Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Tau Protein on the Antidepressant Effects of Ketamine in the Chronic Unpredictable Mild Stress Model

Tau protein is known to play an important role in maintaining microtubule assembly and stabilization, and maintaining the normal morphology of neurons, but several studies have found that chronic stress leads to Tau hyperphosphorylation. A large number of clinical trials have found that ketamine, which is an N-methyl-D-aspartate receptor antagonist, produces a rapid, long-lasting, and potent antidepressant effect in patients suffering from major depression. This rapid antidepressant effect of ketamine, which involves many mechanisms, has attracted wide attention. However, the relationship between ketamine’s antidepressant effects and Tau protein has rarely been examined. We used C57BL/6 and Tau KO mice exposed to 42 days of chronic unpredictable mild stress (the CUMS model) to investigate the effect of ketamine on behavioral changes and synaptic functioning of the hippocampus. The results showed that a single treatment of ketamine rapidly relieved the CUMS-induced anhedonia, depression-like, and anxious behaviors of the C57BL/6 mice. The abnormal behaviors were accompanied by increased levels of specific alterations of hyperphosphorylated Tau protein in cytoplasm and synapse in the hippocampus of the C57BL/6 mice, but ketamine reduced the aggregation of hyperphosphorylated Tau protein only in the synapse. We also found that CUMS exposure reduced the levels of GluA1 and PSD95 in the hippocampus of the C57BL/6 mice and that these deficits were reversed by ketamine. However, the Tau KO mice did not develop any stress-induced depressive behaviors or deficits of hippocampal function. The antidepressant effect of ketamine may decrease the levels of hyperphosphorylated Tau protein in synapse of C57BL/6 mice.
Gait Synthesis with Reduced Proprioceptive Requirements George Council

Sensory and motor neural signaling is comparatively limited in bandwidth and irregular in timing compared to human-designed electronic channels. Despite this, legged animals routinely out-perform robots in leggedlocomotion tasks. One possible contributor to the performance differential is predicted by event-selected systems. Event-selected vector fields, recently formalized by Burden and Revzen [1] to model simultaneous contacts in legged systems, predict a strategy to synthesize a gait as a function of the limb states that is structurally persistent despite irregular or imperfect knowledge in ground contact events, and has looser bandwidth requirements than reference-signal policies that are widely used to drive robots. Empirical analysis of trotting horses by Yuan et. al [2] suggested that event-selected phenomena were contributing to the stability of a horse gait, but left open the possibly that other mechanisms were at work. In order to show that the regime may not just be contributory, but be entirely sufficient to generate a rhythmic stride, an event-selected control scheme was implemented on a Robotic Hexapod (RHex) robot, a six-limbed legged device. A RHex was chosen as RHex robots have been shown to be capable dynamic locomotor when driven [3], [4] with a reference trajectory the Buehler clock, which generates an alternating sequence of footfalls in a prescribed pattern regardless of the environment. Using the solution curve of an event-selected vector field, an analogous, but interactive, gait created was with low (10-20 Hz) closed loop bandwidth between the actuators and the central authority commanding the limbs. The relaxed tracking requirements, structural stability, and timing characteristics results of event-selected synchronization theory suggest a possible resolution, compatible with musculoskeletal signaling limitations, to how animals are able to achieve remarkable performance on rugged terrain.
Spatial scale dependency of the modelled climatic response to deforestation

