Miracle-dz/UniFAR-FTUs huggingface dataset:
Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr(-1) (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr(-1).
Mandarin lexical tone recognition in sensorineural hearing-impaired listeners and cochlear implant users

Abstract Conclusions: As the hearing loss becomes more severe, the tone recognition performance of hearing-impaired listeners gradually but slowly reduces. The tone recognition performance of cochlear implant listeners is below or close to the performance of severely hearing-impaired listeners. Objectives: The present study aimed to investigate the Mandarin lexical tone recognition performance of sensorineural hearing-impaired listeners and post-lingually deafened cochlear implant users. Methods: Tone recognition performance was measured for 30 normal-hearing subjects, 41sensorineural hearing-impaired listeners, and 12 cochlear implant users using 128 monosyllables recorded by a male and a female adult native Mandarin speaker. Results: The results indicated that the accuracy of tone recognition was 99.3%, 96.4%, 93.7%, 83.9%, and 81.0% for the normal-hearing, moderate, moderate to severe, severely hearing-impaired, and cochlear implant subjects, respectively. For the hearing-impaired subjects, a significantly negative correlation was observed between tone recognition performance and the audiometric hearing thresholds. For cochlear implant subjects, Tone 3 was the easiest one to perceive and Tone 2 was the hardest one to perceive. They tended to misperceive Tone 1 as Tone 2, and misperceive Tone 2 as Tones 1 and 3.
Lessons in learning

Scientists wanting to reach beyond academia to improve public appreciation and understanding of research face a number of challenges. Perhaps the first of these is the question of which of the many potential audiences to address. Many scientists and science communicators focus their efforts on school children, perhaps because they are perceived to be particularly open to new ideas and knowledge. However, not all school audiences are the same. We chose to discuss concepts of stem cell science with high school students before they made the curriculum choices that put them on a path towards or away from science. Although high school outreach offers the chance to enthuse future scientists, our motivation was to reach those who would not choose science as their career. Engaging these people is essential to enhance the general level of scientific literacy in society. However, this particular audience poses some challenges, particularly as by this age, some students may already have dismissed science as irrelevant to them, while others who might be interested have little understanding of cell biology. Our challenge was therefore to convey the key concepts of stem cell biology in a way that efficiently engaged the students, demonstrated the relevance of science to their lives, was fun for all involved and enabled all students to place science appropriately within their imagined futures. We developed a series of three lessons for 12‐ to 14‐year‐olds to address the basic concepts, applications and ethics of stem cell biology (Table 1; Box Description of the content of the three lessons). Working together—one of us is a scientist and the other is a science communicator—we focused on designing a set of educational modules with an emphasis on interactivity, experiments, games and discussion to actively engage students in the topic. In addition, we pursued a longer‐term outreach strategy …
Exploration of Dynamic Elastic Modulus Changes on Glioblastoma Cell Populations with Aberrant EGFR Expression as a Potential Therapeutic Intervention Using a Tunable Hyaluronic Acid Hydrogel Platform

Glioblastoma (GBM) is one of most aggressive forms of brain cancer, with a median survival time of 14.6 months following diagnosis. This low survival rate could in part be attributed to the lack of model systems of this type of cancer that faithfully recapitulate the tumor architecture and microenvironment seen in vivo in humans. Therapeutic studies would provide results that could be translated to the clinic efficiently. Here, we assess the role of the tumor microenvironment physical parameters on the tumor, and its potential use as a biomarker using a hyaluronic acid hydrogel system capable of elastic modulus tuning and dynamic elastic moduli changes. Experiments were conducted to assess the sensitivity of glioblastoma cell populations with different mutations to varying elastic moduli. Cells with aberrant epithelial growth factor receptor (EGFR) expression have a predilection for a stiffer environment, sensing these parameters through focal adhesion kinase (FAK). Importantly, the inhibition of FAK or EGFR generally resulted in reversed elastic modulus preference. Lastly, we explore the concept of therapeutically targeting the elastic modulus and dynamically reducing it via chemical or enzymatic degradation, both showing the capability to reduce or stunt proliferation rates of these GBM populations.
Toxoplasma gondii sequesters centromeres to a specific nuclear region throughout the cell cycle

