Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning and visualizing statistical relationships between protein distributions from microscopy images

Multichannel microscopy has emerged as a technique for imaging multiple targets (molecules, protein distributions, etc.) simultaneously. Discovering the relative changes in these targets (i.e. distribution of different proteins) is fundamental for understanding cell structure and function. We describe a new method for quantifying and visualizing relationships between multiple targets, from a set of segmented multichannel cells. The method is based on combining the canonical correlation analysis technique with a framework for analyzing images based on the concept of optimal mass transportation. We apply the method towards understanding chromatin distribution in cancer nuclei as a function of nuclear envelope shape. We also show that sub cellular distribution of mitochondria can be used to predict the sub cellular localization of actin fibers in yeast cells. Finally, we also describe the application of the method towards understanding relationships between nuclear and cellular shapes in 2D HeLa cells. We believe that the method could serve as a general tool for mining relationships between different sub cellular protein/molecule distributions as well as organelle shapes.
A surface approximation algorithm for complex shapes

In the paper, we propose one surface approximation algorithm which could handle the geometrical and topological errors contained by the complex shapes. The algorithm firstly builds one initial coarse envelop based on the voxel hulls of the input shape, then one iterative approximation is processed by two alternative steps: matching the envelop to the input shape by using the Laplacian deformation, and the Laplacian fairing. The experiments demonstrate that our algorithm could efficiently build one surface that approximates the input shape, which could be in by arbitrary representations, such as meshes, polygon soups, and point sets.
L1198F Mutation Resensitizes Crizotinib to ALK by Altering the Conformation of Inhibitor and ATP Binding Sites

The efficacy of anaplastic lymphoma kinase (ALK) positive non-small-cell lung cancer (NSCLC) treatment with small molecule inhibitors is greatly challenged by acquired resistance. A recent study reported the newest generation inhibitor resistant mutation L1198F led to the resensitization to crizotinib, which is the first Food and Drug Administration (FDA) approved drug for the treatment of ALK-positive NSCLC. It is of great importance to understand how this extremely rare event occurred for the purpose of overcoming the acquired resistance of such inhibitors. In this study, we exploited molecular dynamics (MD) simulation to dissect the molecular mechanisms. Our MD results revealed that L1198F mutation of ALK resulted in the conformational change at the inhibitor site and altered the binding affinity of ALK to crizotinib and lorlatinib. L1198F mutation also affected the autoactivation of ALK as supported by the identification of His1124 and Tyr1278 as critical amino acids involved in ATP binding and phosphorylation. Our findings are valuable for designing more specific and potent inhibitors for the treatment of ALK-positive NSCLC and other types of cancer.
Minimum jerk based prediction of user actions for a ball catching task

The present paper examines minimum jerk models for human kinematics as a tool to predict user input in teleoperation with significant dynamics. Predictions of user input can be a powerful tool to bridge time-delays and to trigger autonomous sub-sequences. In this paper an example implementation is presented, along with the results of a pilot experiment in which a virtual reality simulation of a teleoperated ball-catching scenario is used to test the predictive power of the model. The results show that delays up to 100 ms can potentially be bridged with this approach.
MEMORY EFFICIENT WDR (WAVELET DIFFERENCE REDUCTION) using INVERSE OF ECHELON FORM by EQUATION SOLVING

This is an attempt to devise a memory efficient WDR (Wavelet Difference Reduction) algorithm by decomposing a matrix using customized Echelon algorithm and applying WDR on it in parts. The standard process of WDR algorithm requires the entire matrix to be available in RAM (random access memory) which might not be feasible always or for a longer duration till the entire matrix is encoded. This idea takes advantage of working on matrix in parts without having to partition the matrix in any predefined way. The encoded matrix can be reconstructed using symbolic computations by creating equations and solving them against decomposed matrices.
MS vs. HD: Can white matter and subcortical gray matter pathology be distinguished neuropsychologically?

