Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of optineurin E50K disrupts Rab8 interaction and leads to a progressive retinal degeneration in mice

Glaucoma is one of the leading causes of bilateral blindness affecting nearly 8 million people worldwide. Glaucoma is characterized by a progressive loss of retinal ganglion cells (RGCs) and is often associated with elevated intraocular pressure (IOP). However, patients with normal tension glaucoma (NTG), a subtype of primary open-angle glaucoma (POAG), develop the disease without IOP elevation. The molecular pathways leading to the pathology of NTG and POAG are still unclear. Here, we describe the phenotypic characteristics of transgenic mice overexpressing wild-type (Wt) or mutated optineurin (Optn). Mutations E50K, H486R and Optn with a deletion of the first (amino acids 153–174) or second (amino acids 426–461) leucine zipper were used for overexpression. After 16 months, histological abnormalities were exclusively observed in the retina of E50K mutant mice with loss of RGCs and connecting synapses in the peripheral retina leading to a thinning of the nerve fiber layer at the optic nerve head at normal IOP. E50K mice also showed massive apoptosis and degeneration of entire retina, leading to approximately a 28% reduction of the retina thickness. At the molecular level, introduction of the E50K mutation disrupts the interaction between Optn and Rab8 GTPase, a protein involved in the regulation of vesicle transport from Golgi to plasma membrane. Wt Optn and an active GTP-bound form of Rab8 complex were localized at the Golgi complex. These data suggest that alternation of the Optn sequence can initiate significant retinal degeneration in mice.
Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms (Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs. res.in/myosinome.
Voice Conversion Using RNN Pre-Trained by Recurrent Temporal Restricted Boltzmann Machines

This paper presents a voice conversion (VC) method that utilizes the recently proposed probabilistic models called recurrent temporal restricted Boltzmann machines (RTRBMs). One RTRBM is used for each speaker, with the goal of capturing high-order temporal dependencies in an acoustic sequence. Our algorithm starts from the separate training of one RTRBM for a source speaker and another for a target speaker using speaker-dependent training data. Because each RTRBM attempts to discover abstractions to maximally express the training data at each time step, as well as the temporal dependencies in the training data, we expect that the models represent the linguistic-related latent features in high-order spaces. In our approach, we convert (match) features of emphasis for the source speaker to those of the target speaker using a neural network (NN), so that the entire network (consisting of the two RTRBMs and the NN) acts as a deep recurrent NN and can be fine-tuned. Using VC experiments, we confirm the high performance of our method, especially in terms of objective criteria, relative to conventional VC methods such as approaches based on Gaussian mixture models and on NNs.
Schedule integration framework for time-triggered automotive architectures

Automotive Electrical/Electronic (E/E)-architectures consist of various components which are generally developed independently. Due to the increasing size and complexity, component integration is highly challenging and already slight modifications to components or subsystems often require expensive re-testing and re-validation. As a remedy, we propose a framework for modular architectures based on a data-centric description and a fully time-triggered scheduling. This modular design approach is enabled by a novel methodology for schedule integration where local schedules are defined independently for subsystems before being integrated into a global schedule. This divide-and-conquer approach significantly reduces the integration complexity while the system becomes highly composable. Our experimental results give evidence of the efficiency and versatility of the proposed approach, using networks based on a time-triggered automotive Ethernet.
Group Ratio Round-Robin: An O(1) Proportional Share Scheduler

Proportional share resource management provides a flexible and useful abstraction for multiplexing time-shared resources. We present Group Ratio Round-Robin (GR), a proportional share scheduler that combines accurate proportional fairness scheduling behavior with O(1) scheduling overhead. GR uses a novel client grouping strategy to organize clients into groups of similar processor allocations which can be more easily scheduled. Using this grouping strategy, GR combines the benefits of low overhead round-robin execution with a novel ratio-based scheduling algorithm. We analyze the behavior of GR and show that it can provide fairness within a constant factor of the ideal generalized processor sharing model for client weights with a fixed upper bound. GR can be easily implemented using simple data structures. We have implemented GR in Linux and measured its performance against other schedulers commonly used in research and practice, including the standard Linux scheduler, Weighted Fair Queueing, Virtual-Time Round-Robin, and Smoothed Round-Robin. Our experimental results demonstrate that GR can provide much lower scheduling overhead and much better scheduling accuracy in practice than these other approaches.
Using Tag Co-occurrence for Recommendation

