Miracle-dz/UniFAR-FTUs huggingface dataset:
An Efficient Genetic Screen in Drosophila to Identify Nuclear-Encoded Genes With Mitochondrial Function

We conducted a screen for glossy-eye flies that fail to incorporate BrdU in the third larval instar eye disc but exhibit normal neuronal differentiation and isolated 23 complementation groups of mutants. These same phenotypes were previously seen in mutants for cytochrome c oxidase subunit Va. We have molecularly characterized six complementation groups and, surprisingly, each encodes a mitochondrial protein. Therefore, we believe our screen to be an efficient method for identifying genes with mitochondrial function.
The Intertwining of Transposable Elements and Non-Coding RNAs

Growing evidence shows a close association of transposable elements (TE) with non-coding RNAs (ncRNA), and a significant number of small ncRNAs originate from TEs. Further, ncRNAs linked with TE sequences participate in a wide-range of regulatory functions. Alu elements in particular are critical players in gene regulation and molecular pathways. Alu sequences embedded in both long non-coding RNAs (lncRNA) and mRNAs form the basis of targeted mRNA decay via short imperfect base-pairing. Imperfect pairing is prominent in most ncRNA/target RNA interactions and found throughout all biological kingdoms. The piRNA-Piwi complex is multifunctional, but plays a major role in protection against invasion by transposons. This is an RNA-based genetic immune system similar to the one found in prokaryotes, the CRISPR system. Thousands of long intergenic non-coding RNAs (lincRNAs) are associated with endogenous retrovirus LTR transposable elements in human cells. These TEs can provide regulatory signals for lincRNA genes. A surprisingly large number of long circular ncRNAs have been discovered in human fibroblasts. These serve as “sponges” for miRNAs. Alu sequences, encoded in introns that flank exons are proposed to participate in RNA circularization via Alu/Alu base-pairing. Diseases are increasingly found to have a TE/ncRNA etiology. A single point mutation in a SINE/Alu sequence in a human long non-coding RNA leads to brainstem atrophy and death. On the other hand, genomic clusters of repeat sequences as well as lncRNAs function in epigenetic regulation. Some clusters are unstable, which can lead to formation of diseases such as facioscapulohumeral muscular dystrophy. The future may hold more surprises regarding diseases associated with ncRNAs andTEs.
Cellular Expression Profile for Interstitial Cells of Cajal in Bladder - A Cell Often Misidentified as Myocyte or Myofibroblast

Background Interstitial cells of Cajal (ICC) have been identified in urinary bladder of several species, but their presence in mice remains uncertain. Meanwhile, dozens of reports indicate that dysregulation of connexin 43 plays an important role in bladder overactivity, but its localization has not been clearly defined, with reports of expression in either the smooth muscle or in myofibroblasts. We recently identified a population of ectonucleoside triphosphate diphosphohydrolase 2 (NTPDase2) positive cells that resemble ICC and are distinct from smooth muscle, fibroblasts, myofibroblasts and neurons. Thus we sought to define more clearly the molecular signature of ICC and in doing so resolve some of these uncertainties. Principle findings Immunofluorescent localization revealed that NTPDase2-positive cells lie closely adjacent to smooth muscle but are separate from them. NTPDase2 positive cells exhibited co-localization with the widely accepted ICC marker - c-kit. They were further shown to co-localize with other ICC markers CD34 and Ano1, but not with mast cell marker tryptase. Significantly, they show convincing co-localization with connexin 43, which was not present in smooth muscle. The identity of these cells as ICC was further confirmed by the presence of three mesenchymal markers – vimentin, desmin, and PDGFβ receptor, which indicates their mesenchymal origin. Finally, we observed for the first time, the presence of merlin/neurofibromin 2 in ICC. Normally considered a neuronal protein, the presence of merlin suggests ICC in bladder may have a role in neurotransmission. Conclusions NTPDase2 positive cells in mice bladder are ICC, which can be defined by the presence of c-Kit, CD34, Ano1, NTPDase2, connexin 43, vimentin, desmin, PDGFβ receptor and merlin/NF2. These data establish a definitive molecular expression profile, which can be used to assist in explorations of their functional roles, and the presence of NTPDase2 suggests that purinergic signaling plays a role in regulation of ICC function.
The chaperone domain BRICHOS prevents CNS toxicity of amyloid-β peptide in Drosophila melanogaster

