Miracle-dz/UniFAR-FTUs huggingface dataset:
A new approach to measure visual field progression in glaucoma patients using variational bayes linear regression.

PURPOSE We generated a variational Bayes model to predict visual field (VF) progression in glaucoma patients. METHODS This retrospective study included VF series from 911 eyes of 547 glaucoma patients as test data, and VF series from 5049 eyes of 2858 glaucoma patients as training data. Using training data, variational Bayes linear regression (VBLR) was created to predict VF progression. The performance of VBLR was compared against ordinary least-squares linear regression (OLSLR) by predicting VFs in the test dataset. The total deviation (TD) values of test patients' 11th VFs were predicted using TD values from their second to 10th VFs (VF2-10), the root mean squared error (RMSE) associated with each approach then was calculated. Similarly, mean TD (mTD) of test patients' 11th VFs was predicted using VBLR and OLSLR, and the absolute prediction errors compared. RESULTS The RMSE resulting from VBLR averaged 3.9 ± 2.1 (SD) and 4.9 ± 2.6 dB for prediction based on the second to 10th VFs (VF2-10) and the second to fourth VFs (VF2-4), respectively. The RMSE resulting from OLSLR was 4.1 ± 2.0 (VF2-10) and 19.9 ± 12.0 (VF2-4) dB. The absolute prediction error (SD) for mTD using VBLR was 1.2 ± 1.3 (VF2-10) and 1.9 ± 2.0 (VF2-4) dB, while the prediction error resulting from OLSLR was 1.2 ± 1.3 (VF2-10) and 6.2 ± 6.6 (VF2-4) dB. CONCLUSIONS The VBLR more accurately predicts future VF progression in glaucoma patients compared to conventional OLSLR, especially in short VF series.
Influence of Statistical Fluctuation on Reproducibility and Accuracy of SUVmax and SUVpeak: A Phantom Study

Standardized uptake values (SUVs) have been widely used in the diagnosis of malignant tumors and in clinical trials of tumor therapies as semiquantitative metrics of tumor 18F-FDG uptake. However, SUVs for small lesions are liable to errors due to partial-volume effect and statistical noise. The purpose of this study was to evaluate the reproducibility and accuracy of maximum and peak SUV (SUVmax and SUVpeak, respectively) of small lesions in phantom experiments. Methods: We used a body phantom with 6 spheres in a quarter warm background. The PET data were acquired for 1,800 s in list-mode, from which data were extracted to generate 15 PET images for each of the 60-, 90-, 120-, 150-, and 180-s scanning times. The SUVmax and SUVpeak of the hot spheres in the 1,800-s scan were used as a reference (SUVref,max and SUVref,peak). Coefficients of variation for both SUVmax and SUVpeak in hot spheres (CVmax and CVpeak) were calculated to evaluate the variability of the SUVs. On the other hand, percentage differences between SUVmax and SUVref,max and between SUVpeak and SUVref,peak were calculated for evaluation of the accuracy of SUV. We additionally examined the coefficients of variation of background activity and the percentage background variability as parameters for the physical assessment of image quality. Results: Visibility of a 10-mm-diameter hot sphere was considerably different among scan frames. The CVmax and CVpeak increased as the sphere size became smaller and as the acquisition time became shorter. SUVmax was generally overestimated as the scan time shortened and the sphere size increased. The SUVmax and SUVpeak of a 37-mm-diameter sphere for 60-s scans had average positive biases of 28.3% and 4.4%, compared with the reference. Conclusion: SUVmax was variable and overestimated as the scan time decreased and the sphere size increased. In contrast, SUVpeak was a more robust and accurate metric than SUVmax. The measurements of SUVpeak (or SUVpeak normalized to lean body mass) in addition to SUVmax are desirable for reproducible and accurate quantification in clinical situations.
Story-Wall: Supporting Agile Software Development in a Distributed Context