Abstract. Deforestation is associated with increased atmospheric CO2 and alterations to the surface energy and mass balances that can lead to local and global climate changes. Previous modelling studies show that the global surface air temperature (SAT) response to deforestation depends on latitude, with most simulations showing that high latitude deforestation results in cooling, low latitude deforestation causes warming and that the mid latitude response is mixed. These earlier conclusions are based on simulated large scale land cover change, with complete removal of trees from whole latitude bands. Using a global climate model we determine effects of removing fractions of 5% to 100% of forested areas in the high, mid and low latitudes. All high latitude deforestation scenarios reduce mean global SAT, the opposite occurring for low latitude deforestation, although a decrease in SAT is registered over low latitude deforested areas. Mid latitude SAT response is mixed. For all simulations deforested areas tend to become drier and have lower surface air temperature, although soil temperatures increase over deforested mid and low latitude grid cells. For high latitude deforestation fractions of 45% and above, larger net primary productivity, in conjunction with colder and drier conditions after deforestation, cause an increase in soil carbon large enough to generate a previously not reported net drawdown of CO2 from the atmosphere. Our results support previous indications of the importance of changes in cloud cover in the modelled temperature response to deforestation at low latitudes. They also show the complex interaction between soil carbon dynamics and climate and the role this plays on the climatic response to land cover change.
Twitter Sentiment Analysis using Distributed Word and Sentence Representation

An important part of the information gathering and data analysis is to find out what people think about, either a product or an entity. Twitter is an opinion rich social networking site. The posts or tweets from this data can be used for mining people's opinions. The recent surge of activity in this area can be attributed to the computational treatment of data, which made opinion extraction and sentiment analysis easier. This paper classifies tweets into positive and negative sentiments, but instead of using traditional methods or preprocessing text data here we use the distributed representations of words and sentences to classify the tweets. We use Long Short Term Memory (LSTM) Networks, Convolutional Neural Networks (CNNs) and Artificial Neural Networks. The first two are used on Distributed Representation of words while the latter is used on the distributed representation of sentences. This paper achieves accuracies as high as 81%. It also suggests the best and optimal ways for creating distributed representations of words for sentiment analysis, out of the available methods.
Dose‐dependent modulation of the visually evoked N1/N170 by perceptual surprise: a clear demonstration of prediction‐error signalling

Prediction‐error checking processes play a key role in predictive coding models of perception. However, neural indices of such processes have yet to be unambiguously demonstrated. To date, experimental paradigms aiming to study such phenomena have relied upon the relative frequency of stimulus repeats and/or ‘unexpected’ events that are physically different from ‘expected’ events. These features of experimental design leave open alternative explanations for the observed effects. A definitive demonstration requires that presumed prediction error‐related responses should show contextual dependency (rather than simply effects of frequency or repetition) and should not be attributable to low‐level stimulus differences. Most importantly, prediction‐error signals should show dose dependency with respect to the degree to which expectations are violated. Here, we exploit a novel experimental paradigm specifically designed to address these issues, using it to interrogate early latency event‐related potentials (ERPs) to contextually expected and unexpected visual stimuli. In two electroencephalography (EEG) experiments, we demonstrate that an N1/N170 evoked potential is robustly modulated by unexpected perceptual events (‘perceptual surprise’) and shows dose‐dependent sensitivity with respect to both the influence of prior information and the extent to which expectations are violated. This advances our understanding of perceptual predictions in the visual domain by clearly identifying these evoked potentials as an index of visual surprise.
High Quality Degree Based Heuristics for the Influence Maximization Problem

The problem of influence maximization is to select the most influential individuals in a social network. With the popularity of social network sites, and the development of viral marketing, the importance of the problem has been increased. The influence maximization problem is NP-hard, and therefore, there will not exist a polynomial-time algorithm to solve the problem unless P=NP. Many heuristics are proposed to find a nearly good solution in a shorter time. In this paper, we propose two heuristic algorithms to find good solutions. The heuristics are based on two ideas: (1) vertices of high degree have more influence in the network, and (2) nearby vertices influence on almost analogous sets of vertices. We evaluate our algorithms on several well-known data sets and show that our heuristics achieve better results (up to $15\%$ in influence spread) for this problem in a shorter time (up to $85\%$ improvement in the running time).
Regulation of Neuropeptide Processing Enzymes by Catecholamines in Endocrine Cells

