Miracle-dz/UniFAR-FTUs huggingface dataset:
The Conformationally Dynamic C Helix of the RIα Subunit of Protein Kinase A Mediates Isoform-specific Domain Reorganization upon C Subunit Binding*

Different isoforms of the full-length protein kinase A (PKA) regulatory subunit homodimer (R2) and the catalytic (C) subunit-bound holoenzyme (R2C2) have very different global structures despite similar molecular weights and domain organization within their primary sequences. To date, it has been the linker sequence between the R subunit dimerization/docking domain and cAMP-binding domain A that has been implicated in modulating domain interactions to give rise to these differences in global structure. The small angle solution scattering data presented here for three different isoforms of PKA heterodimer (ΔR-C) complexes reveal a role for another conformationally dynamic sequence in modulating inter-subunit and domain interactions, the C helix that connects the cAMP-binding domains A and B of the R subunit. The ΔR-C heterodimer complexes studied here were each formed with a monomeric N-terminal deletion mutant of the R subunit (ΔR) that contains the inhibitor sequence and both cAMP-binding domains. The scattering data show that type IIα and type IIβ ΔR-C heterodimers are relatively compact and globular, with the C subunit contacting the inhibitor sequence and both cAMP-binding domains. In contrast, the type Iα heterodimer is significantly more extended, with the C subunit interacting with the inhibitor sequence and cAMP-binding domain A, whereas domain B extends out such that its surface is almost completely solvent exposed. These data implicate the C helix of RIα in modulating isoform-specific interdomain communication in the PKA holoenzyme, adding another layer of structural complexity to our understanding of signaling dynamics in this multisubunit, multidomain protein kinase.
The choice between current and retrospective evaluations of pain

Daniel Kahneman and his colleagues have made an interesting discovery about people's preferences. In several experiments, subjects underwent two separate ordeals of pain, identical except that one ended with an added amount of diminishing pain. When asked to evaluate these episodes after experiencing both, subjects generally preferred the longer episode--even though it had a greater objective quantity of pain. These data raise an ethical question about whether to respect such preferences when acting on another's behalf. John Broome thinks that it is wrong to add extra pain in order to satisfy a person's preference for a better ending. His explanation for this intuition is that pain is intrinsically bad. I argue against this explanation, and raise several doubts about the moral intuition Broome endorses. In doing so, I offer alternate interpretations of Kahneman's data, and show that these each yield different values which are relevant to the ethical question .
Human &bgr;-Defensin 2 Is a Novel Opener of Ca2+-Activated Potassium Channels and Induces Vasodilation and Hypotension in Monkeys

Human &bgr;-defensin 2 (HBD2) is a cysteine-rich cationic antimicrobial peptide known for its important role in innate immune system. Intensive studies have demonstrated its antimicrobial and chemotactic activities in vitro. In this study, ELISA analysis showed that HBD2 was significantly downregulated in sera of patients with hypertension. It relaxed vessel smooth muscle by acting on the major regulatory pathways, contributing to vessel smooth muscle contraction. Electrophysiology analysis indicated that HBD2 acted as an opener of large-conductance Ca2+-activated potassium (BKCa)-mSlo+h&bgr;1 channels and increased BKCa currents. Mutation analysis revealed that HBD2 activated BKCa-mSlo+h&bgr;1 channels via interacting with Leu41 and Gln43 of &bgr;1-loop. In vivo experiments suggested that HBD2 at 4× to 6× of physiological concentration exerted hypotensive effect in monkeys significantly, whereas the selective blocker of BKCa channels, Paxilline, inhibited the effect. HBD2 is the first peptide opener of BKCa-mSlo+h&bgr;1 channels. It may be a novel regulator of blood pressure and provides a new therapeutic target for the treatment of hypertension. The HBD2 blockade of the BKCa channels may represent a new type of cross-talk between immune and cardiovascular systems.
Mass-Vaccination Programmes and the Value of Respect for Autonomy

Respect for autonomy is problematic in relation to public health programmes such as vaccination, as the success of such programmes depends on widespread compliance. European countries have different policies for dealing with objectors to vaccination programmes. In some countries compliance is compulsory, while in others objectors are exempted or allowed to enter the programme under specific conditions. In this paper I argue that the objectors should not be treated as a homogenous group as is done in the above-mentioned policies. Objectors have different arguments for not participating in vaccination programmes. Considering the value of respect for autonomy, some but not all of these arguments need to be accommodated by authorities. The concept of 'narrative autonomy' provides criteria to distinguish between tenable and untenable claims to the right to refuse vaccination. Narrative autonomy understands autonomy as essentially linked to identity, as this provides the moral framework with which we assess our first-order preferences. The above-mentioned concept of autonomy is derived from the concept of narrative identity as described by Marya Schechtman. She suggests that the application of the Articulation Constraint and the Reality Constraint enables us to establish the validity of personal narratives. Additionally, form and content features of identity, as proposed by Anthony Laden, will be used as criteria to establish the compatibility of the defectors' arguments with shared scientific and political values. Such compatibility is essential to accommodate respect for autonomy in the context of public health.
Micro- and Macro-Justicein the Allocation of Resources between in-Group and Out-Group Members

