Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal EEG/MEG source analysis based on a parametric noise covariance model

A method is described to incorporate the spatiotemporal noise covariance matrix into a spatiotemporal source analysis. The essential feature is that the estimation problem is split into two parts. First, a model is fitted to the observed noise covariance matrix. This model is a Kronecker product of a spatial and a temporal matrix. The spatial matrix models the spatial covariances by a function dependent on sensor distance. The temporal matrix models the temporal covariances as lag dependent. In the second part, sources are estimated given this noise model, which can be done very efficiently due to the Kronecker formulation. An application to real electroencephalogram (EEG) data shows that the noise model fits the data very well. Simulation results show that the resulting source estimates are more precise than those obtained from a standard analysis neglecting the noise covariance. In addition, the estimated standard errors of the source parameter estimates are far more precise than those obtained from a standard analysis. Finally, the source parameter standard errors are used to investigate the effects of temporal sampling. It is shown that increasing the sampling by a factor x, decreases the standard errors of all source parameters with the square root of x.
ERCC1 and XRCC1 as biomarkers for lung and head and neck cancer

Advanced stage non-small cell lung cancer and head and neck squamous cell carcinoma are both treated with DNA damaging agents including platinum-based compounds and radiation therapy. However, at least one quarter of all tumors are resistant or refractory to these genotoxic agents. Yet the agents are extremely toxic, leading to undesirable side effects with potentially no benefit. Alternative therapies exist, but currently there are no tools to predict whether the first-line genotoxic agents will work in any given patient. To maximize therapeutic success and limit unnecessary toxicity, emerging clinical trials aim to inform personalized treatments tailored to the biology of individual tumors. Worldwide, significant resources have been invested in identifying biomarkers for guiding the treatment of lung and head and neck cancer. DNA repair proteins of the nucleotide excision repair pathway (ERCC1) and of the base excision repair pathway (XRCC1), which are instrumental in clearing DNA damage caused by platinum drugs and radiation, have been extensively studied as potential biomarkers of clinical outcomes in lung and head and neck cancers. The results are complex and contradictory. Here we summarize the current status of single nucleotide polymorphisms, mRNA, and protein expression of ERCC1 and XRCC1 in relation to cancer risk and patient outcomes.
Longitudinal and cross-sectional analysis of atrophy in pharmacoresistant temporal lobe epilepsy

Background: Whether recurrent epileptic seizures induce brain damage is debated. Disease progression in epilepsy has been evaluated only in a few community-based studies involving patients with seizures well controlled by medication. These studies concluded that epilepsy does not inevitably lead to global cerebral damage. Objective: To track the progression of neocortical atrophy in pharmacoresistant temporal lobe epilepsy (TLE) using longitudinal and cross-sectional designs. Methods: Using a fully automated measure of cortical thickness on MRI, we studied a homogeneous sample of patients with pharmacoresistant TLE. In the longitudinal analysis (n = 18), fixed-effect models were used to quantify cortical atrophy over a mean interscan interval of 2.5 years (range = 7 to 90 months). In the cross-sectional analysis (n = 121), we correlated epilepsy duration and thickness. To dissociate normal aging from pathologic progression, we compared aging effects in TLE to healthy controls. Results: The longitudinal analysis mapped progression in ipsilateral temporopolar and central and contralateral orbitofrontal, insular, and angular regions. In patients with more than 14 years of disease, atrophy progressed more rapidly in frontocentral and parietal regions that in those with shorter duration. The cross-sectional study showed progressive atrophy in the mesial and superolateral frontal, and parietal cortices. Conclusions: Our combined cross-sectional and longitudinal analysis in patients with pharmacoresistant temporal lobe epilepsy demonstrated progressive neocortical atrophy over a mean interval of 2.5 years that is distinct from normal aging, likely representing seizure-induced damage. The cumulative character of atrophy underlies the importance of early surgical treatment in this group of patients.
Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution

Horizontal transfer (HT) is the transmission of genetic material between non‐mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non‐LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution.
The Decoherence of the Electron Spin and Meta-Stability of 13C Nuclear Spins in Diamond

Following the recent successful experimental manipulation of entangled 13C atoms on the surface of Diamond, we calculate the decoherence of the electron spin in Nitrogen Vacancy NV centers of Diamond via a nonperturbative treatment of the time-dependent Greens function of a Central-Spin model in order to identify the Replica Symmetry Breaking mechanism associated with intersystem mixing between the ms = 0 sublevel of the 3A2 and 1A1 states of the NV− centers, which we identify as mediated via the meta-stability of 13C nuclei bath processes in our calculations. Rather than the standard exciton-based calculation scheme used for quantum dots, we argue that a new scheme is needed to formally treat the Replica Symmetry Breaking of the 3A2 → 3E excitations of the NV− centers, which we define by extending the existing Generalized Master Equation formalism via the use of fractional time derivatives. Our calculations allow us to accurately quantify the dangerously irrelevant scaling associated with the Replica Symmetry Breaking and provide an explanation for the experimentally observed room temperature stability of Diamond for Quantum Computing applications.
Early detection of patients with poor risk diffuse large B-cell lymphoma

More than 60% of patients with diffuse large B-cell lymphoma (DLBCL) will be cured with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). However, the outcome following secondary therapies remains poor. Early identification of high-risk patients would allow alternative treatment strategies to be considered. Clinical prognostic factors, such as the International Prognostic Index remain useful, but can no longer identify patients with a very poor outcome. Identification of molecular prognostic markers will be required to improve risk stratification. A large number of molecular markers have been reported to be prognostic in patients with DLBCL treated with CHOP, and more recently with R-CHOP. These markers require further validation before clinical utility can be established. Continuous reassessment of clinical and molecular markers in the context of prospective clinical trials is necessary to ensure ongoing relevance.
Working Paper Series

This paper constructs a model of trade consequences of terrorism, where firms in trading nations face different costs arising from domestic and transnational terrorism. Using dyadic dataset in a gravity model, we test terrorism’s effects on overall trade, exports, and imports, while allowing for disaggregation by primary commodities and manufacturing goods. While terrorism has little or no influence on trade of primary products, terrorism reduces trade of manufactured goods. This novel finding pinpoints the avenue by which terrorism harms trade and suggests why previous studies that looked at all trade found modest impacts. Moreover, the detrimental effect of transnational terrorism on total manufactured trade, exports, and imports as well as on various classes of manufactured trade is substantially larger than that of domestic terrorism. Generally, this adverse impact is more pronounced for imports than for exports.
An efficient high-probability algorithm for Linear Bandits

For the linear bandit problem, we extend the analysis of algorithm CombEXP from [R. Combes, M. S. Talebi Mazraeh Shahi, A. Proutiere, and M. Lelarge. Combinatorial bandits revisited. In C. Cortes, N. D. Lawrence, D. D. Lee, M. Sugiyama, and R. Garnett, editors, Advances in Neural Information Processing Systems 28, pages 2116--2124. Curran Associates, Inc., 2015. URL this http URL] to the high-probability case against adaptive adversaries, allowing actions to come from an arbitrary polytope. We prove a high-probability regret of \(O(T^{2/3})\) for time horizon \(T\). While this bound is weaker than the optimal \(O(\sqrt{T})\) bound achieved by GeometricHedge in [P. L. Bartlett, V. Dani, T. Hayes, S. Kakade, A. Rakhlin, and A. Tewari. High-probability regret bounds for bandit online linear optimization. In 21th Annual Conference on Learning Theory (COLT 2008), July 2008. this http URL], CombEXP is computationally efficient, requiring only an efficient linear optimization oracle over the convex hull of the actions.
Chronic Exercise Increases Plasma Brain-Derived Neurotrophic Factor Levels, Pancreatic Islet Size, and Insulin Tolerance in a TrkB-Dependent Manner