Members of the eukaryotic phylum Apicomplexa are the cause of important human diseases including malaria, toxoplasmosis, and cryptosporidiosis. These obligate intracellular parasites produce new invasive stages through a complex budding process. The budding cycle is remarkably flexible and can produce varied numbers of progeny to adapt to different host-cell niches. How this complex process is coordinated remains poorly understood. Using Toxoplasma gondii as a genetic model, we show that a key element to this coordination is the centrocone, a unique elaboration of the nuclear envelope that houses the mitotic spindle. Exploiting transgenic parasite lines expressing epitope-tagged centromeric H3 variant CenH3, we identify the centromeres of T. gondii chromosomes by hybridization of chromatin immunoprecipitations to genome-wide microarrays (ChIP-chip). We demonstrate that centromere attachment to the centrocone persists throughout the parasite cell cycle and that centromeres localize to a single apical region within the nucleus. Centromere sequestration provides a mechanism for the organization of the Toxoplasma nucleus and the maintenance of genome integrity.
Short duration waveforms recorded extracellularly from freely moving rats are representative of axonal activity

While extracellular somatic action potentials from freely moving rats have been well characterized, axonal activity has not. We report direct extracellular tetrode recordings of putative axons whose principal feature is a short duration waveform (SDW) with an average peak-trough length less than 179 μs. While SDW recordings using tetrodes have previously been treated as questionable or classified as cells, we hypothesize that they are representative of axonal activity. These waveforms have significantly shorter duration than somatic action potentials, are triphasic and are therefore similar to classic descriptions of microelectrode recordings in white matter and of in vitro action potential propagation along axons. We describe SDWs recorded from pure white-matter tracts including the alveus and corpus callosum. Recordings of several SDWs in the alveus exhibit grid-like firing patterns suggesting these axons carry spatial information from entorhinal cortical neurons. Finally, we locally injected the GABAA agonist Muscimol into layer CA1 of the hippocampus while simultaneously recording somatic activity and SDWs on the same tetrodes. The persistent activity of SDWs during Muscimol inactivation of somatic action potentials indicates that SDWs are representative of action potential propagation along axons projecting from more distal somata. This characterization is important as it illustrates the dangers of exclusively using spike duration as the sole determinant of unit type, particularly in the case of interneurons whose peak-trough times overlap with SDWs. It may also allow future studies to explore how axonal projections from disparate brain regions integrate spatial information in the hippocampus, and provide a basis for studying the effects of pharmaceutical agents on signal transmission in axons, and ultimately to aid in defining the potential role of axons in cognition.
Age Before Stage: Insulin Resistance Rises Before the Onset of Puberty

OBJECTIVE Insulin resistance (IR) is associated with diabetes. IR is higher during puberty in both sexes, with some studies showing the increase to be independent of changes in adiposity. Few longitudinal studies have reported on children, and it remains unclear when the rise in IR that is often attributed to puberty really begins. We sought to establish from longitudinal data its relationship to pubertal onset, and interactions with age, sex, adiposity, and IGF-1. RESEARCH DESIGN AND METHODS The EarlyBird Diabetes study is a longitudinal prospective cohort study of healthy children aged 5–14 years. Homeostasis model assessment (HOMA-IR), skinfolds (SSF), adiposity (percent fat, measured by dual-energy X-ray absorptiometry), serum leptin, and IGF-1 were measured annually in 235 children (134 boys). Pubertal onset was adduced from Tanner stage (TS) and from the age at which luteinizing hormone (LH) first became serially detectable (≥0.2 international units/L). RESULTS IR rose progressively from age 7 years, 3–4 years before TS2 was reached or LH became detectable. Rising adiposity and IGF-1 together explained 34% of the variance in IR in boys and 35% in girls (both P < 0.001) over the 3 years preceding pubertal onset. The contribution of IGF-1 to IR was greater in boys, despite their comparatively lower IGF-1 levels. CONCLUSIONS IR starts to rise in mid-childhood, some years before puberty. Its emergence relates more to the age of the child than to pubertal onset. More than 60% of the variation in IR prior to puberty was unexplained. The demography of childhood diabetes is changing, and prepubertal IR may be important.
Survival and Growth of Triploid Crassostrea virginica (Gmelin, 1791) and C. ariakensis (Fujita, 1913) in Bottom Environments of Chesapeake Bay: Implications for an Introduction