Respondents from Turkey and the United States solved micro- and macro-justice dilemmas requiring them to allocate scholarships and governance board memberships. Recipients were either groups or individuals who were members of respondents’in-groups or out-groups. Turkish respondents showed a stronger preference than U.S. respondents for macro deservingness only when recipients were from their in-groups and, in general, preferred in-group over out-group recipients. Both U.S. and Turkish respondents used macro principles more with group versus individual recipients.
The unified theory of repression

Repression has become an empirical fact that is at once obvious and problematic. Fragmented clinical and laboratory traditions and disputed terminology have resulted in a Babel of misunderstandings in which false distinctions are imposed (e.g., between repression and suppression) and necessary distinctions not drawn (e.g., between the mechanism and the use to which it is put, defense being just one). “Repression” was introduced by Herbart to designate the (nondefensive) inhibition of ideas by other ideas in their struggle for consciousness. Freud adapted repression to the defensive inhibition of “unbearable” mental contents. Substantial experimental literatures on attentional biases, thought avoidance, interference, and intentional forgetting exist, the oldest prototype being the work of Ebbinghaus, who showed that intentional avoidance of memories results in their progressive forgetting over time. It has now become clear, as clinicians had claimed, that the inaccessible materials are often available and emerge indirectly (e.g., procedurally, implicitly). It is also now established that the Ebbinghaus retention function can be partly reversed, with resulting increases of conscious memory over time (hypermnesia). Freud's clinical experience revealed early on that exclusion from consciousness was effected not just by simple repression (inhibition) but also by a variety of distorting techniques, some deployed to degrade latent contents (denial), all eventually subsumed under the rubric of defense mechanisms (“repression in the widest sense”). Freudian and Bartlettian distortions are essentially the same, even in name, except for motive (cognitive vs. emotional), and experimentally induced false memories and other “memory illusions” are laboratory analogs of self-induced distortions.
THE CONTRIBUTION OF CLOSED LOOP TRACKING CONTROL OF MOTION PLATFORM ON LATERALLY INDUCED POSTURAL INSTABILITY OF THE DRIVERS AT SAAM DYNAMIC SIMULATOR

This paper explains the effect of a motion platform closed loop control comparing to the static condition for driving simulators on postural instability. The postural instabilities of the participants (N=18, 15 male and 3 female subjects) were measured as lateral displacements of subject body centre of pressure (YCP ) just before and after each driving session via a balance platform. After having completed the experiments, the two-tailed Mann-Whitney U test was applied to analyze the objective data for merely the post-exposure cases. The objective data analysis revealed that the YCP for the dynamic case indicated a significant lower value than the static situation (U(18), p < 0,0001). It can be concluded that the closed loop tracking control of the hexapod platform of the driving simulator (dynamic platform condition) decreased significantly the lateral postural stability compared to the static operation condition. However the two-tailed Mann-Whitney U test showed that no significant difference was obtained between the two conditions in terms of psychophysical perception.
Developing Teachers' Classroom Interactions: A Description of a Video Review Process for Early Childhood Education Students

This article describes a video review process for providing feedback to students and documents students' teaching practices using the CLASS in a practicum course and student teaching. Students videotaped themselves in their field-based settings and then met with the course instructors and classmates in small groups to review strengths and challenges of their teaching using the CLASS framework of teacher–child interactions. These videos were also coded by trained CLASS observers across 10 dimensions in the areas of emotional support, classroom organization, and instructional support. Results from preservice teachers' CLASS ratings indicate a pattern similar to national data sets using the CLASS, higher scores in the emotional support and classroom organization domains than in the domain of instructional support. Also, findings from the current study revealed that CLASS scores declined from students' practicum placement to the end of student teaching in the domain of emotional support and specifically in the dimensions of regard for student perspectives and behavior management. The process of using videos for providing feedback in field-based experiences is discussed as well as implications for teacher development in light of students' CLASS scores and changes in CLASS scores.
Relationship between apoE4 allele and excitatory amino acid levels after traumatic brain injury

