Miracle-dz/UniFAR-FTUs huggingface dataset:
fMRI Retinotopic Mapping—Step by Step

fMRI retinotopic mapping provides detailed information about the correspondence between the visual field and its cortical representation in the individual subject. Besides providing for the possibility of unambiguously localizing functional imaging data with respect to the functional architecture of the visual system, it is a powerful tool for the investigation of retinotopic properties of visual areas in the healthy and impaired brain. fMRI retinotopic mapping differs conceptually from a more traditional volume-based, block-type, or event-related analysis, in terms of both the surface-based analysis of the data and the phase-encoded paradigm. Several methodological works related to fMRI retinotopic mapping have been published. However, a detailed description of all the methods involved, discussing the steps from stimulus design to the processing of phase data on the surface, is still missing. We describe here step by step our methodology for the complete processing chain. Besides reusing methods proposed by other researchers in the field, we introduce original ones: improved stimuli for the mapping of polar angle retinotopy, a method of assigning volume-based functional data to the surface, and a way of weighting phase information optimally to account for the SNR obtained locally. To assess the robustness of these methods we present a study performed on three subjects, demonstrating the reproducibility of the delineation of low order visual areas.
The Usability of Open Source Software

Open source communities have successfully developed a great deal of software although most computer users only use proprietary applications. The usability of open source software is often regarded as one reason for this limited distribution. In this paper we review the existing evidence of the usability of open source software and discuss how the characteristics of open source development influence usability. We describe how existing human-computer interaction techniques can be used to leverage distributed networked communities, of developers and users, to address issues of usability.
Determination of cell type‐specific proteome signatures of primary human leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts and melanocytes by comparative proteome profiling

Cells gain their functional specialization by different protein synthesis. A lot of knowledge with respect to cell type‐specific proteins has been collected during the last thirty years. This knowledge was built mainly by using antibodies. Nowadays, modern MS, which supports comprehensive proteome analyses of biological samples, may render possible the search for cell type‐specific proteins as well. However, a therefore necessary systematic MS study comprising many different cell types has not been performed until now. Here we present a proteome analysis strategy supporting the automated and meaningful comparison of any biological samples. We have presently applied this strategy to six different primary human cell types, namely leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts, and melanocytes. Comparative analysis of the resulting proteome profiles allowed us to select proteins specifically identified in one of the six cell types and not in any of the five others. Based on these results, we designated cell type‐specific proteome signatures consisting each of six such characteristic proteins. These signatures independently reproduced well‐known marker proteins already established for FACS analyses in addition to novel candidate marker proteins. We applied these signatures for the interpretation of proteome profiles obtained from the analyses of hepatocellular carcinoma‐associated tissue homogenates and normal liver tissue homogenates. The identification of members of the above described signatures gave us an indication of the presence of characteristic cells in the diseased tissues and thus supported the interpretation of the proteomics data of these complex biological samples.
Sliding mode control of coupled tanks using conditional integrators

This paper is on set point regulation of the liquid level in coupled tanks, using continuous sliding mode control (SMC) with integral action. The integrator action occurs only conditionally inside the boundary layer. This "conditional integrator" (CI) design results in improved transient performance over conventional SMC with integral action. It also retains the robustness to uncertain system parameters and disturbances that ideal SMC exhibits, but without control chattering, which is important, because chattering can cause valve wear and tear. We consider two cases: (i) a SISO system with 2 tanks, and (ii) a MIMO system of quadruple tanks. Our controller happens to be a saturated PID controller with anti-windup structure in the SISO case, and 2 decentralized PI controllers in the MIMO case. This is of particular significance because while the application of nonlinear control strategies such as feedback linearization, adaptive/neural control and nonlinear model predictive control has reached considerable maturity for process systems, industrial practice has traditionally relied on PI/PID controllers. Simulation results show that good tracking performance is achieved, in spite of disturbances and unmodeled dynamics.
Adaptive Prony Method for the Calculation of Power-Quality Indices in the Presence of Nonstationary Disturbance Waveforms