This study was conducted to examine the neuropsychological effects of white matter and subcortical gray matter pathology. Nineteen patients with multiple sclerosis (MS), 16 with Huntington's disease (HD), and 17 normal controls (NC) participated. Participants completed the California Verbal Learning Test (CVLT), Rotary Pursuit (RP) and Mirror Tracing (MT) tasks, and the Symbol Digit Modalities Test (SDMT). The principal findings pertain to a dissociation in procedural memory: on RP, the HD group demonstrated impaired sequence learning compared to the MS group, which performed similarly to the NC group, yet on MT, the MS and HD groups demonstrated normal perceptual-motor integration learning. On the CVLT, both patient groups performed better on recognition than on recall. On the SDMT, both patient groups performed worse than the NC group, with the HD group performing more poorly than the MS and NC groups. These results suggest that involvement of white and subcortical gray matter may produce different neuropsychological effects.
Compact UWB bandpass filter on hybrid microstrip/slotline structure with improved out-of-band performances

A compact ultra-wideband (UWB) bandpass filter with good in-band and out-of-band performances is proposed and implemented on hybrid microstrip/slotline structure. A multiple-mode slotline resonator with stepped-impedance configuration is first properly constructed, aiming to allocate its first three resonances occurring at desired positions within the UWB passband. Two 50 Omega microstrip feed lines are then placed perpendicular to this slotline resonator on the opposite side of the substrate. As a result, an initial back-to-back microstrip-slotline bandpass filter is constituted with the targeted UWB passband. Later the slotline resonator is twisted and an additional coupling between two open-ends of feed lines is introduced, resulting in miniaturizing its overall circuitry size and enhancing the roll-off skirts out of the passband. In final, defected ground structures (DGSs) are formed on the two feed lines to improve the upper stopband performance. Two UWB bandpass filters are designed, fabricated and measured. Measured results demonstrate an UWB passband from 3.25 to 10.21 GHz with in-band return loss >10.43 dB and group delay variation <0.34 ns.
Proposta de indicadores para um observatório de empreendedorismo no Brasil

Este estudo tem por objetivo levantar indicadores que auxiliem na criacao e desenvolvimento de um observatorio do empreendedorismo no Brasil. Esta pesquisa e considerada um ensaio teorico, com abordagem qualitativa e analise documental. Com base nos estudos de Vesper (1977), foram levantados 10 (dez) indicadores, agrupados em quatro grandes areas. No grupo G1 – Educacao, levantaram-se seis indicadores: 1) pessoas com ensino fundamental; 2) cursos de graduacao em universidades federais e estaduais com a disciplina de Empreendedorismo em sua matriz curricular; 3) cursos de pos-graduacao stricto sensu em Administracao com a disciplina de Empreendedorismo em sua matriz curricular; 4) eventos em empreendedorismo; 5) artigos publicados com tema “empreendedorismo”; e, 6) teses/dissertacoes divulgadas com o tema “empreendedorismo”. No grupo G2 – Desenvolvimento Economico, foram relacionados os indicadores: 7) incubadoras instaladas; 8) empreendedorismo social; 9) capacitacao e credito para empreendedores pelo governo federal; e 10) taxa de desocupacao. No grupo G3 – Micro e Pequenas Empresas, foram selecionados indicadores constantes no relatorio do SEBRAE (2011). E, finalmente, no grupo G4 – Empreendedor, foram classificados e agrupados indicadores do relatorio GEM (2009).
LUOPAN: Light utility-oriented placement of actuator nodes in sensor/actuator networks

We develop a light utility-oriented placement of actuator nodes (LUOPAN) for wireless sensor/actuator networks (WSAN) to spread serving duties among actuator nodes (ANs). Through appropriate placement of ANs and allocation of serving duties, system deployment cost can be reduced, and the system longevity can be improved. By considering utility consumption and geographic distribution of required services, LUOPAN outperforms existing strategies (e.g. area coverage approach and greedy approach) in terms of operation efficiency and setup cost. A mixed integer linear programming is used to obtain an optimal solution in a discretized search space, with considerations of service fading and multi-scenario placements.
Effects of prevailing hypoxaemia, acidaemia or hypoglycaemia upon the cardiovascular, endocrine and metabolic responses to acute hypoxaemia in the ovine fetus

