Miracle-dz/UniFAR-FTUs huggingface dataset:
Being Flexible: The Voltage-Controllable Activation Gate of Kv Channels

Kv channels form voltage-dependent potassium selective pores in the outer cell membrane and are composed out of four α-subunits, each having six membrane-spanning α-helices (S1–S6). The α-subunits tetramerize such that the S5–S6 pore domains co-assemble into a centrally located K+ pore which is surrounded by four operational voltage-sensing domains (VSD) that are each formed by the S1–S4 segments. Consequently, each subunit is capable of responding to changes in membrane potential and dictates whether the pore should be conductive or not. K+ permeation through the pore can be sealed off by two separate gates in series: (a) at the inner S6 bundle crossing (BC gate) and (b) at the level of the selectivity filter (SF gate) located at the extracellular entrance of the pore. Within the last years a general consensus emerged that a direct communication between the S4S5-linker and the bottom part of S6 (S6c) constitutes the coupling with the VSD thus making the BC gate the main voltage-controllable activation gate. While the BC gate listens to the VSD, the SF changes its conformation depending on the status of the BC gate. Through the eyes of an entering K+ ion, the operation of the BC gate apparatus can be compared with the iris-like motion of the diaphragm from a camera whereby its diameter widens. Two main gating motions have been proposed to create this BC gate widening: (1) tilting of the helix whereby the S6 converts from a straight α-helix to a tilted one or (2) swiveling of the S6c whereby the S6 remains bent. Such motions require a flexible hinge that decouples the pre- and post-hinge segment. Roughly at the middle of the S6 there exists a highly conserved glycine residue and a tandem proline motif that seem to fulfill the role of a gating hinge which allows for tilting/swiveling/rotations of the post-hinge S6 segment. In this review we delineate our current view on the operation of the BC gate for controlling K+ permeation in Kv channels.
A development of a new mechanism of an autonomous unicycle

We propose a new mechanism of a unicycle. One feature of this robot is the shape of the wheel which is similar to a rugby ball. The other feature is that the body is separated into upper and lower parts. We give the details of a mechanism of the robot, simple controller system, and some results of a performance experiment using the designed controller. We present experimental results that show that the robot can move in a straight line and steer itself by the proposed mechanism.
The Remembering Self: Construction and Accuracy in the Self-Narrative

1. Self-narratives: true and false Ulric Neisser 2. Literary and psychological models of the self Daniel Albright 3. The remembered self Jerome Bruner 4. Composing protoselves through improvisation Craig R. Barclay 5. Mind, text and society: self-memory in social context Kenneth J. Gergen 6. Personal identity and autobiographical recall Greg J. Niemeyer and April E. Metzler 7. Constructing narrative, emotion, and self in parent-child conversations about the past Robyn Fivush 8. Narrative practices: their role in socialization and self-construction Peggy J. Miller 9. Emotionality and narrative in the emergence of the self-concept Rebecca A. Eder 10. Is memory self-serving? Wilem A. Wagenaar 11. Creative remembering Michael Ross and Roger Buehler 12. The remembered self and the enacted self Alan Baddeley 13. The authenticity and utility of memories Eugene Winograd 14. The remembered self in amnesics William Hirst 15. Perception is to self as memory is to selves Edward S. Reed.
Clients’ experiences of dynamic interpersonal therapy (DIT): opportunities and challenges for brief, manualised psychodynamic therapy in the NHS

Dynamic interpersonal therapy (DIT) is a brief manualised psychodynamic intervention for depression. This is a first study exploring clients’ experiences of DIT specifically and brief, manualised psychodynamic psychotherapy (PP) in general. Interpretative phenomenological analysis was the methodology employed. Five participants completed a semi-structured interview, three weeks to ten months after completing DIT. The scores of pre- and post-therapy outcome measures of depression and anxiety were also available. Two emerging superordinate themes are presented here: (1) ‘The Distinct Features of DIT’, referring to how its therapeutic style and time limitations were experienced and (2) the ‘Impact of Therapy’, referring to perceived outcomes. While previous findings showed that therapist’s perceived limited activity in long-term PP was experienced as hindering/unhelpful, the perceived sense of direction in DIT appeared adequate to most participants. Secondly, the time limitations provoked complex responses. Reactions to the distinct elements of DIT are to be treated both as therapeutic opportunities and as challenges. Further, in line with psychoanalytic theory, most participants described relational changes that went beyond symptom relief and remained in progress after therapy ended. Intriguingly, there was no consistency between participants’ qualitative accounts of change and the scores of the outcome measures.
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