The presence of the new liberalized markets has increased the interest in power-quality (PQ) disturbances due to their economic effect. In particular, in the case of disturbances caused by a single event (such as a capacitor switching or voltage sag), the waveform assessment can be difficult due to the rapid variations in waveform spectral component characteristics; these difficulties require a suitable choice of signal-processing techniques for spectral analysis and, in particular, the resort to time-frequency representations. In this paper, the adaptive Prony method is proposed to calculate PQ indices based on a time-frequency analysis of waveforms. Numerical applications on a simulated transient due to capacitor switching, a measured voltage sag, and a test waveform are also presented and discussed in order to investigate the validity of the proposed method.
A new data forwarding algorithm for mobile opportunistic networks

In this paper, the forwarding objective and the mobility law of nodes in opportunistic networks are investigated to establish a mathematical model for further analysis, and then a new data forwarding algorithm is proposed. In this algorithm, according to the distance between the data holders and the destination, some intermediate nodes are selected to relay the data. Especially, the forwarding copies will be increased when the forwarding delay has reached a threshold, and thus the delivery ratio can be guaranteed. The simulation results show that the proposed algorithm can effectively reduce the storage occupancies of nodes, reduce the forwarding delay, and guarantee the delivery ratio.
Sleep complaints predict coronary artery disease mortality in males: a 12‐year follow‐up study of a middle‐aged Swedish population

Abstract. Mallon L, Broman J‐E, Hetta J (University Hospital, Uppsala, and Falun Hospital, Falun; and Institute of Clinical Neuroscience, Göteborg; Sweden). Sleep complaints predict coronary artery disease mortality in males: a 12‐year follow‐up study of a middle‐aged Swedish population. J Intern Med 2002; 251: 207–216.
Phase behavior and formulation of structured drops in triphasic systems

1 Abstract—This work sets a first step towards the formulation of a two-domain drug carrier formed by an ATPS (Aqueous Two Phase System) of a solution of two biocompatible polymers, gelatin and poly(ethylene glycol) diacrylate (PEG-diAc), dispersed in an organic solvent. The main objectives of the work are the study of the phase behaviour and to achieve control over the morphology of the ATPS drops at micro and nanoscale by adjusting different parameters of the emulsification process, followed by optical microscopy.
A novel Mcl1 variant inhibits apoptosis via increased Bim sequestration

Members of the Bcl-2 protein family are frequently deregulated in tumors as they critically control cell death induction in mammalian cells. Alterations of these proteins may cause resistance to chemotherapy-induced cell death and immune responses. By serendipity we cloned a variant of the anti-apoptotic Bcl2-family member Myeloid cell leukemia-1 (Mcl1) from human neuroblastoma and leukemia cells. This Mcl1L variant lacks a 45 bp sequence that codes for 15 highly conserved amino acids ranging from Gly158 to Asp172. This region is part of the so called PEST-sequence of Mcl1L and contains two phosphorylation sites (Ser159 and Thr163) that regulate Mcl1L stability. A caspase 3/caspase 8 cleavage site at Asp157 which has been reported to be critical for death-receptor-induced apoptosis and for the conversion of Mcl1L into a pro-apoptotic protein is also missing in this novel variant. Importantly, Mcl1LdelGly158-Asp172 bound significantly more pro-apoptotic Bim compared to Mcl1L and showed increased anti-proliferative and anti-apoptotic activity compared to Mcl1L during death receptor-induced cell death. This suggests that this novel Mcl1L variant efficiently protects tumor cells against extrinsic death signalling and therefore may provide a survival advantage for highly aggressive tumors.
Stress-Induced p38 Mitogen-Activated Protein Kinase Activation Mediates κ-Opioid-Dependent Dysphoria

