Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics

The biomedical literature presents a uniquely challenging text mining problem. Sentences are long and complex, the subject matter is highly specialized with a distinct vocabulary, and producing annotated training data for this domain is time consuming and expensive. In this environment, unsupervised text mining methods that do not rely on annotated training data are valuable. Here we investigate the use of random indexing, an automated method for producing vector-space semantic representations of words from large, unlabeled corpora, to address the problem of term normalization in sentences describing drugs and genes. We show that random indexing produces similarity scores that capture some of the structure of PHARE, a manually curated ontology of pharmacogenomics concepts. We further show that random indexing can be used to identify likely word candidates for inclusion in the ontology, and can help localize these new labels among classes and roles within the ontology.
Longitudinal tracking of muscle sympathetic nerve activity and its relationship with blood pressure in subjects with prehypertension

Abstract Prehypertension is associated with increased cardiovascular events. While the “tracking phenomenon” is an important longitudinal characteristic of blood pressure (BP), changes in muscle sympathetic nerve activity (MSNA) over time remain unclear. This study tested the hypothesis that MSNA tracking contributes to BP trends in prehypertension. BP and MSNA were assessed in 13 prehypertensive males at rest, during hand grip and mental stressors at baseline and after 8 years. Baseline office BP averaged 127 ± 2/81 ± 2 mmHg and MSNA 24 ± 4 bursts/min. BP increased by 7 ± 2/5 ± 2 mmHg (P < 0.01) and MSNA by 11 ± 2 bursts/min (P < 0.001) at follow-up. SBP and DBP were interrelated at baseline (r = 0.65, P = 0.02) and at follow-up (r = 0.78, P = 0.002). MSNA tracking (r = 0.82; P < 0.001) was similar to BP. MSNA was strongly related to DBP at baseline (r = 0.73; P < 0.01) and follow-up (r = 0.64; P = 0.01), more so than SBP. BMI increased (P < 0.001) at follow-up but was unrelated to BP or MSNA. Despite comparable pressor and cardiac increases to handgrip and mental stressors, sympathetic responses were blunted, more pronounced to isometric test (P < 0.006) at follow-up. In conclusion, the trend in MSNA corresponds with BP changes over time suggesting that tonic sympathetic activation may contribute to time-related increase in resting BP and the development of sustained hypertension in prehypertension.
Relationships between form, morphology, density and energy in urban environments

In some cities, per capita energy consumption has grown at approximately the same rate as their spatial growth (Baynes and Bai, 2009). From an urban metabolic viewpoint, energy is one of the most critical resource flows in urban environments. It is a primary driver of both the physical and economic systems; in the form of fossil fuels it is also a primary source of greenhouse gas (GHG) emissions and a driver of human-induced climate change.
Cross-Layer Design for Interference-Limited Spectrum Sharing Systems

In this paper, we consider a dynamic spectrum sharing system consisting of a primary user, whose licensed spectrum is allowed to be accessed by a secondary user as long as it does not violate the prescribed interference limit inflicted on the primary user. Assuming the Nakagami-m blockfading environment, we aim at maximizing the performance of secondary user's link in terms of average spectral efficiency (ASE) and error performance under the specified packet error rate (PER) and average interference limit constraints. To this end, we employ a cross-layer design policy which combines adaptive power and coded discrete M-QAM modulation scheme at the physical layer with a truncated automatic repeat request (ARQ) protocol at the data link layer, and simultaneously satisfies the aforementioned constraints. Numerical results affirm that the secondary link of spectrum sharing system combining ARQ with adaptive modulation and coding (AMC) achieves significant gain in ASE depending on the maximum number of retransmissions initiated by the ARQ protocol. The results further indicate that the ARQ protocol essentially improves the packet loss rate performance of the secondary link.
Isolation, characterization and hypolipidemic activity of ferulic acid in high-fat-diet-induced hyperlipidemia in laboratory rats

