Miracle-dz/UniFAR-FTUs huggingface dataset:
A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements

The computational and cognitive properties of neural systems are often thought to be implemented in terms of their (stochastic) network dynamics. Hence, recovering the system dynamics from experimentally observed neuronal time series, like multiple single-unit recordings or neuroimaging data, is an important step toward understanding its computations. Ideally, one would not only seek a (lower-dimensional) state space representation of the dynamics, but would wish to have access to its statistical properties and their generative equations for in-depth analysis. Recurrent neural networks (RNNs) are a computationally powerful and dynamically universal formal framework which has been extensively studied from both the computational and the dynamical systems perspective. Here we develop a semi-analytical maximum-likelihood estimation scheme for piecewise-linear RNNs (PLRNNs) within the statistical framework of state space models, which accounts for noise in both the underlying latent dynamics and the observation process. The Expectation-Maximization algorithm is used to infer the latent state distribution, through a global Laplace approximation, and the PLRNN parameters iteratively. After validating the procedure on toy examples, and using inference through particle filters for comparison, the approach is applied to multiple single-unit recordings from the rodent anterior cingulate cortex (ACC) obtained during performance of a classical working memory task, delayed alternation. Models estimated from kernel-smoothed spike time data were able to capture the essential computational dynamics underlying task performance, including stimulus-selective delay activity. The estimated models were rarely multi-stable, however, but rather were tuned to exhibit slow dynamics in the vicinity of a bifurcation point. In summary, the present work advances a semi-analytical (thus reasonably fast) maximum-likelihood estimation framework for PLRNNs that may enable to recover relevant aspects of the nonlinear dynamics underlying observed neuronal time series, and directly link these to computational properties.
Spontaneous cortical activity is transiently poised close to criticality

Brain activity displays a large repertoire of dynamics across the sleep-wake cycle and even during anesthesia. It was suggested that criticality could serve as a unifying principle underlying the diversity of dynamics. This view has been supported by the observation of spontaneous bursts of cortical activity with scale-invariant sizes and durations, known as neuronal avalanches, in recordings of mesoscopic cortical signals. However, the existence of neuronal avalanches in spiking activity has been equivocal with studies reporting both its presence and absence. Here, we show that signs of criticality in spiking activity can change between synchronized and desynchronized cortical states. We analyzed the spontaneous activity in the primary visual cortex of the anesthetized cat and the awake monkey, and found that neuronal avalanches and thermodynamic indicators of criticality strongly depend on collective synchrony among neurons, LFP fluctuations, and behavioral state. We found that synchronized states are associated to criticality, large dynamical repertoire and prolonged epochs of eye closure, while desynchronized states are associated to sub-criticality, reduced dynamical repertoire, and eyes open conditions. Our results show that criticality in cortical dynamics is not stationary, but fluctuates during anesthesia and between different vigilance states.
Journal of Geophysical Research : Atmospheres Spectral Characteristics of VLF Sferics Associated With RHESSI TGFs

We compared the modeled energy spectral density of very low frequency (VLF) radio emissions from terrestrial gamma ray flashes (TGFs) with the energy spectral density of VLF radio sferics recorded by Duke VLF receiver simultaneously with those TGFs. In total, six events with world wide lightning location network (WWLLN) defined locations were analyzed to exhibit a good fit between the modeled and observed energy spectral densities. In VLF range the energy spectral density of the TGF source current moment is found to be dominated by the contribution of secondary low-energy electrons and independent of the relativistic electrons which play their role in low-frequency (LF) range. Additional spectral modulation by the multiplicity of TGF peaks was found and demonstrated a good fit for two TGFs whose VLF sferics consist of two overlapping pulses each. The number of seeding pulses in TGF defines the spectral shape in VLF range, which allows to retrieve this number from VLF sferics, assuming they were radiated by TGFs. For two events it was found that the number of seeding pulses is small, of the order of 10. For the rest of the events the lower boundary of the number of seeding pulses was found to be between 10 to 103.
Prediction of mycoplasma hominis proteins targeting in mitochondria and cytoplasm of host cells and their implication in prostate cancer etiology

Although the idea of bacteria causing different types of cancer has exploded about century ago, the potential mechanisms of carcinogenesis is still not well established. Many reports showed the involvement of M. hominis in the development of prostate cancer, however, mechanistic approach for growth and development of prostate cancer has been poorly understood. In the current study, we predicted M. hominis proteins targeting in the mitochondria and cytoplasm of host cells and their implication in prostate cancer. A total of 77 and 320 proteins from M. hominis proteome were predicted to target in the mitochondria and cytoplasm of host cells respectively. In particular, various targeted proteins may interfere with normal growth behaviour of host cells, thereby altering the decision of programmed cell death. Furthermore, we investigated possible mechanisms of the mitochondrial and cytoplasmic targeted proteins of M. hominis in etiology of prostate cancer by screening the whole proteome.
The role of procalcitonin in the diagnosis of bacterial infection after major abdominal surgery