The molecular mechanisms mediating stress-induced dysphoria in humans and conditioned place aversion in rodents are unknown. Here, we show that repeated swim stress caused activation of both κ-opioid receptor (KOR) and p38 mitogen-activated protein kinase (MAPK) coexpressed in GABAergic neurons in the nucleus accumbens, cortex, and hippocampus. Sites of activation were visualized using phosphoselective antibodies against activated κ receptors (KOR-P) and against phospho-p38 MAPK. Surprisingly, the increase in P-p38-IR caused by swim-stress exposure was completely KOR dependent; P-p38-IR did not increase in KOR(−/−) knock-out mice subjected to the same swim-paradigm or in wild-type mice pretreated with the KOR antagonist norbinaltorphimine. To understand the relationship between p38 activation and the behavioral effects after KOR activation, we administered the p38 inhibitor SB203580 [4-(4-fluorophenyl)-2-(4-methylsulfonylphenyl)-5-(4-pyridyl)-1H-imidazole (i.c.v.)] and found that it selectively blocked the conditioned place aversion caused by the κ agonist trans-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl]-benzeneacetamide (U50488) and the KOR-dependent swim stress-induced immobility while not affecting κ-opioid analgesia or nonselectively affecting associative learning. We found that the mechanism linking KOR and p38 activation in vivo was consistent with our previous in vitro data suggesting that β-arrestin recruitment is required; mice lacking G-protein-coupled receptor kinase 3 also failed to increase p-p38-IR after KOR activation in vivo, failed to show swim stress-induced immobility, or develop conditioned place aversion to U50488. Our results indicate that activation of p38 MAPK signaling by the endogenous dynorphin-κ-opioid system likely constitutes a key component of the molecular mechanisms mediating the aversive properties of stress.
Suppressor mutations identify amino acids in PAA-1/PR65 that facilitate regulatory RSA-1/B″ subunit targeting of PP2A to centrosomes in C. elegans

Summary Protein phosphorylation and dephosphorylation is a key mechanism for the spatial and temporal regulation of many essential developmental processes and is especially prominent during mitosis. The multi-subunit protein phosphatase 2A (PP2A) enzyme plays an important, yet poorly characterized role in dephosphorylating proteins during mitosis. PP2As are heterotrimeric complexes comprising a catalytic, structural, and regulatory subunit. Regulatory subunits are mutually exclusive and determine subcellular localization and substrate specificity of PP2A. At least 3 different classes of regulatory subunits exist (termed B, B′, B″) but there is no obvious similarity in primary sequence between these classes. Therefore, it is not known how these diverse regulatory subunits interact with the same holoenzyme to facilitate specific PP2A functions in vivo. The B″ family of regulatory subunits is the least understood because these proteins lack conserved structural domains. RSA-1 (regulator of spindle assembly) is a regulatory B″ subunit required for mitotic spindle assembly in Caenorhabditis elegans. In order to address how B″ subunits interact with the PP2A core enzyme, we focused on a conditional allele, rsa-1(or598ts), and determined that this mutation specifically disrupts the protein interaction between RSA-1 and the PP2A structural subunit, PAA-1. Through genetic screening, we identified a putative interface on the PAA-1 structural subunit that interacts with a defined region of RSA-1/B″. In the context of previously published results, these data propose a mechanism of how different PP2A B-regulatory subunit families can bind the same holoenzyme in a mutually exclusive manner, to perform specific tasks in vivo.
Criterion to Evaluate Input-Offset Voltage of a Latch-Type Sense Amplifier

In advanced CMOS technologies where device mismatches are of major reliability concern, predicting the input-offset voltage of the sensing circuit is a crucial step in the design process as it has a direct impact on the yield. This work uses the Taylor expansion to derive a criterion to evaluate input-offset voltage of a latch-type voltage-mode sense amplifier. By innovatively setting the correct sensing criterion, this method provides a very simple, yet accurate and robust model to quantify the input-offset of the sense amplifier. The resulting offset expression incorporates three types of device mismatches, namely the threshold voltage (Vth), the trans-conductance ( K = ¿C0x W/L) and the capacitance (C). The model is then analyzed under the worst-case scenario. It is shown that Vth has the greatest influence on the offset voltage, followed by K and C mismatches. Second-order approximation is also considered when high-level mismatches are present. Extensive simulations have also been carried out to verify the accuracy of the model using three different CMOS technologies.
Success of the state pain initiatives: moving pain management forward.