Treatment of cultured bovine adrenal chromaffin cells with the catecholamine transport blocker reserpine was shown previously to increase enkephalin levels severalfold. To explore the biochemical mechanism of this effect, we examined the effect of reserpine treatment on the activities of three different peptide precursor processing enzymes: carboxypeptidase E (CPE) and the prohormone convertases (PCs) PC1/3 and PC2. Reserpine treatment increased both CPE and PC activity in extracts of cultured chromaffin cells; total protein levels were unaltered for any enzyme. Further analysis showed that the increase in CPE activity was due to an elevated Vmax, with no change in the Km for substrate hydrolysis or the levels of CPE mRNA. Reserpine activation of endogenous processing enzymes was also observed in extracts prepared from PC12 cells stably expressing PC1/3 or PC2. In vitro experiments using purified enzymes showed that catecholamines inhibited CPE, PC1/3, and PC2, with dopamine quinone the most potent inhibitor (IC50 values of ∼50–500 μM); dopamine, norepinephrine, and epinephrine exhibited inhibition in the micromolar range. The inhibition of purified CPE with catecholamines was time-dependent and, for dopamine quinone, dilution-independent, suggesting covalent modification of the protein by the catecholamine. Because the catecholamine concentrations found to be inhibitory to PC1/3, PC2, and CPE are well within the physiological range found in chromaffin granules, we conclude that catecholaminergic transmitter systems have the potential to exert considerable dynamic influence over peptidergic transmitter synthesis by altering the activity of peptide processing enzymes.
Authenticated Key-Value Stores with Hardware Enclaves

Authenticated data storage on an untrusted platform is an important computing paradigm for cloud applications ranging from big-data outsourcing, to cryptocurrency and certificate transparency log. These modern applications increasingly feature update-intensive workloads, whereas existing authenticated data structures (ADSs) designed with in-place updates are inefficient to handle such workloads. In this paper, we address this issue and propose a novel authenticated log-structured merge tree (eLSM) based key-value store by leveraging Intel SGX enclaves. We present a system design that runs the code of eLSM store inside enclave. To circumvent the limited enclave memory (128 MB with the latest Intel CPUs), we propose to place the memory buffer of the eLSM store outside the enclave and protect the buffer using a new authenticated data structure by digesting individual LSM-tree levels. We design protocols to support query authentication in data integrity, completeness (under range queries), and freshness. The proof in our protocol is made small by including only the Merkle proofs at selective levels. We implement eLSM on top of Google LevelDB and Facebook RocksDB with minimal code change and performance interference. We evaluate the performance of eLSM under the YCSB workload benchmark and show a performance advantage of up to 4.5X speedup.
Modal dependent type theory and dependent right adjoints

Abstract In recent years, we have seen several new models of dependent type theory extended with some form of modal necessity operator, including nominal type theory, guarded and clocked type theory and spatial and cohesive type theory. In this paper, we study modal dependent type theory: dependent type theory with an operator satisfying (a dependent version of) the K axiom of modal logic. We investigate both semantics and syntax. For the semantics, we introduce categories with families with a dependent right adjoint (CwDRA) and show that the examples above can be presented as such. Indeed, we show that any category with finite limits and an adjunction of endofunctors give rise to a CwDRA via the local universe construction. For the syntax, we introduce a dependently typed extension of Fitch-style modal λ-calculus, show that it can be interpreted in any CwDRA, and build a term model. We extend the syntax and semantics with universes.
Learning from Barres

