Miracle-dz/UniFAR-FTUs huggingface dataset:
Common-input models for multiple neural spike-train data

Recent developments in multi-electrode recordings enable the simultaneous measurement of the spiking activity of many neurons. Analysis of such multineuronal data is one of the key challenge in computational neuroscience today. In this work, we develop a multivariate point-process model in which the observed activity of a network of neurons depends on three terms: (1) the experimentally-controlled stimulus; (2) the spiking history of the observed neurons; and (3) a hidden term that corresponds, for example, to common input from an unobserved population of neurons that is presynaptic to two or more cells in the observed population. We consider two models for the network firing-rates, one of which is computationally and analytically tractable but can lead to unrealistically high firing-rates, while the other with reasonable firing-rates imposes a greater computational burden. We develop an expectation-maximization algorithm for fitting the parameters of both the models. For the analytically tractable model the expectation step is based on a continuous-time implementation of the extended Kalman smoother, and the maximization step involves two concave maximization problems which may be solved in parallel. The other model that we consider necessitates the use of Monte Carlo methods for the expectation as well as maximization step. We discuss the trade-off involved in choosing between the two models and the associated methods. The techniques developed allow us to solve a variety of inference problems in a straightforward, computationally efficient fashion; for example, we may use the model to predict network activity given an arbitrary stimulus, infer a neuron's ring rate given the stimulus and the activity of the other observed neurons, and perform optimal stimulus decoding and prediction. We present several detailed simulation studies which explore the strengths and limitations of our approach.
Office Blood Pressure, Ambulatory Blood Pressure Monitoring, and Echocardiographic Abnormalities in Women With Polycystic Ovary Syndrome: Role of Obesity and Androgen Excess

Whether or not blood pressure (BP) and heart function of women with polycystic ovary syndrome (PCOS) are altered remains unclear, albeit subtle abnormalities in the regulation of BP observed in these women might suggest a mild masculinization of their cardiovascular system. To study the influence of obesity and androgen excess on BP and echocardiographic profiles of women with the syndrome, we conducted a cross-sectional case–control study comparing office and ambulatory BP monitoring, as well as echocardiographic assessments, in 63 premenopausal women with the classic phenotype, 33 nonhyperandrogenic women with regular menses, and 25 young men. Forty-nine subjects were lean and 72 had weight excess (body mass index ≥25 kg/m2). Participants had no previous history of hypertension and were nonsmokers. Men showed the highest BP readings, and the lowest readings were observed in control women, whereas women with PCOS had intermediate values. Undiagnosed hypertension was more common in subjects with weight excess irrespective of sex and hyperandrogenism. Women with PCOS and weight excess showed frequencies of previously undiagnosed hypertension that were similar to those of men with weight excess and higher than those observed in nonhyperandrogenic women. Lastly, male sex, weight excess and hypertension, the latter in men as well as in women with PCOS, increased left ventricular wall thickness. In summary, our results show that patients with classic PCOS and weight excess frequently have undiagnosed BP abnormalities, leading to target organ damage.
Autonomic Function is Associated with Fitness Level in HIV-Infected Individuals.

BACKGROUND Cardiovascular fitness can improve autonomic function (AF) in human immunodeficiency virus (HIV)-infected individuals. METHODS Cross-sectional study investigating relationship between AF and cardiovascular fitness in HIV+ individuals on antiretroviral therapy. Participants' (n=29) maximal oxygen consumption (VO2MAX) were assessed by graded exercise test and scaled allometrically, then divided into tertiles by fitness level (Unfit, Low-fit, and Moderately-fit). Heart rate variability (HRV) and the Autonomic Reflex Screen were used to assess AF. RESULTS Median VO2MAX were 104.9, 130.5, and 150.2 mL•kg-. 67•min-1 for Unfit (n=10), Low-fit (n=10), and Moderately-fit (n= 9) groups respectively (p<0.05). Positive correlations were found between VO2MAX and HRV (Spearman's rho range 0.383 to 0.553) were found. Quantitative Sudomotor Axon Reflex Test (QSART) Distal Leg volumes was lower in Unfit compared to Low-fit (p=0.007) and Moderately-fit groups (p=0.018). Unfit QSART total volumes was lower than Moderately-fit (p=0.014). CONCLUSION A positive relationship existed between AF and fitness levels. HIV+ individuals could benefit from improved fitness.
High-resolution palaeoclimatic records for the last millennium: interpretation, integration and comparison with General Circulation Model control-run temperatures