PURPOSE The purpose of this article is to describe the history of the State Cancer Pain Initiative (CPI) movement and current initiative activities that are directed at improving the management of cancer pain. OVERVIEW The undertreatment of pain is a major public health problem in the United States. State CPIs strive to remove the barriers to effective cancer pain management through the provision of innovative professional, patient, and public educational programs, through institutional change projects, and through public advocacy. Collaboration with organizations that share common goals is important in sustaining and maximizing the impact of the movement. CLINICAL IMPLICATIONS Professionals, patients, and families benefit from the work of the State Initiatives. By enhancing the knowledge and skills of clinicians, supporting institutional change, and teaching patients and families the importance of effective pain control, the Initiatives help to improve the quality of life for all cancer survivors. Models of intervention that respond to local needs are discussed, and legislative and advocacy efforts that affect care also are noted.
Proceedings of Usits '03: 4th Usenix Symposium on Internet Technologies and Systems Symphony: Distributed Hashing in a Small World

We present Symphony, a novel protocol for maintaining distributed hash tables in a wide area network. The key idea is to arrange all participants along a ring and equip them with long distance contacts drawn from a family of harmonic distributions. Through simulation, we demonstrate that our construction is scalable, exible, stable in the presence of frequent updates and o ers small average latency with only a handful of long distance links per node. The cost of updates when hosts join and leave is small.
Progress in Exosome Isolation Techniques

Exosomes are one type of membrane vesicles secreted into extracellular space by most types of cells. In addition to performing many biological functions particularly in cell-cell communication, cumulative evidence has suggested that several biological entities in exosomes like proteins and microRNAs are closely associated with the pathogenesis of most human malignancies and they may serve as invaluable biomarkers for disease diagnosis, prognosis, and therapy. This provides a commanding impetus and growing demands for simple, efficient, and affordable techniques to isolate exosomes. Capitalizing on the physicochemical and biochemical properties of exosomes, a number of techniques have been developed for the isolation of exosomes. This article summarizes the advances in exosome isolation techniques with an emphasis on their isolation mechanism, performance, challenges, and prospects. We hope that this article will provide an overview of exosome isolation techniques, opening up new perspectives towards the development more innovative strategies and devices for more time saving, cost effective, and efficient isolations of exosomes from a wide range of biological matrices.
Geometric mapping assisted multi-view depth video coding

Multi-view plus depth (MVD), as a video representation supporting view synthesis based on depth video, has attracted more and more attention for the free view video (FVV) application. It is a challenge to efficiently compress the multi-view depth data in MVD format. In this paper, we explore the geometric relationships in 3D space and propose a geometric mapping assisted (GMA) multi-view depth video coding algorithm. The proposed GMA utilizes the mapped depth image as a reference candidate during prediction. Furthermore, the inpainting method is employed to fill in the holes in mapped depth images. Experimental results demonstrate the gains of up to 2.45 dB for the depth coding, as well as better quality of synthesized views.
V2 Receptor–Mediated Autocrine Role of Somatodendritic Release of AVP in Rat Vasopressin Neurons Under Hypo-Osmotic Conditions

