Miracle-dz/UniFAR-FTUs huggingface dataset:
Miro phosphorylation sites regulate Parkin recruitment and mitochondrial motility

Significance In mitophagy, damaged mitochondria stabilize PTEN-induced putative kinase 1 (PINK1) and recruit Parkin, an E3-ligase that ubiquitinates proteins on the outer membrane and targets mitochondria for degradation. The crucial roles of PINK1 phosphorylation of Parkin and ubiquitin in mitophagy are well-established. Other substrates of PINK1, however, have also been reported but the significance of those phosphorylations is less clear. We now show that Miro phosphorylations can regulate Parkin recruitment to Miro and trigger Miro degradation. The consequence of this branch of the PINK1/Parkin pathway is the disruption of mitochondrial motility, an event that may spatially restrict the deleterious effects of mitochondrial damage prior to the mitophagic removal of the organelle. The PTEN-induced putative kinase 1 (PINK1)/Parkin pathway can tag damaged mitochondria and trigger their degradation by mitophagy. Before the onset of mitophagy, the pathway blocks mitochondrial motility by causing Miro degradation. PINK1 activates Parkin by phosphorylating both Parkin and ubiquitin. PINK1, however, has other mitochondrial substrates, including Miro (also called RhoT1 and -2), although the significance of those substrates is less clear. We show that mimicking PINK1 phosphorylation of Miro on S156 promoted the interaction of Parkin with Miro, stimulated Miro ubiquitination and degradation, recruited Parkin to the mitochondria, and via Parkin arrested axonal transport of mitochondria. Although Miro S156E promoted Parkin recruitment it was insufficient to trigger mitophagy in the absence of broader PINK1 action. In contrast, mimicking phosphorylation of Miro on T298/T299 inhibited PINK1-induced Miro ubiquitination, Parkin recruitment, and Parkin-dependent mitochondrial arrest. The effects of the T298E/T299E phosphomimetic were dominant over S156E substitution. We propose that the status of Miro phosphorylation influences the decision to undergo Parkin-dependent mitochondrial arrest, which, in the context of PINK1 action on other substrates, can restrict mitochondrial dynamics before mitophagy.
Time-dependent shortest path with discounted waits

We study a variant of the shortest path problem in a congested environment. In this setting, the travel time of each arc is represented by a piecewise continuous aﬃne function of departure time. Besides, the driver is allowed to wait at nodes to avoid wasting time in traﬃc. While waiting, the driver is able to perform useful tasks for her job or herself, so the objective is to minimize only driving time. Although optimal solutions may contain cycles and pseudo-polynomially many arcs, we provide a representation of the solutions that is polynomial in the absolute value of the inverse of the slopes as well as in the dimensions of the graph. We further prove that the problem is NP -Hard when the slopes are integer. We introduce a restriction of the problem where waits must be integer and propose pseudo-polynomial algorithms for the latter. We also provide a pseudo-FPTAS, polynomial in the ratio between the bound on the total waiting time and the minimum travel time. Finally, we discuss harder variants of the problem and show their inapproximability.
LEARNING IN CONNECTIONIST SPEECH RECOGNITION

Humans do not learn new tasks in isolation: for instance speech recognition interacts with speaker recognition. Multitask Learning (MTL) attempts to take advantage of these interactions by adding additional, related tasks to the main task. In this work, we present applications of MTL to Automatic Speech Recognition in noise, incorporating speech enhancement and gender recognition as additional tasks. A Recurrent Neural Net architecture is used to integrate multiple tasks. Results show that related extra tasks can indeed produce significant improvements to performance on the main task, i.e. ASR.
New approach for quantitation of short echo time in vivo 1H MR spectra of brain using AMARES