Prosopis cineraria (L.) Druce (Leguminosae) (syn. Prosopis spicigera L.) has antidiabetic and antioxidant potential. Earlier we reported its hypolipidemic activity obtained from ethanol extract (ET-PCF). Object of this work was to isolate ferulic acid (FA) from ET-PCF and evaluate hypolipidemic activity against high-fat diet (HFD)-induced hyperlipidemic laboratory rats. ET-PCF was subjected to flash column chromatography to isolate FA. The chemical structure of the isolated compound was elucidated by UV, IR, 1H NMR,13C NMR and LC-MS. Further, the antihyperlipidemic effect of FA (10, 20 and 40 mg/kg, p.o.) in HFD-induced hyperlipidemic rats was investigated. Hyperlipidemia was induced in male Sprague-Dawley rats by feeding with HFD for 60 days. Lipid parameters such as total cholesterol (TC), Low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) levels were measured in serum and hepatic tissue. Hepatic oxido-nitrosative stress (SOD, GSH, MDA and NO) were also determined. Histological evaluation of liver tissue was carried out. The structure of the isolated compound was characterized based on spectral data and confirmed as FA. HFD induced an alteration in serum, and hepatic lipid profile (triglyceride, cholesterol, HDL, and LDL) was significantly restored (p < 0.001) by administration of FA (20 and 40 mg/kg, p.o.). The elevated level of oxido-nitrosative stress in liver was significantly reduced (p < 0.001) by FA (20 and 40 mg/kg, p.o.). Histological aberration induced in the liver after HFD ingestion were restored by FA administration. Ferulic acid isolated from ET-PCF showed hypolipidemic effects in HFD-induced hyperlipidemic rats via modulation of elevated oxido-nitrosative stress.
Network calculus and queueing theory: two sides of one coin: invited paper

Network calculus is a theory dealing with queueing type problems encountered in computer networks, with particular focus on quality of service guarantee analysis. Queueing theory is the mathematical study of queues, proven to be applicable to a wide area of problems, generally concerning about the (average) quantities in an equilibrium state. Since both network calculus and queueing theory are analytical tools for studying queues, a question arises naturally as is if and where network calculus and queueing theory meet. In this paper, we explore queueing principles that underlie network calculus and exemplify their use. Particularly, based on the network calculus queueing principles, we show that for GI/GI/1, similar inequalities in the theory of queues can be derived. In addition, we prove that the end-to-end performance of a tandem network is independent of the order of servers in the network even under some general settings. Through these, we present a network calculus perspective on queues and relate network calculus to queueing theory.
Optimizing two-photon multiple fluorophore imaging of the human trabecular meshwork

Purpose Advances in two-photon (2P) deep tissue imaging provide powerful options for simultaneously viewing multiple fluorophores within tissues. We determined imaging parameters for optimally visualizing three fluorophores in the human trabecular meshwork (TM) to simultaneously detect broad-spectrum autofluorescence and multiple fluorophores through a limited number of emission filters. Methods 2P imaging of viable human postmortem TM was conducted to detect Hoechst 33342–labeled nuclei, Alexa-568-conjugated phalloidin labeling of filamentous actin, and autofluorescence of the structural extracellular matrix (ECM). Emission detection through green (500–550 nm), near-red (565–605 nm), and far-red (590–680 nm) filters following 2P excitation at 750, 800, 850, and 900 nm was analyzed. Region-of-interest (ROI) image analysis provided fluorescence intensity values for each fluorophore. Results Red-channel Alexa 568 fluorescence was of highest intensity with 2P 750 nm and 800 nm excitation. Alexa 568 was imperceptible with 900 nm excitation. With excitation at 750 nm and 800 nm, Hoechst 33,342 intensity swamped autofluorescence in the green channel, and marked bleed-through into red channels was seen. 850 nm excitation yielded balanced Hoechst 33342 and autofluorescence intensities, minimized their bleed-through into the far-red channel, and produced reasonable Alexa 568 intensities in the far-red channel. Conclusions 2P excitation at 850 nm and long-wavelength emission detection in the far-red channel allowed simultaneous visualization of the specific mix of endogenous and exogenous fluorophores with reasonably balanced intensities while minimizing bleed-through when imaging the human TM.
Nature versus nurture in T cell cytokine production

Both extrinsic and intrinsic factors influence the development of cytokine expression patterns in T lymphocytes. The models proposed to accommodate these factors are often separated into two types: deterministic (or instructional) and probabilistic (or stochastic). In this review we compare these two types of models and examine how they account for different stages of T cell cytokine responses to antigen stimulation. We conclude by showing how a reconciliation of the two types of models may be possible, perhaps through the regulatory potential of heritable epigenetic mechanisms. This type of reconciliation may open up new avenues for manipulating T cell cytokine expression and redirecting immune responses. J. Leukoc. Biol. 66: 869–875; 1999.
Fisher information of sampled packets: an application to flow size estimation