The untimely death of Ben Barres (Figure 1) on the December 27, 2017 signifies a terrible loss for science and for those who ever enjoyed his company. Ben’s fascinating personality, his wondrous life and his remarkable achievements have been honored elsewhere (Allen & Daneman, 2018; Butt, Nedergaard, & Verkhratsky, 2018; Huberman, 2018; Raff, 2018; Tessier-Lavigne, 2018). I would like to present some lessons that I have learned from Ben, formerly known as Barbara. My advice may be of interest to neuroscientists starting their career in the glia field and beyond. Given Ben’s passion for teaching and mentorship, I think he would endorse my intention. My “history” with Barres started in 1993. While finishing my PhD project with Hans-Dieter Lux at the Max-Planck-Institute of Psychiatry (now Neurobiology) in Martinsried (Germany), I decided to follow my simmering wish to study glial cells, and I applied for a postdoc position in Martin Raff’s lab in London. In his friendly, handwritten reply, Dr. Raff turned down my application and advised me to get in touch with his postdoc, Barbara Barres. The latter was about to become assistant professor at Stanford University. So, I wrote a letter to Barbara, who responded immediately. Figures 2 and 3 document this first exchange: The content and length of the kind and encouraging response to my admittedly cursory letter indicates already some qualities of Barres: carefulness, reliability, and enthusiasm. A first face-to-face encounter at Stanford in January 1994 revealed another trait that I appreciated very much: Barres’ sense of humor. From September 1994 to spring 1997, I worked in the Barres lab as a postdoctoral fellow studying the impact of glial cells on synapses.
Ruminal fatty acid outflow in dry cows fed different sources of linoleic acid: reticulum and omasum as alternative sampling sites to abomasum

ABSTRACT This study was designed to determine the rumen outflow of fatty acids (FA) and biohydrogenation (BH) extent using alternative sampling sites (reticulum and omasum) to abomasum in dry cows fed different sources of FA. Four Holstein non-pregnant dry cows (≥3 parturitions, and 712 ± 125 kg BW), cannulated in the rumen and abomasum, were randomly assigned to a 4 × 4 Latin square design experiment, containing the following treatments: 1) control (CON); 2) soya bean oil (SO), dietary inclusion at 30 g/kg; 3) whole raw soya beans (WS), dietary inclusion at 160 g/kg; and 4) calcium salts of FA (CSFA), dietary inclusion at 32 g/kg. Rumen outflow of nutrients was estimated using the three markers reconstitution system (cobalt-EDTA, ytterbium chloride, and indigestible neutral detergent fibre [NDF]). Diets with FA sources decreased feed intake and increased FA intake. No differences in nutrient intake and digestibility were detected among cows fed diets supplemented with different FA sources. Diets with FA sources reduced the rumen outflow of DM and NDF, hence decreasing their passage rates. In addition, SO diet reduced the ruminal outflow of DM and NDF in comparison with WS and CSFA. Omasal sampling yielded the highest values of rumen outflow of NDF and potentially degradable NDF (pdNDF), whereas the reticular and abomasal samplings yielded intermediate and least values, respectively. The interaction effect between diet and sampling site was observed for rumen outflow of majority FA (except for C16:0, C18:0, and C18:2 trans-10, cis-12) and BH extension of C18:1 cis, C18:2, and C18:3. Calculations derived from abomasal sampling revealed that WS and CSFA diets had lower BH extent of C18:1 cis and C18:2 in comparison with SO, whereas cows fed CSFA had greater BH extent of C18:3 and lower BH extent of C18:1 cis compared to those fed WS. However, the latter results were not similar when calculations were performed based on the reticular and omasal samplings. Thus, there is evidence that neither reticular nor omasal samplings are suitable for estimating rumen outflow of FA in dry cows. In addition, WS and CSFA diets can increase the abomasal flow of polyunsaturated FA in dry cows.
First-Principles Study of the Impact of Grain Boundary Formation in the Cathode Material LiFePO4

Motivated by the need to understand the role of internal interfaces in Li migration occurring in lithium-ion batteries, a first-principles study of a coincident site lattice grain boundary in LiFePO4 cathode material and in its delithiated counterpart FPO4 is performed. The structure of the investigated grain boundary is obtained, and the corresponding interface energy is calculated. Other properties, such as ionic charges, magnetic moments, excess free volume, and the lifetime of positrons trapped at the interfaces are determined and discussed. The results show that while the grain boundary in LiFePO4 has desired structural and bonding characteristics, the analogous boundary in FePO4 needs to be yet optimized to allow for an efficient Li diffusion study.
Immunogenicity and safety of three consecutive production lots of the non replicating smallpox vaccine MVA: A randomised, double blind, placebo controlled phase III trial