Aggregation of the amyloid-β peptide (Aβ) into toxic oligomers and amyloid fibrils is linked to the development of Alzheimer’s disease (AD). Mutations of the BRICHOS chaperone domain are associated with amyloid disease and recent in vitro data show that BRICHOS efficiently delays Aβ42 oligomerization and fibril formation. We have generated transgenic Drosophila melanogaster flies that express the Aβ42 peptide and the BRICHOS domain in the central nervous system (CNS). Co-expression of Aβ42 and BRICHOS resulted in delayed Aβ42 aggregation and dramatic improvements of both lifespan and locomotor function compared with flies expressing Aβ42 alone. Moreover, BRICHOS increased the ratio of soluble:insoluble Aβ42 and bound to deposits of Aβ42 in the fly brain. Our results show that the BRICHOS domain efficiently reduces the neurotoxic effects of Aβ42, although significant Aβ42 aggregation is taking place. We propose that BRICHOS-based approaches should be explored with an aim towards the future prevention and treatment of AD.
Monocular 3D scene understanding with explicit occlusion reasoning

Scene understanding from a monocular, moving camera is a challenging problem with a number of applications including robotics and automotive safety. While recent systems have shown that this is best accomplished with a 3D scene model, handling of partial object occlusion is still unsatisfactory. In this paper we propose an approach that tightly integrates monocular 3D scene tracking-by-detection with explicit object-object occlusion reasoning. Full object and object part detectors are combined in a mixture of experts based on their expected visibility, which is obtained from the 3D scene model. For the difficult case of multi-people tracking, we demonstrate that our approach yields more robust detection and tracking of partially visible pedestrians, even when they are occluded over long periods of time. Our approach is evaluated on two challenging sequences recorded from a moving camera in busy pedestrian zones and outperforms several state-of-the-art approaches.
Comparing vocal parameters in spontaneous and posed child-directed speech

Research on the facial expression of emotion distinguishes between correlates of posed vs. spontaneous emotion expression. Similar research in the vocal domain is lacking. In this study, we compare changes in a range of vocal parameters between posed vs. spontaneous adult-directed (AD) and child–directed (CD) speech. CDS is a highly affectively charged speech register which lends itself well to the study of posed vs. spontaneous emotion expression. A group of mother addressed an adult and their child, and a group of non-mothers addressed an imaginary adult and an imaginary child. The results confirm adjustments in pitch, formants and speech rate typically reported for CDS in both groups. At the same time, they show that source parameters not in service of linguistic function, such as shimmer (perturbations in fundamental period amplitude) and harmonics-to-noise ratio show clear group effects suggesting that they may constitute veridical indicators of spontaneous emotion expression.
Annular Height-to-Commissural Width Ratio of Annulolasty Rings In Vivo

Background—A “saddle-shaped” mitral annulus with an optimal ratio between annular height and commissural diameter may reduce leaflet and chordal stress and is purported to be conserved across mammalian species. Whether annuloplasty rings maintain this relationship is unknown. Methods and Results—Twenty-three adult sheep underwent implantation of radiopaque markers on the left ventricle and mitral annulus. Eight animals underwent implantation of a Carpentier-Edwards Physio ring, 7 underwent a Medtronic Duran flexible ring, and 8 served as controls. Animals were studied with biplane videofluoroscopy 7 to 10 days postoperatively. Annular height and commissural width (CW) were determined from 3D marker coordinates, and annular height:CW ratio (AHWCR) was calculated. Annular height was similar in Control and Duran animals but significantly lower in the Physio group at end diastole (8.4±3.8, 6.7±2.3, and 3.4±0.6 mm, respectively, for Control, Duran, and Physio; ANOVA=0.005) and at end systole (14.5±6.2, 10.5±5.5, and 5.8±2.5 mm, respectively, for Control, Duran, and Physio; ANOVA=0.004). Both ring groups reduced CW significantly relative to Control. AHCWR did not differ between Control and Duran but was lower in Physio (23±11%, 24±7%, and 12±2% at end diastole and 42±17%, 37±17%, and 21±10% at end systole, respectively, for Control, Duran, and Physio, respectively; ANOVA <0.05 for both). Conclusions—Mitral annular height and AHWCR of the native valve were unchanged by a Duran ring, whereas the Physio ring led to a lower AHWCR. Theoretically, such a flexible annuloplasty ring may provide better leaflet stress distribution by maintaining normal AHWCR.
Comments on "Capacity with explicit delay guarantees for generic sources over correlated Rayleigh channel"