Packet sampling is widely used in network monitoring. Sampled packet streams are often used to determine flow-level statistics of network traffic. To date there is conflicting evidence on the quality of the resulting estimates. In this paper we take a systematic approach, using the Fisher information metric and the Cramér-Rao bound, to understand the contributions that different types of information within sampled packets have on the quality of flow-level estimates. We provide concrete evidence that, without protocol information and with packet sampling rate p = 0.005, any accurate unbiased estimator needs approximately 1016 sampled flows. The required number of sampled flows drops to roughly 104 with the use of TCP sequence numbers. Furthermore, additional SYN flag information significantly reduces the estimation error of short flows. We present a Maximum Likelihood Estimator (MLE) that relies on all of this information and show that it is efficient, even when applied to a small sample set. We validate our results using Tier-1 Internet backbone traces and evaluate the benefits of sampling from multiple monitors. Our results show that combining estimates from several monitors is 50% less accurate than an estimate based on all samples.
Smell and taste disorders: a primary care approach.

Smell and taste disorders are common in the general population, with loss of smell occurring more frequently. Although these disorders can have a substantial impact on quality of life and may represent significant underlying disease, they are often overlooked by the medical community. Patients may have difficulty recognizing smell versus taste dysfunction and frequently confuse the concepts of "flavor" and "taste. " While the most common causes of smell disturbance are nasal and sinus disease, upper respiratory infection and head trauma, frequent causes of taste disturbance include oral infections, oral appliances (e.g., dentures), dental procedures and Bell's palsy. Medications can interfere with smell and taste, and should be reviewed in all patients with reported dysfunction. In addition, advancing age has been associated with a natural impairment of smell and taste ability. A focused history and a physical examination of the nose and mouth are usually sufficient to screen for underlying pathology. Computed tomographic scanning or magnetic resonance imaging of affected areas, as well as commercially available standardized tests, may be useful in selected patients. The causes of olfactory dysfunction that are most amenable to treatment include obstructing polyps or other masses (treated by excision) and inflammation (treated with steroids). Enhancement of food flavor and appearance can improve quality of life in patients with irreversible dysfunction.
Principle of Emergence in Text and Linguistics

The entire, long history of linguistics is characterised by one type of reductionism: the context of the analysed language formants is mostly reduced to sentences and/or to lower units which are constituents of sentences. The extraction of analysed language objects from their broader connections in texts was one of the ways to make language description less complicated. The notion of ‘text’ did not occur among the analytical instruments used for the descriptive aims and even in stylistics it was applied as a free, non-specified term. This is quite understandable: the task of linguistics (or better: philology) was and still is to offer such a sorting of language units, which can serve for cultivation of mother languages and for learning foreign languages. Regardless of all the new developments in language cognition, these aims, according to our opinion, will still remain valid in the future for specialists dealing with languages, and that classical approaches with their classificatory achievements will con.
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Motivation: Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima or to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions. Results: We propose the use of Answer Set Programming to explore exhaustively the space of feasible logic models. Toward this end, we have developed caspo, an open-source Python package that provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of Answer Set Programming. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11 700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input–output behavior of the models. We find 91 behaviors across the 11 700 models and we suggest new experiments to discriminate among them. Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design. Availability: caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest. org/. Supplementary information: Supplementary materials are available at Bioinformatics online. Contact: santiago.videla@irisa.fr
Automatic induction of translation lexicons from aligned parallel corpus

Translation lexicons are one of the most important linguistic resources for machine translation. However, this bilingual set of word and multiword correspondences requires a lot of manual work to be built. This paper describes a method to automatically build translation lexicons by extracting knowledge from PoS-tagged and lexically aligned parallel corpora. Preliminary experiments were carried out on Brazilian Portuguese, Spanish and English parallel texts. The results showed that 85% of pt–es and 89% ofpt–en entries are plausible correspondences. These results were obtained taking into consideration only the classes of entries which achieved the best results.
CapE, a 47-Amino-Acid Peptide, Is Necessary for Bacillus anthracis Polyglutamate Capsule Synthesis

ABSTRACT Polyglutamate is found in various bacteria, but displays different functions depending on the species and their environment. Here, we describe a minimal polyglutamate synthesis system in Bacillus anthracis. In addition to the three genes previously described as sufficient for polyglutamate synthesis, this system includes a small open reading frame, capE, belonging to the cap operon. The polyglutamate system's requirement for the five cap genes, for capsulation and anchoring, was assayed in nonpolar mutants. The capA, capB, capC, and capE genes are all necessary and are sufficient for polyglutamate synthesis by B. anthracis. capD is required for polyglutamate anchoring to the peptidoglycan. The 47-amino-acid peptide encoded by capE is localized in the B. anthracis membrane. It is not a regulator and it is required for polyglutamate synthesis, suggesting that it has a structural role in polyglutamate synthesis. CapE appears to interact with CapA. Bacillus subtilis ywtC is similar to capE and we named it pgsE. Genes similar to capE or pgsE were found in B. subtilis natto, Bacillus licheniformis, and Staphylococcus epidermidis, species that produce polyglutamate. All the bacterial polyglutamate synthesis systems analyzed show a similar genetic organization and, we suggest, the same protein requirements.
Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