Short echo time in vivo STEAM 1H MR spectra (4.7 T, TE =16 ms) of normal rat brain were fitted in the time domain using a VARPRO‐like algorithm called AMARES which allows an inclusion of a large amount of prior knowledge. The prior knowledge was derived from phantom spectra of pure metabolite solutions measured under the same experimental conditions as the in vivo spectra. The prior knowledge for the in vivo spectra was constructed as follows: for each VARPRO‐fitted phantom spectrum one peak (the most prominent one in the in vivo spectrum) was chosen and left unconstrained in the AMARES fitting while all the other peaks in the metabolite spectrum (i.e. their corresponding parameters—amplitudes, damping factors, frequencies and phases) were fixed to the parameter values of the unconstrained peak via amplitude and damping ratios and frequency and phase shifts. Including N ‐acetyl‐aspartate, glutamate, total creatine, cholines, glucose and myo ‐inositol into the fits provided results which were in agreement with published data. An inclusion of glutamine into the set of fitted metabolites was also investigated. © 1998 John Wiley & Sons, Ltd.
Effects of erythromycin on the phenotypic and genotypic biofilm expression in two clinical Staphylococcus capitis subspecies and a functional analysis of Ica proteins in S. capitis.

The ica operon encoding polysaccharide intercellular adhesion, which facilitates biofilm formation in staphylococci, has been extensively studied in Staphylococcus epidermidis and Staphylococcus aureus. Based on in silico analysis, we suggest the following functional model for Ica proteins in S. capitis. IcaA is responsible for polysaccharide synthesis. IcaA and IcaD complete transferring the growing sugar chain to the cell surface; IcaB is a deacetylase, with the same function as IcaB of S. epidermidis. IcaC mainly modifies the synthesized glucan by acetylation. We also examined the effects of subinhibitory concentrations of erythromycin on phenotypic biofilm expression and transcription of biofilm-related genes, using isolates representing the two subspecies of Staphylococcus capitis and different biofilm and resistance phenotypes. On induction with erythromycin, biofilm density was strongly elevated in two erythromycin-resistant S. capitis, but not in three susceptible isolates. In the representative erythromycin-resistant S. capitis subsp. urealyticus, there were significant upregulations of the icaA gene and its positive regulator sarA on transition to the stationary phase without erythromycin induction. There were also significant increases in the transcription levels of icaA, rsbU and sigB corresponding to a very strong biofilm phenotype in the stationary phase on erythromycin stress. In contrast, the representative erythromycin-susceptible S. capitis subsp. capitis displayed upregulation only of altE on entry into the stationary phase with erythromycin induction, but this change was not associated with enhancement of biofilm production. These findings suggest that the two subspecies of S. capitis adopt different pathogenesis and survival strategies to adapt to a hostile environment. Received 2 December 2014 Accepted 17 March 2015
The Lived Experience of Lupus Flares: Features, Triggers, and Management in an Australian Female Cohort

Individuals living with lupus commonly experience daily backgrounds of symptoms managed to acceptable tolerance levels to prevent organ damage. Despite management, exacerbation periods (flares) still occur. Varied clinical presentations and unpredictable symptom exacerbation patterns provide management and assessment challenges. Patient perceptions of symptoms vary with perceived impact, lifestyles, available support, and self-management capacity. Therefore, to increase our understanding of lupus' health impacts and management, it was important to explore lupus flare characteristics from the patient viewpoint. Lupus flares in 101 Australian female patients were retrospectively explored with the use of a novel flare definition. Qualitative methods were used to explore patient-perceived flare symptoms, triggers, and management strategies adopted to alleviate symptom exacerbations. A mean of 29.9 flare days, with 6.8 discrete flares, was experienced. The study confirmed that patients perceive stress, infection, and UV light as flare triggers and identified new potential triggers of temperature and weather changes, work, and chemical exposure from home cleaning. The majority of flares were self-managed with patients making considered management choices without medical input. Barriers to seeking medical support included appointment timings and past negative experiences reflecting incongruence between clinician and patient views of symptom impact, assessment, and ultimately flare occurrence.
Weight Based KNN Recommender System