Palaeoclimatology provides our only means of assessing climatic variations before the beginning of instrumental records. The various proxy variables used, however, have a number of limitations which must be adequately addressed and understood. Besides their obvious spatial and seasonal limitations, different proxies are also potentially limited in their ability to represent climatic variations over a range of different timescales. Simple correlations with instrumental data over the period since ad 1881 give some guide to which are the better proxies, indicating that coral- and ice-core-based reconstructions are poorer than tree-ring and historical ones. However, the quality of many proxy time series can deteriorate during earlier times. Suggestions are made for assessing proxy quality over longer periods than the last century by intercomparing neighbouring proxies and, by comparisons with less temporally resolved proxies such as borehole temperatures. We have averaged 17 temperature reconstructions (representing various seasons of the year), all extending back at least to the mid-seventeenth century, to form two annually resolved hemispheric series (NH10 and SH7). Over the 1901–91 period, NH10 has 36% variance in common with average NH summer (June to August) temperatures and 70% on decadal timescales. SH7 has 16% variance in common with average SH summer (December to February) temperatures and 49% on decadal timescales, markedly poorer than the reconstructed NH series. The coldest year of the millennium over the NH is ad 1601, the coldest decade 1691–1700 and the seventeenth is the coldest century. A Principal Components Analysis (PCA) is performed on yearly values for the 17 reconstructions over the period ad 1660–1970. The correlation between PC1 and NH10 is 0.92, even though PC1 explains only 13.6% of the total variance of all 17 series. Similar PCA is performed on thousand-year-long General Circulation Model (GCM) data from the Geophysical Fluid Dynamics Laboratory (GFDL) and the Hadley Centre (HADCM2), sampling these for the same locations and seasons as the proxy data. For GFDL, the correlation between its PC1 and its NH10 is 0.89, while for HADCM2 the PCs group markedly differently. Cross-spectral analyses are performed on the proxy data and the GFDL model data at two different frequency bands (0.02 and 0.03 cycles per year). Both analyses suggest that there is no large-scale coherency in the series on these timescales. This implies that if the proxy data are meaningful, it should be relatively straightforward to detect a coherent near-global anthropogenic signal in surface temperature data.
Cyanobacteriochrome SesA Is a Diguanylate Cyclase That Induces Cell Aggregation in Thermosynechococcus*♦

Background: Cyanobacteriochrome photoreceptors have diverse spectral properties and regulate photosynthetic antenna composition and motility of cyanobacteria. Results: A blue/green-responsive cyanobacteriochrome SesA is a blue light-dependent diguanylate cyclase and induces cell aggregation of Thermosynechococcus under blue light. Conclusion: SesA regulates sessility in a light-dependent way likely via cyclic diguanylate signaling. Significance: SesA is the first cyanobacteriochrome photoreceptor that regulates sessility. Cyanobacteria have unique photoreceptors, cyanobacteriochromes, that show diverse spectral properties to sense near-UV/visible lights. Certain cyanobacteriochromes have been shown to regulate cellular phototaxis or chromatic acclimation of photosynthetic pigments. Some cyanobacteriochromes have output domains involved in bacterial signaling using a second messenger cyclic dimeric GMP (c-di-GMP), but its role in cyanobacteria remains elusive. Here, we characterize the recombinant Tlr0924 from a thermophilic cyanobacterium Thermosynechococcus elongatus, which was expressed in a cyanobacterial system. The protein reversibly photoconverts between blue- and green-absorbing forms, which is consistent with the protein prepared from Escherichia coli, and has diguanylate cyclase activity, which is enhanced 38-fold by blue light compared with green light. Therefore, Tlr0924 is a blue light-activated diguanylate cyclase. The protein's relatively low affinity (10.5 mm) for Mg2+, which is essential for diguanylate cyclase activity, suggests that Mg2+ might also regulate c-di-GMP signaling. Finally, we show that blue light irradiation under low temperature is responsible for Thermosynechococcus vulcanus cell aggregation, which is abolished when tlr0924 is disrupted, suggesting that Tlr0924 mediates blue light-induced cell aggregation by producing c-di-GMP. Given our results, we propose the name “sesA (sessility-A)” for tlr0924. This is the first report for cyanobacteriochrome-dependent regulation of a sessile/planktonic lifestyle in cyanobacteria via c-di-GMP.
Zinc accumulation after target loss: an early event in retrograde degeneration of thalamic neurons

