Miracle-dz/UniFAR-FTUs huggingface dataset:
The insect-protected CTC91087-6 sugarcane event expresses Cry1Ac protein preferentially in leaves and presents compositional equivalence to conventional sugarcane

ABSTRACT A Cry1Ac-expressing sugarcane cultivar, CTC91087-6, has been developed by Centro de Tecnologia Canavieira (CTC) to be resistant to the sugarcane borer (Diatraea saccharalis). This genetically modified event was developed using Agrobacterium-mediated transformation and the help of the selectable marker phosphinothricin N-acetyltransferase (PAT) expressed from bar gene. We describe here a detailed characterization of CTC91087-6 event with respect to protein expression, nutritional composition, and assessment of its derived DNA and proteins in raw sugar. Expression of the Cry1Ac and PAT (bar) proteins produced by CTC91087-6 was evaluated in different tissues and at different times during the growing season. The new proteins are preferentially expressed in leaves, are produced at low levels in stalks, and are near the limits of detection in root tissues. The levels of Cry1Ac were much higher than PAT in all evaluated tissues. Furthermore, Cry1Ac levels in CTC91087-6 leaves are stable at various times during sugarcane cultivation cycle, assuring borer control throughout the complete crop cycle. Assessment of CTC91087-6 tissues for key food and feed nutrients as recommended by OECD to assess the safety of new varieties of sugarcane showed compositional equivalence to the conventional counterpart CTC9001 and to other commercial sugarcane varieties used as references. Raw sugar samples produced from CTC91087-6 did not contain DNA corresponding to cry1Ac and bar genes nor DNA specifically derived from CTC91087-6. In a similar way, there is no detection of Cry1Ac and PAT proteins in raw sugar produced from CTC91087-6. Taken together these results show that CTC91087-6 stably expresses Cry1Ac and PAT proteins and is substantially equivalent to the conventional counterpart CTC9001.
Impact of Physical Exercise on Symptoms of Depression and Anxiety in Pre-adolescents: A Pilot Randomized Trial

Aim The intensity of the most appropriate exercise to use in depressed youth is unclear due to differences in methodology and the lack of evidence documenting the effect of physical activity in children. Therefore, the authors of this study attempted to document the effectiveness of different training intensities to reduce symptoms of depression and anxiety in pre-teens. Methods The study included twenty-seven, randomly selected pre-adolescents (aged between 9–11 years of age) all of whom had Primary education. The participants were enrolled and, over a 5-week period, were subject to either intensive or low-to-moderate exercise programs four times a week. Psychological self-reports, as well as physical examinations, were conducted before and after such programs in blinded assessments. Psychological effects were considered the primary outcome, whilst physical condition was secondary. Results Four subjects were lost and twenty-three were analyzed. General linear model with 2 criteria revealed significant changes (p = 0.05) in trait anxiety symptoms over time in the low-to-moderate intensity group (LMIG). Within group changes followed a significant decrease in levels of anxiety (38.82 ± 2.20 to 33.36 ± 2.83, p = 0.004) and depression (10.36 ± 2.83 to 6.73 ± 1.88, p = 0.006) related symptoms amongst those in the LMIG. Interpretation This study indicated that depression and anxiety symptoms were reduced amongst a non-clinical sample of Primary educated pre-adolescents when they were subject to a low-to-moderate exercise program. The program focused on associating movement with pleasure, encouraged positive and non-competitive interactions between participants. Clinical Trial Registration www.ClinicalTrials. gov, identifier NCT02970825, autumn 2016, updated May 7, 2018 (https://clinicaltrials.gov/ct2/show/NCT02970825).
Legitimate and Reliable Determination of the Age-Related Intestinal Microbiome in Young Piglets; Rectal Swabs and Fecal Samples Provide Comparable Insights

A prerequisite for reliable microbiota analysis is having an effective and consistent sampling method. Fecal sampling, commonly used to study the intestinal microbiome, might not be suitable in all situations, especially considering the potential difficulties in obtaining fresh feces from young animals. Indeed, this study shows that the success rate of collecting fecal samples from young piglets (<2 weeks of age) was very low. Therefore, we evaluated rectal swabs as an alternative sample type (to feces) for studying porcine microbiome development and performed a comparative analysis of microbiome composition obtained from fresh fecal samples and rectal swabs in 15 healthy piglets at seven (6 piglets) and 20 (9 piglets) days of age. Three samples (fresh feces, rectal swab before and after defecation) were collected from individual piglets and microbiome composition was assessed by 16S rRNA gene sequencing. The results demonstrated that rectal swabs and fecal samples provide similar microbiome composition profiles, with samples clustering predominantly by individual animal rather than sample type. Furthermore, regardless of the sample type, the biological interpretation with respect to microbiota colonization patterns associated with different ages (7 and 20 days) was found to be comparable. Independent of sample type, we observed age-related changes like increasing microbiota diversity and alterations in relative abundances of the phyla Firmicutes, Bacteroidetes, and Fusobacteria, which was also reflected in consistent family- and genus-level microbiota changes. This study establishes that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early life, when fecal sampling is challenging.
Application of Bioengineered Materials in the Surgical Management of Heart Failure