The majority of commercial requirements management tools tend to be costly, document-driven and used by large organizations undertaking traditional forms of software development. While they are not immediately in the spirit of the agile philosophy, which advocates live dialogue over documentation and encourages small teams of developers to do the simplest thing possible to satisfy a requirement, there are some fundamental practices supported by these tools that play a role in more agile forms of software development. This paper examines the core requirements management needs that are common to software development of all flavors, at a high level, and describes a tool concept designed to bring lightweight requirements management to the agile (predominantly XP) context. This work is based on the experiences of a globally distributed team that uses agile development practices to develop and maintain ibm.com, and on their transition from manually handling paper-based story cards to the use of first generation story management tools.
Ecological divergence combined with ancient allopatry in lizard populations from a small volcanic island

Population divergence and speciation are often explained by geographical isolation, but may also be possible under high gene flow due to strong ecology‐related differences in selection pressures. This study combines coalescent analyses of genetic data (11 microsatellite loci and 1 Kbp of mtDNA) and ecological modelling to examine the relative contributions of isolation and ecology to incipient speciation in the scincid lizard Chalcides sexlineatus within the volcanic island of Gran Canaria. Bayesian multispecies coalescent dating of within‐island genetic divergence of northern and southern populations showed correspondence with the timing of volcanic activity in the north of the island 1.5–3.0 Ma ago. Coalescent estimates of demographic changes reveal historical size increases in northern populations, consistent with expansions from a volcanic refuge. Nevertheless, ecological divergence is also supported. First, the two morphs showed non‐equivalence of ecological niches and species distribution modelling associated the northern morph with mesic habitat types and the southern morph with xeric habitat types. It seems likely that the colour morphs are associated with different antipredator strategies in the different habitats. Second, coalescent estimation of gene copy migration (based on microsatellites and mtDNA) suggest high rates from northern to southern morphs demonstrating the strength of ecology‐mediated selection pressures that maintain the divergent southern morph. Together, these findings underline the complexity of the speciation process by providing evidence for the combined effects of ecological divergence and ancient divergence in allopatry.
Systemic treatment for alopecia areata

Of the world population, 1.7% is suffering from alopecia areata at some point in their lives. The exact etiology of this disease is still unknown, and the course of the disease is unpredictable. Effective treatments, especially for severe multifocal alopecia areata, alopecia areata totalis, and alopecia areata universalis, are lacking. The present article will discuss side effects and relapse rates of different systemic agents for treatment of severe and rapid progressive alopecia areata.
Dynamic Dwell Timer for Hybrid Vertical Handover in 4G Coupled Networks

Cellular networks coupled with wireless local area networks would be very common in the next- generation wireless environments. This integration would be made possible by employing techniques of vertical handover across different radio access networks. Finding precise timing to carry out vertical handover is an important problem and is the topic of this research work. We propose a hybrid vertical handoff (HVH) initiation by intelligent fusion of adaptive threshold, signal trend detection and variable width dwell timer. Simulation studies have shown that our proposed approach results in a better vertical handoff experience as compared to existing techniques.
Resource Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Casey A. Gifford,1,2,3,9 Michael J. Ziller,1,2,3,9 Hongcang Gu,1 Cole Trapnell,1,3 Julie Donaghey,1,2,3 Alexander Tsankov,1,2,3 Alex K. Shalek,4 David R. Kelley,1,3 Alexander A. Shishkin,1 Robbyn Issner,1 Xiaolan Zhang,1 Michael Coyne,1 Jennifer L. Fostel,1 Laurie Holmes,1 Jim Meldrim,1 Mitchell Guttman,1 Charles Epstein,1 Hongkun Park,4 Oliver Kohlbacher,5 John Rinn,1,3,6 Andreas Gnirke,1 Eric S. Lander,1,7 Bradley E. Bernstein,1,8 and Alexander Meissner1,2,3,* 1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 2Harvard Stem Cell Institute, Cambridge, MA 02138, USA 3Department of Stem Cell and Regenerative Biology 4Department of Chemistry Harvard University, Cambridge, MA 02138, USA 5Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tübingen, 72076 Tübingen, Germany 6Beth Israel Deaconess Hospital, Boston, MA 02115, USA 7Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 8Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA 9These authors contributed equally to this work *Correspondence: alexander_meissner@harvard.edu http://dx.doi. org/10.1016/j.cell. 2013.04. 037
Direct Power Control of variable-speed micro-hydropower plant based on propeller turbine