Accumulation of cytoplasmic zinc is linked with a cascade of events leading to neuronal death. In many in vivo models of zinc‐induced cell death, toxic concentrations of synaptically released zinc enter vulnerable neurons via neurotransmitter‐ or voltage‐gated ion channels. In vitro studies demonstrate, in addition, that zinc can be liberated from intracellular stores following oxidative stress and contribute to cell death processes, including apoptosis. Here we describe accumulation of intracellular zinc in an in vivo model of cell death in the absence of presynaptic zinc release. We focused on the lateral geniculate nucleus (LGN) because LGN neurons undergo apoptosis when separated from their target, the primary visual cortex (V1), and the LGN is mostly devoid of zinc‐containing presynaptic terminals. Infant and adult rats and adult mice received unilateral ablation of V1, either by aspiration or kainate injection. One to 14 days later, brain sections were stained with selenium autometallography or fluorescently labeled to localize zinc, or stained immunochemically for activated caspase‐3. V1 lesions led to zinc accumulation in LGN neurons in infant and adult subjects. Zinc‐containing neurons were evident 1–3 days after aspiration lesions, depending on age, but not until 14 days after kainate injection. Zinc accumulation was followed rapidly by immunostaining for activated caspase‐3. Our data indicate that like neurotrauma and excitotoxicity, target deprivation leads to accumulation of zinc in apoptotic neurons. Moreover, zinc accumulation in vivo can occur in the absence of presynaptic zinc release. Together these findings suggest that accumulation of intracellular zinc is a ubiquitous component of the cell death cascade in neurons.
Otka-nnf 78918 " Molecular Diversity and Plasticity of Endocannabinoid Signaling at Cortical Synapses " Publications Supported by the Otka-nnf 78918 Grant Publicity Measures, Participation at Conferences Posters

(2011) Complementary synaptic distribution of enzymes responsible for synthesis and inactivation of the endocannabinoid 2-arachidonoylglycerol in the human hippocampus. (2011) Uncoupling of the endocannabinoid signalosome in a mouse model of fragile X. (2010) Synaptic localization of the enzymatic machinery responsible for 2-arachidonoylglycerol synthesis and degradation in the human hippocampus. Development of perisomatic innervation of pyramidal neurons arising from CB1-and parvalbumin-positive basket cells in the mouse visual cortex. (2010) Synaptic localization of enzymes responsible for the synthesis and degradation of the endocannabinoid 2-arachidonoylglycerol in human hippocampus. Summary of the scientific achievements Specific aim 1 Endocannabinoids (eCBs) are retrograde lipid messengers regulating short-and long-term forms of synaptic plasticity throughout the nervous system (Chevaleyre et al., 2006). The substantial role of the eCB system in neuronal function is well supported by its involvement in various diseases of the CNS (Pacher et al., 2006). Several different mechanisms of eCB-dependent synaptic plasticity have been described in different layers of the neocortex, including stimulation-induced, pairing-induced, and spike-timing dependent depression The exact molecular composition of synaptic eCB signaling is well described in some brain regions, e.g. the hippocampus, where activation of metabotropic glutamate receptors leads to the postsynaptic production of 2-arachidonoylglycerol (2-AG) by diacylglycerol
NMDA Receptor GluN 2 B ( GluR 2 / NR 2 B ) Subunit Is Crucial for Channel Function , Postsynaptic Macromolecular Organization , and Actin Cytoskeleton at Hippocampal CA 3 Synapses