Today, the personalized recommendation is one of the most important technologies in the Internet and e-commerce system, along with the increasing number of users and commodities. Among personalized recommendation algorithms, CF (Collaborate Filtering) has been researched for many years. The similarity computation method, which is the key in personalized recommender, like cosine theorem or pearson correlation coefficient, does not consider the distinguish degree of the items. In this paper, we will propose weight Based similarity algorithm, called IR-IUF++, which updates pearson correlation coefficient. IR-IUF++ performs better than traditional similarity algorithm in our experiment.
GENETIC CHARACTERIZATION OF COMMON EIDERS BREEDING IN THE YUKON-KUSKOKWIM DELTA, ALASKA

Abstract We assessed population genetic subdivision among four colonies of Common Eiders (Somateria mollissima v-nigrum) breeding in the Yukon-Kuskokwim Delta (YKD), Alaska, using microsatellite genotypes and DNA sequences with differing modes of inheritance. Significant, albeit low, levels of genetic differentiation were observed between mainland populations and Kigigak Island for nuclear intron lamin A and mitochondrial DNA (mtDNA) control region. Intercolony variation in haplotypic frequencies also was observed at mtDNA. Positive growth signatures assayed from microsatellites, nuclear introns, and mtDNA indicate recent colonization of the YKD, and may explain the low levels of structuring observed. Gene flow estimates based on microsatellites, nuclear introns, and mtDNA suggest asymmetrical gene flow between mainland colonies and Kigigak Island, with more individuals on average dispersing from mainland populations to Kigigak Island than vice versa. The directionality of gene flow observed may be explained by the colonization of the YKD from northern glacial refugia or by YKD metapopulation dynamics.
Modeling and Comparing the Influence of Neighbors on the Behavior of Users in Social and Similarity Networks

Social networks are becoming more and more popular with the advent of numerous online social networking services. In this paper, we explore social rating networks, which record not only social relations but also user ratings for items. We analyze and model the effects of social influence and correlational influence in such networks, based on influence coefficients that measure the degree of influence in a network. We distinguish two types of user behavior: adopting an item and adopting a rating value for that item. We propose models to analyze and measure the influence of neighbors on both item and rating adoption behavior of users. Our experiments demonstrate that social influence has a much stronger impact on user behavior than correlational influence. Social and correlational influence are global effects in the entire network. However, there are local differences, i.e. certain users have a stronger social influence than others. To model this effect, we introduce the novel concept of social authority of individual users. We also propose an objective way to evaluate the social authority measure by injecting it into a simple recommender system.
Viscous Transonic Decretion in Disks of Be Stars

We study the characteristics of the outflow in disks of Be stars, based on the viscous decretion disk scenario. In this scenario, the matter ejected from the equatorial surface of the star drifts outward because of the effect of viscosity, and forms the disk. For simplicity, we adopt the alpha-prescription for the viscous stress, and assume the disk to be isothermal. Solving the resulting wind equations, we find that a transonic solution exists for any value of alpha. The sonic point is located at r>100R for plausible values of parameters, where R is the stellar radius. The sonic radius is smaller for higher temperature and/or larger radiative force. We also find that the topology of the sonic point is nodal for alpha>0.95, while it is of saddle type for alpha<0.9. We expect that the sonic point in the former case is unstable, whereas that in the latter case is stable. The outflow is highly subsonic in the inner part of the disk. Roughly, the outflow velocity increases linearly with r and the surface density decreases as r^{-2}. Interestingly, the disk is near Keplerian in the inner subsonic region, while it is angular momentum conserving in the outer subsonic region and in the supersonic region. Our results, together with the observed range of the base density for Be star disks, suggest that the mass loss rate in the equatorial region is at most comparable with that in the polar region.
Non-obstructive room-level locating system in home environments using activity fingerprints from smartwatch