Tagging with free form tags is becoming an increasingly important indexing mechanism. However, free form tags have characteristics that require special treatment when used for searching or recommendation because they show much more variation than controlled keywords. In this paper we present a method that puts this large variation to good use. We introduce second order co-occurrence and a related distance measure measure for tag similarities that is robust against the variation in tags. From this distance measure it is straightforward to derive methods to analyze user interest and compute recommendations. We evaluate the use of tag based recommendation on the Movielens dataset and a dataset of tagged books.
A Systematic Review of the Reliability of Rehabilitative Ultrasound Imaging for the Quantitative Assessment of the Abdominal and Lumbar Trunk Muscles

Study Design. Systematic review. Objective. To systematically review the literature on the rater reliability of Rehabilitative Ultrasound Imaging (RUSI) measurements to assess the morphology of the abdominal and lumbar trunk musculature. Summary of Background Data. RUSI is an increasingly popular method of evaluating the morphology and function of muscles with real-time ultrasound. Conclusions regarding the reliability of measurements obtained by RUSI, need to be established before recommending its wider use. Methods. A systematic approach to searching and identifying original research articles reporting quantitative RUSI measurements was undertaken. Reliability data were extracted and methodologic quality was evaluated by 2 independent reviewers. Results. Of the 24 studies included, 6 were deemed to be of high methodologic quality. Among high quality studies, some reported the measurement error associated with performing repeated measurements of the same image (intraimage analysis), whereas others reported the reliability of obtaining and measuring unique RUSI images (interimage analysis). Intraimage measurements demonstrated good intrarater and interrater reliability (ICC: >0.93). Interimage measurements demonstrated good reliability between raters (ICC: >0.90). Interimage, intrarater correlation coefficients were more variable with ICC values ranging from 0.62 to 0.97. Conclusion. The methodologic quality of research investigating the reliability of RUSI to measure the abdominal and lumbar trunk muscles needs to be improved. The majority of results of high quality studies indicate that RUSI has good levels of rater reliability. Improved reliability was observed among studies examining muscle thickness, and when using mean measurement values obtained by more experienced examiners.
Semantic Annotation to Support Description of the Art Market

The estimation of prices on the art market has been investigated as a research topic for many years, but only recently new approaches to this problem have been applied. One of these approaches concerns extending data on a work of art with data from the Internet to improve the quality of assessment. This, however, creates a lot of challenges mostly regarding the information extraction. Semantic annotation and enrichment of the crawled data enable additional reasoning and introduce new features into existing methods, resulting in a better estimation of indices for the art market. The problem tackled by this paper is as follows: what kind of semantic enrichment on documents collected from the Internet can be introduced to extend the data on the artwork and inuence the eciency and quality of indices calculated for artworks.
Happiness Is a Personal(ity) Thing

Subjective well-being is known to be related to personality traits. However, to date, nobody has examined whether personality and subjective well-being share a common genetic structure. We used a representative sample of 973 twin pairs to test the hypothesis that heritable differences in subjective well-being are entirely accounted for by the genetic architecture of the Five-Factor Model's personality domains. Results supported this model. Subjective well-being was accounted for by unique genetic influences from Neuroticism, Extraversion, and Conscientiousness, and by a common genetic factor that influenced all five personality domains in the directions of low Neuroticism and high Extraversion, Openness, Agree-ableness, and Conscientiousness. These findings indicate that subjective well-being is linked to personality by common genes and that personality may form an “affective reserve” relevant to set-point maintenance and changes in set point over time.
HUMAN DIGNITY: SEVERAL INTERPRETATIONS WITH DIFFERENT CONSEQUENCES

The Swiss National Bioethics Committee has recently organized a convent to discuss about „The culture of death”; it envisaged the contribution of philosophers and professional medical care staff. The human dignity has been significantly invoked. This term is considered by aestheticians and the Anglo-Saxon scholars (Ruth Macklin, Peter Singer, Steven Pinker) as an useless concept … but it still remains fundamental from the viewpoint of the Universal Declaration of Human Rights and generally for ethics and European law. It corresponds to a strong intuition. Our debate recalls the various usages of the “dignity” notion. The dignity may be understood as „decency”, non-degradation or, better, as selfesteem: the refusal to live with no dignity. A second meaning, often associated with the previous one, is the dignity seen as autonomy providing the individuals the right to make free will decisions on their course of life. We may state that those ¾ of the Swiss population who, according to repeated surveys, want the assistance to suicide to become an option (although few people would actually use it) formulate such an opinion. They might not clearly understand this notion but they feel this way and need no theories in this regard (this is what I believed I could say in a debate in North America – [1]). An approach rather inductive than deductive. The ontological aspect of the essence of human beings, a metaphysical notion, is significantly different; the human being is provided with dignity as a pure element, independent from any other consideration. I humbly believe that the human dignity is a construction gradually built in various ways depending on the society (the story about facts and ideas seems to justify this notion) rather than given by God. This human construction imposes requirements, and it is our responsibility to defend and improve it permanently. In fact, the notion of respect might be more pertinent: what really matters is to respect all human beings, regardless their nature, in our constant and voluntarily diligences. „Firstly, the dignity logically involves owing respect […] by being responsible for creating a world of respect, humans create in fact their own dignity” [2] In the name of this metaphysical essence, those accepting the ontological dignity oppose to the idea of people’s free will in respect of their own life. In practice, this
Safety culture assessment in community pharmacy: development, face validity, and feasibility of the Manchester Patient Safety Assessment Framework