Abstract Postsurgical infections represent an important cause of morbidity after abdominal surgery. The microbiological diagnosis is not achieved in at least 30% of culture with consequent worsening of patient outcome. In this study, procalcitonin measurement, during the first 3 days after abdominal surgery, has been evaluated for the early diagnosis of postsurgical infection. Ninety consecutive patients subjected to major abdominal surgery at the University Campus Bio-Medico of Rome, have been included. PCT concentrations were measured by time-resolved amplified cryptate emission (TRACE) assay at admission and at the first, second, and third day after surgery. PCT levels were compared using the Mann–Whitney test and by ANOVA test for variance analysis. Receiver operating characteristic (ROC) analysis was performed to define the diagnostic ability of PCT in case of postsurgical infections. PCT values resulted significantly different between patients developing or not developing postsurgical infections. PCT >1.0 ng/mL at first or second day after surgery and >0.5 ng/mL at third day resulted diagnostic for infectious complication, whereas a value <0.5 ng/mL at the fifth day after surgery was useful for early and safety discharge of patients. In conclusion, PCT daily measurement could represent a useful diagnostic tool improving health care in the postsurgical period following major abdominal surgery and should be recommended.
Early rehospitalizations of frail elderly patients – the role of medications: a clinical, prospective, observational trial

Background and objective Early readmissions of frail elderly patients after an episode of hospital care are common and constitute a crucial patient safety outcome. Our purpose was to study the impact of medications on such early rehospitalizations. Patients and methods This is a clinical, prospective, observational study on rehospitalizations within 30 days after an acute hospital episode for frail patients over the age of 75 years. To identify adverse drug reactions (ADRs), underuse of evidence-based treatment and avoidability of rehospitalizations, the Naranjo score, the Hallas criteria and clinical judgment were used. Results Of 390 evaluable patients, 96 (24.6%) were rehospitalized. The most frequent symptoms and conditions were dyspnea (n = 25) and worsened general condition (n = 18). The most frequent diagnoses were heart failure (n = 17) and pneumonia/acute bronchitis (n = 13). By logistic regression analysis, independent risk predictors for rehospitalization were heart failure (odds ratio [OR] = 1.8; 95% CI = 1.1–3.1) and anemia (OR = 2.3; 95% CI = 1.3–4.0). The number of rehospitalizations due to probable ADRs was 13, of which two were assessed as avoidable. The number of rehospitalizations probably due to underuse of evidence-based drug treatment was 19, all of which were assessed as avoidable. The number of rehospitalizations not due to ADRs or underuse of evidence-based drug treatment was 64, of which none was assessed as avoidable. Conclusion One out of four frail elderly patients discharged from hospital was rehospitalized within 1 month. Although ADRs constituted an important cause of rehospitalization, underuse of evidence-based drug treatment might be an even more frequent cause. Potentially avoidable rehospitalizations were more frequently associated with underuse of evidence-based drug treatment than with ADRs. Efforts to avoid ADRs in frail elderly patients must be balanced and combined with evidence-based drug therapy, which can benefit these patients.
Mesh Blending

A new method for smoothly connecting different patches on triangle meshes with arbitrary connectivity, called mesh blending, is presented. A major feature of mesh blending is to move vertices of the blending region to a virtual blending surface by choosing an appropriate parameterization of those vertices. Once blending is completed, the parameterization optimization is performed to perfect the final meshes. Combining mesh blending with multiresolution techniques, an effective blending technique for meshes is obtained. Our method has several advantages: (1) the user can intuitively control the blending result using different blending radii, (2) the shape of cross-section curves can be adjusted to flexibly design complex models, and (3) the resulting mesh has the same connectivity as the original mesh. In this paper, some examples about smoothing, sharpening, and mesh editing show the efficiency of the method.
Phase-Variable Changes in the Position of O-Methyl Phosphoramidate Modifications on the Polysaccharide Capsule of Campylobacter jejuni Modulate Serum Resistance