Background Physical exercise improves glucose metabolism and insulin sensitivity. Brain-derived neurotrophic factor (BDNF) enhances insulin activity in diabetic rodents. Because physical exercise modifies BDNF production, this study aimed to investigate the effects of chronic exercise on plasma BDNF levels and the possible effects on insulin tolerance modification in healthy rats. Methods Wistar rats were divided into five groups: control (sedentary, C); moderate- intensity training (MIT); MIT plus K252A TrkB blocker (MITK); high-intensity training (HIT); and HIT plus K252a (HITK). Training comprised 8 weeks of treadmill running. Plasma BDNF levels (ELISA assay), glucose tolerance, insulin tolerance, and immunohistochemistry for insulin and the pancreatic islet area were evaluated in all groups. In addition, Bdnf mRNA expression in the skeletal muscle was measured. Principal Findings Chronic treadmill exercise significantly increased plasma BDNF levels and insulin tolerance, and both effects were attenuated by TrkB blocking. In the MIT and HIT groups, a significant TrkB-dependent pancreatic islet enlargement was observed. MIT rats exhibited increased liver glycogen levels following insulin administration in a TrkB-independent manner. Conclusions/Significance Chronic physical exercise exerted remarkable effects on insulin regulation by inducing significant increases in the pancreatic islet size and insulin sensitivity in a TrkB-dependent manner. A threshold for the induction of BNDF in response to physical exercise exists in certain muscle groups. To the best of our knowledge, these are the first results to reveal a role for TrkB in the chronic exercise-mediated insulin regulation in healthy rats.
The path dependency theory: analytical framework to study institutional integration. The case of France

Background The literature on integration indicates the need for an enhanced theorization of institutional integration. This article proposes path dependence as an analytical framework to study the systems in which integration takes place. Purpose PRISMA proposes a model for integrating health and social care services for older adults. This model was initially tested in Quebec. The PRISMA France study gave us an opportunity to analyze institutional integration in France. Methods A qualitative approach was used. Analyses were based on semi-structured interviews with actors of all levels of decision-making, observations of advisory board meetings, and administrative documents. Results Our analyses revealed the complexity and fragmentation of institutional integration. The path dependency theory, which analyzes the change capacity of institutions by taking into account their historic structures, allows analysis of this situation. The path dependency to the Bismarckian system and the incomplete reforms of gerontological policies generate the coexistence and juxtaposition of institutional systems. In such a context, no institution has sufficient ability to determine gerontology policy and build institutional integration by itself. Conclusion Using path dependence as an analytical framework helps to understand the reasons why institutional integration is critical to organizational and clinical integration, and the complex construction of institutional integration in France.
Chronic Obstructive Pulmonary Disease-Related Non-Small-Cell Lung Cancer Exhibits a Low Prevalence of EGFR and ALK Driver Mutations

Lung cancer and chronic obstructive pulmonary disease (COPD) are two major lung diseases. Epidermal growth factor receptor (EGFR) mutations, v‐Ki‐ras2 Kirsten rat sarcoma (KRAS) mutations and anaplastic lymphoma kinase (ALK) gene rearrangements represent driver mutations that are frequently assessed on initial evaluation of non-small-cell lung cancer (NSCLC). The present study focused on the expression of driver mutations in NSCLC patients presenting with COPD and further evaluated the association between NSCLC and COPD. Data from 501 consecutive patients with histologically proven recurrent or metastatic NSCLC were analyzed retrospectively. The patients underwent spirometry and genotyping of EGFR, ALK, and KRAS in tissue samples. Patient characteristics and expression of driver mutations were compared between the COPD and non-COPD groups. Among 350 patients with spirometric results, 106 (30.3%) were diagnosed with COPD, 108 (30.9%) had EGFR mutations, 31 (8.9%) had KRAS mutations, and 34 (9.7%) showed ALK rearrangements. COPD was independently associated with lower prevalences of EGFR mutations (95% confidence interval [CI], 0.254–0.931, p = 0.029) and ALK rearrangements (95% CI, 0.065–0.600, p = 0.004). The proportions of EGFR mutations and ALK rearrangements decreased as the severity of airflow obstruction increased (p = 0.001). In never smokers, the prevalence of EGFR mutations was significantly lower in the COPD group than in the non-COPD group (12.7% vs. 49.0%, p = 0.002). COPD-related NSCLC patients exhibited low prevalences of EGFR mutations and ALK rearrangements compared with the non-COPD group. Further studies are required regarding the molecular mechanisms underlying lung cancer associated with COPD.
Complement Coercion: The Joint Effects of Type and Typicality