ObjectiveApolipoprotein E isoform (E4) has been posited to affect outcomes after central nervous system injury. This project sought to determine the relationship between the apoE4 allele and the recovery of amino acid neurotransmitters (aspartate, glutamate, and lactate/pyruvate ratio [L/P]) following a traumatic brain injury (TBI) after controlling for patient characteristics. DesignThis prospective clinical study examined neurotransmitters and L/P within the cerebrospinal fluid and compared the trends by apoE genotypes. SettingAdults with TBI were recruited from a neurotrauma intensive care unit within a trauma I university medical center. PatientsNinety-one patients were enrolled into the study after a severe TBI (Glasgow Coma Scale [GCS] score, ≤8). Cerebrospinal fluid was serially sampled from a ventriculostomy every 4 hrs for the first 24 hrs and every 6 hrs for 25–120 hrs after injury. Measurements and Main ResultsHierarchical linear modeling analyses were used to compare the change of glutamate, aspartate, and L/P over time by the presence or absence of the apoE4 allele, with GCS score, sex, race, and therapeutic hypothermias included as covariates. There was a significant apoE4 allele group effect on both the linear and quadratic slopes in aspartate. In glutamate, the rate of change in glutamate was statistically related to GCS score. There was no significant difference in the glutamate response over time by the presence of the apoE4 allele. There was a significant difference in the change in L/P across time, with faster recovery when the apoE4 allele was absent. ConclusionsRecovery of aspartate and L/P differed depending on the presence of the apoE4 allele. Patients with the allele had significant increased and sustained levels of aspartate and L/P after TBI. Changes in glutamate were related to severity of illness and were independent of the presence of the apoE4 allele.
apid identification of bacterial and fungal pathogens from positive blood ultures by MALDI-TOF MS

Sepsis is a syndrome characterized by a systemic inflammatory response due to severe infection. Early detection of causal agents and appropriate antimicrobial treatment reduce mortality. Conventional microbiological methods often do not provide time critical results for an optimal early management. We used an in-house protocol based on Tween 80 to process 109 positive blood cultures for bacteria and yeast identification by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and results were compared to standard reference or automated methods. MALDI-TOF MS correctly identified 91.7% of the isolates. Correct identification was obtained for 57/62 (91.9%) aerobic/facultative anaerobic Gram-positive isolates, 53 (85.5%) at species level, and 4 (6.4%) at the genus
Rapid Synthesis of Silver Nanowires

The presence of either copper(I) or copper(II) chloride in the polyol reduction of silver nitrate facilitates the production of silver nanowires. Silver nanowires have applications in many areas, including electronics and catalysis. These wires are produced quickly (in approximately one hour), with the synthesis being easily performed in disposable glass vials, using only pipettes to deliver reagents. Specifically, silver nitrate is reduced by ethylene glycol in the presence of poly(vinylpyrrolidone) (PVP) and copper(II) chloride. PVP acts as a stabilizing agent, while the copper chloride likely controls the rate of silver(I) reduction and initial seed formation. Our results indicate that both the copper and chloride ions are necessary to synthesize the wires; otherwise, ill-defined silver particles are formed. Scanning electron microscopy (SEM) has been used to characterize the wires.
Reply to Cohene

It is difficult to avoid accepting the nu11 hypothesis when the results of an appropriately designed test prove null. The present test seems theoretically appropriate, since it has long been accepted that obtaining reports on unattended material constitutes evidence for iconic storage and it has also been accepted that the integration of dot letters provides confirmation for the theory. Our experiments have combined these two approaches, showing that the predicted effect does not occur. It seems unlikely that the experiments are methodologically inappropriate since our results, where the conditions are comparable, closely resemble those of the critic. Cohene (1974) obtained little more than 30% accuracy for bigram integration at an interstimulus-interval of 0 sec. (corrected for item guessing), while Cohene and Bechtoldc (1975) only found 70% accuracy in what corresponds to our superimposed condition. It is true that the attentional demands of the task were high, but this problem is inherent in the basic claim that iconic storage provides access to a large reserve of unattended stimuli. As for the nature of the information to be integrated, one might wish to accept Campbell and Mewhort's (1980) partition of the icon into a feature buffer and a postcategorical character buffer, assigning dot storage to the feature buffer. However, as our experiment shows no excess storage of any kind, it seems that whatever features are held prove insufficient to generate any character surplus. Even a modified, postcategorical view of the icon finds no support. Since Haber (1983) has recently argued that an icon could have no practical utility, except perhaps to explain flashlight viewing or "reading in a lightning storm" (p. 16), it may now be advisable to omit iconic memory from our description of information processing.
High availability using virtualization