Background Modified Vaccinia Ankara (MVA) is a live, viral vaccine under advanced development as a non-replicating smallpox vaccine. A randomised, double-blind, placebo-controlled phase III clinical trial was conducted to demonstrate the humoral immunogenic equivalence of three consecutively manufactured MVA production lots, and to confirm the safety and tolerability of MVA focusing on cardiac readouts. Methods The trial was conducted at 34 sites in the US. Vaccinia-naïve adults aged 18-40 years were randomly allocated to one of four groups using a 1:1:1:1 randomization scheme. Subjects received either two MVA injections from three consecutive lots (Groups 1-3), or two placebo injections (Group 4), four weeks apart. Everyone except personnel involved in vaccine handling and administration was blinded to treatment. Safety assessment focused on cardiac monitoring throughout the trial. Vaccinia-specific antibody titers were measured using a Plaque Reduction Neutralization Test (PRNT) and an Enzyme-Linked Immunosorbent Assay (ELISA). The primary immunogenicity endpoint was Geometric Mean Titers (GMTs) after two MVA vaccinations measured by PRNT at trial visit 4. This trial is registered with ClinicalTrials.gov, number NCT01144637. Results Between March 2013 and May 2014, 4005 subjects were enrolled and received at least one injection of MVA (n = 3003) or placebo (n = 1002). The three MVA lots induced equivalent antibody titers two weeks after the second vaccination, with seroconversion rates of 99·8% (PRNT) and 99·7% (ELISA). Overall, 180 (6·0%) subjects receiving MVA and 29 (2·9%) subjects in the placebo group reported at least one unsolicited Adverse Event (AE) that was considered trial-related. Vaccination was well tolerated without significant safety concerns, particularly regarding cardiac assessment. Conclusions The neutralizing and total antibody titers induced by each of the three lots were equivalent. No significant safety concerns emerged in this healthy trial population, especially regarding cardiac safety, thus confirming the excellent safety and tolerability profile of MVA. Trial registration ClinicalTrials.gov NCT01144637
HELP project - a dreamed-of multiwavelength dataset for SED fitting: The influence of used models for the main physical properties of galaxies

Abstract The Herschel Extragalactic Legacy Project (HELP) focuses to publish an astronomical multiwavelength catalogue of millions of objects over 1300 deg2 of the Herschel Space Observatory survey fields. Millions of galaxies with ultraviolet–far infrared photometry make HELP a perfect sample for testing spectral energy distribution fitting models, and to prepare tools for next-generation data. In the frame of HELP collaboration we estimated the main physical properties of all galaxies from the HELP database and we checked a new procedure to select peculiar galaxies from large galaxy sample and we investigated the influence of used modules for stellar mass estimation.
Urine Organic Acids as Potential Biomarkers for Autism-Spectrum Disorder in Chinese Children

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that lacks clear biological biomarkers. Existing diagnostic methods focus on behavioral and performance characteristics, which complicates the diagnosis of patients younger than 3 years-old. The purpose of this study is to characterize metabolic features of ASD that could be used to identify potential biomarkers for diagnosis and exploration of ASD etiology. We used gas chromatography-mass spectrometry (GC/MS) to evaluate major metabolic fluctuations in 76 organic acids present in urine from 156 children with ASD and from 64 non-autistic children. Three algorithms, Partial Least Squares-Discriminant Analysis (PLS-DA), Support Vector Machine (SVM), and eXtreme Gradient Boosting (XGBoost), were used to develop models to distinguish ASD from typically developing (TD) children and to detect potential biomarkers. In an independent testing set, full model of XGBoost with all 76 acids achieved an AUR of 0.94, while reduced model with top 20 acids discovered by voting from these three algorithms achieved 0.93 and represent a good collection of potential ASD biomarkers. In summary, urine organic acids detection with GC/MS combined with XGBoost algorithm could represent a novel and accurate strategy for diagnosis of autism and the discovered potential biomarkers could be valuable for future research on the pathogenesis of autism and possible interventions.