Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro and In Vivo Characterization of the Alkaloid Nuciferine

Rationale The sacred lotus (Nelumbo nucifera) contains many phytochemicals and has a history of human use. To determine which compounds may be responsible for reported psychotropic effects, we used in silico predictions of the identified phytochemicals. Nuciferine, an alkaloid component of Nelumbo nucifera and Nymphaea caerulea, had a predicted molecular profile similar to antipsychotic compounds. Our study characterizes nuciferine using in vitro and in vivo pharmacological assays. Methods Nuciferine was first characterized in silico using the similarity ensemble approach, and was followed by further characterization and validation using the Psychoactive Drug Screening Program of the National Institute of Mental Health. Nuciferine was then tested in vivo in the head-twitch response, pre-pulse inhibition, hyperlocomotor activity, and drug discrimination paradigms. Results Nuciferine shares a receptor profile similar to aripiprazole-like antipsychotic drugs. Nuciferine was an antagonist at 5-HT2A, 5-HT2C, and 5-HT2B, an inverse agonist at 5-HT7, a partial agonist at D2, D5 and 5-HT6, an agonist at 5-HT1A and D4 receptors, and inhibited the dopamine transporter. In rodent models relevant to antipsychotic drug action, nuciferine blocked head-twitch responses and discriminative stimulus effects of a 5-HT2A agonist, substituted for clozapine discriminative stimulus, enhanced amphetamine induced locomotor activity, inhibited phencyclidine (PCP)-induced locomotor activity, and rescued PCP-induced disruption of prepulse inhibition without induction of catalepsy. Conclusions The molecular profile of nuciferine was similar but not identical to that shared with several approved antipsychotic drugs suggesting that nuciferine has atypical antipsychotic-like actions.
Dynamic Hebbian Cross-Correlation Learning Resolves the Spike Timing Dependent Plasticity Conundrum

Spike Timing-Dependent Plasticity has been found to assume many different forms. The classic STDP curve, with one potentiating and one depressing window, is only one of many possible curves that describe synaptic learning using the STDP mechanism. It has been shown experimentally that STDP curves may contain multiple LTP and LTD windows of variable width, and even inverted windows. The underlying STDP mechanism that is capable of producing such an extensive, and apparently incompatible, range of learning curves is still under investigation. In this paper, it is shown that STDP originates from a combination of two dynamic Hebbian cross-correlations of local activity at the synapse. The correlation of the presynaptic activity with the local postsynaptic activity is a robust and reliable indicator of the discrepancy between the presynaptic neuron and the postsynaptic neuron's activity. The second correlation is between the local postsynaptic activity with dendritic activity which is a good indicator of matching local synaptic and dendritic activity. We show that this simple time-independent learning rule can give rise to many forms of the STDP learning curve. The rule regulates synaptic strength without the need for spike matching or other supervisory learning mechanisms. Local differences in dendritic activity at the synapse greatly affect the cross-correlation difference which determines the relative contributions of different neural activity sources. Dendritic activity due to nearby synapses, action potentials, both forward and back-propagating, as well as inhibitory synapses will dynamically modify the local activity at the synapse, and the resulting STDP learning rule. The dynamic Hebbian learning rule ensures furthermore, that the resulting synaptic strength is dynamically stable, and that interactions between synapses do not result in local instabilities. The rule clearly demonstrates that synapses function as independent localized computational entities, each contributing to the global activity, not in a simply linear fashion, but in a manner that is appropriate to achieve local and global stability of the neuron and the entire dendritic structure.
LOFAR Lightning Imaging: Mapping Lightning With Nanosecond Precision

Lightning mapping technology has proven instrumental in understanding lightning. In this work we present a pipeline that can use lightning observed by the LOw‐Frequency ARray (LOFAR) radio telescope to construct a 3‐D map of the flash. We show that LOFAR has unparalleled precision, on the order of meters, even for lightning flashes that are over 20 km outside the area enclosed by LOFAR antennas (∼3,200 km2), and can potentially locate over 10,000 sources per lightning flash. We also show that LOFAR is the first lightning mapping system that is sensitive to the spatial structure of the electrical current during individual lightning leader steps.
Molecular, Cellular, and Developmental Biology Developmental Regulation of Nutrient Transporter and Enzyme Mrna Abundance in the Small Intestine of Broilers 1

The objective of this study was to investigate intestinal nutrient transporter and enzyme mRNA in broilers selected on corn-and soybean-based (line A) or wheat-based (line B) diets. We investigated the peptide transporter PepT1, 10 amino acid transporters GLUT5, and GLUT2), and a digestive enzyme (aminopep-tidase N). Intestine was collected at embryo d 18 and 20, day of hatch, and d 1, 3, 7, and 14 posthatch. The mRNA abundance of each gene was assayed using real-time PCR and the absolute quantification method. For PepT1, line B had greater quantities of mRNA compared with line A (P = 0.001), suggesting a greater capacity for absorption of amino acids as peptides. Levels of PepT1 mRNA were
Distributed Coloring in Sparse Graphs with Fewer Colors

