Miracle-dz/UniFAR-FTUs huggingface dataset:
Health Status in Long-Term Survivors of Pediatric Craniopharyngiomas

Craniopharyngiomas are the third most common pediatric brain tumor and most common pediatric suprasellar tumor. Contemporary treatment of craniopharyngiomas uses limited surgery and radiation in an effort to minimize morbidity, but the long-term health status of patients treated in this fashion has not been well described. The purpose of this study was to analyze the health status of long-term survivors of pediatric craniopharyngioma treated primarily with radiation and conservative surgical resection. Medical records of all long-term survivors of craniopharyngioma treated at St. Jude Children's Research Hospital and then transferred to the long-term follow-up clinic were reviewed. The initial cohort comprised 55 patients. Of these, 51 (93%) were alive at the time of this analysis. The median age at diagnosis was 7.1 years (range, 1.2-17.6 years), and 29 (57%) were male. At the time of analysis, the median survival was 7.6 years (range, 5.0-21.3 years). Diagnosis and treatment included surgical biopsy, resection (n = 50), and radiation therapy (n = 48). Only 1 patient received chemotherapy. Polyendocrinopathy was the most common morbidity, with hypothyroidism (96%), adrenocorticotropic hormone deficiency (84%), and diabetes insipidus (53%) occurring most frequently. Half of the patients were hypogonadal, and 33 (65%) were overweight or obese. The most common neurologic problems included shunt dependence (37%), seizures (28%), and headaches (39%). Psychological and educational deficits were also identified in a significant number of these individuals. Despite efforts to reduce morbidity in these patients, many survivors remain burdened with significant medical complications. In a small percentage of patients, complications may result in death even during extended remission of craniopharyngioma. Because of the broad spectrum or morbidities experienced, survivors of craniopharyngioma continue to benefit from multidisciplinary care.
2-D CMUT wafer bonded imaging arrays with a row-column addressing scheme

This paper presents fabrication and characterization results of two-dimensional capacitive micromachined ultrasonic transducer arrays which use a row-column addressing scheme. The devices are fabricated using a wafer bonding process where both the insulation layer and the membrane are user deposited silicon nitride. Two types of arrays with different resonant frequencies are presented. One is a 32×32 element array which has a resonant frequency of 15 MHz. In immersion, when transmitting and receiving with columns a centre frequency of 5.45 MHz is measured with a relative -6 dB bandwidth of 119%. Using rows, a centre frequency of 5.75 MHz is measured with a −6 dB bandwidth of 135%. The other device is a 32×32 element array with a resonant frequency of 28 MHz and in immersion has a centre frequency of ∼12 MHz. Membrane resonant frequency uniformity across the 15 MHz device has a measured standard deviation of 0.3%.
The control of developmental phase transitions in plants

Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs – miR156 and miR172 – and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.
Single trial P300 detection in children using expert knowledge and SOM

Preliminary results of an automatic system for single trial P300 visual evoked potential events detection are presented. For each single trial P300, several candidate events were generated, and then filtered, using 3 wave features. The surviving candidate events were fed into a SOM-based classifier. A context filter was applied before the final output. No stationary condition of the P300 is involved in the algorithms. Recordings of 27 assessment sessions, each with 120 trials, were visually inspected by experts to identify and mark the P300 events, which was accomplished in about one third of the trials. The dataset was divided in training (18) and testing (9) subsets. The system identifies the initial and end times of the P300; it obtained a sensitivity of 53.9%, a specificity of 64.0% and an accuracy of 61.2% in the testing dataset.
Opportunistic Spectrum Access in Unknown Dynamic Environment: A Game-Theoretic Stochastic Learning Solution