Although it is established that the fetus can successfully withstand a single, acute hypoxaemic challenge during gestation, little is known about what effects prevailing adverse intrauterine conditions might have on the fetal response to acute hypoxaemia. The aims of this study were therefore: (1) to characterise the effects of prevailing and sustained hypoxaemia, acidaemia or hypoglycaemia on the fetal cardiovascular responses to an episode of acute hypoxaemia; and (2) to determine the effects of these adverse intrauterine conditions on mechanisms mediating these cardiovascular responses. Thirty‐three Welsh Mountain sheep fetuses were chronically instrumented (1–2 % halothane) between 117 and 125 days of gestation (term is ca 145 days) with amniotic and vascular catheters and with a transit‐time flow probe around a femoral artery. The animals were divided retrospectively into four groups based upon post‐surgical, sustained, basal blood oxygen (chronically hypoxaemic; Pa,O2, 17.3 ± 0.5 mmHg; n= 8), glucose (chronically hypoglycaemic; blood glucose, 0.49 ± 0.03 mmol l−1; n= 6) and acid‐base (chronically acidaemic; pHa, 7.25 ± 0.01; n= 5) status. Values for compromised fetuses were −2 s.d. from a group of control (n= 14) fetuses. At 130 ± 4 days, a 1 h episode of acute, isocapnic hypoxaemia (9 % O2 in N2, to reduce carotid Pa,O2 to 12 ± 1 mmHg) was induced in all fetuses by reducing the maternal inspired O2 fraction (FI,O2). Fetal cardiovascular variables were recorded at 1 s intervals throughout the experimental protocol and arterial blood samples taken at appropriate intervals for biophysical (blood gases, glucose, lactate) and endocrine (catecholamines, vasopressin, cortisol, ACTH) measures. During acute hypoxaemia all fetuses elicited hypertension, bradycardia and femoral vasoconstriction. However, prevailing fetal compromise altered the cardiovascular and endocrine responses to a further episode of acute hypoxaemia, including: (1) enhanced pressor and femoral vasoconstriction; (2) greater increments in plasma noradrenaline and vasopressin during hypoxaemia; and (3) basal upward resetting of hypothalamic‐pituitary‐adrenal axis function. Only chronically hypoxaemic fetuses had significantly elevated basal concentrations of noradrenaline and enhanced chemoreflex function during acute hypoxaemia. These data show that prevailing adverse intrauterine conditions alter the capacity of the fetus to respond to a subsequent episode of acute hypoxaemia; however, the partial contributions of hypoxaemia, acidaemia or hypoglycaemia to mediating these responses can vary.
Background calibration techniques for multistage pipelined ADCs with digital redundancy

The proposed digital background calibration scheme, applicable to multistage (pipelined or algorithmic/cyclic) analog-to-digital converters (ADCs), corrects the linearity errors resulting from capacitor mismatches and finite opamp gain. A high-accuracy calibration is achieved by recalculating the digital output based on each stage's equivalent radix. The equivalent radices are extracted in the background by using a digital correlation method. The proposed calibration technique takes advantage of the digital redundancy architecture inherent to most pipelined ADCs. In the proposed method, the SNR is not degraded from the pseudorandom noise sequence injected into the system. A two-channel ADC architecture with negligible overhead is also proposed to significantly improve the efficiency of the digital correlation. Simulation results confirm that 16-bit linearity can be achieved after calibration for an ADC with /spl sigma/=0.1% capacitor mismatches and 60 dB opamp gain.
Finite-element-simulation-assisted optimized design of an asymmetrical high-power inductive coupler with a large air gap for EV charging

Wireless Power Transfer (WPT) has become very popular due to improved safety and convenience provided by the cordless environment. Compared to wireless charging of small electronics, wireless charging of EVs has less variability in distance between transmitter coil (Tx) to receiver coil (Rx). Also, it is highly desirable to minimize the weight and size of Rx mounted on a car, while a larger Tx is employed on the charging platform to provide stronger and/or more uniform magnetic field. Most of the WPT papers for EVs in the literature [1]-[3] describe the realization of inductive couplers using air coils, while some authors use a high-permeability magnetic core [4], [5]. However, a well-defined approach on how to design the coupler is missing. This paper describes how a 3D FES program is used to optimize the coupler. It shows that for a typical design it is preferable to use a ferrite core and suggests how to optimize the core geometry as a function of the air gap.
Training Caregivers to Provide Virtual Reality Intervention for Adults With Severe Intellectual and Developmental Disability