More than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed HaploReg (http://compbio.mit.edu/HaploReg) to aid the functional dissection of genome-wide association study (GWAS) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. Since first launching the website in 2011, we have greatly expanded HaploReg, increasing the number of chromatin state maps to 127 reference epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eQTL) variants and their tissue-specific target genes from GTEx, Geuvadis, and other recent studies. We present these updates as HaploReg v4, and illustrate a use case of HaploReg for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms.
A Polymer/Oil Based Nanovaccine as a Single-Dose Immunization Approach

The recognized necessity for new antigen delivery carriers with the capacity to boost, modulate and prolong neutralizing immune responses prompted our approach, in which we describe a multifunctional nanocarrier consisting of an oily nanocontainer protected by a polymeric shell made of chitosan (CS), named CS nanocapsules (CSNC). The CS shell can associate the antigen on its surface, whereas the oily core might provide additional immunostimulating properties. In this first characterization of the system, we intended to study the influence of different antigen organizations on the nanocarrier's surface (using the recombinant hepatitis B surface antigen –rHBsAg– as a model antigen) on their long-term immunopotentiating effect, without any additional immunostimulant. Thus, two prototypes of antigen-loaded CSNC (CSNC+ and CSNC−), exhibiting similar particle size (200 nm) and high antigen association efficiency (>80%), were developed with different surface composition (polymer/antigen ratios) and surface charge (positive/negative, respectively). The biological evaluation of these nanovaccines evidenced the superiority of the CSNC+ as compared to CSNC- and alum-rHBsAg in terms of neutralizing antibody responses, following intramuscular vaccination. Moreover, a single dose of CSNC+ led to similar IgG levels to the positive control. The IgG1/IgG2a ratio suggested a mixed Th1/Th2 response elicited by CSNC+, in contrast to the typical Th2-biased response of alum. Finally, CSNC+ could be freeze-dried without altering its physicochemical properties and adjuvant effect in vivo. In conclusion, the evaluation of CSNC+ confirms its interesting features for enhancing, prolonging and modulating the type of immune response against subunit antigens, such as rHBsAg.
Prefrontal Cortex and Somatosensory Cortex in Tactile Crossmodal Association : An Independent Component Analysis of ERP Recordings

1 Department of Neurosurgery, Johns Hopkins University, Baltimore, Maryland, United States of America, 2 Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, Maryland, United States of America, 3 Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, United States of America, 4 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America, 5 The Institute of Cognitive Neuroscience, East China Normal University, Shanghai, People’s Republic of China, 6 The Music Intelligence Neural Development Institute, Costa Mesa, California, United States of America, 7 Tsinghua University, Beijing, People’s Republic of China
Prediction of Gas Emission Based on Partial Correlation Analysis and SVR

The prediction model of gas emission is established based on partial correlation analysis and support vector regression (SVR) in order to accurately predict gas emission of working face under the condition of small samples. Not only are the problems of small samples and nonlinear prediction effectively resolved by applying SVR, but also the main control factors of gas emission are selected by applying partial correlation analysis method, which can re duce variables space dimension of the model to improve prediction accuracy. Through empirical analysis, the superiority of the model is proved by prediction results that are quite close to the measured values.
An Experimental Test of the Effect of Incentives on Recruitment of Ethnically Diverse Colorectal Cancer Cases and Their First-Degree Relatives into a Research Study

Background: Optimizing participant response rates is important for obtaining representative samples and the timely completion of studies. It is a common practice to use participant incentives to boost response rates, but few studies have systematically examined their effectiveness, particularly among minority groups. Methods: We experimentally tested three incentive strategies for their effectiveness in improving response rates among colorectal cancer cases (n = 3,816) and their relatives (n = 2,353). A 2 × 2 × 2 factorial design compared (a) registered versus first class mail, (b) $5 cash with the initial mailing (yes/no), and (c) $20 promise (yes/no) upon completion of the information form (for cases) or $10 promise (yes/no) upon completion of the baseline survey (for relatives). Outcome measures were provision of contact information on first-degree relatives for cases and completion of the baseline survey for relatives. Results: The response rate among cases was low in all ethnic groups (28-37%) and incentive strategies did not have an effect. Among relatives, the overall baseline survey response rate was 71%, ranging from 66% among Asians to 76% among Whites. Modest absolute increases were observed for payment schedules that included a $5 cash enclosure with the initial mailing in the total sample [odds ratio (OR), 1.65 and 1.47] and among Latinos (OR, 1.94 and 1.74) but not among Asians (OR, 1.61 and 1.55) or African Americans (OR, 1.19 and 1.02). Response rates were not influenced by registered versus first-class mailing. Conclusion: The effects of incentives in this study were modest with some suggestion of differences by ethnic group and type of incentive. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2620–5)
Dispersion and Characterization of Coplanar Waveguide Based On Conformal Mapping Technique