High availability has always been one of the main problems for a data center. Till now high availability was achieved by host per host redundancy, a highly expensive method in terms of hardware and human costs. A new approach to the problem can be offered by virtualization. Using virtualization, it is possible to achieve a redundancy system for all the services running on a data center. This new approach to high availability allows to share the running virtual machines over the servers up and running, by exploiting the features of the virtualization layer: start, stop and move virtual machines between physical hosts. The system (3RC) is based on a finite state machine with hysteresis, providing the possibility to restart each virtual machine over any physical host, or reinstall it from scratch. A complete infrastructure has been developed to install operating system and middleware in a few minutes. To virtualize the main servers of a data center, a new procedure has been developed to migrate physical to virtual hosts. The whole Grid data center SNS-PISA is running at the moment in virtual environment under the high availability system. As extension of the 3RC architecture, several storage solutions have been tested to store and centralize all the virtual disks, from NAS to SAN, to grant data safety and access from everywhere. Exploiting virtualization and ability to automatically reinstall a host, we provide a sort of host on-demand, where the action on a virtual machine is performed only when a disaster occurs.
Utilizing State-of-the-art Parsers to Diagnose Problems in Treebank Annotation for a Less Resourced Language

The recent success of statistical parsing methods has made treebanks become important resources for building good parsers. However, constructing highquality annotated treebanks is a challenging task. We utilized two publicly available parsers, Berkeley and MST parsers, for feedback on improving the quality of part-of-speech tagging for the Vietnamese Treebank. Analysis of the treebank and parsing errors revealed how problems with the Vietnamese Treebank influenced the parsing results and real difficulties of Vietnamese parsing that required further improvements to existing parsing technologies.
Women‐friendly HRM and organizational commitment: A study among women and men of organizations in Hong Kong

This study found that women-friendly policies are not prevalent in organizations in Hong Kong. To ascertain if organizations that are more women-friendly have more committed employees, working men and women in the territory were surveyed. Controlling for ‘national origin of organization’, the research results indicate that family- and work-related factors impact on both women's and men's organizational commitment. But women-friendly policies have a positive impact only on women—and only on their affective commitment, not on continuance commitment. The finding indicates that employees who are more likely to benefit directly from progressive policies that symbolize concern for them would become psychologically more attached to their organizations than those who perceive little value in the policies for their work lives.
‘We Are All Managers Now’; ‘We Always Were’: On the Development and Demise of Management

The existence of an identifiable group of people who are labelled ‘managers’ has been one of the most significant aspects of the organization of work and society for well over a century. This separation of managers from others has been questioned for some years by critical writers, not least because it ignores the many managerial activities performed by non‐managers both in and outside the workplace. This argument suggests that the development of the ‘special’ status of managers is a construction which requires explanation. Accepting this, three broad types of explanation are reviewed in the paper: technical, elite and political approaches. Notwithstanding these explanations, in recent years the logic – although not necessarily the actuality – of organizational change programmes, and especially of the concept of empowerment, has been suggestive of the ‘demise’ of management, most especially middle management. This demise has implied an erosion of the distinction between managers and managed. Now, organizational members are told that ‘we are all managers’, and the three approaches have various ways of explaining this, which are reviewed. Critics may reply that ‘we always were’, thus welcoming a more democratic notion of management, but this paper argues that such a reply reflects an inadequate, and potentially oppressive, understanding of management
Scientific literacy as collective praxis

In this article, we conceive of scientific literacy as a property of collective activity rather than individual minds. We think of knowing and learning science as situated in and distributed across social and material aspects of a setting. To support the proposed conception, we provide several detailed cases from our three-year multi-site ethnographic study of science in one community, featuring different types of citizens who walk a creek, interact during an environment-oriented open-house event, discuss water problems, collect data, and have different conceptions of human-environment relations. The case studies show that collectively, much more advanced forms of scientific literacy are produced than any individual (including scientists) could produce. Creating opportunities for scientific literacy to emerge from collective activity, irrespective of whether one or more participants know some basic scientific facts, presents challenges to science educators very different from teaching basic facts and skills to individuals.
Fuzzy Logic in Medicine and Bioinformatics

The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions) and in bioinformatics (comparison of genomes).
Why Reasons May Not Be Causes

: This paper considers Davidson's (1963) arguments for construing reasons as causes and attempts to show that he has failed to provide positive reasons for introducing causation into his analysis of rationalizing explanation. I consider various ways of spelling out his intuition that something is missing from explanation if we consider only the justificatory relation between reasons and action, and I argue that to the extent that there is anything missing, it should not be provided by construing reasons as causes. What is ostensibly missing, and what I think Davidson is after, is some kind of determinate relation between explanans and explanandum. I argue that this is too strong a requirement to place on rationalizing explanation.