Background. Individuals with intellectual and developmental disabilities (IDD) are in need of effective physical fitness training programs, leisure time opportunities, and strategies to improve their participation in daily life activities.1 Purpose. This study sought to present an educational program that enabled the implementation of a virtual reality (VR) program operated by in‐house caregivers for adults at a severe level of IDD. Methods. During the initial stages of this series of studies, 2 groups of participants underwent a video‐capture, VR‐based, game‐like, exercise program. The first study group (N = 33; mean age = 28.1 ± 5.3 years; moderate IDD) was trained by an experienced occupational therapist, and the second study group (N = 30; mean age = 52.3 ± 5.8 years; moderate IDD) was trained by occupational therapy students. Changes in physical fitness were monitored for all participants in comparison to matched control groups. A third study group (N = 20; mean age = 48.1 ± 8.6 years; severe IDD) was trained by in‐house caregiver staff. An educational program including gathering appropriate caregivers, presenting theoretical background for the program, as well as providing on going technical support was implemented. Results. The strategy used to enable the implementation of a VR program by in‐house caregivers was shown to be feasible. The VR intervention program promoted activity and was motivating to and enjoyable by all participants with mild to moderate IDD and to most individuals with severe IDD. Significant (P < .05) improvements in physical fitness were demonstrated for all research groups in comparison to the matched control groups, supporting the effectiveness of this educational program. Conclusion. VR technology was found as fully effective tool to engage adults with mild to moderate IDD, and some with severe levels of IDD, in a variety of activities by caregivers from different educational backgrounds and professions.
Mitochondrial DNA and RNA increase in peripheral blood mononuclear cells from HIV-1-infected patients randomized to receive stavudine-containing or stavudine-sparing combination therapy.

BACKGROUND Mitochondrial DNA (mtDNA) in peripheral blood mononuclear cells (PBMCs) has been suggested as a potential marker of mitochondrial toxicity associated with nucleoside analogue reverse-transcriptase inhibitor-containing therapy. METHODS We quantified mtDNA and mitochondrial RNA (mtRNA) in PBMCs over the course of 48 weeks in 78 patients infected with human immunodeficiency virus type 1 (HIV-1) who were randomly assigned to receive ritonavir-boosted indinavir and efavirenz with or without stavudine. Furthermore, we analyzed the association of mtDNA and mtRNA with clinical signs and symptoms and/or abnormalities in laboratory markers attributed to mitochondrial toxicity. RESULTS No statistically significant difference was found in mtDNA and mtRNA content over time between the 2 treatment arms. When arms were combined, both median mtDNA and mtRNA content showed statistically significant increases over the course of 48 weeks, from 206 to 278 copies/cell (P < .001) and from 154 to 288 copies/cell (P = .003), respectively. No statistically significant difference in mtDNA and mtRNA content was found between patients with and those without adverse events attributed to mitochondrial toxicity. CONCLUSIONS The observed increases in mtDNA and mtRNA content during the first year of treatment may represent a restorative trend resulting from suppression of HIV-1 infection, independent of the treatment used. Future studies should focus on well-defined mitochondrial toxicities and changes in these markers within the corresponding affected tissues simultaneously with those in PBMCs. Furthermore, with respect to studies of peripheral blood, mtDNA and mtRNA content in individual cell subtypes rather than in PBMCs may be better markers of toxicity and deserve further investigation.
Localization and Role of Manganese Superoxide Dismutase in a Marine Diatom1[OA]