This paper is concerned with efficiently coloring sparse graphs in the distributed setting with as few colors as possible. According to the celebrated Four Color Theorem, planar graphs can be colored with at most 4 colors, and the proof gives a (sequential) quadratic algorithm finding such a coloring. A natural problem is to improve this complexity in the distributed setting. Using the fact that planar graphs contain linearly many vertices of degree at most 6, Goldberg, Plotkin, and Shannon obtained a deterministic distributed algorithm coloring n-vertex planar graphs with 7 colors in O(log n) rounds. Here, we show how to color planar graphs with 6 colors in polylog(n) rounds. Our algorithm indeed works more generally in the list-coloring setting and for sparse graphs (for such graphs we improve by at least one the number of colors resulting from an efficient algorithm of Barenboim and Elkin, at the expense of a slightly worst complexity). Our bounds on the number of colors turn out to be quite sharp in general. Among other results, we show that no distributed algorithm can color every n-vertex planar graph with 4 colors in o(n) rounds.
Texture Segmentation Based Video Compression Using Convolutional Neural Networks

There has been a growing interest in using different approaches to improve the coding efficiency of modern video codec in recent years as demand for web-based video consumption increases. In this paper, we propose a model-based approach that uses texture analysis/synthesis to reconstruct blocks in texture regions of a video to achieve potential coding gains using the AV1 codec developed by the Alliance for Open Media (AOM). The proposed method uses convolutional neural networks to extract texture regions in a frame, which are then reconstructed using a global motion model. Our preliminary results show an increase in coding efficiency while maintaining satisfactory visual quality.
Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

High efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
Relevance Ranking for Geographic IR

In this paper, we introduce a geographic similarity operator that computes the relatedness between two geographic places and describe how it is combined with textual ranking. The effectiveness of the geographic ranking is evaluated on the GeoCLEF 2005 collection. We considered various strategies for query formulation and for combining textual ant geographical ranking. For some queries, geographic ranking significantly improves results, while for other queries it does not have a positive impact.
Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island

An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here, we use genetic pedigree analyses to examine 3 seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered. We determined that 8 of 9 founding individuals were assigned parentage to at least 1 of 130 offspring produced, though there was considerable reproductive skew. In addition, we observed that genetic diversity of the progeny was lower than that of the founders. Despite the observed reproductive skew, we did not see evidence for assortative mating based on relatedness, but there was a trend toward reduced fitness when more related individuals bred. Finally, we found that the majority of progeny had ancestry assigned to the Floreana species (mean ± SE = 0.51 ± 0.02), though individual estimates varied. The success of these pilot seasons bodes well for a larger breeding program to help restore the previously extinct tortoise from Floreana island. Future efforts should continue to monitor for reproductive skew and assortative mating to maintain allelic diversity. We would also recommend forming smaller breeding groups and rotating individuals among them to prevent long-term reproductive skew among pairs.
luctuations in the open time of synaptic channels : An application to noise nalysis based on charge

Synaptic channels are stochastic devices. Even recording from large ensembles of channels, the fluctuations, described by Markov transition matrices, can be used to extract single channel properties. Here we study fluctuations in the open time of channels, which is proportional to the charge flowing eywords: ynaptic transmission oise analysis tochastic channels eural variability through the channel. We use the results to implement a novel type of noise analysis that uses the charge rather than the current to extract fundamental channel parameters. We show in simulations that this charge based noise analysis is more robust if the synapse is located on the dendrites and thus subject to cable filtering. However, we also demonstrate that when multiple synapses are distributed on the dendrites, noise analysis breaks down. We finally discuss applications of our results to other biological processes.
Alcohol abuse/dependence symptoms among hospital employees exposed to a SARS outbreak.