Many smart home applications, such as monitoring for the elderly and home automation, require location information for individual occupants. Several techniques have been proposed for tracking occupants in a home environment. However, the current techniques do not provide a seamless in-home locating system owing to the occupants' device-free movement and the lack of cost-effective infrastructure for home location tracking. In this paper, we propose a home occupant tracking system that uses a smartphone and an off-the-shelf smartwatch without additional infrastructure. In our system, activity fingerprints are automatically generated from the microphone and the inertial sensors of the smartwatch, and location information is periodically obtained from the smartphone. We designed a hidden Markov model using the relationship between home activities and the room's location. Extensive experiments showed that our system tracks the location of users with 87% accuracy, even when there is no manual training for activities.
Protection against allograft rejection with intercellular adhesion molecule-1 antisense oligodeoxynucleotides.

BACKGROUND We designed an antisense phosphorothioate oligodeoxynucleotide (oligo) to specifically inhibit the expression of rat intercellular adhesion molecule-1 (ICAM-1) mRNA (IP-9125). METHODS IP-9125 oligo was delivered intravenously by osmotic pump alone or in combination with cyclosporine (CsA) to recipients in order to prevent the rejection of kidney or heart allografts. In additional experiments, kidney allografts were perfused with IP-9125 before grafting. RESULTS IP-9125 inhibited ICAM-1 mRNA and ICAM-1 protein expression in rat aortic endothelial cells; scrambled controls IP-12140 and IP-13944 were ineffective. Untreated ACI (RT1a) recipients rejected Lewis (RT1l) kidney allografts at a mean survival time of 8.5+/-1.1 days. A 14-day intravenous administration of 2.5 mg/kg/day IP-9125 prolonged the survival of kidney allografts to 39.2+/-16.4 days; 5.0 mg/kg/day, to 43.0+/-17.5 days; and 10.0 mg/kg/day, to 50.4+/-21.6 days. In contrast, a scrambled control IP-12140 was not effective. A combination of 10 mg/kg/day IP-9125 and 1.0 mg/kg/day CsA delivered for 14 days synergistically extended kidney allograft survival times 88.5+/-7.5 days. In contrast, the combination of 10.0 mg/kg/day control IP-12140 with CsA was ineffective (20.7+/-3.2 days) when compared with CsA alone (20.2+/-4.0 days). Similar results were obtained for heart transplants in recipients treated with IP-9125 alone or in combination with CsA. Furthermore, in situ immunostaining showed that IP-9125 significantly reduced the expression of ICAM-1 protein in kidney allografts. Finally, perfusion of kidney grafts alone with 20.0 mg per 2 ml of IP-9125 protected kidney allografts from rejection (37.5+/-7.5 days; P < 0.001), whereas perfusion with 20 mg per 2 ml of control IP-12140 was ineffective (12.6+/-5.0 days). CONCLUSIONS Rat ICAM-1 IP-9125 oligo inhibits ICAM-1 protein expression in vitro and in vivo as well as blocks allograft rejection when used for pretreatment of donors, graft perfusion, or postoperative treatment of recipients.
Exchanging focus groups for individual interviews when collecting qualitative data.

BACKGROUND Focus group data are created through interactions between participants whereas data from individual interviews are created through a dialogue between the participant and researcher, whose questions set the agenda. Focus groups and individual interviews are therefore used for different reasons and produce different data. However, sometimes researchers exchange focus groups for individual interviews when collecting data. AIM To discuss the rationale for using focus groups, reasons for exchanging focus groups for interviews when collecting qualitative data and any implications for the quality of research in doing so. DISCUSSION The author first considers the unique features of focus groups and how these contrast with individual interviews. The reasons why individual interviews are added to studies designed for focus groups are then considered, based on the author's experience and a selection of research studies. Researchers showed flexibility, adapting plans to include particular individuals, but they could have provided clearer rationales for using focus groups and changing their designs. CONCLUSION Researchers should rationalise their choices of research methods and adopt a transparent and systematic approach, with a clear account of the research process and explanations about any changes to their original designs. IMPLICATIONS for practice Researchers should recognise the differences between focus group and interview data, reflect on their rationales for using each method, and justify their choices. If recruitment is likely to be difficult, researchers intending to use focus groups could nevertheless include individual interviews in their initial design.
Efficient Estimation of Software System Using Fuzzy Technique