This paper presents a Direct Power Control of variable-speed micro hydropower plant (MHPP). This control is applied to a micro axial-flow hydraulic turbine rigidly coupled to permanent magnet synchronous generator. A back-to-back two level Voltage Source Inverters are interfacing the generator to the grid. The main topic is to directly control the DC-bus power injected to the grid without speed control loop for robustness and simplicity. PI and resonant controllers are used to control the power electronics interface converters and DC-link voltage. The proposed control technique has been simulated under Matlab Simulink and the obtained results show the benefit of the proposed technique to simplify the whole control of the MHPP.
Self-Reported Everyday Memory and Depression in Patients With Multiple Sclerosis

Depression and memory difficulties are among the most common complaints voiced by patients with multiple sclerosis (MS). Nevertheless, little is known about how depression might affect patients’ perceptions of their memory difficulties. The present investigation was designed to explore this issue. Results supported a model that integrates aspects of Beck’s theory of depression and the concept of depressive realism. Consistent with the depressive realism literature, nondepressed MS patients significantly overestimated their everyday memory compared with their actual performance on verbal memory and attention/concentration indices, whereas moderately depressed patients’ everyday memory ratings mirrored their actual neuropsychological performance. Supporting Beck’s negative cognitive schema notion, mildly depressed patients significantly overestimated their memory difficulties. Implications for the treatment of memory problems among MS patients are discussed.
Métabolomique par spectroscopie RMN HRMAS appliquée à l’hyperparathyroïdie et aux tumeurs pancréatiques

La spectroscopie RMN Haute Resolution en Rotation a l’Angle Magique (HRMAS) permet la caracterisation metabolomique tissulaire. Nous avons caracterise par RMN HRMAS le profil metabolomique des glandes parathyroidiennes hypersecretantes. Celui de l’hyperparathyroidie primaire (HPT1) a ete compare a celui des HPT renales. Au sein des HPT1, la distinction a pu etre faite entre pathologie uni- et multi-glandulaire. Le profil metabolomique du tissu pancreatique sain a ete compare a celui du tissu tumoral. Aussi, les patients longs/courts-survivants ont pu etre distingues. La relation entre le phenotype metabolique et la survie des patients a ete etudiee. Le profil metabolomique des TIPMP a ete caracterise. Les TIPMP non degenerees et degenerees ont ete comparees. Le risque de degenerescence a ete correle au profil metabolomique. Nos resultats montrent que la spectroscopie RMN HRMAS est une technique prometteuse pour l’etude du profil metabolomique des HPT et des pathologies pancreatiques.
Stress-Induced Production of Biofilm in the Hyperthermophile Archaeoglobus fulgidus

Archaeoglobus fulgidus, an anaerobic marine hyperthermophile, forms a biofilm in response to environmental stresses. The biofilm is a heterogeneous, morphologically variable structure containing protein, polysaccharide, and metals. Production of the biofilm can be induced by nonphysiological extremes of pH and temperature, by high concentrations of metals, and by addition of antibiotics, xenobiotics, or oxygen. Cells within the biofilm show an increased tolerance to otherwise toxic environmental conditions. Metals sequestered within the biofilm stimulate growth of A. fulgidus cells in metal-depleted medium. These data suggest that cells may produce biofilm as a mechanism for concentrating cells and attaching to surfaces, as a protective barrier, and as a reserve nutrient. Because similar biofilms are formed by Archaeoglobus profundus, Methanococcus jannaschii, and Methanobacterium thermoautotrophicum, biofilm formation might be a common stress response mechanism among the archaea.
The Evolution of Cooperation: The Role of Costly Strategy Adjustments

