Miracle-dz/UniFAR-FTUs huggingface dataset:
Objects tell us what action we can expect: dissociating brain areas for retrieval and exploitation of action knowledge during action observation in fMRI

Objects are reminiscent of actions often performed with them: knife and apple remind us on peeling the apple or cutting it. Mnemonic representations of object-related actions (action codes) evoked by the sight of an object may constrain and hence facilitate recognition of unrolling actions. The present fMRI study investigated if and how action codes influence brain activation during action observation. The average number of action codes (NAC) of 51 sets of objects was rated by a group of n = 24 participants. In an fMRI study, different volunteers were asked to recognize actions performed with the same objects presented in short videos. To disentangle areas reflecting the storage of action codes from those exploiting them, we showed object-compatible and object-incompatible (pantomime) actions. Areas storing action codes were considered to positively co-vary with NAC in both object-compatible and object-incompatible action; due to its role in tool-related tasks, we here hypothesized left anterior inferior parietal cortex (aIPL). In contrast, areas exploiting action codes were expected to show this correlation only in object-compatible but not incompatible action, as only object-compatible actions match one of the active action codes. For this interaction, we hypothesized ventrolateral premotor cortex (PMv) to join aIPL due to its role in biasing competition in IPL. We found left anterior intraparietal sulcus (IPS) and left posterior middle temporal gyrus (pMTG) to co-vary with NAC. In addition to these areas, action codes increased activity in object-compatible action in bilateral PMv, right IPS, and lateral occipital cortex (LO). Findings suggest that during action observation, the brain derives possible actions from perceived objects, and uses this information to shape action recognition. In particular, the number of expectable actions quantifies the activity level at PMv, IPL, and pMTG, but only PMv reflects their biased competition while observed action unfolds.
Glucose & sodium chloride induced biofilm production & ica operon in clinical isolates of staphylococci

Background & objectives: All colonizing and invasive staphylococcal isolates may not produce biofilm but may turn biofilm producers in certain situations due to change in environmental factors. This study was done to test the hypothesis that non biofilm producing clinical staphylococci isolates turn biofilm producers in presence of sodium chloride (isotonic) and high concentration of glucose, irrespective of presence or absence of ica operon. Methods: Clinical isolates of 100 invasive, 50 colonizing and 50 commensal staphylococci were tested for biofilm production by microtiter plate method in different culture media (trypticase soy broth alone or supplemented with 0.9% NaCl/ 5 or 10% glucose). All isolates were tested for the presence of ica ADBC genes by PCR. Results: Biofilm production significantly increased in the presence of glucose and saline, most, when both glucose and saline were used together. All the ica positive staphylococcal isolates and some ica negative isolates turned biofilm producer in at least one of the tested culture conditions. Those remained biofilm negative in different culture conditions were all ica negative. Interpretation & conclusions: The present results showed that the use of glucose or NaCl or combination of both enhanced biofilm producing capacity of staphylococcal isolates irrespective of presence or absence of ica operon.
Histamine Transmission Modulates the Phenotype of Murine Narcolepsy Caused by Orexin Neuron Deficiency

Narcolepsy type 1 is associated with loss of orexin neurons, sleep-wake derangements, cataplexy, and a wide spectrum of alterations in other physiological functions, including energy balance, cardiovascular, and respiratory control. It is unclear which narcolepsy signs are directly related to the lack of orexin neurons or are instead modulated by dysfunction of other neurotransmitter systems physiologically controlled by orexin neurons, such as the histamine system. To address this question, we tested whether some of narcolepsy signs would be detected in mice lacking histamine signaling (HDC-KO). Moreover, we studied double-mutant mice lacking both histamine signaling and orexin neurons (DM) to evaluate whether the absence of histamine signaling would modulate narcolepsy symptoms produced by orexin deficiency. Mice were instrumented with electrodes for recording the electroencephalogram and electromyogram and a telemetric arterial pressure transducer. Sleep attacks fragmenting wakefulness, cataplexy, excess rapid-eye-movement sleep (R) during the activity period, and enhanced increase of arterial pressure during R, which are hallmarks of narcolepsy in mice, did not occur in HDC-KO, whereas they were observed in DM mice. Thus, these narcolepsy signs are neither caused nor abrogated by the absence of histamine. Conversely, the lack of histamine produced obesity in HDC-KO and to a greater extent also in DM. Moreover, the regularity of breath duration during R was significantly increased in either HDC-KO or DM relative to that in congenic wild-type mice. Defects of histamine transmission may thus modulate the metabolic and respiratory phenotype of murine narcolepsy.
Changes in MicroRNA Expression Contribute to Pancreatic β-Cell Dysfunction in Prediabetic NOD Mice

