, a web-based framework for NGS analysis in microbiology

Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.

Availability and implementation: Orione is available online at http://orione.crs4.it.

Contact:gianmauro.cuccuru@crs4.it

Supplementary information:Supplementary data are available at Bioinformatics online.

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

Background

The data-driven inference of intracellular networks is one of the key challenges of computational and systems biology. As suggested by recent works, a simple yet effective approach for reconstructing regulatory networks comprises the following two steps. First, the observed effects induced by directed perturbations are collected in a signed and directed perturbation graph (PG). In a second step, Transitive Reduction (TR) is used to identify and eliminate those edges in the PG that can be explained by paths and are therefore likely to reflect indirect effects.

Results

In this work we introduce novel variants for PG generation and TR, leading to significantly improved performances. The key modifications concern: (i) use of novel statistical criteria for deriving a high-quality PG from experimental data; (ii) the application of local TR which allows only short paths to explain (and remove) a given edge; and (iii) a novel strategy to rank the edges with respect to their confidence. To compare the new methods with existing ones we not only apply them to a recent DREAM network inference challenge but also to a novel and unprecedented synthetic compendium consisting of 30 5000-gene networks simulated with varying biological and measurement error variances resulting in a total of 270 datasets. The benchmarks clearly demonstrate the superior reconstruction performance of the novel PG and TR variants compared to existing approaches. Moreover, the benchmark enabled us to draw some general conclusions. For example, it turns out that local TR restricted to paths with a length of only two is often sufficient or even favorable. We also demonstrate that considering edge weights is highly beneficial for TR whereas consideration of edge signs is of minor importance. We explain these observations from a graph-theoretical perspective and discuss the consequences with respect to a greatly reduced computational demand to conduct TR. Finally, as a realistic application scenario, we use our framework for inferring gene interactions in yeast based on a library of gene expression data measured in mutants with single knockouts of transcription factors. The reconstructed network shows a significant enrichment of known interactions, especially within the 100 most confident (and for experimental validation most relevant) edges.

Conclusions

This paper presents several major achievements. The novel methods introduced herein can be seen as state of the art for inference techniques relying on perturbation graphs and transitive reduction. Another key result of the study is the generation of a new and unprecedented large-scale in silico benchmark dataset accounting for different noise levels and providing a solid basis for unbiased testing of network inference methodologies. Finally, applying our approach to Saccharomyces cerevisiae suggested several new gene interactions with high confidence awaiting experimental validation.

A distal renal tubular acidosis showing hyperammonemia and hyperlactacidemia

INTRODUCTION

distal renal tubular acidosis (dRTA) presents itself with variable clinical manifestations and often with late expressions that impact on prognosis.

CASE REPORT

A 45-day-old male infant was admitted with stopping growth, difficult feeding and vomiting after meals. Clinical tests and labs revealed a type 1 renal tubular acidosis, even if the first blood tests showed ammonium and lactate increase. We had to exclude metabolic diseases before having a certain diagnosis.

CONCLUSIONS

blood and urine investigations and genetic tests are fundamental to formulate dRTA diagnosis and to plan follow-up, according to possible phenotypic expressions of recessive and dominant autosomal forms in patients with dRTA.

Simulating systems genetics data with SysGenSIM

SUMMARY

SysGenSIM is a software package to simulate Systems Genetics (SG) experiments in model organisms, for the purpose of evaluating and comparing statistical and computational methods and their implementations for analyses of SG data [e.g. methods for expression quantitative trait loci (eQTL) mapping and network inference]. SysGenSIM allows the user to select a variety of network topologies, genetic and kinetic parameters to simulate SG data ( genotyping, gene expression and phenotyping) with large gene networks with thousands of nodes. The software is encoded in MATLAB, and a user-friendly graphical user interface is provided.

AVAILABILITY

The open-source software code and user manual can be downloaded at: http://sysgensim.sourceforge.net/

CONTACT

alf@crs4.it.

Impact of adjuvant chemotherapy on time to relapse in cholangiocarcinoma

299

Background: Biliary tract cancer is a rare malignancy with poor prognosis. Surgery is the only potential curative approach, but even if surgical intervention is performed correctly the relapse risk remains very high. In adjuvant setting only few randomized trials using no standard treatments and producing controversial data are reported in literature.

Methods: This is a retrospective analysis on 144 consecutive biliary tract cancer patients (pts), undergone potentially curative resection in our institution (109 pts with R0 surgery and 31 pts with R1 surgery). The series included 57 intrahepatic cholangiocarcinomas (ICC), 68 extrahepatic cholangiocarcinomas (ECC), 19 gallbladder cancers (GBC) (Table). Median age was 63, 80 pts were males and 64 pts were females. 80 (60 R0 and 20 R1) out of 144 pts received adjuvant chemotherapy and the remaining 64 pts (49 R0 and 15 R1) started a follow-up program. Adjuvant chemotherapy schedule was gemcitabine 1000 mg/m2 at day 1, 8, 15 every 28, for six months.

Results: Median time to relapse (TTR) in the treatment group and in the follow-up group were 18 months and 11 months respectively (p=0.038). No grade 3-4 chemotherapy-related adverse events were observed and only grade 1-2 thrombocytopenia occurred. This hematologic toxicity did not affect treatment dose intensity.

Conclusions: Our preliminary retrospective analysis suggests a significant advantage of adjuvant treatment on TTR in radically resected biliary tract cancer patients, although further placebo-controlled double blind trials are required.

[Table: see text]

No significant financial relationships to disclose.