We address a major flaw in the abovementioned paper, which proposes to calculate effective capacity of random channels by the use of central limit theorem. We analytically show that the authors are incorrect in finding the effective capacity by first taking the limit of cumulative random process rather than taking the limit of moment generating function of the same process. We later quantify our results over a correlated ON-OFF process.
Stochastic Real-Time Scheduling of Wind-Thermal Generation Units in an Electric Utility

The objective of the dynamic economic dispatch (DED) problem is to find the optimal dispatch of generation units in a given operation horizon to supply a prespecified demand while satisfying a set of constraints. In this paper, an efficient method based on optimality-condition-decomposition technique is proposed to solve the DED problem in real-time environment while considering wind power generation and pool market. The uncertainties of wind power generation, as well as the electricity prices, are also taken into account. The aforementioned uncertainties are handled using a scenario-based approach. To illustrate the effectiveness of the proposed approach, it is applied on 40 and 54 thermal generation units and a large-scale practical system with 391 thermal generation units. The obtained results substantiate the applicability of the proposed method for solving the real-time DED problem with uncertain wind power generation.
Epigenetic RELN Dysfunction in Schizophrenia and Related Neuropsychiatric Disorders

REELIN (RELN) is a large (420 kDa) glycoprotein that in adulthood is mostly synthesized in GABAergic neurons of corticolimbic structures. Upon secretion in the extracellular matrix (ECM), RELN binds to VLDL, APOE2, and α3β2 Integrin receptors located on dendritic shafts and spines of postsynaptic pyramidal neurons. Reduced levels of RELN expression in the adult brain induce cognitive impairment and dendritic spine density deficits. RELN supplementation recovers these deficits suggesting a trophic action for RELN in synaptic plasticity. We and others have shown that altered RELN expression in schizophrenia (SZ) and bipolar (BP) disorder patients is difficult to reconcile with classical Mendelian genetic disorders and it is instead plausible to associate these disorders with altered epigenetic homeostasis. Support for the contribution of altered epigenetic mechanisms in the down-regulation of RELN expression in corticolimbic structures of psychotic patients includes the concomitant increase of DNA-methyltransferases and the increased levels of the methyl donor S-adenosylmethionine (SAM). It is hypothesized that these conditions lead to RELN promoter hypermethylation and a reduction in RELN protein amounts in psychotic patients. The decreased synthesis and release of RELN from GABAergic corticolimbic neurons could serve as a model to elucidate the epigenetic pathophysiological mechanisms acting at pyramidal neuron dendrites that regulate synaptic plasticity and cognition in psychotic and non-psychotic subjects.
A 0.92-THz SiGe Power Radiator Based on a Nonlinear Theory for Harmonic Generation

We propose a nonlinear device model and a systematic methodology to generate maximum power at any desired harmonic. The proposed power optimization technique is based on the Volterra-Wiener theory of nonlinear systems. By manipulating the device nonlinearity and optimizing the embedding network, optimum conditions for harmonic power generation are provided. Using this theory, a 920–944-GHz frequency quadrupler is designed in a 130-nm SiGe:C process. The circuit achieves the peak output power of −17.3 and −10 dBm of effective isotropic radiated power and consumes 5.7 mW of dc power. To the best of our knowledge, this circuit demonstrates the highest generated power among Si/SiGe-based sources at this frequency range.
Performances of OFDM‐CDMA receivers with MIMO communications