AIMS The aim of this study was to examine alcohol abuse/dependence symptoms among hospital employees exposed to a severe acute respiratory syndrome (SARS) outbreak, and the relationship between types of exposure to the SARS outbreak and subsequent alcohol abuse/dependence symptoms. METHODS A survey was conducted among 549 randomly selected hospital employees in Beijing, China, concerning the psychological impact of the 2003 SARS outbreak. Subjects were assessed on sociodemographic factors and types of exposure to the outbreak, and on symptoms of post-traumatic stress (PTS), alcohol abuse/dependence and depression. RESULTS Current alcohol abuse/dependence symptom counts 3 years after the outbreak were positively associated with having been quarantined, or worked in high-risk locations such as SARS wards, during the outbreak. However, having had family members or friends contract, SARS was not related to alcohol abuse/dependence symptom count. Symptoms of PTS and of depression, and having used drinking as a coping method, were also significantly associated with increased alcohol abuse/dependence symptoms. The relationship between outbreak exposure and alcohol abuse/dependence symptom count remained significant even when sociodemographic and other factors were controlled for. When the intrusion, avoidance and hyperarousal PTS symptom clusters were entered into the model, hyperarousal was found to be significantly associated with alcohol abuse/dependence symptoms. CONCLUSIONS Exposure to an outbreak of a severe infectious disease can, like other disaster exposures, lead not only to PTSD but also to other psychiatric conditions, such as alcohol abuse/dependence. The findings will help policy makers and health professionals to better prepare for potential outbreaks of diseases such as SARS or avian flu.
Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies

Abstract Mass spectrometry based clinical proteomics has emerged as a powerful tool for high-throughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in biomedical research. However, the complexity of the proteomic expression introduces new statistical challenges in summarizing and analyzing the acquired data. Statistical methods for optimally processing proteomic data are currently a growing field of research. In this paper we present simple, yet appropriate methods to preprocess, summarize and analyze high-throughput MALDI-FTICR mass spectrometry data, collected in a case-control fashion, while dealing with the statistical challenges that accompany such data. The known statistical properties of the isotopic distribution of the peptide molecules are used to preprocess the spectra and translate the proteomic expression into a condensed data set. Information on either the intensity level or the shape of the identified isotopic clusters is used to derive summary measures on which diagnostic rules for disease status allocation will be based. Results indicate that both the shape of the identified isotopic clusters and the overall intensity level carry information on the class outcome and can be used to predict the presence or absence of the disease.
Wiki3C: exploiting wikipedia for context-aware concept categorization

Wikipedia is an important human generated knowledge base containing over 21 million articles organized by millions of categories. In this paper, we exploit Wikipedia for a new task of text mining: Context-aware Concept Categorization. In the task, we focus on categorizing concepts according to their context. We exploit article link feature and category structure in Wikipedia, followed by introducing Wiki3C, an unsupervised and domain independent concept categorization approach based on context. In the approach, we investigate two strategies to select and filter Wikipedia articles for the category representation. Besides, a probabilistic model is employed to compute the semantic relatedness between two concepts in Wikipedia. Experimental evaluation using manually labeled ground truth shows that our proposed Wiki3C can achieve a noticeable improvement over the baselines without considering contextual information.
Adaptive recursive higher order polynomial filter

In this paper we present an adaptive recursive nonlinear filter based on the higher order Volterra series infinite impulse response (IIR) structure. The proposed work is an extension of the work of Roy et al [9] in which they limit the Volterra recursive filter to the second order. Adaptive algorithms based on the exact and the approximate gradient will be derived. Stability issues based on the Extended Kalman Filter will be discussed. Simulations results highlight the usefulness of the proposed algorithms. Improvement on the convergence and stability behavior will be evaluated.
Correlation between epicardial fat thickness and aortic valve sclerosis

Background Epicardial fat is a true visceral fat deposit with adverse effects through the secretion of numerous proinflammatory and proatherogenic cytokines. Previous studies showed an association between aortic valve sclerosis and coronary artery disease. The aim of this study was to determine the correlation between epicardial fat thickness and aortic valve sclerosis. Method The study involved 225 patients who were admitted for coronary angiography due to new-onset angina. They underwent transthoracic echocardiography and epicardial fat thickness was determined. The sclerosis scoring of each aortic cusp, average aortic valve sclerosis score index, and left ventricular ejection fraction were determined. The variables of left ventricular diastolic function obtained included the early diastolic velocity determined by transmitral pulsed Doppler, and early mitral annular velocity measured by tissue Doppler. Results Patients with an epicardial fat thickness ≥7 mm were older (p = 0.006), with more hypertension (p = 0.045) and hyperlipidemia (p < 0.001). Their average aortic valve sclerosis score index was higher (1.4 ± 1.02 vs. 0.86 ± 0.85, p = 0.001), and left ventricular ejection fraction and early mitral annular velocity were lower (p < 0.001 and 0.03, respectively). They also exhibited more left ventricular hypertrophy (p = 0.026) and a trend towards more significant coronary artery disease and 3-vessel disease (p = 0.086 and 0.073, respectively). Conclusion Our findings confirm that epicardial fat as a marker of visceral adipose tissue may have an important role in promoting inflammatory and atherosclerotic changes in the aortic valve.
A non-linear elastic constitutive framework for replicating plastic deformation in solids.