In this paper we proposed the estimation of the characteristic impedance, effect of dispersion, and the effective dielectric constant of Coplanar Waveguide (CPW) using conformal mapping theory and performances are analyzed. Numerically efficient and accurate formulae based on the conformal mapping method for the analysis of coplanar waveguide structures are presented. The analysis formulas for Coplanar Waveguides are derived and verified with Matlab. The Characteristic Impedance of CPW for different dielectric material using finite substrate as well as for infinite thickness of the substrate material and peering effect of dispersion is under consideration in this work. With the help of CPW transmission techniques, substantial amount of efficiency has been achieved. The design equation obtained by conformal mapping technique which is the simplest and most often used quasi-static method consists of complete elliptical integral.
Citizens, dictators and networks: A game theory approach

In a society composed of citizens and a dictator, what are the conditions for a successful citizens’ revolt? What kind of strategies do governments follow to prevent such revolts? In this article, we argue that the concept of networks is a very powerful tool to understand these issues, as shown, for example, by the prominent role of social networks during the recent revolts in the Arab world. More specifically, we model these types of societies as a game played between a leader, who has to decide the distribution of the aggregate income, and a group of citizens who have the opportunity to revolt if they are unhappy with the distribution (or if they dislike the regime). Coordinated action by citizens is possible because they form nodes in a communication network. However, communication through the network is distorted, which could preclude the emergence of collective action among citizens. The network structure and the distortion level are determinants of the political equilibrium and wealth distribution. The model explains how the dictator could use propaganda, cooptation, and repression to increase his expected utility. We also use our framework to provide a formal proof of Wintrobe’s Dictator’s Dilemma. Finally, the model is illustrated by applying it to cases in Nigeria, Zaire/Congo, and Libya.
Does the Butcher-on-the-Bus Phenomenon Require a Dual-Process Explanation? A Signal Detection Analysis

The butcher-on-the-bus is a rhetorical device or hypothetical phenomenon that is often used to illustrate how recognition decisions can be based on different memory processes (Mandler, 1980). The phenomenon describes a scenario in which a person is recognized but the recognition is accompanied by a sense of familiarity or knowing characterized by an absence of contextual details such as the person’s identity. We report two recognition memory experiments that use signal detection analyses to determine whether this phenomenon is evidence for a recollection plus familiarity model of recognition or is better explained by a univariate signal detection model. We conclude that there is an interaction between confidence estimates and remember-know judgments which is not explained fully by either single-process signal detection or traditional dual-process models.
Bringing 3D to teleradiology

The NOVICE project (Network-Oriented Visualization in a Clinical Environment) is developing a system for medical image data analysis and visualization through the Web with the intention of demonstrating the effectiveness of such a system in a clinical environment. One element being addressed by NOVICE is the provision of teleradiology tools. The paper describes how three-dimensional models can be included in a teleradiology application by utilising the Virtual Reality Modelling Language (VRML) and multi-user extensions, including annotation tools. The result is the world's first Web based system for 3D teleradiology. We present a detailed overview of the implementation and operation of this system, and indicate results from early use.
Fluoride Anion Recognition by a Multifunctional Urea Derivative: An Experimental and Theoretical Study

In this work we demonstrate the ability of a multifaceted N,N′-disubstituted urea to selectively recognize fluoride anion (F−) among other halides. This additional function is now added to its already reported organocatalytic and organogelator properties. The signaling mechanism relies on the formation of a charge-transfer (CT) complex between the urea-based sensor and F¯ in the ground state with a high association constant as demonstrated by absorption and fluorescence spectroscopy. The nature of the hydrogen bonding interaction between the sensor and F¯ was established by 1H-NMR studies and theoretical calculations. Moreover, the recovery of the sensor was achieved by addition of methanol.
Psychometric Validation of the Taiwanese Version of the Job Satisfaction of Persons with Disabilities Scale in a Sample of Individuals with Poliomyelitis

Objective: To evaluate the measurement structure of the Taiwanese Version of the Job Satisfaction of Persons with Disabilities Scale (JSPDS). Design: A quantitative descriptive research design using exploratory factor analysis (EFA). Participants: One hundred and thirty-two gainfully employed individuals from Taiwan with poliomyelitis participated in this study. Results: EFA result indicated a three-factor structure accounting for 54.1 per cent of the total variance. The internal consistency reliability coefficients for the integrated work environment, job quality, and alienation factors were 0.91, 0.77, and 0.59, respectively. Only the integrated work environment and job quality factors showed positive correlations with life satisfaction. People with higher educational attainment also reported higher levels of job satisfaction than people with lower educational attainment. Conclusion: The three-factor measurement structure of the JSPDS appears to be parsimonious, psychologically meaningful, and interpretable, and can be used to improve the comprehensiveness of vocational rehabilitation outcome evaluation.
Effects of Informal Caregivers' Health on Care Recipients