This paper considers the joint design of OFDM and code division multiple access (CDMA) with MIMO communications. The receivers for both Bell Labs Layered Space Time system and space–time block code are designed in this paper. The performances of the MIMO‐OFDM‐CDMA receivers are investigated in several typical fading channels. The maximum likelihood, zero forcing, and minimum mean square error receivers for the MIMO‐OFDM‐CDMA systems are derived, and the performances in the typical fading channels are verified by the simulations. Copyright © 2012 John Wiley & Sons, Ltd.
Protein NMR Spectroscopy: Principles and Practice

Preliminary Table of Contents 1. Classical NMR Spectroscopy 2. Theoretical Description of NMR Spectroscopy 3. Experimental Aspects of NMR Spectroscopy 4. Multi-Dimensional NMR Spectroscopy 5. Relaxation and Dynamic Processes 6. Experimental 1H NMR Methods 7. Heteronuclear NMR Experiments 8. Experimental NMR Relaxation Methods 9. Larger Proteins and Molecular Interactions 10. Sequential Assignment, Structure Determination and Other Applications
A Threshold Equation for Action Potential Initiation

In central neurons, the threshold for spike initiation can depend on the stimulus and varies between cells and between recording sites in a given cell, but it is unclear what mechanisms underlie this variability. Properties of ionic channels are likely to play a role in threshold modulation. We examined in models the influence of Na channel activation, inactivation, slow voltage-gated channels and synaptic conductances on spike threshold. We propose a threshold equation which quantifies the contribution of all these mechanisms. It provides an instantaneous time-varying value of the threshold, which applies to neurons with fluctuating inputs. We deduce a differential equation for the threshold, similar to the equations of gating variables in the Hodgkin-Huxley formalism, which describes how the spike threshold varies with the membrane potential, depending on channel properties. We find that spike threshold depends logarithmically on Na channel density, and that Na channel inactivation and K channels can dynamically modulate it in an adaptive way: the threshold increases with membrane potential and after every action potential. Our equation was validated with simulations of a previously published multicompartemental model of spike initiation. Finally, we observed that threshold variability in models depends crucially on the shape of the Na activation function near spike initiation (about −55 mV), while its parameters are adjusted near half-activation voltage (about −30 mV), which might explain why many models exhibit little threshold variability, contrary to experimental observations. We conclude that ionic channels can account for large variations in spike threshold.
Improving reviews by extended traceability

When defining a new system, the history and functionality of the system to be replaced should be considered. This avoids repeating errors and neglecting important system functionality. The properties and the rationale behind the existing system are typically elicited by analysing concrete system usage-scenarios. The results of the analysis of the existing system are typically represented using conceptual models. To establish conceptual models of high quality, reviewing the models is common practice. The problem faced with when reviewing conceptual models, is that the reviewer cannot assess and therefore understand the basis (concrete system usage) on which the conceptual models where build. In this paper, we present an approach to overcome this problem. We argue to establish extended traceability, by recording concrete system usage scenarios using rich media (e.g. video, speech, graphic) and interrelating the recorded observations with the conceptual models. We discuss the main improvements for review processes resulting from the extended traceability and illustrate the advantages with excerpts from a case study performed in a mechanical engineering company.
Thin-Film Thermal Conductivity Measurement Using Microelectrothermal Test Structures and Finite-Element-Model-Based Data Analysis

We present a new method for measuring thermal conductivities of films with nanoscale thickness. The method combines a micro electrothermal test structure with a finite-element- based data analysis procedure. The test device consists of two serpentine nickel structures, which serve as resistive heaters and resistance temperature detectors, on top of the sample. The sample is supported by a silicon nitride membrane. Analytical solution of the heat flow is infeasible, making interpretation of the data difficult. To address this, we use a finite-element model of the test structure and apply nonlinear least-squares estimation to extract the desired material parameter values. The approach permits simultaneous extraction of multiple parameters. We demonstrate our technique by simultaneously obtaining the thermal conductivity of a 280 mum x 80 mum x 140 nm thick aluminum sample and the 360 mum x 160 mum x 180 nm thick silicon nitride support membrane. The thermal conductivity measured for the silicon nitride thin film is 2.1 W/mK, which is in agreement with reported values for films of this thickness. The thermal conductivity of the Al thin film is found to be 94 W/mK, which is significantly lower than reported bulk values and consistent both with reported trends for thin metallic films and with values that were obtained using electrical resistivity measurements and the Wiedemann-Franz law.
2D visual servoing for a long range navigation in a cluttered environment