Superoxide dismutase (SOD) catalyzes the transformation of superoxide to molecular oxygen and hydrogen peroxide. Of the four known SOD isoforms, distinguished by their metal cofactor (iron, manganese [Mn], copper/zinc, nickel), MnSOD is the dominant form in the diatom Thalassiosira pseudonana. We cloned the MnSOD gene, sodA, using the expression vector pBAD, overexpressed the product in Escherichia coli, and purified the mature protein (TpMnSOD). This recombinant enzyme was used to generate a polyclonal antibody in rabbit that recognizes MnSOD in T. pseudonana. Based on quantitative immunoblots, we calculate that in vivo concentrations of TpMnSOD are approximately 0.9 amol cell−1 using the recombinant protein as a standard. Immunogold staining indicates that TpMnSOD is localized in the chloroplasts, which is in contrast to most other eukaryotic algae (including chlorophytes and embryophytes) where MnSOD is localized exclusively in mitochondria. Based on the photosynthetic Mn complex in photosystem II, cellular Mn budgets cannot account for 50% to 80% of measured Mn within diatom cells. Our results reveal that chloroplastic MnSOD accounts for 10% to 20% of cellular Mn, depending on incident light intensity and cellular growth rate. Indeed, our analysis indicates that TpMnSOD accounts for 1.4% (±0.2%) of the total protein in the cell. The TpMnSOD has a rapid turnover rate with an apparent half-life of 6 to 8 h when grown under continuous light. TpMnSOD concentrations increase relative to chlorophyll, with an increase in incident light intensity to minimize photosynthetic oxidative stress. The employment of a Mn-based SOD, linked to photosynthetic stress in T. pseudonana, may contribute to the continued success of diatoms in the low iron regions of the modern ocean.
CSMAC: A novel DS-CDMA based MAC protocol for wireless sensor networks

This paper proposes CSMAC (CDMA sensor MAC), a novel self-organizing, location-aware media-access control (MAC) protocol for DS-CDMA based sensor networks for applications such as battlefield surveillance that feature higher traffic and stringent latency requirements. Previously proposed MAC protocols for sensor networks such as S-MAC [W. Ye et al., June 2002] primarily prioritize energy efficiency over latency, Our protocol design balances the considerations of energy efficiency, latency, accuracy, and fault-tolerance in sensor networks. CSMAC uses a combination of DS-CDMA and frequency division in channel allocation to reduce channel interference and consequently the message latency in the network. It exploits location awareness of sensor nodes to enable efficient network formation for collaborative sensing applications using two algorithms - turn off redundant node (TORN) and select minimum neighbor (SMN). Our simulation results show that CSMAC significantly reduces mean message latency and mean energy consumption per message in comparison to traditional sensor network MAC protocols.
Real-time processing of range-monitoring queries in heterogeneous mobile databases

Unlike conventional range queries, a range-monitoring query is a continuous query. It requires retrieving mobile objects inside a user-defined region and providing continuous updates as the objects move into and out of the region. In this paper, we present an efficient technique for real-time processing of such queries. In our approach, each mobile object is associated with a resident domain, and when an object moves, it monitors its spatial relationship with its resident domain and the monitoring areas inside it. An object reports its location to the server when it crosses over some query boundary or moves out of its resident domain. In the first case, the server updates the affected query results accordingly, while in the second case, the server determines a new resident domain for the object. This distributive approach achieves an accurate and real-time monitoring effect with minimal mobile communication and server processing costs. Our approach also allows a mobile object to negotiate a resident domain based on its computing capability. By having a larger resident domain, a more capable object has less of a chance of moving out of it and having to request a new one. As a result, both communication and server processing costs are reduced. Our comprehensive performance study shows that the proposed technique can be highly scalable in supporting location-based services in a wireless environment that consists of a large number of mobile devices.
ENSEMBLE CLASSIFICATION OF DATA STREAMS

-Data stream classification is a challenging task. For real-time data concepts of instances keep varying with time, such as weather prediction or intrusion detection etc. The concept changes in continuously evolving data streams are termed as concept drifts. To address this issue, idea of an adaptive ensemble classifier is presented. The classification approach is ensemble-based rather than using a single classifier. The set of classifiers are updated with respect to accuracy achieved during classification. This work includes initial experiments and results carried out using MOA, a data stream mining framework.