We investigate the problem of distributed channel selection using a game-theoretic stochastic learning solution in an opportunistic spectrum access (OSA) system where the channel availability statistics and the number of the secondary users are apriori unknown. We formulate the channel selection problem as a game which is proved to be an exact potential game. However, due to the lack of information about other users and the restriction that the spectrum is time-varying with unknown availability statistics, the task of achieving Nash equilibrium (NE) points of the game is challenging. Firstly, we propose a genie-aided algorithm to achieve the NE points under the assumption of perfect environment knowledge. Based on this, we investigate the achievable performance of the game in terms of system throughput and fairness. Then, we propose a stochastic learning automata (SLA) based channel selection algorithm, with which the secondary users learn from their individual action-reward history and adjust their behaviors towards a NE point. The proposed learning algorithm neither requires information exchange, nor needs prior information about the channel availability statistics and the number of secondary users. Simulation results show that the SLA based learning algorithm achieves high system throughput with good fairness.
LAT-MAC: A Latency Energy Aware MAC Protocol for Wireless Sensor Networks

The mobile nodes in Ad hoc networks move freely, but their batteries have limited energy. Reducing energy consumption in mobile ad hoc networks and sensors is a major challenge. Several protocols called Energy-aware protocols have been proposed. Another important parameter is the latency. It is a common attribute for most MAC protocols. Its importance depends on real applications. We studied the different Energy-aware protocols, and simulated SMAC protocol as one of the main protocols that save energy. However, SMAC has one main inconvenient which is the latency. We proposed a new Latency Energy Aware Protocol for Wireless Sensor Networks (LATMAC) which solves the problem of energy and latency at the same time. After comparison of LATMAC with SMAC, we can observe its importance and performance.
Degenerative Intraspinal Cyst of the Cervical Spine: Case Report and Literature Review

Study Design. A case report and a literature review are presented. Objective. To describe and review the clinical presentations, characteristic findings from imaging studies, and treatment of synovial and ganglion cysts arising within the cervical spinal canal. Summary of Background Data. Synovial and ganglion cysts in the cervical spine are rare. To the authors’ knowledge, 24 sporadic cases in all, designated by various terms, have been reported in the literature. Methods. Three cases of synovial and ganglion cysts in the cervical spine are reported as well as a review of the literature. Results. Characteristic findings from imaging studies included a fluid-containing extradural lesion demonstrated on magnetic resonance images and gas content in the lesion demonstrated on ordinary or sagittally reconstructed computed tomography images. A laminectomy with removal of the cyst was the treatment of choice in most cases. Conclusions. Neither communication with an adjacent facet joint nor histopathology of the cyst wall provides a persuasive basis for differentiating ganglion, synovial cyst, and cyst arising from the ligaments. To accommodate the varied presentations, the authors propose a comprehensive term for these lesions: “degenerative intraspinal cyst. ”
CHARACTERISTICS OF MOULD FLUX FILMS FOR CASTING MC AND LC STEELS

The characteristics of mould flux films developed while casting MC and LC steels taken from a continuous casting mould have been investigated. These characteristics include appearance, porosity, crystallinity, mineralogical phases, cross-sectional microstructure, and element distribution and thickness of solid/liquid layers. The following are discussed: (i) the effect of chemical compositions of mould fluxes on the characteristics of the films and (ii) the mechanisms responsible for crystallisation and porosity formation. Two mould flux films for casting MC and LC steel grades were taken at around 300 mm from the top of the mould in the end of casting. The crystallinity of flux films was investigated by direct observation of optical microscope and SEM. XRD was used to detect the mineralogical phases in the mould flux films. The microstructure and cross-sectional element distribution were studied by SEM/SEM -EDS. The porosity and appearance of flux films were determined by imagine analysis system. It was verified that the horizontal heat transfer between shell and mould is controlled by (i) thickness of the solid slag film and (ii) the surface roughness (equivalent to an air gap) formed when the initial glassy slag film crystallises. Both the surface roughness and the crystalline fraction (90%) of the slag film for casting MC grades were greater than those for casting LC grades. The crystalline fraction can be related to the flux composition by using the parameter “modified NBO/T”. The mechanism for the crystallisation and porosity formation of the flux films is discussed.
The Antimicrobial Defense of the Pacific Oyster, Crassostrea gigas. How Diversity may Compensate for Scarcity in the Regulation of Resident/Pathogenic Microflora

