Miracle-dz/UniFAR-FTUs huggingface dataset:
Central Hypersensitivity in Chronic Pain After Whiplash Injury

ObjectiveThe mechanisms underlying chronic pain after whiplash injury are usually unclear. Injuries may cause sensitization of spinal cord neurons in animals (central hypersensitivity), which results in increased responsiveness to peripheral stimuli. In humans, the responsiveness of the central nervous system to peripheral stimulation may be explored by applying sensory tests to healthy tissues. The hypotheses of this study were: (1) chronic whiplash pain is associated with central hypersensitivity; (2) central hypersensitivity is maintained by nociception arising from the painful or tender muscles in the neck. DesignComparison of patients with healthy controls. SettingPain clinic and laboratory for pain research, university hospital. PatientsFourteen patients with chronic neck pain after whiplash injury (car accident) and 14 healthy volunteers. Outcome MeasuresPain thresholds to: single electrical stimulus (intramuscular), repeated electrical stimulation (intramuscular and transcutaneous), and heat (transcutaneous). Each threshold was measured at neck and lower limb, before and after local anesthesia of the painful and tender muscles of the neck. ResultsThe whiplash group had significantly lower pain thresholds for all tests, except heat, at both neck and lower limb. Local anesthesia of the painful and tender points affected neither intensity of neck pain nor pain thresholds. ConclusionsThe authors found a hypersensitivity to peripheral stimulation in whiplash patients. Hypersensitivity was observed after cutaneous and muscular stimulation, at both neck and lower limb. Because hypersensitivity was observed in healthy tissues, it resulted from alterations in the central processing of sensory stimuli (central hypersensitivity). Central hypersensitivity was not dependent on a nociceptive input arising from the painful and tender muscles.
Managing Metadata Variability within a Hierarchy of Annotation Schemas

The paper describes the theoretical basis of the ALPE1 model, a hierarchy of annotation formats used to guide the automatic computation of processing flows capable of performing complex linguistic processing tasks. The hierarchy is comprised of a core, which is a direct acyclic graph whose nodes represent XML annotation formats, and a halo which contains additional annotation formats. The core hierarchy also serves as a standardization hub for annotated documents. The focus of the paper is the description of the new additions to the model, allowing the integration and usage of non-XML formats in processing flows and new equivalence relations between XML formats. This type of hierarchy is implemented in the ALPE system, which is also briefly described in the paper.
Endosome fusion induced by diphtheria toxin translocation domain

Endosomal cargo travels through a dynamic vesicle network en route to degradation by lysosomes or recycling through the Golgi apparatus back to the cell surface. Rab5 is a key determinant of the early endosomes by organizing effector proteins in specific subdomains and mediating early endosome fusion. We find that early endosome morphogenesis and maturation is disrupted by diphtheria toxin (DT). Rab5 bound endosomes increase in size and in Rab5 content due to luminal toxin exposure, whereas Rab7 positive endosomes are not detectably altered. These changes appear to be caused by an activity of the toxin entry domain (T domain) as mutations inactivating either the receptor binding (CRM107) or ADP-ribosyl transferase (CRM197) activities do not inhibit the effect of DT on endosome morphogenesis. In contrast, mutations in the T domain or diminishing the endosomal pH gradient, which prevents T domain membrane insertion, inhibit these endosome changes. The change in size appears to be due to changing the early endosome fission-fusion equilibrium. The Rab5 membrane exchange rate, assessed with photoactivatable GFP-Rab5, decreases in the presence of DT. These changes to endosomes may reflect activities of the T domain that mediate toxin entry to the cytosol. The nontoxic mutant DT, CRM197, yields a new tool to manipulate endosome dynamics in living cells.
The effect of executive function on stress, depression, anxiety, and quality of life in multiple sclerosis

The experience of cognitive deficits and emotional dysfunction are prevalent in people with multiple sclerosis (PwMS), although research examining their interaction has provided inconsistent findings. The current study examined the ability of executive function to predict psychosocial adjustment in PwMS. One hundred and seven PwMS underwent cognitive assessment and completed measures of stress, depression, anxiety, and quality of life (QoL). There was limited support for a relationship. There was no relationship between objective cognitive tasks and state or trait anxiety, mental health QoL, overall QoL, or stress frequency. The only relationship with depression was found when the Beck Depression Inventory Fast-Screen was used, with a task of planning when the timing element was removed. A measure of error rates on a task of cognitive flexibility predicted physical health QoL, and severity, but not frequency, of stress was predicted by a task of working memory. The results of this study highlight the need for further research into the relationship between cognitive deficits and psychosocial adjustment because of the conflicting findings between studies and call for a common measurement framework for future investigation.
Kto zasługuje na pomoc? Poparcie dla wybranych inicjatyw prospołecznych wśród studentów uczelni warszawskich