Software effort estimation is the greatest challenge for software developers. Software effort estimation is the process of predicting most realistic use of effort required to develop or maintain software based on incomplete and uncertain input.There are various models suggested by researchers for calculating effort.But no one can give accurate result.The best result are achieved by using soft computing technique.the various methodology used in soft computing for effort estimation are based on fuzzy logic, neural netwok and genetic algorithm.In this paper we have used the fuzzy logic approach. Rather than using a single number software size is regarded as triangular fuzzy number. The developed model are tested on 10 NASA [2]software project. Comparison of various models have been done and it is found that developed model provide better solution. KeywordsLOC based model, NASA software project, fuzzy logic, triangular fuzzy number, membership fuction and fuzziness.
Supple Laws in Psychology and Biology

The nature and status of psychological laws are a long-standing controversy. I will argue that part of the controversy stems from the distinctive nature of an important subset of those laws, which I’ll call “supple laws. ” An emergent-model strategy taken by the new interdisciplinary field of artificial life provides a strikingly successful understanding of analogously supple laws in biology. So, after reviewing the failures of the two evident strategies for understanding supple psychological laws, I’ll turn for inspiration to emergent-models explanations of supple laws in biology. I’ll conclude by inferring what an emergent model of supple laws in psychology should be like.
Smart phone accessibility and mHealth use in a limited resource setting

AIM To determine smartphone access and use including future opportunities for mHealth and potential ethical implications among health care professionals practicing at a health care facility in Bengaluru, India. BACKGROUND The evolution of smart phones can provide convenient, portable, and rapid access to resources for health care professionals. While mobile phone accessibility has improved in recent years in many low and middle-income countries, the use of smart phones to address health priorities remains limited in some limited resource settings. DESIGN A quantitative descriptive design was used. METHODS A survey was administered in November of 2016 to nurses and physicians at a tertiary care hospital in India. RESULTS/FINDINGS All respondents had a mobile phone, and the majority owned a smart phone that was used for text messaging, email, accessing internet, and downloading apps. Participants recommended smart phone use to improve health care provider access to continuing education and to improve patient knowledge about health. Physicians had better access to mHealth resources compared with nurses. CONCLUSION Credible, evidence-based, affordable mobile applications are needed to provide a platform for continuing health education to health professionals and patients in India and limited resource settings. Nurses need equitable access to mHealth resources to build successful mHealth initiatives.
Integrating jason in a multi-agent platform with support for interaction protocols.

Agent communication is a core issue when studying all possible ways for agents to organize and collaborate to achieve their goals. We can count on communication standards, as the FIPA Interaction Protocols. On the other hand we can count on high level agent programming languages, like AgentSpeak, which allow us to model and represent the agent and its knowledge and behavior. In this paper we present a proposal to add to Jason (an interpreter of an extended version of AgentSpeak) a new level of abstraction in the task of programming conversations between agents. The agent communication follows the FIPA interaction protocols. A new entity called Communicator Manager acts as an interface between the agent programming language (Jason) and the platform communication facilities (Magentix 2). This approach allows the programmer to focus on programming the agent knowledge and reasoning parts instead of the interaction protocols. An agent can call the communication manager to start a conversation. The communication manager will control the different steps of the conversation and will modify the agent belief base to represent the results of the different steps of the conversation protocol. Therefore, the agents can use this knowledge in its reasoning process. This approach can be easily transfered to others agent programming languages and platforms.