ABSTRACT Survival and growth of triploid Crassostrea virginica and triploid C. ariakensis were investigated at four sites surrounding Chesapeake Bay, United States, that varied in salinity, tidal regime, water depth, predation intensity and disease pressure. Four experimental treatments were established at each site: C. virginica; C. ariakensis; 50:50 of C. virginica: C. ariakensis; and shell only. Oysters were deployed at mean shell heights of 12.80 mm and 13.85 mm (C. virginica and C. ariakensis, respectively), at an overall density of 347.5 oysters m-2. Oyster survival and growth varied significantly with site and species. Survival was significantly higher in C. virginica than C. ariakensis at the intertidal site, and significantly higher in C. ariakensis than C. virginica at the highest salinity, subtidal site. Survival did not differ significantly between species at the mid and low salinity, subtidal sites. For both species, survival differed significantly between sites, with lowest survival in both species occurring at the intertidal site. Among the subtidal sites, C. virginica survival varied inversely with salinity, whereas C. ariakensis had the lowest survival at the mid salinity site. Eight months after deployment C. ariakensis were significantly larger than C. virginica at all sites. This difference generally persisted throughout the experiment, though the size differences between oyster species at the lowest salinity site were small (< 10%). Shell heights within single-species treatments differed significantly between sites; highest growth rates were observed at the high salinity, subtidal site, whereas lowest growth rates were observed at the high salinity, intertidal site. At low and mid salinity subtidal sites, C. ariakensis shell heights were significantly greater in the single-species treatment compared with the mixed-species treatment. Perkinsus marinus infections occurred in both species at all sites, with prevalences varying between sites. In C. virginica, moderate and high intensity infections were only common at the two higher salinity sites, whereas infections in C. ariakensis were generally low to rare. Haplosporidium nelsoni infections in C. virginica were only observed at the two higher salinity sites and prevalences were generally low. Two out of 53 C. ariakensis tested at the high salinity, subtidal site had rare H. nelsoni infections. Bonamia spp. infections were never observed. Our study supports previous laboratory findings and observations from its native range that C. ariakensis survives poorly in intertidal habitats. In subtidal habitats, however, C. ariakensis displayed broad environmental tolerances, often exceeding native oyster survival and growth rates. Post-introduction C. ariakensis populations would be shaped by the survival and growth patterns described here, but also by their reproductive success, larval survival, predator-prey interactions and prevailing disease dynamics.
In vivo and in vitro metabolism of trans-resveratrol by human gut microbiota 1 – 3

Background: Strong interindividual differences in the microbial conversion of some dietary polyphenols have been reported. Indepth studies of trans-resveratrol metabolism by human gut microbiota, however, are lacking, and only one bacterial metabolite, namely dihydroresveratrol, has been described. Objective: The aim of this study was to elucidate interindividual differences in trans-resveratrol metabolism by human gut microbiota and to identify bacterial strains involved. Design: In the first part of the study, in vitro fermentation experiments were performed with feces samples from 7 healthy volunteers, and metabolite formation was measured by liquid chromatography– ultraviolet/visible (UV/Vis)–mass spectrometry (MS)/MS detection. Microbial diversities in 3 feces samples were analyzed by highthroughput pyrosequencing and quantitative real-time polymerase chain reaction. In addition, trans-resveratrol conversion experiments were conducted with selected fecal bacterial strains in pure culture. The second part of the study was a controlled intervention study with 12 healthy volunteers. After a washout period, all of the subjects received a one-time oral dose of 0.5 mg trans-resveratrol/kg body weight in the form of a grapevine-shoot supplement, and 24-h urine samples were analyzed by liquid chromatography–UV/Vis–
A Multi-agent Genetic Algorithm for Multi-objective Optimization

In this paper a new multi-agent genetic algorithm for multi-objective optimization (MAGAMO) is presented. The algorithm based on the dynamical interaction of synchronized agents which are interdepended genetic algorithms (GAs) having own separate evolutions of their populations. This approach has some similarities with well known "island model" of GA. In both methods is used a migration of individuals from agents ("islands") to the main process ("continent"). In contrast, the intelligent agents in MAGAMO are able to decompose the dimensions space to form evolutions of subpopulations (instead of distribution of initial population as in the standard "island model"). In the same time, the main (central) process is responsible for the coordination of agents only and their selection according Pareto rules (without evolution). Intelligent agents seek local sub optimal solutions for a global optimization, which will be completed in the result of the interaction of all agents. In the result of this, the amount of needed recalculating the fitness-functions can be significantly reduced. It is especially important for the multi-objective optimization related to a large-scale problem. Besides, the proposed approximating approach allows solving complex optimization problems for real big systems (like an oil company, plants, corporations, etc.).
Tet family proteins and 5-hydroxymethylcytosine in development and disease