ABSTRACT Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these bacterial communities respond to diarrheal disease and its treatment. Here, we report that after Vibrio cholerae infection, the human gut microbiota undergoes an orderly and reproducible succession that features transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest that multiple mechanisms drive microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure but is driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea. IMPORTANCE Disability after diarrhea is a major burden on public health in the developing world. Gut bacteria may affect this recovery, but it remains incompletely understood how resident microbes in the digestive tract respond to diarrheal illness. Here, we observed an orderly and reproducible succession of gut bacterial groups after cholera in humans. Genomic analyses associated the succession with bacterial dispersal in food, an altered microbial environment, and changing phage levels. Our findings suggest that it may one day be feasible to manage resident bacterial populations in the gut after infectious diarrhea. Disability after diarrhea is a major burden on public health in the developing world. Gut bacteria may affect this recovery, but it remains incompletely understood how resident microbes in the digestive tract respond to diarrheal illness. Here, we observed an orderly and reproducible succession of gut bacterial groups after cholera in humans. Genomic analyses associated the succession with bacterial dispersal in food, an altered microbial environment, and changing phage levels. Our findings suggest that it may one day be feasible to manage resident bacterial populations in the gut after infectious diarrhea.
Particle Swarm Optimization with Time Varying Acceleration Coefficients for Congestion Management

This paper presents an application of Particle Swarm Optimization with Time Varying Acceleration Coefficients (PSO-TVAC) algorithm for Congestion Management (CM) using optimal re-scheduling of real power generation. The optimal rescheduling of powers in a pool model is formulated as a constrained nonlinear optimization problem. The PSO-TVAC algorithm is proposed to assess the generation re-schedule to relieve the congestion optimally. The generators participating in the congestion management are selected based on real power transmission congestion distribution factors (PTCDFs). The effectiveness of the proposed method has been tested on 39-bus New England Test system. The simulation experiments reveal that the proposed method performs better than conventional PSO.
Intermediate Coupling between Aboveground and Belowground Biomass Maximises the Persistence of Grasslands

Aboveground and belowground biomass compartments of vegetation fulfil different functions and they are coupled by complex interactions. These compartments exchange water, carbon and nutrients and the belowground biomass compartment has the capacity to buffer vegetation dynamics when aboveground biomass is removed by disturbances such as herbivory or fire. However, despite their importance, root-shoot interactions are often ignored in more heuristic vegetation models. Here, we present a simple two-compartment grassland model that couples aboveground and belowground biomass. In this model, the growth of belowground biomass is influenced by aboveground biomass and the growth of aboveground biomass is influenced by belowground biomass. We used the model to explore how the dynamics of a grassland ecosystem are influenced by fire and grazing. We show that the grassland system is most persistent at intermediate levels of aboveground-belowground coupling. In this situation, the system can sustain more extreme fire or grazing regimes than in the case of strong coupling. In contrast, the productivity of the system is maximised at high levels of coupling. Our analysis suggests that the yield of a grassland ecosystem is maximised when coupling is strong, however, the intensity of disturbance that can be sustained increases dramatically when coupling is intermediate. Hence, the model predicts that intermediate coupling should be selected for as it maximises the chances of persistence in disturbance driven ecosystems.
WIC-Based Interventions to Promote Breastfeeding Among African-American Women in Baltimore: Effects on Breastfeeding Initiation and Continuation

We evaluated the single and combined effects of introducing a motivational video and peer counseling into four matched WIC clinics on breastfeeding initiation and continuation at 7-10 days among African-American WIC participants. Of the 242 women with complete data, 48% initiated breastfeeding, but only 31% were still breastfeeding at 7-10 days. Initiation was associated with cesarean delivery, infant feeding instruction, no artificial milk discharge pack, attending the peer counselor only-intervention site, and intention to breastfeed. Continuation was influenced by infant feeding instruction, no artificial milk discharge pack, and intention to breastfeed. Overall, trends toward a positive impact of the breastfeeding promotion activities were evident but weak, and largely gone by 7-10 days postpartum.