Ductile metals and other materials typically deform plastically under large applied loads; a behavior most often modeled using plastic deformation constitutive models. However, it is possible to capture some of the key behaviors of plastic deformation using only the framework for nonlinear elastic mechanics. In this paper, we develop a phenomenological, hysteretic, nonlinear elastic constitutive model that captures many of the features expected of a plastic deformation model. This model is based on calculating a secant modulus directly from a material's stress-strain curve. Scalar stress and strain values are obtained in three dimensions by using the von Mises invariants. Hysteresis is incorporated by tracking an additional history variable and assuming an elastic unloading response. This model is demonstrated in both single- and multi-element simulations under varying strain conditions.
Cerebellar ataxia and glutamic acid decarboxylase antibodies: immunologic profile and long-term effect of immunotherapy.

IMPORTANCE Current clinical and immunologic knowledge on cerebellar ataxia (CA) with glutamic acid decarboxylase 65 antibodies (GAD65-Abs) is based on case reports and small series with short-term follow-up data. OBJECTIVE To report the symptoms, additional antibodies, prognostic factors, and long-term outcomes in a cohort of patients with CA and GAD65-Abs. DESIGN, SETTING, AND PARTICIPANTS Retrospective cohort study and laboratory investigations at a center for autoimmune neurologic disorders among 34 patients with CA and GAD65-Abs, including 25 with long-term follow-up data (median, 5.4 years; interquartile range, 3.1-10.3 years). MAIN OUTCOMES AND MEASURES Analysis of clinicoimmunologic features and predictors of response to immunotherapy. Immunochemistry on rat brain, cultured neurons, and human embryonic kidney cells expressing GAD65, GAD67, α1-subunit of the glycine receptor, and a repertoire of known cell surface autoantigens were used to identify additional antibodies. Twenty-eight patients with stiff person syndrome and GAD65-Abs served as controls. RESULTS The median age of patients was 58 years (range, 33-80 years); 28 of 34 patients (82%) were women. Nine patients (26%) reported episodes of brainstem and cerebellar dysfunction or persistent vertigo several months before developing CA. The clinical presentation was subacute during a period of weeks in 13 patients (38%). Nine patients (26%) had coexisting stiff person syndrome symptoms. Systemic organ-specific autoimmunities (type 1 diabetes mellitus and others) were present in 29 patients (85%). Twenty of 25 patients with long-term follow-up data received immunotherapy (intravenous immunoglobulin in 10 and corticosteroids and intravenous immunoglobulin or other immunosuppressors in 10), and 7 of them (35%) improved. Predictors of clinical response included subacute onset of CA (odds ratio [OR], 0.50; 95% CI, 0.25-0.99; P = .047) and prompt immunotherapy (OR, 0.98; 95% CI, 0.96-0.99; P = .01). Similar frequencies of serum GAD67-Abs were found in patients with CA (24 of 34 patients [71%]) and in patients with stiff person syndrome (20 of 28 patients [71%]). However, GAD67-Abs were found in all of the cerebrospinal fluid samples examined (22 samples from patients with CA and 17 samples from patients with stiff person syndrome). Glycine receptor antibodies but not other cell surface antibodies were identified in 4 patients with CA. The presence of glycine receptor antibodies did not correlate with any specific clinical feature. CONCLUSIONS AND RELEVANCE In patients with CA and GAD65-Abs, subacute onset of symptoms and prompt immunotherapy are associated with good outcome. Persistent vertigo or brainstem and cerebellar episodes can herald CA and should lead to GAD65-Ab testing, particularly in patients with systemic organ-specific autoimmunities.
Inferring and Asserting Distributed System Invariants

Distributed systems are difficult to debug and understand. A key reason for this is distributed state, which is not easily accessible and must be pieced together from the states of the individual nodes in the system. We propose Dinv, an automatic approach to help developers of distributed systems uncover the runtime distributed state properties of their systems. Dinv uses static and dynamic program analyses to infer relations between variables at different nodes. For example, in a leader election algorithm, Dinv can relate the variable leader at different nodes to derive the invariant forall ∀ nodes i, j, leader_i = leader_j. This can increase the developer's confidence in the correctness of their system. The developer can also use Dinv to convert an inferred invariant into a distributed runtime assertion on distributed state. We applied Dinv to several popular distributed systems, such as etcd Raft, Hashicorp Serf, and Taipei-Torrent, which have between 1.7K and 144K LOC and are widely used. Dinv derived useful invariants for these systems, including invariants that capture the correctness of distributed routing strategies, leadership, and key hash distribution. We also used Dinv to assert correctness of the inferred etcd Raft invariants at runtime, using these asserts to detect injected silent bugs.