The article presents a study concerning the attitudes towards selected prosocial initiatives among the students of various universities in Warsaw in perspective of Melvin Lerner’s just-world fallacy and Roland Inglehart’s postmaterialism theory. The results of the study show that the responsibility for one’s own situation decreases the willingness to support the person in need. The support for proecological initiatives turned out to be low.
Dynameomics: Large‐scale assessment of native protein flexibility

Structure is only the first step in understanding the interactions and functions of proteins. In this paper, we explore the flexibility of proteins across a broad database of over 250 solvated protein molecular dynamics simulations in water for an aggregate simulation time of ∼6 μs. These simulations are from our Dynameomics project, and these proteins represent approximately 75% of all known protein structures. We employ principal component analysis of the atomic coordinates over time to determine the primary axis and magnitude of the flexibility of each atom in a simulation. This technique gives us both a database of flexibility for many protein fold families and a compact visual representation of a particular protein's native‐state conformational space, neither of which are available using experimental methods alone. These tools allow us to better understand the nature of protein motion and to describe its relationship to other structural and dynamical characteristics. In addition to reporting general properties of protein flexibility and detailing many dynamic motifs, we characterize the relationship between protein native‐state flexibility and early events in thermal unfolding and show that flexibility predicts how a protein will begin to unfold. We provide evidence that fold families have conserved flexibility patterns, and family members who deviate from the conserved patterns have very low sequence identity. Finally, we examine novel aspects of highly inflexible loops that are as important to structural integrity as conventional secondary structure. These loops, which are difficult if not impossible to locate without dynamic data, may constitute new structural motifs.
iWorlds: Generating artificial control systems for simulated humans using virtual worlds and intelligent environments

This paper highlights research into using virtual worlds, intelligent environments and mixed reality to create artificial control systems for simulated humans. Following a brief explanation of this project, the beneficial contribution provided by virtual worlds, intelligent environments and mixed reality systems is outlined. Throughout this project a series of experimental iWorlds, (virtual and mixed reality intelligent environments) have been used to profile the actions and decisions of humans to generate sets of realistic behaviours and test the project research hypothesis. These worlds consist of a mixed-reality household experiment plus two supporting game-like behaviour experiments, namely ‘Bar-World’ and ‘Battleships’ which were designed to explore and reinforce aspects of the underlying theory. As a core part of this work a description of a new profile generation mechanism is presented, which comprises a genetic programming mechanism that blends real user behaviour data to produce varied artificial profiles for non-player computer characters. In support of this a set of experimental results are presented that reveal the new artificial intelligence mechanism does indeed advance the project aim to create realistic simulated humans. A discussion is included that describes the potential benefits that could be gained by incorporating these methodologies into computer games and professional intelligent environment development systems.
Specificity of the polycation-stimulated (type-2A) and ATP,Mg-dependent (type-1) protein phosphatases toward substrates phosphorylated by P34cdc2 kinase.

p34cdc2 kinase, a critical regulator of the cell cycle, has been shown to recognize the consensus sequence S/TP in proteins such as histone H1, the retinoblastoma gene product RB and the carboxyl-terminal domain of eukaryotic RNA polymerase II. Using phosphorylated synthetic peptides, representing the p34cdc2 phosphorylation sites in these proteins and histone H1 protein as substrates, we investigated the substrate specificity of the different oligomeric forms of the polycation-stimulated (PCS/type-2A) protein phosphatase and the active catalytic subunit of the ATP,Mg-dependent (AMDc/type 1) protein phosphatase. The results show that the oligomeric structure of the PCS phosphatases is an important determinant for efficient dephosphorylation. The trimeric PCSH1 and PCSM phosphatases are about 10-20-fold-better histone H1 phosphatases than the dimeric PCSH2 and PCSL phosphatases and about 100-fold better than the catalytic subunit (PCSC), suggesting a regulatory role for the 72-kDa, 65-kDa and 55-kDa subunits. The RB peptide = INGS(P)PRT(P)PRRGQNR, is preferred over phosphorylase a (8-fold) by the PCSH1 phosphatase and is about a 40-fold and 95-fold-better substrate for the PCSH1 phosphatase than for the PCSM and PCSL phosphatases, respectively. The primary structure surrounding the S/T(P)P motif, by itself a strong negative determinant for dephosphorylation, can harbour positive features which relieve the constraint imposed by the carboxyl-terminal proline. Thus, the RB peptide INGS(P)PRT(P)PRRGQNR, in which the T(P)P configuration is preferred over the S(P)P sequence, is an extremely good and specific substrate for the PCSH1 phosphatase (Km = 10 microM, Vmax = 3882 nmol.min-1.mg-1). The AMDC phosphatase is a poor phosphatase for all the phosphopeptides tested, unless Mn2+ is added. Its histone H1 phosphatase activity is much less sensitive than its phosphorylase a and phosphopeptide phosphatase activity to inhibition by the modulator or inhibitor-1. The results strongly suggest a role for the trimeric PCSH1 phosphatase in reversing the p34cdc2 phosphorylations.
“We beat the path by walking”