ABSTRACT Campylobacter jejuni polysaccharide capsules (CPS) are characterized by the presence of nonstoichiometric O-methyl phosphoramidate (MeOPN) modifications. The lack of stoichiometry is due to phase variation at homopolymeric tracts within the MeOPN transferase genes. C. jejuni strain 81-176 contains two MeOPN transferase genes and has been shown previously to contain MeOPN modifications at the 2 and 6 positions of the galactose (Gal) moiety in the CPS. We demonstrate here that one of the two MeOPN transferases, encoded by CJJ81176_1435, is bifunctional and is responsible for the addition of MeOPN to both the 2 and the 6 positions of Gal. A new MeOPN at the 4 position of Gal was observed in a mutant lacking the CJJ81176_1435 transferase and this was encoded by the CJJ81176_1420 transferase. During routine growth of 81-176, the CJJ81176_1420 transferase was predominantly in an off configuration, while the CJJ81176_1435 transferase was primarily on. However, exposure to normal human serum selected for cells expressing the CJJ81176_1420 transferase. MeOPN modifications appear to block binding of naturally occurring antibodies to the 81-176 CPS. The absence of MeOPN-4-Gal resulted in enhanced sensitivity to serum killing, whereas the loss of MeOPN-2-Gal and MeOPN-6-Gal resulted in enhanced resistance to serum killing, perhaps by allowing more MeOPN to be put onto the 4 position of Gal. IMPORTANCE Campylobacter jejuni undergoes phase variation in genes encoding surface antigens, leading to the concept that a strain of this organism consists of multiple genotypes that are selected for fitness in various environments. Methyl phosphoramidate modifications on the capsule of C. jejuni block access of preexisting antibodies in normal human sera to the polysaccharide chain, thus preventing activation of the classical arm of the complement cascade. We show that the capsule of strain 81-176 contains more sites of MeOPN modifications than previously recognized and that one site, on the 4 position of galactose, is more critical to complement resistance than the others. Exposure to normal human serum selects for variants in the population expressing this MeOPN modification.
Sedentary Behavior Is an Independent Predictor of Mortality in Subjects With COPD

BACKGROUND: The terms sedentary behavior and physical inactivity have been confusingly mixed. Although the association between physical inactivity and mortality has been shown previously in subjects with COPD, this association had not yet been investigated with regard to sedentarism. The aim of this work was to investigate the impact of sedentary behavior on mortality of subjects with COPD and to propose a cutoff point of sedentarism with prognostic value. METHODS: In this retrospective cohort study, sedentary behavior was assessed with 2 activity monitors (DynaPort and Sensewear armband) in 101 subjects with COPD from 2006 to 2011. Vital status was then ascertained in 2015. The following 6 variables of sedentary behavior were analyzed: average of metabolic equivalent of task (MET)/d (reflecting intensity); time spent/d lying, sitting, and lying + sitting (reflecting duration of sedentary postures); and time spent/d in activities requiring <1.5 MET and <2 MET (reflecting intensity and duration of sedentary time). Cutoff points for sedentarism and their respective prognostic values were investigated for each variable. RESULTS: Forty-one subjects (41%) died over a median (interquartile range) follow-up period of 62 (43–88) months. After adjusting for potential confounders in the Cox regression model, cutoff points from variables that combine duration of sedentary time and intensity <1.5 MET or <2 MET were associated with the increased risk of mortality. The strongest independent cutoff for predicting mortality was ≥8.5 h/d spent in sedentary activities <1.5 MET (area under the curve 0.76; hazard ratio 4.09, 95% CI 1.90–8.78; P < .001). CONCLUSIONS: Sedentary behavior was an independent predictor of mortality in subjects with COPD, even adjusting for moderate-to-vigorous physical activity and a number of other variables. Mortality was higher in subjects with COPD who spend ≥8.5 h/d in activities requiring <1.5 MET. These findings may open room for future studies aiming at decreasing sedentary time as a promising strategy to reduce mortality risk in subjects with COPD.
A DNA Vaccine Expressing Consensus Hemagglutinin-Esterase Fusion Protein Protected Guinea Pigs from Infection by Two Lineages of Influenza D Virus