During the initial phases of type 1 diabetes, pancreatic islets are invaded by immune cells, exposing β-cells to proinflammatory cytokines. This unfavorable environment results in gene expression modifications leading to loss of β-cell functions. To study the contribution of microRNAs (miRNAs) in this process, we used microarray analysis to search for changes in miRNA expression in prediabetic NOD mice islets. We found that the levels of miR-29a/b/c increased in islets of NOD mice during the phases preceding diabetes manifestation and in isolated mouse and human islets exposed to proinflammatory cytokines. Overexpression of miR-29a/b/c in MIN6 and dissociated islet cells led to impairment in glucose-induced insulin secretion. Defective insulin release was associated with diminished expression of the transcription factor Onecut2, and a consequent rise of granuphilin, an inhibitor of β-cell exocytosis. Overexpression of miR-29a/b/c also promoted apoptosis by decreasing the level of the antiapoptotic protein Mcl1. Indeed, a decoy molecule selectively masking the miR-29 binding site on Mcl1 mRNA protected insulin-secreting cells from apoptosis triggered by miR-29 or cytokines. Taken together, our findings suggest that changes in the level of miR-29 family members contribute to cytokine-mediated β-cell dysfunction occurring during the initial phases of type 1 diabetes.
Supporting Selective Undo in a Code Editor

Programmers often need to revert some code to an earlier state, or restore a block of code that was deleted a while ago. However, support for this backtracking in modern programming environments is limited. Many of the backtracking tasks can be accomplished by having a selective undo feature in code editors, but this has major challenges: there can be conflicts among edit operations, and it is difficult to provide usable interfaces for selective undo. In this paper, we present AZURITE, an Eclipse plug-in that allows programmers to selectively undo fine-grained code changes made in the code editor. With AZURITE, programmers can easily perform backtracking tasks, even when the desired code is not in the undo stack or a version control system. AZURITE also provides novel user interfaces specifically designed for selective undo, which were iteratively improved through user feedback gathered from actual users in a preliminary field trial. A formal lab study showed that programmers can successfully use AZURITE, and were twice as fast as when limited to conventional features.
Stochastic Approximation for Consensus: A New Approach via Ergodic Backward Products

This paper considers both synchronous and asynchronous consensus algorithms with noisy measurements. For stochastic approximation based consensus algorithms, the existing convergence analysis with dynamic topologies heavily relies on quadratic Lyapunov functions, whose existence, however, may be difficult to ensure for switching directed graphs. Our main contribution is to introduce a new analytical approach. We first show a fundamental role of ergodic backward products for mean square consensus in algorithms with additive noise. Subsequently, we develop ergodicity results for backward products of degenerating stochastic matrices converging to a 0-1 matrix via a discrete time dynamical system approach. These results complement the existing ergodic theory of stochastic matrices and provide an effective tool for analyzing consensus problems. Under a joint connectivity assumption, our approach may deal with switching topologies, delayed measurements and correlated noises, and it does not require the double stochasticity condition typically assumed for the existence of quadratic Lyapunov functions.
Classifying finite localizations of quasicoherent sheaves