The epicardial surface of the heart is readily accessible during cardiac surgery and presents an opportunity for therapeutic intervention for cardiac repair and regeneration. As an important anatomic niche for endogenous mechanisms of repair, targeting the epicardium using decellularized extracellular matrix (ECM) bioscaffold therapy may provide the necessary environmental cues to promote functional recovery. Following ischemic injury to the heart caused by myocardial infarction (MI), epicardium derived progenitor cells (EPDCs) become activated and migrate to the site of injury. EPDC differentiation has been shown to contribute to endothelial cell, cardiac fibroblast, cardiomyocyte, and vascular smooth muscle cell populations. Post-MI, it is largely the activation of cardiac fibroblasts and the resultant dysregulation of ECM turnover which leads to maladaptive structural cardiac remodeling and loss of cardiac function. Decellularized ECM bioscaffolds not only provide structural support, but have also been shown to act as a bioactive reservoir for growth factors, cytokines, and matricellular proteins capable of attenuating maladaptive cardiac remodeling. Targeting the epicardium post-MI using decellularized ECM bioscaffold therapy may provide the necessary bioinductive cues to promote differentiation toward a pro-regenerative phenotype and attenuate cardiac fibroblast activation. There is an opportunity to leverage the clinical benefits of this innovative technology with an aim to improve the prognosis of patients suffering from progressive heart failure. An enhanced understanding of the utility of decellularized ECM bioscaffolds in epicardial repair will facilitate their growth and transition into clinical practice. This review will provide a summary of decellularized ECM bioscaffolds being developed for epicardial infarct repair in coronary artery bypass graft (CABG) surgery.
Cross-Species Co-analysis of Prefrontal Cortex Chronic Ethanol Transcriptome Responses in Mice and Monkeys

Despite recent extensive genomic and genetic studies on behavioral responses to ethanol, relatively few new therapeutic targets for the treatment of alcohol use disorder have been validated. Here, we describe a cross-species genomic approach focused on identifying gene networks associated with chronic ethanol consumption. To identify brain mechanisms underlying a chronic ethanol consumption phenotype highly relevant to human alcohol use disorder, and to elucidate potential future therapeutic targets, we conducted a genomic study in a non-human primate model of chronic open-access ethanol consumption. Microarray analysis of RNA expression in anterior cingulate and subgenual cortices from rhesus macaques was performed across multiple cohorts of animals. Gene networks correlating with ethanol consumption or showing enrichment for ethanol-regulated genes were identified, as were major ethanol-related hub genes within these networks. A subsequent consensus module analysis was used to co-analyze monkey data with expression data from a chronic intermittent ethanol vapor-exposure and consumption model in C57BL/6J mice. Ethanol-related gene networks conserved between primates and rodents were enriched for genes involved in discrete biological functions, including; myelination, synaptic transmission, chromatin modification, Golgi apparatus function, translation, cellular respiration, and RNA processing. The myelin-related network, in particular, showed strong correlations with ethanol consumption behavior and displayed marked network reorganization between control and ethanol-drinking animals. Further bioinformatics analysis revealed that these networks also showed highly significant overlap with other ethanol-regulated gene sets. Altogether, these studies provide robust primate and rodent cross-species validation of gene networks associated with chronic ethanol consumption. Our results also suggest potential novel focal points for future therapeutic interventions in alcohol use disorder.
Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution

Adaptive laboratory evolution (ALE) is used to find causal mutations that underlie improved strain performance under the applied selection pressure. ALE studies have revealed that mutator populations tend to outcompete their non-mutator counterparts following the evolutionary trajectory. Among them, mutS-inactivated mutator cells, characterize d by a dysfunctional methyl-mismatch repair system, are frequently found in ALE experiments. Here, we examined mutS inactivation as an approach to facilitate ALE of Escherichia coli. The wild-type E. coli MG1655 and mutS knock-out derivative (ΔmutS) were evolved in parallel for 800 generations on lactate or glycerol minimal media in a serial-transfer experiment. Whole-genome re-sequencing of each lineage at 100-generation intervals revealed that (1) mutations emerge rapidly in the ΔmutS compared to in the wild-type strain; (2) mutations were more than fourfold higher in the ΔmutS strain at the end-point populations compared to the wild-type strain; and (3) a significant number of random mutations accumulated in the ΔmutS strains. We then measured the fitness of the end-point populations on an array of non-adaptive carbon sources. Interestingly, collateral fitness increases on non-adaptive carbon sources were more pronounced in the ΔmutS strains than the parental strain. Fitness measurement of single mutants revealed that the collateral fitness increase seen in the mutator lineages can be attributed to a pool of random mutations. Together, this study demonstrates that short-term mutator ALE extensively expands possible genotype space, resulting in versatile bacteria with elevated fitness levels across various carbon sources.
Trends of Postoperative Radiotherapy for Completely Resected Non-small Cell Lung Cancer in China: A Hospital-Based Multicenter 10–Year (2005–2014) Retrospective Clinical Epidemiological Study