We study the evolution of cooperation in the indefinitely repeated prisoner’s dilemma when it is costly for players to adjust their strategy. Our experimental interface allows subjects to design a comprehensive strategy that then selects actions for them in every period. We conduct lab experiments in which subjects can adjust their strategies during a repeated game but may incur a cost for doing so. We find three main results. First, subjects learn to cooperate more when adjustments are costless than when they are costly. Second, subjects make more adjustments to their strategies when adjustments are costless, but they still make adjustments even when they are costly. Finally, we find that cooperative strategies emerge over time when adjustments are costless but not when adjustments are costly. These results highlight that within-game experimentation is critical to the rise of cooperative behavior. We provide simulations based on an evolutionary algorithm to support these results. (JEL C71, C72, C73, C91)
Commande Robuste de la Machine Synchrone à AimantsPermanents

Le travail presente dans cette these porte sur les lois de commande non lineaire robuste dediees aux moteurs synchrones a aimants permanents . Nous avons presente deux aspects, le premier aspect concerne la commande par modes glissants d’ordre superieur et plus precisement aux modes glissants d’ordre deux. Un autre type de commande utilisant un concept different de linearisation a ete aborde. Cette technique repose principalement sur la notion des systemes plats associee a des regulateurs auto-ajustable type Lineaire a Parametres Variant (LPV). Elle a pour ambition de proposer un outil de synthese et d’analyse des lois de commande robuste des systemes non lineaires en utilisant le concept de platitude. Dans un premier temps, nous avons propose une approche destinee a la modelisation des systemes non lineaires plats perturbes sous forme de systemes LPV. L'approche est basee sur un changement de coordonnees sur les sorties plates, sur un diffeomorphisme et sur le developpement en serie de Taylor. L'approche permet d'abord de determiner en boucle ouverte, en tenant compte de certains objectifs, les trajectoires de references des sorties plates du systeme et des commandes nominales associees. Elle permet ensuite d'obtenir un modele, non lineaire, du comportement dynamique de l'ecart (l'erreur entre le modele de reference et modele nominale) des trajectoires induit par des erreurs de modele ou des perturbations exogenes. Apres linearisation du modele non lineaire de l'ecart le long des trajectoires de references des sorties plates, le comportement dynamique du modele linearise obtenu est represente par un modele LPV. Dans un second temps l’utilisation des outils de la commande robuste, a base des LMI et la modelisation polytopique, vont nous permettre d’obtenir une loi de commande LPV assurant la stabilite et les performances du systeme.
Noyau Linux : à propos des outils de trace

Linux est un programme complexe par nature. La comprehension de ce que le systeme execute, et de comment et quand il l'execute est necessaire pour obtenir des metriques de performances, pour s'approprier son fonctionnement ou pour analyser du code ajoute quand on developpe un module ou lorsqu'on ajoute du code au sein meme du noyau. Afin d'obtenir des informa- tions d'execution sans etre dependant d'un support d'execution particulier, du code est ajoute au systeme pour produire des traces. Leur production doit induire un surcout le plus faible possible pour reduire les risques de perturber le code observe. Un nombre important d'ou- tils est apparu pour permettre ce type de mise en œuvre. L'article apporte un eclairage sur les points de conception associes a leur developpement dans un contexte d'execution multicœur, et propose une etude comparee de 11 outils.
Inhibition in Task Switching: The Reliability of the n − 2 Repetition Cost

The n − 2 repetition cost seen in task switching is the effect of slower response times performing a recently completed task (e.g. an ABA sequence) compared to performing a task that was not recently completed (e.g. a CBA sequence). This cost is thought to reflect cognitive inhibition of task representations and as such, the n − 2 repetition cost has begun to be used as an assessment of individual differences in inhibitory control; however, the reliability of this measure has not been investigated in a systematic manner. The current study addressed this important issue. Seventy-two participants performed three task switching paradigms; participants were also assessed on rumination traits and processing speed—measures of individual differences potentially modulating the n − 2 repetition cost. We found significant n − 2 repetition costs for each paradigm. However, split-half reliability tests revealed that this cost was not reliable at the individual-difference level. Neither rumination tendencies nor processing speed predicted this cost. We conclude that the n − 2 repetition cost is not reliable as a measure of individual differences in inhibitory control.
4-(Methylsulfonyl)piperazin-1-ium chloride