Objective: To develop a framework that could be used by community pharmacies to self-assess their current level of safety culture maturity, which has high face validity and is both acceptable and feasible for use in this setting. Design: An iterative review process in which the framework was developed and evaluated through a series of 10 focus groups with a purposive sample of 67 community pharmacists and support staff in the UK. Main outcome measures: Development of the framework and qualitative process feedback on its acceptability, face validity, and feasibility for use in community pharmacies. Results: Using this process, a version of the Manchester Patient Safety Assessment Framework (MaPSAF) was developed that is suitable for application to community pharmacies. The participants were able to understand the concepts, recognised differences between the five stages of safety culture maturity, and concurred with the descriptions from personal experience. They also indicated that they would be willing to use the framework but recognised that staff would require protected time in order to complete the assessment. Conclusions: In practice the MaPSAF is likely to have a number of uses including raising awareness about patient safety and illustrating any differences in perception between staff, stimulating discussion about the strengths and weaknesses of patient safety culture within the pharmacy, identifying areas for improvement, and evaluating patient safety interventions and tracking changes over time. This will support the development of a mature safety culture in community pharmacies.
Reduction of Eddy-Current Losses in Fractional-Slot Concentrated-Winding Synchronous PM Motors

This paper focuses on the reduction of eddy-current losses in fractional-slot inset permanent magnet motors. The flux paths of the armature reaction is modified based on pulsewidth modulation technique. Undesirable harmonic contents of the air-gap flux density can be reduced. This improves back electromotive force waveform quality and reduces the amplitude of eddy currents in the solid rotor and magnets. Rotor losses are strongly reduced by this technique.
Optimal power flow: Closing the loop over corrupted data

Recently the power system state estimator was shown to be vulnerable to malicious deception attacks on the measurements, resulting in biased estimates. In this work we analyze the behavior of the Optimal Power Flow (OPF) algorithm in the presence of such maliciously biased estimates and the resulting consequences to the system operator. In particular, we characterize the set of attacks that may lead the operator to apply the erroneous OPF recommendation. Such characterization is used to improve a previously proposed security index by also considering the attack impact, which may be used for allocation and prioritization of protective measures. Additionally, we propose an analytical expression for the optimal solution of a simplified OPF problem with corrupted measurements. A small analytical example is discussed to illustrate and motivate our contributions.
A CMOS 64×48 Single Photon Avalanche Diode Array with Event-Driven Readout

This paper presents a CMOS array of 64times48 pixels capable of detecting single photons with timing accuracies better than 80ps. Upon photon arrival, a digital pulse is generated and routed by an event-driven digital readout scheme to a specific location for further processing. This method allows non-sequential row-wise and simultaneous column-wise detection while preserving photon arrival timing information. The readout scheme is scalable and it is shown to have minimal impact on timing accuracy. Time-correlated fluorescence spectroscopy and optical rangefinders are among the target applications for this technology
Rhinovirus disrupts the barrier function of polarized airway epithelial cells.

