Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability. We here examine factors that systematically promote non-conservative mutations at the proteome level. Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered. Similarly, whether and how molecular chaperones, which have been shown to buffer destabilizing mutations in individual proteins, generally provide robustness during proteome evolution remains unclear. To this end, we introduce an evolutionary parameter λ that directly estimates the rate of non-conservative substitutions. Our analysis of λ in Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens sequences reveals how co- and post-translationally acting chaperones differentially promote non-conservative substitutions in their substrates, likely through buffering of their destabilizing effects. We further find that λ serves well to quantify the evolution of intrinsically disordered proteins even though the unstructured, thus generally variable regions in proteins are often flanked by very conserved sequences. Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher λ at the expense of enhanced chaperone assistance. Our findings thus highlight an intricate interplay of molecular chaperones and protein disorder in the evolvability of protein networks. Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. We feel that the development of λ may be a valuable addition to the toolbox applied to understand the molecular basis of evolution.
Ammonium is a key determinant on the dietary restriction of yeast chronological aging in culture medium

New evidences have recently emerged from studies in yeast and in higher eukaryotes showing the importance of nutrient balance in dietary regimes and its effects on longevity regulation. We have previously shown that manipulation ofammoniumconcentration in the culture and/or aging medium can drastically affect chronological lifespan (CLS) of Saccharomyces cerevisiae, especially in amino acid restricted cells. Here we describe that the CLS shortening under amino acid restriction can be completely reverted by removing ammonium from the culture medium. Furthermore, the absence of ammonium, and of any rich nitrogen source, was so effective in extending CLS that no beneficial effect could be observed by further imposing calorie restriction conditions. When present in the culture medium,ammoniumimpaired the consumption of theauxotrophy-complementing amino acidsand caused in an improper cell cycle arrest of the culture. TOR1 deletion reverted ammonium effects both in amino acid restricted and non-restricted cultures, whereas, Ras2p and Sch9p seem to have only a milder effect in the mediation ofammonium toxicity under amino acid restriction and no effect on non-restricted cultures. Our studies highlight ammonium as a key effector in the nutritional equilibrium between rich and essential nitrogen sources and glucose required for longevity promotion.
A novel high-speed sense-amplifier-based flip-flop

A new sense-amplifier-based flip-flop is presented. The output latch of the proposed circuit can be considered as an hybrid solution between the standard NAND-based set/reset latch and the NC-/sup 2/MOS approach. The proposed flip-flop provides ratioless design, reduced short-circuit power dissipation, and glitch-free operation. The simulation results, obtained for a 0.25-/spl mu/m technology, show improvements in the clock-to-output delay and the power dissipation with respect to the recently proposed high-speed flip-flops. The new circuit has been successfully employed in a high-speed direct digital frequency synthesizer chip, highlighting the effectiveness of the proposed flip-flop in high-speed standard cell-based applications.
Test method for embedded real-time systems

Testing is an ultimate phase of product life cycle to which particular attention is paid, namely when dependability is of great importance. This work is concerned with the checking of dependability requirements by means of tests experiments. Here we address real-time embedded systems for which validation encounters a complexity problem due to real-time requirements. In this paper we propose a partial technique aimed at avoiding this problem and illustrate it with an example.
Efficient Cluster-Based Fault-Tolerant Schemes for Wireless Sensor Networks

The deployment of wireless sensor networks (WSNs) over a geographical area for monitoring physical phenomena is prone to several failures due to energy depletion, environmental hazards, hardware failure, communication link errors, etc. These failures prevent them to fulfill their tasks normally. In addition, in safety applications, these failures lead to hazardous consequences. Thus, it is necessary to adopt an efficient fault-tolerant approach to ensure the availability of sensor data anytime and anywhere in WSNs. In this paper, we proposed two efficient cluster-based fault-tolerant schemes enabling to reduce communication and processing overhead. These schemes are respectively denoted ECFS-1 and ECFS-2. ECFS-1 could tolerate link failures and therefore guarantee routing reliability while ECFS-2 could tolerate both sensor faults and links failures. Finally, we conducted several simulations to illustrate the effectiveness of our contribution and compared obtained results to other schemes.
Characterization of High Q Transmission Line Structure for Advanced CMOS Processes