This paper considers the collective knowledge about housing design and construction that was developed over 30 years by the Indian Alliance of the Society for the Promotion of Area Resource Centres (SPARC), Mahila Milan and the National Slum Dwellers’ Federation (NSDF) in its pursuit of secure shelter for the pavement dwellers in Mumbai, the most vulnerable people in the city. It traces the learning and innovations developed by these women pavement dwellers, mostly illiterate, in this one specific aspect of their much larger joint journey towards a safe, secure home in the city, something that seemed almost inconceivable when they began. The deeply political aspects of this larger journey are only briefly touched on here, allowing space to describe the hands-on learning about planning, design and building that was also essential in this process. The paper is one of an ongoing series tracing the work of this Indian partnership since 1986, examining the critical milestones that have emerged from discussion, reflections and collective exploration.
Improved Mitochondrial and Methylglyoxal‐Related Metabolisms Support Hyperproliferation Induced by 50 Hz Magnetic Field in Neuroblastoma Cells

Extremely low frequency magnetic fields (ELF‐MF) are common environmental agents that are suspected to promote later stages of tumorigenesis, especially in brain‐derived malignancies. Even though ELF magnetic fields have been previously linked to increased proliferation in neuroblastoma cells, no previous work has studied whether ELF‐MF exposure may change key biomolecular features, such as anti‐glycative defence and energy re‐programming, both of which are currently considered as crucial factors involved in the phenotype and progression of many malignancies. Our study investigated whether the hyperproliferation that is induced in SH‐SY5Y human neuroblastoma cells by a 50 Hz, 1 mT ELF magnetic field is supported by an improved defense towards methylglyoxal (MG), which is an endogenous cancer‐static and glycating α‐oxoaldehyde, and by rewiring of energy metabolism. Our findings show that not only the ELF magnetic field interfered with the biology of neuron‐derived malignant cells, by de‐differentiating further the cellular phenotype and by increasing the proliferative activity, but also triggered cytoprotective mechanisms through the enhancement of the defense against MG, along with a more efficient management of metabolic energy, presumably to support the rapid cell outgrowth. Intriguingly, we also revealed that the MF‐induced bioeffects took place after an initial imbalance of the cellular homeostasis, which most likely created a transient unstable milieu. The biochemical pathways and molecular targets revealed in this research could be exploited for future approaches aimed at limiting or suppressing the deleterious effects of ELF magnetic fields. J. Cell. Physiol. 231: 2014–2025, 2016. © 2016 Wiley Periodicals, Inc.
Capture of homotopy classes with probabilistic road map

Feasibility tests in virtual reality for nuclear power plant maintenance or dismantling operations are a source of problems for motion planning because finding a way in a cluttered environment is not easy for the bulky loads, mobile devices and robots used in such operations. Standard probabilistic roadmap methods (PRM) have been successfully used to answer such feasibility problems. These methods provide, at the most a single solution but do not provide a complete overview of the possible motions which have to be evaluated in a complete engineering task. We focus here on the open question of building probabilistic roadmaps which can provide an exhaustive list of all the solutions which can not be distorted from one to another while staying collision free. We call such roadmaps homotopy preserving probabilistic roadmap (HPPR). We propose a new algorithm for creating HPPR.
Foundations of aggregation and synchronization in distributed systems

A distributed system consists of several autonomous devices that are capable of performing certain (computational) tasks and that have a means to communicate with each other. A computer network system, such as the Internet, is a prototypical example of a distributed system. While a distributed system has many advantages over a single computational unit, e.g., the combined computational power of all entities of a distributed system typically exceeds the power of any single computational device considerably, the decentralized nature of distributed systems also poses significant challenges. In this thesis, two fundamental problems of distributed systems are studied. The first part of this thesis focuses on the problem of computing global functions that depend on the state of all devices in the system. Since each device stores only a small part of the state of the entire system, interaction between the devices is required in order compute such functions. If the bandwidth of the communication channels is bounded, it may not be an efficient solution to simply encode the state of each entity and forward this information to a single participant in the system, which could then compute the result of the function locally. Instead, the devices may attempt to aggregate the data received from other devices in the system and use this information to compute partial solutions of the global function. Such aggregation techniques may greatly reduce the bandwidth consumption when computing global functions in a distributed manner. The goal is to gain a deeper understanding of the complexity of computing global functions using in-network aggregation. In the second part of this thesis, we consider the problem that several distributed applications and protocols require that all computational devices maintain a common notion of time, but the devices do not have access to a global timer. If each device possesses its own clock, the different clock rates of these clocks necessitate the use of a clock synchronization algorithm whose purpose is to compensate for the clock drifts by exchanging timing information and adjusting the clock values according to the received information. Synchronizing clocks is a challenging task mainly due to the uncontrollable and potentially varying message delays, which render it impossible for the devices to determine how accurate the timing information is that they receive from other devices. The objective is thus to analyze the feasible degree of synchronization, which not only depends on the message delays and the clock drift rates, but also on other parameters such as the frequency of communication.
Introduction to monoclonal antibodies.