ABSTRACT Two lineages of influenza D virus (IDV) have been found to infect cattle and promote bovine respiratory disease complex, one of the most commonly diagnosed causes of morbidity and mortality within the cattle industry. Furthermore, IDV can infect other economically important domestic livestock, including pigs, and has the potential to infect humans, which necessitates the need for an efficacious vaccine. In this study, we designed a DNA vaccine expressing consensus hemagglutinin-esterase fusion (HEF) protein (FluD-Vax) and tested its protective efficacy against two lineages of IDV (D/OK and D/660) in guinea pigs. Animals that received FluD-Vax (n = 12) developed appreciable titers of neutralizing antibodies against IDV lineage representatives, D/OK and D/660. Importantly, vaccinated animals were protected against intranasal challenge with IDV [3 × 105 50% tissue culture infective dose(s) (TCID50)] D/OK (n = 6) or D/600 (n = 6), based on the absence of viral RNA in necropsied tissues (5 and 7 days postchallenge) using quantitative reverse transcription-PCR and in situ hybridization. In contrast, animals that received a sham DNA vaccine (n = 12) had no detectable neutralizing antibodies against IDV, and viral RNA was readily detectable in respiratory tract tissues after intranasal challenge (3 × 105 TCID50) with IDV D/OK (n = 6) or D/660 (n = 6). Using a TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) assay, we found that IDV D/OK and D/600 infections induced apoptosis in epithelial cells lining alveoli and bronchioles, as well as nonepithelial cells in lung tissues. Our results demonstrate for the first time that the consensus IDV HEF DNA vaccine can elicit complete protection against infection from two lineages of IDV in the guinea pig model. IMPORTANCE Influenza D virus (IDV) infection has been associated with bovine respiratory disease complex, one of the most devastating diseases of the cattle population. Moreover, with broad host range and high environmental stability, IDV has the potential to further gain virulence or even infect humans. An efficacious vaccine is needed to prevent infection and stop potential cross-species transmission. In this study, we designed a DNA vaccine encoding the consensus hemagglutinin-esterase fusion (HEF) protein of two lineages of IDV (D/OK and D/660) and tested its efficacy in a guinea pig model. Our results showed that the consensus DNA vaccine elicited high-titer neutralizing antibodies and achieved sterilizing protection against two lineage-representative IDV intranasal infections. To our knowledge, this is the first study showing that a DNA vaccine expressing consensus HEF is efficacious in preventing different lineages of IDV infections.
A parallel vector quantization processor eliminating redundant calculations for real-time motion picture compression

A technique to eliminate redundant distance calculations is used in a vector quantization (VQ) processor which handles 2048 template vectors with a single chip. A real-time motion picture compression system employing this chip can transmit five QVGA (320/spl times/240 pixels) images per second at <64 kb/s.
30 years of ad hoc networking research: what about humanitarian and disaster relief solutions? what are we still missing?

In this invited talk, we will start by surveying the research works conducted during the last 30 years on wireless networking technologies from ad hoc, mesh to delay-tolerant opportunistic networks. We present how these networking technology may be applied to uphold communications in the event of a disaster where the communication infrastructure can be wiped-out (earthquakes, floods), overloaded (surge of traffic and flash crowds) or not existing in the first place (developing countries). We summarize the advantages and disadvantages of each unique approach, how they can be combined together (and with legacy systems), and focus on recent advances in the field. In a second part we will present, Twimight, our Twitter application relying on opportunistic communications to spread tweets and sensor data in an epidemic fashion. Twimight is an open source Twitter client for Android phones featured with a "disaster mode", which users enable upon losing connectivity. In the disaster mode, tweets are not sent to the online Twitter servers but stored on the phone, carried around as people move, and forwarded opportunistically via Bluetooth or WiFi Direct when in proximity with other smartphones. We will demonstrate how opportunistic technologies such as Twimight can be of great value right after a disaster by enabling the self-organization of victims and a better coordination with first rescue organizations. Eventually, we will conclude with the main challenges still to overcome and provide directions for future research in this emerging field from protocol and system design to security and data privacy. We will stress the need for cross-disciplinary approaches to better understand the psychology of distressed victims and their interaction with innovative communication technologies.
Metabolism and proteomics of large and small dense LDL in combined hyperlipidemia: effects of rosuvastatin1[S]

Small dense LDL (sdLDL) has been reported to be more atherogenic than large buoyant LDL (lbLDL). We examined the metabolism and protein composition of sdLDL and lbLDL in six subjects with combined hyperlipidemia on placebo and rosuvastatin 40 mg/day. ApoB-100 kinetics in triglyceride-rich lipoproteins (TRLs), lbLDL (density [d] = 1.019–1.044 g/ml), and sdLDL (d = 1.044–1.063 g/ml) were determined in the fed state by using stable isotope tracers, mass spectrometry, and compartmental modeling. Compared with placebo, rosuvastatin decreased LDL cholesterol and apoB-100 levels in TRL, lbLDL, and sdLDL by significantly increasing the fractional catabolic rate of apoB-100 (TRL, +45%; lbLDL, +131%; and sdLDL, +97%), without a change in production. On placebo, 25% of TRL apoB-100 was catabolized directly, 37% was converted to lbLDL, and 38% went directly to sdLDL; rosuvastatin did not alter these distributions. During both phases, sdLDL apoB-100 was catabolized more slowly than lbLDL apoB-100 (P < 0.01). Proteomic analysis indicated that rosuvastatin decreased apoC-III and apoM content within the density range of lbLDL (P < 0.05). In our view, sdLDL is more atherogenic than lbLDL because of its longer plasma residence time, potentially resulting in more particle oxidation, modification, and reduction in size, with increased arterial wall uptake. Rosuvastatin enhances the catabolism of apoB-100 in both lbLDL and sdLDL.