RATIONALE Secondary bacterial infection following rhinovirus (RV) infection has been recognized in chronic obstructive pulmonary disease. OBJECTIVES We sought to understand mechanisms by which RV infection facilitates secondary bacterial infection. METHODS Primary human airway epithelial cells grown at air-liquid interface and human bronchial epithelial (16HBE14o-) cells grown as polarized monolayers were infected apically with RV. Transmigration of bacteria (nontypeable Haemophilus influenzae and others) was assessed by colony counting and transmission electron microscopy. Transepithelial resistance (R(T)) was measured by using a voltmeter. The distribution of zona occludins (ZO)-1 was determined by immunohistochemistry and immunoblotting. MEASUREMENTS AND MAIN RESULTS Epithelial cells infected with RV showed 2-log more bound bacteria than sham-infected cultures, and bacteria were recovered from the basolateral media of RV- but not sham-infected cells. Infection of polarized airway epithelial cell cultures with RV for 24 hours caused a significant decrease in R(T) without causing cell death or apoptosis. Ultraviolet-treated RV did not decrease R(T), suggesting a requirement for viral replication. Reduced R(T) was associated with increased paracellular permeability, as determined by flux of fluorescein isothiocyanate (FITC)-inulin. Neutralizing antibodies to tumor necrosis factor (TNF)-alpha, IFN-gamma and IL-1beta reversed corresponding cytokine-induced reductions in R(T) but not that induced by RV, indicating that the RV effect is independent of these proinflammatory cytokines. Confocal microscopy and immunoblotting revealed the loss of ZO-1 from tight junction complexes in RV-infected cells. Intranasal inoculation of mice with RV1B also caused the loss of ZO-1 from the bronchial epithelium tight junctions in vivo. CONCLUSIONS RV facilitates binding, translocation, and persistence of bacteria by disrupting airway epithelial barrier function.
THE CORNER: IMAGINE: bRINGING VISION INTO CHILD PROTECTIVE SERVICES

Elizabeth Root, M.A., is a frontline child protection worker with 20 years’ experience helping families. she is also an Associate at the Family-Centered services Project and provides training and consultation to child welfare workers with particular attention to incorporating Collaborative helping in child welfare practice. William Madsen, Ph.d., is the Founder and director of the Family-Centered services Project in Watertown, Massachusetts, a training and consultation organization designed to help develop more respectful and responsive services for families (www.family-centeredservices.org). he has written extensively about collaborative approaches to helping efforts and is the author of Collaborative Therapy With Multi-stressed Families, 2nd ed. (Guilford, 2007), and co-author with kevin Gillespie of an upcoming book, Collaborative Helping: A Strengths Framework for Home-Based Services (Wiley, in press), that offers a principle-based, practice framework for helping efforts across many different contexts. Bill and Beth have been working together to experiment with new approaches to the challenges and dilemmas of child protection work in ways that support both workers and families. This article is the first to describe some of those efforts.
Myelin Basic Protein Cleaves Cell Adhesion Molecule L1 and Promotes Neuritogenesis and Cell Survival*

Background: The cell adhesion molecule L1 plays important roles in the developing and adult nervous system. Results: L1 is cleaved by myelin basic protein (MBP) yielding a L1 fragment that promotes L1-dependent functions. Conclusion: L1 functions in the nervous system depend on MBP. Significance: Study of the L1 and MBP functions may contribute to understanding the pathogenesis of demyelinating and neurodegenerative diseases. The cell adhesion molecule L1 is a Lewisx-carrying glycoprotein that plays important roles in the developing and adult nervous system. Here we show that myelin basic protein (MBP) binds to L1 in a Lewisx-dependent manner. Furthermore, we demonstrate that MBP is released by murine cerebellar neurons as a sumoylated dynamin-containing protein upon L1 stimulation and that this MBP cleaves L1 as a serine protease in the L1 extracellular domain at Arg687 yielding a transmembrane fragment that promotes neurite outgrowth and neuronal survival in cell culture. L1-induced neurite outgrowth and neuronal survival are reduced in MBP-deficient cerebellar neurons and in wild-type cerebellar neurons in the presence of an MBP antibody or L1 peptide containing the MBP cleavage site. Genetic ablation of MBP in shiverer mice and mutagenesis of the proteolytically active site in MBP or of the MBP cleavage site within L1 as well as serine protease inhibitors and an L1 peptide containing the MBP cleavage site abolish generation of the L1 fragment. Our findings provide evidence for novel functions of MBP in the nervous system.
Preterm Birth Rates in Pregnant Women with Sexually Transmitted Infections: Cincinnati Public Health Centers 2005 and 2006 Deliveries

3 Introduction 5 Statement of Purpose 8 Literature Review 9 Summary 39 Methods 40 Results 43 Discussion 56 Limitations and Strengths of Study 63 Conclusions 64 References 66 Appendix (A) Public Health Competencies 84 Appendix (B) Data collection form 87 Appendix (C) Data definitions 89 Appendix (D) Statistical Neighborhood map 90 Appendix (E) 2000 Census Tract and Jurisdictions map 91 Appendix (F) Premature births by neighborhood map 92 Appendix (G) Project Timeline 94 Appendix (H) Cincinnati Health Department IRB approval 95 Appendix (I) Wright State University IRB approval 96 PRETERM BIRTH RATES 3