Healthy oysters are inhabited by abundant microbial communities that vary with environmental conditions and coexist with immunocompetent cells in the circulatory system. In Crassostrea gigas oysters, the antimicrobial response, which is believed to control pathogens and commensals, relies on potent oxygen-dependent reactions and on antimicrobial peptides/proteins (AMPs) produced at low concentrations by epithelial cells and/or circulating hemocytes. In non-diseased oysters, hemocytes express basal levels of defensins (Cg-Defs) and proline-rich peptides (Cg-Prps). When the bacterial load dramatically increases in oyster tissues, both AMP families are driven to sites of infection by major hemocyte movements, together with bactericidal permeability/increasing proteins (Cg-BPIs) and given forms of big defensins (Cg-BigDef), whose expression in hemocytes is induced by infection. Co-localization of AMPs at sites of infection could be determinant in limiting invasion as synergies take place between peptide families, a phenomenon which is potentiated by the considerable diversity of AMP sequences. Besides, diversity occurs at the level of oyster AMP mechanisms of action, which range from membrane lysis for Cg-BPI to inhibition of metabolic pathways for Cg-Defs. The combination of such different mechanisms of action may account for the synergistic activities observed and compensate for the low peptide concentrations in C. gigas cells and tissues. To overcome the oyster antimicrobial response, oyster pathogens have developed subtle mechanisms of resistance and evasion. Thus, some Vibrio strains pathogenic for oysters are equipped with AMP-sensing systems that trigger resistance. More generally, the known oyster pathogenic vibrios have evolved strategies to evade intracellular killing through phagocytosis and the associated oxidative burst.
Overview of the EOS aura mission

Aura, the last of the large Earth Observing System observatories, was launched on July 15, 2004. Aura is designed to make comprehensive stratospheric and tropospheric composition measurements from its four instruments, the High Resolution Dynamics Limb Sounder (HIRDLS), the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), and the Tropospheric Emission Spectrometer (TES). With the exception of HIRDLS, all of the instruments are performing as expected, and HIRDLS will likely be able to deliver most of their planned data products. We summarize the mission, instruments, and synergies in this paper.
Friction Stir Welding and Processing

Abstract Friction stir welding (FSW) is a relatively new solid-state joining process. This joining technique is energy efficient, environment friendly, and versatile. In particular, it can be used to join high-strength aerospace aluminum alloys and other metallic alloys that are hard to weld by conventional fusion welding. FSW is considered to be the most significant development in metal joining in a decade. Recently, friction stir processing (FSP) was developed for microstructural modification of metallic materials. In this review article, the current state of understanding and development of the FSW and FSP are addressed. Particular emphasis has been given to: (a) mechanisms responsible for the formation of welds and microstructural refinement, and (b) effects of FSW/FSP parameters on resultant microstructure and final mechanical properties. While the bulk of the information is related to aluminum alloys, important results are now available for other metals and alloys. At this stage, the technology diffusion has significantly outpaced the fundamental understanding of microstructural evolution and microstructure–property relationships.
BIOINFORMATICS ORIGINAL PAPER