Title NMDA Receptor GluN2B (GluRε2/NR2B) Subunit Is Crucial for Channel Function, Postsynaptic Macromolecular Organization, and Actin Cytoskeleton at Hippocampal CA3 Synapses Author(s) Akashi, Kaori; Kakizaki, Toshikazu; Kamiya, Haruyuki; Fukaya, Masahiro; Yamasaki, Miwako; Abe, Manabu; Natsume, Rie; Watanabe, Masahiko; Sakimura, Kenji Citation The Journal of Neuroscience, 29(35): 10869-10882 Issue Date 2009-09-02 Doc URL http://hdl.handle. net/2115/39397 Right Copyright©2009 Society for Neuroscience
Altered Expression of FAS System Is Related to Adverse Clinical Outcome in Stage I-II Breast Cancer Patients Treated with Adjuvant Anthracycline-Based Chemotherapy

Purpose: To determine the prognostic value of Fas receptor and Fas ligand (FasL) as apoptosis-related biomarkers in the context of chemoresponsiveness in breast cancer (BC) patients submitted to anthracycline-based adjuvant therapy. Experimental Design: Fas and FasL were investigated by immunohistochemistry in surgical samples collected from 167 stage I-IIa-b BC patients enrolled in a prospective clinical trial using epirubicin plus cyclophosphamide in the adjuvant setting. Results: Fas and FasL were significantly associated with tumor stage (P < 0.0001). Multivariate analysis indicated that stage, loss of Fas (relative risk, 8.5 and 9.12; P < 0.0001) and FasL up-regulation (relative risk, 2.38 and 2.88; P = 0.01) were independent prognostic variables influencing both disease-free survival (DFS) and overall survival (OS). A Cox analysis using a four-category Fas/FasL phenotype (+/−, +/+, −/+, −/−) as a stratification factor evidenced a highly positive association between Fas/FasL phenotype and the cumulative hazard of relapse and death in the entire series of patients. We also estimated the DFS and OS for different combinations of the pathological-tumor-node-metastasis (TNM) stage and Fas/FasL by using the K sample log-rank exact test demonstrating that significantly shorter DFS and OS were observed in Fas-negative and FasL-positive patients in both stage I-IIa and IIb. Conclusions: Data presented herein demonstrated that, according to a number of in vitro studies, the prognosis for BC patients receiving adjuvant anthracycline-based chemotherapy strongly depends on the Fas/FasL status. Therefore, a concomitant altered pattern of Fas/FasL expression seems to configure an aggressive tumor phenotype linked to disease progression.
Intra-Cranial Recordings of Brain Activity During Language Production

Recent findings in the neurophysiology of language production have provided a detailed description of the brain network underlying this behavior, as well as some indications about the timing of operations. Despite their invaluable utility, these data generally suffer from limitations either in terms of temporal resolution, or in terms of spatial localization. In addition, studying the neural basis of speech is complicated by the presence of articulation artifacts such as electro-myographic activity that interferes with the neural signal. These difficulties are virtually absent in a powerful albeit much less frequent methodology, namely the recording of intra-cranial brain activity (intra-cranial electroencephalography). Such recordings are only possible under very specific clinical circumstances requiring functional mapping before brain surgery, most notably in patients that suffer from pharmaco-resistant epilepsy. Here we review the research conducted with this methodology in the field of language production, with explicit consideration of its advantages and drawbacks. The available evidence is shown to be diverse, both in terms of the tasks and the cognitive processes tested and in terms of the brain localizations being studied. Still, the review provides valuable information for characterizing the dynamics of the neural events occurring in the language production network. Following modality specific activities (in auditory or visual cortices), there is a convergence of activity in superior temporal sulcus, which is a plausible neural correlate of phonological encoding processes. Later, between 500 and 800 ms, inferior frontal gyrus (around Broca’s area) is involved. Peri-rolandic areas are recruited in the two modalities relatively early (200–500 ms window), suggesting a very early involvement of (pre-) motor processes. We discuss how some of these findings may be at odds with conclusions drawn from available meta-analysis of language production studies.
A Modular Power System Planning and Power Flow Simulation Framework for Generating and Evaluating Power Network Models