Objectives: The role of postoperative radiotherapy (PORT) in the treatment of patients with completely resected non-small cell lung cancer (NSCLC) is not clear. Few study explored the trends of the PORT use. In this study, we examine the status of PORT use of completely resected NSCLC in mainland China. Methods: From 2005 to 2014, patients with primary lung cancer from eight hospitals across seven geographic regions of mainland China were selected. Then patients with staged I–IIIA NSCLC receiving radical surgery were enrolled in this study. The chi-square test was used to compare differences in the use of PORT among the groups of different age, regions and stages. The Cochran-Armitage trend test was used to identify the trend in the PORT use from 2005 to 2014. Results: Totally, 2,253 out of 7,184 patients were with staged I–IIIA NSCLC receiving completely resection. Only 122 patients (5.42%) received PORT. During this decade, the use of PORT declined significantly (p = 0.0002). In high socio-economic areas, the percentage of PORT use was 7.43%, which was significantly higher than 1.34% in the low socio-economic areas (p < 0.0001). Age was also associated with PORT use (p = 0.0747). For N0-1 and N2 NSCLC, the proportions of PORT use were 4.01 and 10.22%, respectively (p < 0.0001). And in N0-1 or N2 NSCLC, the proportions both decreased significantly during this decade (p = 0.009 and 0.026, respectively). For stage I, IIA, IIB and IIIA, the proportions who received PORT were 2.59, 4.65, 5.49, and 10.29%, respectively (p < 0.0001). Modern radiation techniques were widely used, but the volumes and doses varied widely. The proportions of using IMRT and EPID/IGRT increased after 2012. Conclusions: In China, the use of PORT was less than developed countries and had a declined trend. The use of PORT was related to disease stages, patients' age and geographic location. Both in N0-1 and N2 diseases, the use of PORT declined. Proper education of radiation doctors was urgently needed.
Congenital Transmission of Trypanosoma cruzi: A Review About the Interactions Between the Parasite, the Placenta, the Maternal and the Fetal/Neonatal Immune Responses

Chagas disease (CD), caused by the protozoan parasite Trypanosoma cruzi, is considered a neglected tropical disease by the World Health Organization. Congenital transmission of CD is an increasingly relevant public health problem. It progressively becomes the main transmission route over others and can occur in both endemic and non-endemic countries. Though most congenitally infected newborns are asymptomatic at birth, they display higher frequencies of prematurity, low birth weight, and lower Apgar scores compared to uninfected ones, and some suffer from severe symptoms. If not diagnosed and treated, infected newborns are at risk of developing disabling and life-threatening chronic pathologies later in life. The success or failure of congenital transmission depends on interactions between the parasite, the placenta, the mother, and the fetus. We review and discuss here the current knowledge about these parameters, including parasite virulence factors such as exovesicles, placental tropism, potential placental defense mechanisms, the placental transcriptome of infected women, gene polymorphism, and the maternal and fetal/neonatal immune responses, that might modulate the risk of T. cruzi congenital transmission.
Negative Emotional Stimuli Enhance Conflict Resolution Without Altering Arousal

In our daily life, we frequently need to make decisions between competing behavioral options while we are exposed to various contextual factors containing emotional/social information. We examined how changes in emotional/arousal state influence resolving conflict between behavioral rules. Visual stimuli with emotional content (positive, negative and neutral) and music (High/Low tempo), which could potentially alter emotional/arousal states, were included in the task context while participants performed the Wisconsin Card Sorting Test (WCST). The WCST requires the application of abstract matching rules, to resolve conflict between competing behavioral options. We found that conflict influenced both accuracy and response time (RT) in implementing rules. Measuring event-related autonomic responses indicated that these behavioral effects were accompanied by concomitant alterations in arousal levels. Performance in the WCST was modulated by the emotional content of visual stimuli and appeared as a faster response and higher accuracy when trials commenced with negative emotional stimuli. These effects were dependent on the level of conflict but were not accompanied by changes in arousal levels. Here, we report that visual stimuli with emotional content influence conflict processing without trial-by-trial changes in arousal level. Our findings indicate intricate interactions between emotional context and various aspects of executive control such as conflict resolution and suggest that these interactions are not necessarily mediated through alterations in arousal level.
On the Use of Semi-empirical Flame Models for Spreading Chaparral Crown Fire