A new transmission line structure is presented in this work for advanced CMOS processes. This structure has a high quality factor and low attenuation. It allows slow-waves to propagate which results in low dispersion for a given characteristic impedance. It is also designed to satisfy the stringent density requirements of advanced CMOS processes. A model is developed to characterize this structure by analyzing the physical current flowing in the substrate and the shield structure. Test structures were fabricated using CMOS 90 nm process technology with measurements made up to 110 GHz using a transmission-reflection module on a network analyzer. The results correspond well to the proposed model.
Effective ontology-based search for educational resources exploiting semantic similarity

Semantic similarity measure plays an important role in semantic search. However, Intention in educational resources search with semantic similarity has been rarely. In this paper, we proposed ontology based semantic similarity method to compute the user query and provided educational resources, so as to improve the search efficiency. A prototype system has been implemented in light of this approach. Given a keyword combined query, the system outputs a ranked list of relative results according to the semantic similarity. In the experiment, the system achieved the better result than traditional keyword based search.
Computing Gender Difference Using Fisher-Rao Metric from Facial Surface Normals

The aim in this paper is to explore whether the Fisher-Rao metric can be used to characterise the shape changes due to gender difference. We work using a 2.5D representation based on facial surface normals (or facial needle-maps) for gender classification. The needle-map is a shape representation which can be acquired from 2D intensity images using shape-from-shading (SFS). Using the von-Mises Fisher distribution, we compute the elements of the Fisher information matrix, and use this to compute geodesic distance between fields of surface normals to construct a shape-space. We embed the fields of facial surface normals into a low dimensional pattern space using a number of alternative methods including multidimensional scaling, heat kernel embedding and commute time embedding. We present results on clustering the embedded faces using the Max Planck and EAR database.
CpxP, a Stress-Combative Member of the Cpx Regulon

ABSTRACT The CpxA/R two-component signal transduction system ofEscherichia coli can combat a variety of extracytoplasmic protein-mediated toxicities. The Cpx system performs this function, in part, by increasing the synthesis of the periplasmic protease, DegP. However, other factors are also employed by the Cpx system for this stress-combative function. In an effort to identify these remaining factors, we screened a collection of random lacZ operon fusions for those fusions whose transcription is regulated by CpxA/R. Through this approach, we have identified a new locus,cpxP, whose transcription is stimulated by activation of the Cpx pathway. cpxP specifies a periplasmic protein that can combat the lethal phenotype associated with the synthesis of a toxic envelope protein. In addition, we show that cpxPtranscription is strongly induced by alkaline pH in a CpxA-dependent manner and that cpxP and cpx mutant strains display hypersensitivity to growth in alkaline conditions.
Psychometric Properties of the Beck Depression Inventories When Used with an Elderly Population.

The reliability of the 1978 version (BI) and the 13-item Short Form (BDI-SF) of the Beck Depression Inventory forms were investigated using an elderly population participating in a health promotion program (AGE WELL). Five items on the long form were identified as commonly occuring in an elderly population without depression: weight loss, body image, irritability, loss of libido, and sleep disturbance. The psychometric characteristics of these items were investigated as well as their relationship to the total score. A modified version for elderly (BI-E) was suggested. Aging, Older Adults, Depression, Measurement
Chemokine receptor CCR5 promotes leukocyte trafficking to the brain and survival in West Nile virus infection

The molecular immunopathogenesis of West Nile virus (WNV) infection is poorly understood. Here, we characterize a mouse model for WNV using a subcutaneous route of infection and delineate leukocyte subsets and immunoregulatory factors present in the brains of infected mice. Central nervous system (CNS) expression of the chemokine receptor CCR5 and its ligand CCL5 was prominently up-regulated by WNV, and this was associated with CNS infiltration of CD4+ and CD8+ T cells, NK1.1+ cells and macrophages expressing the receptor. The significance of CCR5 in pathogenesis was established by mortality studies in which infection of CCR5−/− mice was rapidly and uniformly fatal. In the brain, WNV-infected CCR5−/− mice had increased viral burden but markedly reduced NK1.1+ cells, macrophages, and CD4+ and CD8+ T cells compared with WNV-infected CCR5+/+ mice. Adoptive transfer of splenocytes from WNV-infected CCR5+/+ mice into infected CCR5−/− mice increased leukocyte accumulation in the CNS compared with transfer of splenocytes from infected CCR5−/− mice into infected CCR5−/− mice, and increased survival to 60%, the same as in infected CCR5+/+ control mice. We conclude that CCR5 is a critical antiviral and survival determinant in WNV infection of mice that acts by regulating trafficking of leukocytes to the infected brain.
Stillbirths in Western Australia 1980–1983: Influence of Race, Residence and Place of Birth