Complement coercion (begin a book →reading) involves a type clash between an event-selecting verb and an entity-denoting object, triggering a covert event (reading). Two main factors involved in complement coercion have been investigated: the semantic type of the object (event vs. entity), and the typicality of the covert event (the author began a book →writing). In previous research, reading times have been measured at the object. However, the influence of the typicality of the subject–object combination on processing an aspectual verb such as begin has not been studied. Using a self-paced reading study, we manipulated semantic type and subject–object typicality, exploiting German word order to measure reading times at the aspectual verb. These variables interacted at the target verb. We conclude that both type and typicality probabilistically guide expectations about upcoming input. These results are compatible with an expectation-based view of complement coercion and language comprehension more generally in which there is rapid interaction between what is typically viewed as linguistic knowledge, and what is typically viewed as domain general knowledge about how the world works.
The role of I-J and Igh determinants on F1-derived suppressor factor in controlling restriction specificity

In the 4-hydroxy-3-nitrophenyl acetyl (NP) contact sensitivity system, the activity of third-order suppressor cells and their factors is restricted by H-2(I-J) and Igh linked genes. The present report analyzes the specificity of NP-specific Ts3 cells and factors derived from H-2 and Igh heterozygous (B6 X C3H)F1 mice. Two approaches were used. First, heterogeneous populations of F1 Ts3 cells were activated in vitro and then assayed in Ts3-depleted recipients which carried different combinations of H-2 and Igh alleles. The second approach was to hybridize the Ts3 cells and analyze the specificity of the F1- derived TsF3. The combined data demonstrated four functionally distinct populations of Ts3 cells. The activity of each population was restricted by a particular combination of H-2 and Igh haplotypes. Thus, Ts3 cells derived from F1 donors can demonstrate an apparent scrambling of H-2 and Igh restriction specificities. There was functional allelic exclusion of the H-2(I-J) and Igh determinants expressed on (B6 X C3H)F1 hybridoma-derived TsF3. Thus, TsF3 from each cloned hybridoma line expressed only one set of I-J and Igh determinants. Furthermore, there was a complete correlation between the I-J and Igh linked determinants expressed on TsF3 and the restriction specificity. In view of the recent findings on the molecular biology of the I-J region, an alternative interpretation of the role of I-J determinants on suppressor cells and factors is offered.
NMDA receptor surface mobility depends on NR2A-2B subunits

The NR2 subunit composition of NMDA receptors (NMDARs) varies during development, and this change is important in NMDAR-dependent signaling. In particular, synaptic NMDAR switch from containing mostly NR2B subunit to a mixture of NR2B and NR2A subunits. The pathways by which neurons differentially traffic NR2A- and NR2B-containing NMDARs are poorly understood. Using single-particle and -molecule approaches and specific antibodies directed against NR2A and NR2B extracellular epitopes, we investigated the surface mobility of native NR2A and NR2B subunits at the surface of cultured neurons. The surface mobility of NMDARs depends on the NR2 subunit subtype, with NR2A-containing NMDARs being more stable than NR2B-containing ones, and NR2A subunit overexpression stabilizes surface NR2B-containing NMDARs. The developmental change in the synaptic surface content of NR2A and NR2B subunits was correlated with a developmental change in the time spent by the subunits within synapses. This suggests that the switch in synaptic NMDAR subtypes depends on the regulation of the receptor surface trafficking.
Phase Synchronization Analysis of EEG during Attentional Blink