Over the past few decades, DNA methylation at the 5-position of cytosine (5-methylcytosine, 5mC) has emerged as an important epigenetic modification that plays essential roles in development, aging and disease. However, the mechanisms controlling 5mC dynamics remain elusive. Recent studies have shown that ten-eleven translocation (Tet) proteins can catalyze 5mC oxidation and generate 5mC derivatives, including 5-hydroxymethylcytosine (5hmC). The exciting discovery of these novel 5mC derivatives has begun to shed light on the dynamic nature of 5mC, and emerging evidence has shown that Tet family proteins and 5hmC are involved in normal development as well as in many diseases. In this Primer we provide an overview of the role of Tet family proteins and 5hmC in development and cancer.
Geographical and temporal variation of injection drug users in Pakistan

Objectives We describe the characteristics of injecting drug users (IDU) in Pakistan in 2006 and 2011, and assess the heterogeneity of IDU characteristics across different cities and years as well as factors associated with HIV infection. Methods Cross-sectional, integrated behavioural-biological surveys of IDU were conducted in 10 cities across Pakistan in 2006 and 2011. Univariate and multivariable analyses were used to describe the differences in HIV prevalence and risk behaviours between cities and over time. Results Large increases in HIV prevalence among injection drug users in Pakistan were observed, with overall HIV prevalence increasing from 16.2% in 2006 to 31.0% in 2011; an increase in HIV prevalence was also seen in all geographic areas except one. There was an increase in risk behaviours between 2006 and 2011, anecdotally related to a reduction in the availability of services for IDU. In 2011, larger proportions of IDU reported injecting several times a day and using professional injectors, and fewer reported always using clean syringes. An increase in the proportion living on the street was also observed and this was associated with HIV infection. Cities differ in terms of HIV prevalence, risk profiles, and healthcare seeking behaviours. Conclusions There is a high prevalence of HIV among injection drug users in Pakistan and considerable potential for further transmission through risk behaviours. HIV prevention programs may be improved through geographic targeting of services within a city and for involving groups that interact with IDU (such as pharmacy staff and professional injectors) in harm reduction initiatives.
Relationships between activation level, knowledge, self-efficacy, and self-management behavior in heart failure patients discharged from rural hospitals

Non-adherence to self-management guidelines accounted for 50% of hospital readmissions in heart failure patients. Evidence showed that patient activation affects self-management behaviors in populations living with chronic conditions. The purpose of this study was to describe patient activation level and its relationship with knowledge, self-efficacy and self-management behaviors in heart failure patients discharged from rural hospitals. Our study populations were recruited from two hospitals in rural areas of Nebraska. We found that two-thirds of the participants reported low activation levels (e.g., taking no action to manage their heart failure condition). In addition, low patient activation levels were associated with inadequate heart failure knowledge (p=.005), low self-efficacy (p<.001) and low engagement in heart failure self-management behaviors (p<.001) after discharge from hospital.
Integrating Naïve Bayes and FOIL

A novel relational learning approach that tightly integrates the naive Bayes learning scheme with the inductive logic programming rule-learner FOIL is presented. In contrast to previous combinations that have employed naive Bayes only for post-processing the rule sets, the presented approach employs the naive Bayes criterion to guide its search directly. The proposed technique is implemented in the NFOIL and TFOIL systems, which employ standard naive Bayes and tree augmented naive Bayes models respectively. We show that these integrated approaches to probabilistic model and rule learning outp erform post-processing approaches. They also yield significantly more accurate models than si mple rule learning and are competitive with more sophisticated ILP systems.
Mindfulness meditation modulates reward prediction errors in a passive conditioning task

Reinforcement learning models have demonstrated that phasic activity of dopamine neurons during reward expectation encodes information about the predictability of reward and cues that predict reward. Self-control strategies such as those practiced in mindfulness-based approaches is claimed to reduce negative and positive reactions to stimuli suggesting the hypothesis that such training may influence basic reward processing. Using a passive conditioning task and fMRI in a group of experienced mindfulness meditators and age-matched controls, we tested the hypothesis that mindfulness meditation influence reward and reward prediction error (PE) signals. We found diminished positive and negative PE-related blood-oxygen level-dependent (BOLD) responses in the putamen in meditators compared with controls. In the meditator group this decrease in striatal BOLD responses to reward PE was paralleled by increased activity in posterior insula, a primary interoceptive region. Critically, responses in the putamen during early trials of the conditioning procedure (run 1) were elevated in both meditators and controls. Overall, these results provide evidence that experienced mindfulness meditators are able to attenuate reward prediction signals to valenced stimuli, which may be related to interoceptive processes encoded in the posterior insula.