Flame geometry plays a key role in shaping fire behavior as it can influence flame spread, radiative heat transfer and fire intensity. For wildland fire, a thorough understanding of relationships between flame geometry including flame length, flame height and flame tilt can help advance the derivation of comprehensive models of wildfire behavior. Within the fire community, a classical flame modeling approach has been the development of semi-empirical models. Many of these models have been derived for surface fuels or for pool fire configurations. However, few have sought to model flame behavior in chaparral crown fires. Thus, the objective of this study was to assess the applicability of existing semi-empirical models on observed chaparral crown fire geometry. Semi-empirical models of flame tilt, flame height and flame length were considered. Comparison with experimental observation of crown fuel layer flame height showed good agreement between two-fifths power law that relates flame height to heat release rate. Predictions of flame tilt were obtained from application of semi-empirical power-law correlations relating flame tilt angle to Froude number. Observed flame tilt values exhibited low correlation with predicted values. Thus, two new power-law correlations were proposed. Coefficients for new models were obtained from regression analysis.
Advancing Our Understandings of Healthcare Team Dynamics From the Simulation Room to the Operating Room: A Neurodynamic Perspective

The initial models of team and team member dynamics using biometric data in healthcare will likely come from simulations. But how confident are we that the simulation-derived high-resolution dynamics will reflect those of teams working with live patients? We have developed neurodynamic models of a neurosurgery team while they performed a peroneal nerve decompression surgery on a patient to approach this question. The models were constructed from EEG-derived measures that provided second-by-second estimates of the neurodynamic responses of the team and team members to task uncertainty. The anesthesiologist and two neurosurgeons developed peaks, often coordinated, of elevated neurodynamic organization during the patient preparation and surgery which were similar to those seen during simulation training, and which occurred near important episodes of the patient preparation and surgery. As the analyses moved down the neurodynamic hierarchy, and the simulation and live patient neurodynamics occurring during the intubation procedure were compared at progressively smaller time scales, differences emerged across scalp locations and EEG frequencies. The most significant was the pronounced suppression of gamma rhythms detected by the frontal scalp sensors during the live patient intubation which was absent in simulation trials of the intubation procedure. These results indicate that while profiles of the second-by-second neurodynamics of teams were similar in both the simulation and live patient environments, a deeper analysis revealed differences in the EEG frequencies and scalp locations of the signals responsible for those team dynamics. As measures of individual and team performance become more micro-scale and dynamic, and simulations become extended into virtual environments, these results argue for the need for parallel studies in live environments to validate the dynamics of cognition being observed.
Improving early warning scores – more data, better validation, the same response

We thank Oglesby et al. for their interesting editorial [1] accompanying our recent paper [2]. We value their interpretation that a single standardised early warning score (EWS) may not be applicable to all types of patients and are grateful for their qualified support of the concept of future population-specific EWS. We are also in agreement that evidence-based models are preferable to consensus-based scores and that external validation is imperative for all EWS. We have a major issue with their criticism that we failed to externally validate our score in a dataset separate from that used to develop the score. Multiple external validation techniques were undertaken and have been available in electronic format in the online supplement since 3 July 2019 [2]. Each centre independently collected four separate datasets. Although these datasets were ultimately merged into one combined database, we retained the ability to use separate databases for external validation purposes. Multiple predictive performance and validation techniques were utilised and these are summarised in the supporting information which accompanies the online version of our paper (Appendix 3: Table A3.4.) [3]. Debray et al. [4] define external validation as using new participant-level data, external to those used for model development, to examine whether the model’s predictions are reliable in individuals from potential population(s) for clinical use. Following that definition, we purposely held back from using some centres to fit/develop the model so that we could then use them to externally validate a model fit for other centres. We even reported all possible combinations of doing this, which were a sensible cut of the dataset to avoid accusations of potential bias. Given the revised evidence-based physiological weightings, novel sub-division of oxygen therapy and potential clinical utility of our app [5] in discriminating between ‘hard’ and ‘soft’ escalation threshold NEWS scores (≥ 5 or ≥ 7), we believe ‘Improving EWS –more data, better validation, a step in the right direction’ may have been a more accurate choice of editorial title.
The PLUG Link Annotator – interactive construction of data from parallel corpora

In this paper an approach of using gold standards to evaluate word alignment systems is described. To make the process of creating gold standards easier, an interactive tool called the PLUG Link Annotator is presented along with the Link Scorer, which automatically evaluates the output from a word alignment system against the gold standard. It is argued that using reference data in this manner has several advantages, the most important being consistency in evaluation criteria as well as savings in time, due to the fact that the reference data only need to be constructed once, but can be applied many times.