Given a quasi-compact, quasi-separated scheme X, a bijection between the tensor localizing subcategories of finite type in Qcoh(X) and the set of all subsets $Y\subseteq X$ of the form $Y=\bigcup_{i\in\Omega}Y_i$, with $X\setminus Y_i$ quasi-compact and open for all $i\in\Omega$, is established. As an application, there is constructed an isomorphism of ringed spaces (X,O_X)-->(Spec(Qcoh(X)),O_{Qcoh(X)}), where $(Spec(Qcoh(X)),O_{Qcoh(X)})$ is a ringed space associated to the lattice of tensor localizing subcategories of finite type. Also, a bijective correspondence between the tensor thick subcategories of perfect complexes $\perf(X)$ and the tensor localizing subcategories of finite type in Qcoh(X) is established.
Basophil activation tests in the evaluation of immediate drug hypersensitivity

Purpose of reviewThe aim of this study was to confirm the applicability of the basophil activation test (BAT) in the in-vitro diagnosis of drug allergy reactions. Recent findingsThe results obtained in terms of sensitivity and specificity with BAT are encouraging and in significant number of cases can establish the diagnosis. SummaryBAT sensitivity in beta-lactam allergy was 50%, and specificity ranged from 89 to 97%. There are several studies to validate the BAT in allergy to muscle relaxants showing a sensitivity ranging from 54 to 64% with a specificity of 100 and 93%. The sensitivity of a test for evaluating immediate allergic reactions to drugs may decrease over time. To date, the BAT is the only in-vitro diagnostic method that has been validated for the diagnosis of both IgE-mediated and hypersensitivity reactions to NSAIDs. With respect to other drugs, they are nonetheless interesting as they include the evaluation of allergy to drugs that cannot be studied by other in-vitro techniques. All these data suggest that although a full validation of the test is required, BAT is a potential diagnostic method for evaluating immediate allergic reactions to drugs and NSAID hypersensitivity reactions.
Staying afloat on Neurath's boat - Heuristics for sequential causal learning

Causal models are key to flexible and efficient exploitation of the environment. However, learning causal structure is hard, with massive spaces of possible models, hard-to-compute marginals and the need to integrate diverse evidence over many instances. We report on two experiments in which participants learnt about probabilistic causal systems involving three and four variables from sequences of interventions. Participants were broadly successful, albeit exhibiting sequential dependence and floundering under high background noise. We capture their behavior with a simple model, based on the “Neurath’s ship” metaphor for scientific progress, that neither maintains a probability distribution, nor computes exact likelihoods.
A comparison of particle mass spectrometers during the 1999 Atlanta Supersite Project

During the Atlanta Supersite Project, four particle mass spectrometers were operated together for the first time: NOAA's Particle Analysis by Laser Mass Spectrometer (PALMS), University of California at Riverside's Aerosol Time-of-Flight Mass Spectrometer (ATOFMS), University of Delaware's Rapid Single-Particle Mass Spectrometer II (RSMS-II), and Aerodyne's Aerosol Mass Spectrometer (AMS). Although these mass spectrometers are generally classified as similar instruments, they clearly have different characteristics due to their unique designs. One primary difference is related to the volatilization/ionization method: PALMS, ATOFMS, and RSMS-II utilize laser desorption/ionization, whereas particles in the AMS instrument are volatilized by impaction onto a heated surface with the resulting components ionized by electron impact. Thus mass spectral data from the AMS are representative of the ensemble of particles sampled, and those from the laser-based instruments are representative of individual particles. In addition, the AMS instrument cannot analyze refractory material such as soot, sodium chloride, and crustal elements, and some sulfate or water-rich particles may not always be analyzed with every laser-based instrument. A main difference among the laser-based mass spectrometers is that the RSMS-II instrument can obtain size-resolved single particle composition information for particles with aerodynamic diameters as small as 15 nm. The minimum sizes analyzed by ATOFMS and PALMS are 0.2 and about 0.35 μm, respectively, in aerodynamic diameter. Furthermore, PALMS, ATOFMS, and RSMS-II use different laser ionization conditions. Despite these differences the laser-based instruments found similar individual particle classifications, and their relative fractions among comparable sized particles from Atlanta were broadly consistent. Finally, the AMS measurements of the nitrate/sulfate mole ratio were highly correlated with composite measurements (r^2 = 0.93). In contrast, the PALMS nitrate/sulfate ion ratios were only moderately correlated (r^2 ∼ 0.7).
A Cryptographic Analysis of the TLS 1.3 Handshake Protocol Candidates