EDITORIAL COMMENT: The stillbirth rate in Western Australia for infants with birth‐weights of at least 1,000 g is commendably low at only 4.91 per 1,000 births. The authors' analysis shows that stillbirths of unknown cause are the largest group (table 3), and most of these occur at term, but before labour (table 2b). We respectfully disagree with the authors' comment that because these deaths are of unknown cause, that few are potentially avoidable/preventable by better obstetric care. The table below shows the neonatal death and stillbirth rates for Victoria for infants with birth‐weight of 1,000 g or more. Although the death rates have not reduced significantly in the past 2 years we believe that further improvement is possible; even if the stillbirth rates in Western Australia for 1984, 1985 and 1986 are the same as for 1983, we should not be prepared to accept that the limits of current obstetric care to favourably influence stillbirth rates have been reached. It should be stressed that this large group of stillbirths of ‘unknown cause’ occur in potentially salvageable infants who are mature and not malformed. The research required to prevent a significant proportion of these deaths may be no more than routine testing of glucose tolerance to diagnose all cases of gestational diabetes.
A 100MHz, 1.2V, ±1V peak-to-peak output, double-bus single ended-to-differential switched-capacitor amplifier for multi-column CMOS image sensors

This paper presents a high-speed (100MHz), low-voltage (1.2V), rail-to-rail (±1V) output, double-bus single ended-to-differential switched-capacitor amplifier built in multi-column CMOS image sensors. The amplifier conditions the incoming video signal for further processing by an analog-to-digital converter (ADC). The amplifier must perform several conflicting and rigorous functions: (1) high-voltage to low-voltage supply conversion (2) DC level-shift analog signal reference ground (3) single ended-to-differential conversion, and (4) correlated double sampling. The amplifier output signal is sampled by the ADC with a 100MHz clock. While the pixel array supply is at 3.3V, the amplifier/ADC must operate with 1.2V supply voltage to reduce analog DC bias power consumption. A typical 4-transistor pixel circuit full-well capacity produces the video signal in the range of 2 volts from fully dark to fully bright conditions. To process ±1V peak-to-peak output signal working with 1.2V supply rail, a special low-voltage, high-speed, rail-to-rail output opamp has been designed. Additionally, the pixel array requires two buses to be processed simultaneously consistent with the red-green-blue color filter pattern of a CMOS imager. The circuit is fabricated in a 1P8M CMOS process with dual-gate 0.09/0. 35μm, dual-voltage 1.2/3.3V transistors from SMIC semiconductor foundry.
An introduction to AI course with guide robot programming assignments

In this paper we describe a collection of course materials designed to be used in an undergraduate introduction to artificial intelligence (AI) course. These materials include three programming assignments, each touching upon core AI topics, which require that the students build the main functionalities of a guide robot. These assignments were carefully designed to allow the same solution to work both with a robot simulator and an inexpensive web-cam as well as with real robots. An overview of the course and the assignments is given along with references to online versions of the resources developed to teach the course.
Kripke Logical Relations and PCF

Abstract Sieber has described a model of PCF consisting of continuous functions that are invariant under certain (finitary) logical relations, and shown that it is fully abstract for closed terms of up to third-order types. We show that one may achieve full abstraction at all types using a form of "Kripke logical relations" introduced by Jung and Tiuryn to characterize λ-definability.
Virtual environment teleoperation of a hydraulic forestry crane

A teleoperation system has been developed for a hydraulic crane, of the type used on a forwarder vehicle, which travels off-road and collects logs cut by a harvester. The system developed consists of a 3D virtual environment, which allows the user to input a desired position for the crane tip using either the mouse or a joystick. The desired position is then transmitted (via UDP/IP) to a local control system. The crane is a redundant manipulator, so movements of the individual links are calculated using a pseudoinverse method, and controlled using PIDs with friction compensation. Encoder data from the crane links are continuously sent back to the user side, and the crane's movement is visualized in the virtual environment. The system has been tested on a real forwarder crane, experimental results and a video of the system's performance are provided.
Psoralea corylifolia Linn.—“Kushtanashini”