In the title molecular salt, C5H13N2O2S+·Cl−, the complete cation is generated by crystallographic mirror symmetry, with both N atoms, the S atom and one C atom lying on the reflecting plane. The chloride ion also lies on the mirror plane. The piperazinium ring adopts a chair conformation and the N—S bond adopts an equatorial orientation. In the crystal structure, the component ions are linked into a three-dimensional framework by intermolecular N—H⋯Cl and C—H⋯Cl hydrogen bonds.
Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis

Abstract Epidermal growth factor receptor variant III (EGFRvIII) is a glycoprotein uniquely expressed in glioblastoma, but not in normal brain tissues. To develop targeted therapies for brain tumors, we selected RNA aptamers against the histidine-tagged EGFRvIII ectodomain, using an Escherichia coli system for protein expression and purification. Representative aptamer E21 has a dissociation constant (Kd) of 33×10-9 m, and exhibits high affinity and specificity for EGFRvIII in ELISA and surface plasmon resonance assays. However, selected aptamers cannot bind the same protein expressed from eukaryotic cells because glycosylation, a post-translational modification present only in eukaryotic systems, significantly alters the structure of the target protein. By transfecting EGFRvIII aptamers into cells, we find that membrane-bound, glycosylated EGFRvIII is reduced and the percentage of cells undergoing apoptosis is increased. We postulate that transfected aptamers can interact with newly synthesized EGFRvIII, disrupt proper glycosylation, and reduce the amount of mature EGFRvIII reaching the cell surface. Our work establishes the feasibility of disrupting protein post-translational modifications in situ with aptamers. This finding is useful for elucidating the function of proteins of interest with various modifications, as well as dissecting signal transduction pathways.
Automatic Prostate Segmentation in MR Images with a Probabilistic Active Shape Model

Segmentation of the prostate gland in Magnetic Resonance (MR) images is an important task for image-guided prostate cancer therapy. The low contrast of the prostate to surrounding tissue in MR images makes automatic segmentation very challenging. In this paper, we propose an automatic approach for robust and accurate prostate segmentation in T2-weighted MR scans. We ﬁrst employ a boosted prostate detector to locate the prostate in the images, and then use a Probabilistic Active Shape Model for the delineation of its contour. Our approach has been quantitatively evaluated on 50 MR images, on which we achieve a median dice coeﬃcient of 0.85 (IQR: 0.09).
Fabricated multilayer SIW system using PCB manufacturing process

The challenge to acquire new and realistic means to practically demonstrate innovative technical-based RF solution has led designers to pursue and optimize available fabrication techniques. In this paper, design properties and versatility exhibited in SIW design have been explored, realized, and characterized in a proposed multilayer SIW prototype solution for 10.0 GHz. The assembled system consists of SMA-microstrip input interface with the low-loss microstrip-taper via transition, two manually stacked SIW structures electrically connected via small rectangular slot opening, and finally radiated by a SIW slot array antenna. The proposed system is designed using CST software and fabricated using conventional Printed Circuit Board (PCB) manufacturing process on Rogers 4003 C with εr = 3.38 and thickness of 0.813 mm. The close agreement between simulated and measured result indicating resonance occurring at 10.0 GHz. The prototype has measured return loss of −21.5 dB, bandwidth of 300 MHz, and gain of 6.1 dBi. Meanwhile, the beamwidth in E-plane and H-plane are 62.0 degrees and 94.0 degrees, respectively. The assembled multilayer SIW system, although fabricated using conventional PCB manufacturing process, shows potential in several RF applications such as satellite and radar application.
Whose DNA Is It, Anyway?

Three of the U.S. National Institutes of Health are trying to open up collections of DNA to spur hunts for disease genes, but clinicians are holding onto their data out of fear that molecular biologists will skim the cream off years of their painstaking work. Also at stake are the rights of donors--many of whom are members of families carrying disease-related genes--to research results derived from their own DNA. Now a patients9 rights organization has taken matters into its own hands by sponsoring research projects with the proviso that data be shared.