The antidiuretic hormone arginine vasopressin (AVP) is also an autocrine signal, allowing the hypothalamic neurons that produce it to maintain their volume during hypotonic stress. Acting Locally as Well as Globally Arginine vasopressin (AVP), which acts as an antidiuretic hormone to decrease plasma osmolarity, is synthesized by osmosensory hypothalamic neurons and released from their terminals in the posterior pituitary into the systemic circulation. Consistent with this homeostatic role, increased plasma osmolarity increases nerve terminal release of AVP, whereas decreased plasma osmolarity decreases it. Here, Sato et al. show that, in contrast to its effect on systemic secretion of AVP, hypo-osmotic stimulation of isolated AVP neurons increased somatodendritic AVP release. AVP acted through the V2 receptor to activate volume-sensitive anion currents and initiate a slow decrease in AVP neuron volume, counteracting the swelling induced by exposure to hypo-osmotic solution. The authors thus conclude that somatodendritic release of AVP acts as an autocrine signal to help AVP neurons maintain an appropriate volume while undergoing hypotonic stress. Arginine vasopressin (AVP) neurons in the hypothalamus are osmosensory neurons that respond to increased or decreased plasma osmolarity by releasing more or less AVP, respectively, from their axon terminals. Here, we found that, in contrast, hypo-osmotic stress enhanced somatodendritic AVP secretion from isolated rat AVP neurons, and this somatodendritic release depended on actin depolymerization. In AVP neurons identified by transgenic expression of green fluorescent protein, hypo-osmotic stimulation led to activation of anion currents and a slow regulatory volume decrease (RVD). Bath application of AVP increased the volume-sensitive anion current and accelerated RVD; these effects were abolished by inhibition of adenylate cyclase or by a specific antagonist of the V2-type vasopressin receptor. The V2 receptor antagonist slowed the RVD rate of AVP neurons even in the absence of exogenous AVP when the volume of bath solution was reduced. Reverse transcription polymerase chain reaction and immunostaining both indicated that the V2 receptor was present in AVP neurons. We conclude that somatodendritic release of AVP under hypo-osmotic conditions acts through the V2 receptor as an autocrine signal to enhance volume-sensitive anion channel activity and thereby facilitate cell volume regulation.
HIV/AIDS in South Africa: how many people died from the disease between 1997 and 2010?

Objectives:Empirical estimates of the number of HIV/AIDS deaths are important for planning, budgeting, and calibrating models. However, there is an extensive misattribution of HIV/AIDS as an underlying cause-of-death. This study estimates the true numbers of AIDS deaths from South African vital statistics between 1997 and 2010. Methods:Individual-level cause-of-death data were grouped according to a local burden of disease list and source causes (i.e. causes under which AIDS deaths are misclassified) that recorded a rapid increase. After adjusting for completeness of registration, the mortality rate of the source causes, by age and sex, was regressed on the lagged HIV prevalence to estimate the rate of increase correlated with HIV. Background trends in the source-cause mortality rates were estimated from the trend experienced among 75–84 year olds. Results:Of 214 causes considered, 19 were identified as potential sources for cause misattribution. High proportions of deaths from tuberculosis, lower respiratory infections (mostly pneumonia), diarrhoeal diseases, and ill-defined natural causes were estimated to be HIV-related, with only 7% of the estimated AIDS deaths being recorded as HIV. Estimated HIV/AIDS deaths increased rapidly, then reversed after 2006, totalling 2.8 million deaths over the whole period. The number was lower than model estimates from Joint United Nations Programme on HIV/AIDS (UNAIDS) and the Global Burden of Disease Study. Conclusion:Empirically based estimates confirm the considerable loss of life from HIV/AIDS and should be used for calibrating models of the AIDS epidemic which generally appear too low for infants but too high for other ages. Doctors are urged to specify HIV on death notifications to provide reliable cause-of-death statistics.
OpenDaylight: Towards a Model-Driven SDN Controller architecture

This paper describes a novel Software-Defined Networking (SDN) Controller architecture that is built on Model-Driven Software Engineering (MDSE) principles. It supports both the “classic” OpenFlow-based approach to SDN and emerging model-driven network management/programmability technologies, such as NETCONF/YANG. The architecture was first implemented in the OpenDaylight Project Hydrogen release, and it is being further evolved in subsequent OpenDaylight releases.