Monoclonal antibodies (mAbs) are a group of antibodies produced by identical clones of B lymphocytes against a particular antigen. mAbs are identical in several properties such as protein sequence, antigen-binding site region, binding affinity for their targets, and identical downstream functional effects. These characteristics of mAbs highlight their differences with the polyclonal antibodies which have heterogenous activities and recognize different epitopes on an antigen. Murine mAbs was the first generation of mAbs developed by hybridoma technology however, because of their murine origin, they can trigger the anti-mouse antibody response in the host which could accelerate mAb clearance and undesirable allergic reactions upon repeated administration. This issue was resolved by developing engineering methods toward producing less immunologic chimeric or humanized antibodies. mAbs applications have become a novel way of targeting antigens in a wide variety of diseases such as autoimmunity, malignancies, and asthma. In addition, high specificity and high affinity binding properties of mAbs make them effective biological reagents in immunodiagnostic assays. They can be used in diagnosis of infectious diseases and detection of certain antigens or in serological assessments for detection of antibodies against a certain antigen. This chapter summarizes the general properties of mAbs, their production processes, and their important diagnostic and therapeutic applications.
Ambiguity Resolution and Evolution of Word Order

We examine the lexical and syntactic ambiguities from an evolutionary perspective of sequential and combinatorial relationships in the prefrontal brain and the evolution of word order as resolution of these ambiguities. We find that there is temporal ambiguity after the verb in SVO sentences, which causes the activation of the inferior frontal gyrus, while there is no activation in SOV sentences. This implicates the earliest human language evolved the SOV word order. We then demonstrate that the postnominal relative clause evolved from the paratactic clause with a non-relativized shared NP. Embedding took place by pulling the head noun to a position before the relative clause to avoid perceptual ambiguity arising from center-embedding which demands too much of our short-term memory. This also produced the word order change from OV to VO. Language evolves procedures to avoid lexical and syntactic ambiguities. It is not specifically lexical or syntactic, but a general cognitive tendency to attempt to resolve ambiguity, or to avoid the burden on working memory in the left inferior frontal gyrus.
The music of speech: electrophysiological approach

This experiment was aimed at studying the changes in the brain electrical activity associated with some aspects of prosodic processing and at comparing the results with those obtained for the melodic processing of short musical phrases, by manipulating the F0 of the final word/note. Both musicians and non-musicians were presented with French sentences, ending with prosodically congruous, weakly or strongly incongruous words, and with short musical phrases ending with congruous, weakly or strongly incongruous notes. Both Reaction Times (RTs) and Evoked Related Potentials (ERPs) were recorded. In both the prosodic and melodic conditions, RTs were shorter for strong incongruities than for weak incongruities and congruous completions. ERP recorded in both conditions showed that large positive components (P600s) were associated with incongruous stimuli. Moreover, in both cases, the amplitude of the P600 component was larger, and its latency was shorter, for the strong than for the weak incongruities. Interestingly, an early negative component (N150) develop in response to strong incongruities. For the musicians, this N150 component is clearly localized over right temporo-frontal electrodes, specifically in the melodic condition. For non-musicians, the N150 is more broadly distributed across scalp sites. These results point to strong similarities in the processing of prosodic and melodic incongruities, and a general cognitive process may be at play in both cases. However, they also point to some early differences which may reflect the effects of musical expertise.
A new approach to assessing observable attributes of the tax compliance behaviors of small business owners

Measurement of individual behavior and attitudes are often based on the recall of respondents of actions that occurred in the past. These responses can often be biased due to incomplete or incorrect recall, or deliberate obfuscation by respondents. This paper discusses a new approach to data collection, through the use of a virtual reality environment, that allows researchers to collect data on respondents’ tax decisions, at the moment they make them, through a simulation of a representative business year and subsequent tax preparation process. Disparate data can be collected and analyzed, providing researchers with greater reliability and validity in their research. A discussion of this data and potential implications on tax research is included.