The Internet Engineering Task Force (IETF) is currently developing the next version of the Transport Layer Security (TLS) protocol, version 1.3. The transparency of this standardization process allows comprehensive cryptographic analysis of the protocols prior to adoption, whereas previous TLS versions have been scrutinized in the cryptographic literature only after standardization. This is even more important as there are two related, yet slightly different, candidates in discussion for TLS 1.3, called draft-ietf-tls-tls13-05 and draft-ietf-tls-tls13-dh-based. We give a cryptographic analysis of the primary ephemeral Diffie-Hellman-based handshake protocol, which authenticates parties and establishes encryption keys, of both TLS 1.3 candidates. We show that both candidate handshakes achieve the main goal of providing secure authenticated key exchange according to an augmented multi-stage version of the Bellare-Rogaway model. Such a multi-stage approach is convenient for analyzing the design of the candidates, as they establish multiple session keys during the exchange. An important step in our analysis is to consider compositional security guarantees. We show that, since our multi-stage key exchange security notion is composable with arbitrary symmetric-key protocols, the use of session keys in the record layer protocol is safe. Moreover, since we can view the abbreviated TLS resumption procedure also as a symmetric-key protocol, our compositional analysis allows us to directly conclude security of the combined handshake with session resumption. We include a discussion on several design characteristics of the TLS 1.3 drafts based on the observations in our analysis.
Xenobiotic-Metabolizing Cytochromes P450 in Human White Adipose Tissue: Expression and Induction

Lipophilic pollutants can accumulate in human white adipose tissue (WAT), and the consequences of this accumulation are still poorly understood. Cytochromes P450 (P450s) have recently been found in rat WAT and shown to be inducible through mechanisms similar to those in the liver. The aim of our study was to describe the cytochrome P450 pattern and their induction mechanisms in human WAT. Explants of subcutaneous and visceral WAT and primary culture of subcutaneous adipocytes were used as WAT models, and liver biopsies and primary culture of hepatocytes were used as liver models to characterize P450 expression in both tissues. The WAT and liver models were then treated with typical P450 inducers (rifampicin, phenobarbital, and 2,3,7,8-tetrachlorodibenzo-p-dioxin) and lipophilic pollutants (lindane, prochloraz, and chlorpyrifos), and the effects on P450 expression were studied. P450 expression was considerably lower in WAT than in the liver, except for CYP1B1 and CYP2U1, which were the most highly expressed adipose P450s in all individuals. 2,3,7,8-Tetrachlorodibenzo-p-dioxin and prochloraz induced CYP1A1 and CYP1B1 expression in both tissues. The aryl hydrocarbon receptor was also present in WAT. In contrast, neither phenobarbital nor rifampicin treatment induced CYP2 or CYP3 mRNA in WAT, and constitutive androstane receptor and pregnane X receptor were almost undetectable. These results suggest that the mechanisms by which P450s of family 1 are regulated in the liver are also functional in human WAT, but those regulating CYP2 and CYP3 expression are not.
Simulation of nitrate transport and fate in groundwater in presence of kaolin