Motivation: In molecular biology, as in many other scientiﬁc ﬁelds, the scale of analyses is ever increasing. Often, complex Monte Carlo simulation is required, sometimes within a large-scale multiple testing setting. The resulting computational costs may be prohibitively high. Results: We here present MCFDR, a simple, novel algorithm for false discovery rate (FDR) modulated sequential Monte Carlo (MC) multiple hypothesis testing. The algorithm iterates between adding MC samples across tests and calculating intermediate FDR values for the collection of tests. MC sampling is stopped either by sequential MC or based on a threshold on FDR. An essential property of the algorithm is that it limits the total number of MC samples whatever the number of true null hypotheses. We show on both real and simulated data that the proposed algorithm provides large gains in computational efﬁciency. Availability: MCFDR is implemented in the Genomic HyperBrowser (http://hyperbrowser.uio.no/mcfdr), a web-based system for genome analysis. All input data and results are available and can be reproduced through a Galaxy Pages document at: http://hyperbrowser.uio. no/mcfdr/u/sandve/p/mcfdr.
Multiple Instance Learning: Algorithms and Applications

Traditional supervised learning requires a training data set that consists of inputs and corresponding labels. In many applications, however, it is difﬁcult or even impossible to accurately and consistently assign labels to inputs. A relatively new learning paradigm called Multiple Instance Learning allows the training of a classiﬁer from ambiguously labeled data. This paradigm has been receiving much attention in the last several years, and has many useful applications in a number of domains (e.g. computer vision, computer audition, bioinformatics, text processing). In this report we review several representative algorithms that have been proposed to solve this problem. Furthermore, we discuss a number of existing and potential applications, and how well the currently available algorithms address the problems presented by these applications.
Indexing, browsing, and searching of digital video

L'A. examine les methodes d'acces aux documents audiovisuels numeriques. Apres une premiere partie consacree aux normes d'encodage et de stockage de l'information video ainsi qu'aux moyens d'acces conventionnels, il s'interesse a la facon dont l'information peut et doit etre structuree et indexee automatiquement en scenes et en prises de facon a faciliter l'acces. Il traite des methodes de navigation et de recherche des videos numeriques, de l'evaluation des performances de recherche notamment avec le TREC (Text REtrieval Conference), de l'acces a partir de plateformes mobiles, et des futures tendances.
High-speed network modeling for full system simulation

The widespread adoption of cluster computing systems has shifted the modeling focus from synthetic traffic to realistic workloads to better capture the complex interactions between applications and architecture. In this context, a full-system simulation environment also needs to model the networking component, but the simulation duration that is practically affordable is too short to appropriately stress the networking bottlenecks. In this paper, we present a methodology that overcomes this problem and enables the modeling of interconnection networks while ensuring representative results with fast simulation turnaround. We use standard network tools to extract simplified models that are statistically validated and at the same time compatible with a full system simulation environment. We propose three models with different accuracy vs. speed ratios that compute network latency times according to the estimated traffic and measure them on a real-world parallel scientific application.
Functional Genomic Analysis of the HY2 Family of Ferredoxin-Dependent Bilin Reductases from Oxygenic Photosynthetic Organisms

Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. Previous biochemical studies have established that phytobilins are synthesized from heme via the intermediacy of biliverdin IXα (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities. By exploiting the sequence of phytochromobilin synthase (HY2) of Arabidopsis, an enzyme that catalyzes the ferredoxin-dependent conversion of BV to the phytochrome chromophore precursor phytochromobilin, genes encoding putative bilin reductases were identified in the genomes of various cyanobacteria, oxyphotobacteria, and plants. Phylogenetic analyses resolved four classes of HY2-related genes, one of which encodes red chlorophyll catabolite reductases, which are bilin reductases involved in chlorophyll catabolism in plants. To test the catalytic activities of these putative enzymes, representative HY2-related genes from each class were amplified by the polymerase chain reaction and expressed in Escherichia coli. Using a coupled apophytochrome assembly assay and HPLC analysis, we examined the ability of the recombinant proteins to catalyze the ferredoxin-dependent reduction of BV to phytobilins. These investigations defined three new classes of bilin reductases with distinct substrate/product specificities that are involved in the biosynthesis of the phycobiliprotein chromophore precursors phycoerythrobilin and phycocyanobilin. Implications of these results are discussed with regard to the pathways of phytobilin biosynthesis and their evolution.
Early Use of Clozapine for Poorly Responding First-Episode Psychosis