In this paper, we consider the problem of realizing a vision-based long range navigation in a cluttered environment. To this aim, we couple a topological environment representation and a supervision algorithm. The latter organizes several elementary tasks which allow to perform image based visual servoing, obstacle avoidance and to estimate on line several required parameters. Well known and new methods based on the tasks function approach are introduced. The dynamical sequencing formalism is used to guarantee the global control law smoothness. Finally, simulation results validate our approach.
Deaf children's non-verbal working memory is impacted by their language experience

Several recent studies have suggested that deaf children perform more poorly on working memory tasks compared to hearing children, but these studies have not been able to determine whether this poorer performance arises directly from deafness itself or from deaf children's reduced language exposure. The issue remains unresolved because findings come mostly from (1) tasks that are verbal as opposed to non-verbal, and (2) involve deaf children who use spoken communication and therefore may have experienced impoverished input and delayed language acquisition. This is in contrast to deaf children who have been exposed to a sign language since birth from Deaf parents (and who therefore have native language-learning opportunities within a normal developmental timeframe for language acquisition). A more direct, and therefore stronger, test of the hypothesis that the type and quality of language exposure impact working memory is to use measures of non-verbal working memory (NVWM) and to compare hearing children with two groups of deaf signing children: those who have had native exposure to a sign language, and those who have experienced delayed acquisition and reduced quality of language input compared to their native-signing peers. In this study we investigated the relationship between NVWM and language in three groups aged 6–11 years: hearing children (n = 28), deaf children who were native users of British Sign Language (BSL; n = 8), and deaf children who used BSL but who were not native signers (n = 19). We administered a battery of non-verbal reasoning, NVWM, and language tasks. We examined whether the groups differed on NVWM scores, and whether scores on language tasks predicted scores on NVWM tasks. For the two executive-loaded NVWM tasks included in our battery, the non-native signers performed less accurately than the native signer and hearing groups (who did not differ from one another). Multiple regression analysis revealed that scores on the vocabulary measure predicted scores on those two executive-loaded NVWM tasks (with age and non-verbal reasoning partialled out). Our results suggest that whatever the language modality—spoken or signed—rich language experience from birth, and the good language skills that result from this early age of acquisition, play a critical role in the development of NVWM and in performance on NVWM tasks.
Equilibrium Vitrification of Mouse Embryos1

Abstract For the cryopreservation of embryos, vitrification has various advantages, but it also has disadvantages because embryos are vitrified with a considerable supercooling (i.e., in nonequilibrium). Here, we tried to develop a novel method in which embryos are vitrified in near-equilibrium. The extent of equilibrium was assessed by examining whether vitrified embryos survive after being kept at −80°C. Two-cell embryos of ICR mice were vitrified with ethylene glycol (EG)-based solutions, either EFSa or EFSc solutions, which were mixtures of EG (30%–40%) and an FSa or FSc solution, respectively. The FSa and FSc solutions were PB1 medium containing 30% Ficoll plus 0.5 or 1.5 M sucrose, respectively. In vitro survival rate was high when embryos vitrified with 30%–40% EG (EFS30a, EFS40a, EFS30c, and EFS40c) were warmed rapidly. When embryos were vitrified and then kept at −80°C for 4 days, large proportions survived with EFS30c and EFS40c. When embryos were vitrified with EFS35c or EFS40c, the survival rate was high even for those kept at −80°C for 10 days. When embryos of ICR and C57BL/6J mice were vitrified with EFS35c or EFS40c and then kept at −80°C for 4 days, the survival rate was high even after recooling in liquid nitrogen; a high proportion (75%) of C57BL/6J embryos vitrified with EFS35c developed to term after transfer. In conclusion, we have developed a novel method by which embryos are vitrified in near-equilibrium. This will be a supreme method for cryopreservation, retaining the advantages of both current vitrification and equilibrium slow freezing.