It has been found that aquifers containing clay particles possess a natural capacity of pollution attenuation and thereby are able to mitigate the effects of contamination. The main objective of this study was to simulate nitrate (NO3) movement and fate in porous media in presence of clay kaolin using a numerical and physical model in order to estimate the pollution attenuation capacity of kaolin. A noncommercial solute transport model known as Ground Water Key (GWK) was used to simulate NO3 concentration in an idealized physical model for this purpose. Nitrate polluted water at level 112.5 mg NO3 L−1 was introduced to the porous media of the physical model for experimental data collection and validation of numerical simulation by GWK. The results revealed that the GWK model can estimate NO3 concentration with a high level of accuracy in porous media in presence of kaolin. Nitrate concentrations in porous media and the dispersion coefficient were found to be sensitive to initial NO3 concentration. The results also revealed that kaolin can retain NO3 and thus is able to reduce NO3 pollution by approximately one-third. It is expected that the study results can be helpful in groundwater monitoring and protection.
A Systematic Review of Psychological Interventions for Adult and Pediatric Patients with Vocal Cord Dysfunction

Background: Vocal cord dysfunction (VCD) or paradoxical vocal-fold motion (PVFM) is a functional disorder of the vocal cords that requires multidisciplinary treatment. Besides relaxation techniques, the use of psychological interventions can help treat the underlying psychological co-morbidities. There is currently no literature that examines the effectiveness of psychological interventions for VCD/PVFM. Objectives: To review the evidence for psychological interventions used for the treatment of patients with VCD/PVFM. Data sources: We searched electronic databases for English medical literature using Pubmed (Medline), PsycInfo, Cochrane Database of Systematic Reviews, Cochrane Central Registry of Controlled Trials, and Clinicaltrials.gov. The date range for our search is from June 1964 to June 2014. Study eligibility criteria, participants, and interventions: We included studies that reported the use of psychological interventions in both adults and children diagnosed with VCD/PVFM. We included randomized controlled trials, case-control studies, retrospective chart reviews, prospective case series, and individual case reports. Results: Most reported studies are small case series or individual case reports that have described the use of interventions such as psychotherapy, behavioral therapy, use of anti-anxiety and anti-depressant medications, and hypnotherapy in conjunction with breathing exercises taught by speech therapists for symptomatic relief. Among the various psychological interventions that have been reported, there is no data regarding effectiveness and/or superiority of one approach over another in either adult or pediatric patients. Conclusions: Psychological interventions have a role to play in the management of adult and pediatric patients with VCD/PVFM. Future prospective studies using uniform approaches for treatment of associated psychopathology may help address this question.
A Comparative Study of Protective Immunity Provided by Oral, Intranasal and Parenteral Canine Bordetella bronchiseptica Vaccines

The present study was designed to determine if an oral live Bordetella bronchiseptica vaccine protects dogs from developing signs of respiratory disease after challenge with virulent Bordetella bronchiseptica. The study was also designed to compare the level of protection induced by the oral vaccine with the protection provided by an intranasal live vaccine and an injected killed vaccine. Forty 6-8 week old beagles, culture and antibody negative to Bordetella bronchiseptica, were randomly distributed to 4 groups. Group 1 (O) received a single dose of attenuated oral Bordetella vaccine at study day 14; Group 2 (IN) received a single dose of attenuated intranasal Bordetella vaccine at study day 14; Group 3 (SCu) received two doses of killed Bordetella vaccine administered subcutaneously at study days 0 and 14; and Group 4 (C) received saline both intranasally and subcutaneously. All dogs were challenged with virulent Bordetella bronchiseptica via nebulization chamber at study day 42. Blood and nasal swabs were collected weekly thru-out the study for serology and bacterial culture. After challenge, daily clinical assessments included body temperature and a weighted score of coughing and other respiratory disease signs. Severe signs of disease in the control group proved the validity of our challenge model. Results of this study showed that the oral Bordetella bronchiseptica vaccine protects dogs from challenge. This protection provided by the oral vaccine was equivalent to that induced by intranasal vaccine, and was superior to protection provided by the killed, subcutaneously administered vaccine.