Although most patients treated for first-episode schizophrenia will experience considerable improvement with initial antipsychotic therapy, a subgroup experiences significant ongoing positive symptoms. Clozapine has unique efficacy in improving treatment-resistant patients with chronic schizophrenia, but its role in the treatment of first-episode patients remains unclear. A standardized treatment algorithm was implemented in our First Episode Psychosis Program, with patients receiving 2 trials with 2 second-generation antipsychotics (olanzapine, quetiapine, or risperidone at low, medium, and high doses), followed by a trial of clozapine as early as 25 weeks into the start of their treatment. Patients progress along the algorithm according to their response as defined by clinical rating scales. To date, 123 patients with first-episode schizophrenia have been treated according to the algorithm. Of these, 93 (76%) responded to the first trial of an antipsychotic. Only 7 (23%) of the remaining 30 patients responded to a second antipsychotic trial; 13 of the remaining 23 individuals agreed to a trial of clozapine. We compared the clozapine-treated group with a group of 9 patients who refused clozapine and chose to continue the same antipsychotic treatment as before. Subjects who received clozapine experienced a mean Brief Psychiatric Rating Scale change of 19 points (from 53.5 to 34.5) and a change in the Clinical Global Inventory severity rating from 5.4 to 3.5 (from severely ill to mildly ill); those who refused clozapine had a 2-point increase in mean Brief Psychiatric Rating Scale (from 53 to 55) and a 0.6-point increase in the mean Clinical Global Inventory severity rating from 5.4 to 6 (remaining markedly to severely ill). In clinical practice, there is a hesitancy to switch individuals to clozapine given its side effect profile and position as treatment of "last resort. " The present findings suggest that clozapine may have an important role in the early treatment of first-episode patients whose psychosis does not remit with other second-generation antipsychotics during the first months of treatment.
Sulfiredoxin-1 exerts anti-apoptotic and neuroprotective effects against oxidative stress-induced injury in rat cortical astrocytes following exposure to oxygen-glucose deprivation and hydrogen peroxide

Sulfiredoxin 1 (Srxn1), an endogenous antioxidant protein, plays an important neuroprotective role in cerebral ischemia. However, the exact mechanisms of action of Srxn1 in cerebral ischemia have not yet been fully elucidated. Therefore, in the present study, rat primary cortical astrocytes transfected with a lentiviral vector encoding short hairpin RNA (shRNA) were exposed to oxygen-glucose deprivation (OGD) for 4 h or to 100 μM hydrogen peroxide (H2O2) for 6 h, in order to construct an in vitro model of cerebral ischemia-induced damage. We found that following exposure to OGD or H2O2, the knockdown of Srxn1 resulted in a decrease in cell viability, as shown by MTS assay, an increase in cell damage, as shown by lactate dehydrogenase assay and an increase in cellular apoptosis, as shown by Hoechst 33342 staining and flow cytometry. Furthermore, we found that following exposure to OGD or H2O2, the knockdown of Srxn1 resulted in a decrease in mitochondrial transmembrane potential (Δψm) as indicated by JC-1 staining, an increase in the cytoplasmic expression of cytochrome c (Cyt.C), caspase-3, caspase-9, poly(ADP-ribose) polymerase (PARP) and Bax protein at the protein level, but a decrease in the expression of the anti-apoptotic Bcl-2 protein; these effects were tightly associated with the mitochondrial apoptotic pathway. However, we found that there was no obvious change in the intracellular calcium ([Ca2+]i) levels and caspase-12 expression following the knockdown of Srxn1. Taken together, the results from the present study demonstrate that Srxn1 protects primary rat cortical astrocytes from OGD- or H2O2-induced apoptosis and that involves the activation of the mitochondrial apoptotic pathway, which suggests that Srxn1 may be a potential target in the treatment of cerebral ischemia.