This work presents a modular power system planning and power flow simulation framework for the generation and evaluation of power network models (PNM) using spatially resolved demand data. It targets users who want to study large-scale power grids having only limited information on the actual power system. Besides creating cost minimal PNMs, users are able to flexibly configure the framework to produce PNMs individually tailored to their specific use cases. Both greenfield and expansion planning are possible. The framework further comprises a built-in ac power flow simulation designed to simulate power flows in large-scale networks. This allows users to conduct a great variety of simulation studies on entire power systems, which would otherwise not be possible without access to comprehensive power grid data. Apart from the presentation of the methodology, this work comprises a demonstration of the power system planning process at the example of Singapore. The investigation shows that the framework is capable of generating a network that matches the topological and electrical metrics of the Singapore power grid.
Potential of probiotics in controlling cardiovascular diseases

The World Health Organization and the Food and Agriculture Organization of the United Nations have defi ned probiotics as “live microorganisms, which, when administered in adequate amounts, confer a health benefi t on the host. ” They are also called “friendly bacteria” or “good bacteria. ” The concept of probiotics arose at the turn of the 20th century from a hypothesis fi rst proposed by the Noble Prize-winning Russian scientist, Elie Metchnikoff. Most probiotics fall into the group of organisms known as lactic acid-producing bacteria, and are normally consumed in the form of yogurt, fermented milks or other fermented foods. [1,2] The valuable effects of food with added live microbes (probiotics) on human health and, in particular, of milk products, are being increasingly promoted by health professionals, and these probiotics can play an important role in systemic health of the person.Read more. ,
Attention function after childhood stroke

We investigated attentional outcome after childhood stroke and orthopedic diagnosis in medical controls. Twenty-nine children with focal stroke lesions and individually matched children with clubfoot or scoliosis were studied with standardized attention and neuroimaging assessments. Stroke lesions were quite varied in location and commonly involved regions implicated in Posner's model of attention networks. Children with stroke lesions performed significantly more poorly regarding attention function compared with controls. Performance on the Starry Night, a test demanding alerting and sensory-orienting but not executive attention function, was significantly associated with lesion size in the alerting and sensory-orienting networks but not the executive attention network. Furthermore, earlier age at lesion acquisition was significantly associated with poorer attention function even when lesion size was controlled. These findings support the theory of dissociable networks of attention and add to evidence from studies of children with diffuse and focal brain damage that early insults are associated with worse long-term outcomes in many domains of neuropsychological function. In addition, these results may provide clues towards the understanding of mechanisms underlying attention in children. (JINS, 2004, 10, 976–986.)
Experimental study of gradient-based visual coverage control on SO(3) toward moving object/human monitoring

This paper presents experimental studies of coverage control for networked camera sensors. Regarding the issue, one of our previous works considered the scenario where the camera sensors with controllable orientations are distributed over the 3-D space to monitor 2-D environment. Then, we presented a visual coverage control scheme based on the gradient descent techniques on SO(3) in combination with an estimation process of the image density function describing the importance of each point over the image. In this paper, we build a testbed with four Pan-Tilt (PT) cameras and demonstrate the total process including the image acquisition, density estimation, gradient computation and camera physical motion. In particular, we show applicability of the presented scheme to a scenario of the human behavior monitoring. In addition, the density function is given in the form of a polynomial function in order to overcome the drawback of the above density estimation process that the magnitude of the motion at each pixel cannot be directly reflected to the resulting density. It is shown through experiments that the new density estimation method together with the new gradient outperforms the conventional method when the environment is rapidly changing.
Accuracy of circulating placental growth factor, vascular endothelial growth factor, soluble fms‐like tyrosine kinase 1 and soluble endoglin in the prediction of pre‐eclampsia: a systematic review and meta‐analysis

Please cite this paper as: Kleinrouweler C, Wiegerinck M, Ris‐Stalpers C, Bossuyt P, van der Post J, von Dadelszen P, Mol B, Pajkrt E, for the EBM CONNECT Collaboration. Accuracy of circulating placental growth factor, vascular endothelial growth factor, soluble fms‐like tyrosine kinase 1 and soluble endoglin in the prediction of pre‐eclampsia: a systematic review and meta‐analysis. BJOG 2012;119:778–787.