Informal care is increasingly important in countries undergoing population aging. Previous research has discussed how the long-term care system may affect the behaviors of informal caregivers but has paid not much attention to how changes in caregivers' circumstances, particularly their health, affect those receiving their care. Using the Japanese Study of Aging and Retirement, we empirically examine how caregivers' health condition may affect the elderly parents receiving their care. We find empirical evidence that declining caregivers' health adversely affects care recipients' health. We see such links between informal caregivers and their in-laws, demonstrating that these effects go beyond genetic influences.
Sirtuin modulators control reactive gliosis in an in vitro model of Alzheimer’s disease

Among neurodegenerative disorders, Alzheimer’s disease (AD) represents the most common cause of dementia in the elderly. Several genetic and environmental factors have been identified; however, aging represents the most important risk factor in the development of AD. To date, no effective treatments to prevent or slow this dementia are available. Sirtuins (SIRTs) are a family of NAD+-dependent enzymes, implicated in the control of a variety of biological processes that have the potential to modulate neurodegeneration. Here we tested the hypothesis that activation of SIRT1 or inhibition of SIRT2 would prevent reactive gliosis which is considered one of the most important hallmark of AD. Primary rat astrocytes were activated with beta amyloid 1-42 (Aβ 1-42) and treated with resveratrol (RSV) or AGK-2, a SIRT1 activator and a SIRT2-selective inhibitor, respectively. Results showed that both RSV and AGK-2 were able to reduce astrocyte activation as well as the production of pro-inflammatory mediators. These data disclose novel findings about the therapeutic potential of SIRT modulators, and suggest novel strategies for AD treatment.
Engineering of 2,3-Butanediol Dehydrogenase To Reduce Acetoin Formation by Glycerol-Overproducing, Low-Alcohol Saccharomyces cerevisiae

ABSTRACT Engineered Saccharomyces cerevisiae strains overexpressing GPD1, which codes for glycerol-3-phosphate dehydrogenase, and lacking the acetaldehyde dehydrogenase Ald6 display large-scale diversion of the carbon flux from ethanol toward glycerol without accumulating acetate. Although GPD1 ald6 strains have great potential for reducing the ethanol contents in wines, one major side effect is the accumulation of acetoin, having a negative sensory impact on wine. Acetoin is reduced to 2,3-butanediol by the NADH-dependent 2,3-butanediol dehydrogenase Bdh1. In order to investigate the influence of potential factors limiting this reaction, we overexpressed BDH1, coding for native NADH-dependent Bdh1, and the engineered gene BDH1221,222,223, coding for an NADPH-dependent Bdh1 enzyme with the amino acid changes 221 EIA 223 to 221 SRS 223, in a glycerol-overproducing wine yeast. We have shown that both the amount of Bdh1 and the NADH availability limit the 2,3-butanediol dehydrogenase reaction. During wine fermentation, however, the major limiting factor was the level of synthesis of Bdh1. Consistent with this finding, the overproduction of native or engineered Bdh1 made it possible to redirect 85 to 90% of the accumulated acetoin into 2,3-butanediol, a compound with neutral sensory characteristics. In addition, the production of diacetyl, a compound causing off-flavor in alcoholic beverages, whose production is increased in glycerol-overproducing yeast cells, was decreased by half. The production of higher alcohols and esters, which was slightly decreased or unchanged in GPD1 ald6 cells compared to that in the control cells, was not further modified in BDH1 cells. Overall, rerouting carbons toward glycerol and 2,3-butanediol represents a new milestone in the engineering of a low-alcohol yeast with desirable organoleptic features, permitting the decrease of the ethanol contents in wines by up to 3°.
Distance-Sensitive Bloom Filters

A Bloom filter is a space-efficient data structure that answers set membership queries with some chance of a false positive. We introduce the problem of designing generalizations of Bloom filters designed to answer queries of the form, "Is x close to an element of S? " where closeness is measured under a suitable metric. Such a data structure would have several natural applications in networking and database applications. We demonstrate how appropriate data structures can be designed using locality-sensitive hash functions as a building block, and we specifically analyze the performance of a natural scheme under the Hamming metric.