The attentional blink (AB) phenomenon occurs when perceivers must report two targets embedded in a sequence of distracters; if the first target precedes the second by 200-600 msec, the second one is often missed. We investigated AB by measuring dynamic cross-lag phase synchronization for 565 electrode pairs in 40-Hz-range EEG. Phase synchrony, on average, was higher in experimental conditions, where two targets are reported, than in control conditions, where only the second target is reported. The effect occurred in electrode pairs covering the whole head. Timing of the synchrony was crucial: Brief episodes of enhanced synchrony occurred 100-500 msec before expected target onset in AB conditions where the second target was correctly reported. These results show that intrinsic brain dynamics produce anticipatory synchronization in transient assemblies of cortical areas. Enhanced levels of anticipatory synchronization occur in response to the demands of the task in conditions where the system's limited capacity is under strain.
The Efficacy of Working Memory Training on Working Memory Capacity, Psychopathology, and Mental Well-being

markdownabstract__Abstract__ Mood and anxiety disorders are the most prevalent psychopathological disorders in the Netherlands (de Graaf, ten Have, Van Gool, & Van Dorsselaer, 2012). Anxiety disorders and major depression, which are the focus of this dissertation, affect respectively 10.1% and 5.2% of the Dutch population yearly. The World Health Organization (WHO) estimates that 150 million people worldwide suffer from depression (WHO, 2008) and 15% of the world population will suffer from an anxiety disorder in his/her life (Kessler et al., 2009). Approximately 85% of these patients suffer from both depression and anxiety (Gorman, 1996). This high comorbidity rate might indicate a shared underlying etiology and is reflected in similar consequences. That is, both psychiatric disorders result in significant social and personal concern, which is associated with reduced quality of life, productivity and even significantly increased mortality (Doris, Ebmeier, & Shajahan, 1999). As a matter of fact, mood and anxiety disorders are responsible for 40% of the costs for work absence and disability to work (Hutschemaekers, Donker, & Richter, 2000). Unfortunately, the prevalence of these disorders has remained stable over decades, which might imply that contemporary treatments are not able to reduce these disorders (de Graaf et al., 2012).
Vocal Analysis of Acoustic Startle Responses

This paper presents an extensive statistical analysis of the acoustic startle response of two vocal parameters: fundamental frequency (F0) and root-mean-square energy (E), as well as of the orbicularis oculi (eyeblink) surface electromyography (sEMG). An experiment was conducted in which fourteen participants were exposed to acoustic startle stimuli of varying parameters, i.e., intensity level, duration, rise time, and spectral type, during periods of sustained phonation. Voice recordings of the phonations were taken alongside several physiological signals, of which only the sEMG was analyzed in this paper. Response features (peak value, peak time, latency, rise time, fall time, and duration) were extracted on F0, E and sEMG data, and statistical analysis was conducted using linear mixed effects models to show the response behavior with the varying stimuli. The results for vocal F0 and E data were congruent with sEMG data and earlier work in the field. The results demonstrated that vocal analysis can be used as a feasible alternative to the sEMG eyeblink analysis of acoustic startle responses.
Cramer-Rao bound for nonlinear filtering with Pd<1 and its application to target tracking

The paper investigates the Cramer-Rao bound for discrete-time nonlinear filtering in the case where the probability of detection of a sensor is less than unity. The theoretical formula involves the evaluation of exponentially growing number of possible miss/detection sequences. An approximation of the theoretical bound for practical applications, such as target tracking, where the number of sensor scans is large, is proposed. An application of the developed techniques to the well-known filtering problem of tracking a re-entry ballistic object is also presented.