Plants have been the basis of many traditional medicines throughout the world for thousands of years and continue to provide new remedies to mankind. Plants have been one of the important sources of medicines since the beginning of human civilization. The recent resurgence of plant remedies resulted from several factors, such as effectiveness of plant medicines and lesser side effects compared with modern medicines. Psoralea corylifolia, commonly known as babchi, is a popular herb, which has since long been used in traditional Ayurvedic and Chinese medicine for its magical effects to cure various skin diseases. This plant is also pharmacologically studied for its chemoprotective, antioxidant, antimicrobial, and antiinflammatory properties. This review attempts to highlight the available literature on P. corylifolia with respect to its ethnobotany, pharmacognostic characteristics, traditional uses, chemical constituents, and summary of its various pharmacologic activities and clinical effects. Other aspects, such as toxicology and precautions are also discussed. This will be helpful to create interest toward babchi and may be useful in developing new formulations with more therapeutic and economical value.
Multi-objective Task Mapping Approach for Wireless NoC in Dark Silicon Age

Hybrid Wireless Network-on-Chip (HWNoC) provides high bandwidth, low latency and flexible topology configurations, making this emerging technology a scalable communication fabric for future Many-Core System-on-Chips (MCSoCs). On the other hand, dark silicon is dominating the chip footage of upcoming MCSoCs since Dennard scaling fails due to the voltage scaling problem that results in higher power densities. Moreover, congestion avoidance and hot-spot prevention are two important challenges of HWNoC-based MCSoCs in dark silicon age, Therefore, in this paper, a novel task mapping approach for HWNoC is introduced in order to first balance the usage of wireless links by avoiding congestion over wireless routers and second spread temperature across the whole chip by utilizing dark silicon. Simulation results show significant improvement in both congestion and temperature control of the system, compared to state-of-the-art works.
Phonological Context Approximation and Homophone Treatment for NEWS 2009 English-Chinese Transliteration Shared Task

This paper describes our systems participating in the NEWS 2009 Machine Transliteration Shared Task. Two runs were submitted for the English-Chinese track. The system for the standard run is based on graphemic approximation of local phonological context. The one for the non-standard run is based on parallel modelling of sound and tone patterns for treating homophones in Chinese. Official results show that both systems stand in the mid range amongst all participating systems.
Treatment for epilepsy in later life

Old age is now the commonest time to develop epilepsy, often as a consequence of underlying cerebrovascular or neurodegenerative disease. Age-related physiological changes can affect the pharmacokinetics and pharmacodynamics of antiepileptic drugs. Only three double-blind, head-to-head, randomised, controlled trials have been undertaken in this patient population and so pharmacological treatment tends to be empirical, often based on what antiepileptic drug not to chose for an individual patient. The available evidence has tended to favour lamotrigine, and perhaps gabapentin, over carbamazepine, based on better tolerability rather than superior efficacy for newly diagnosed epilepsy in this population. Preliminary data with levetiracetam suggest that this drug will also be useful in older people as a consequence of its favourable side-effect profile and lack of idiosyncratic reactions and drug interactions. Despite the dearth of high quality trial evidence, published outcome data hint at a good prognosis with a single antiepileptic drug for the majority of elderly people with epilepsy. A few patients will require low dose combination therapy. Epilepsy surgery is also an occasional option in this population. As life expectancy rises, so will the likelihood of presenting with seizures in later life placing an increasing burden on healthcare resources.
Stress, cortisol and well-being of caregivers and children in home-based child care: a case for differential susceptibility.

BACKGROUND We examined whether children cared for by stressed caregivers show lower socio-emotional well-being and more stress, compared with children cared for by less stressed caregivers. METHODS Perceived stress and cortisol levels of professional caregivers (n = 44), and associations with children's (n = 44) well-being and cortisol levels in home-based child care were examined. RESULTS Caregiver perceived stress and cortisol levels were related to children's well-being but not to children's cortisol levels. Children's social fearfulness acted as a moderator between caregivers' mean ratio of diurnal change in cortisol and children's well-being. When caregiver cortisol levels decreased, more fearful children were reported higher on well-being than less fearful peers. In contrast, when caregiver cortisol levels increased, more fearful children were reported lower on well-being. CONCLUSIONS The findings point to differential susceptibility. Child care organizations and parents need to notice that a non-stressful child care environment is in particular important for children with a difficult temperament.
Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans

Background The identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron. Methodology/Principal Findings Using phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16) that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements. Conclusions/Significance We identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons.