Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute and Chronic Molecular Signatures and Associated Symptoms of Blast Exposure in Military Breachers

Injuries from exposure to explosions rose dramatically during the Iraq and Afghanistan wars, which motivated investigations of blast-related neurotrauma and operational breaching. In this study, military “breachers” were exposed to controlled, low-level blast during a 10-day explosive breaching course. Using an omics approach, we assessed epigenetic, transcriptional, and inflammatory profile changes in blood from operational breaching trainees, with varying levels of lifetime blast exposure, along with daily self-reported symptoms (with tinnitus, headaches, and sleep disturbances as the most frequently reported). Although acute exposure to blast did not confer epigenetic changes, specifically in DNA methylation, differentially methylated regions (DMRs) with coordinated gene expression changes associated with chronic lifetime cumulative blast exposures were identified. The accumulative effect of blast showed increased methylation of PAX8 antisense transcript with coordinated repression of gene expression, which has been associated with sleep disturbance. DNA methylation analyses conducted in conjunction with reported symptoms of tinnitus in the low vs. high blast incidents groups identified DMRS in KCNE1 and CYP2E1 genes. KCNE1 and CYP2E1 showed the expected inverse correlation between DNA methylation and gene expression, which have been previously implicated in noise related hearing loss. Although no significant transcriptional changes were observed in samples obtained at the onset of the training course relative to chronic cumulative blast, we identified a large number of transcriptional perturbations acutely pre- versus post-blast exposure. Acutely, 67 robustly differentially expressed genes (fold change ≥1.5), including UFC1 and YOD1, ubiquitin-related proteins were identified. Inflammatory analyses of cytokines and chemokines revealed dysregulation of MCP-1, GCSF, HGF, MCSF, and RANTES acutely following blast exposure. These data show the importance of an omics approach, revealing that transcriptional and inflammatory biomarkers capture acute low-level blast overpressure exposure, whereas DNA methylation marks encapsulate chronic long-term symptoms.
Monitoring codling moth (Lepidoptera: Tortricidae) with a four‐component volatile blend compared to a sex pheromone‐based blend

Monitoring adult codling moth, Cydia pomonella (L.), is a crucial component in implementing effective integrated management programmes in apple, Malus domestica Borkhausen. Use of sex pheromone lures to track male populations has been the traditional approach, but their use in orchards treated with sex pheromone for mating disruption (MD) has been problematic. Development of kairomone and kairomone–pheromone combination lures has allowed the catch of female moths and has benefited several aspects of codling moth management through improved spray timings and action thresholds. Recently, a new four‐component volatile blend (4‐K) comprised of pear ester, (E,Z)‐2,4‐ethyl decadienoate (PE), (E)‐11 4,8‐dimethyl‐1,3,7‐nonatriene, all isomers of pyranoid linalool oxide and acetic acid (AA) has been characterized that has increased female moth catch threefold versus any previous blend. Field trapping studies were conducted to compare moth catches in traps baited with 4‐K versus the use of sex pheromone, (E,E)‐8,10‐dodecadien‐1‐ol (PH) in combination with PE and AA. Trials were conducted in orchards left either untreated, or treated with PH or PH + PE. Traps baited with 4‐K and 4‐K + PH lures caught significantly more females than traps baited with PH + PE + AA lures. Traps baited with 4‐K + PH lures caught significantly more total moths than traps baited with PH + PE + AA lures in all three orchards. Adding a PH lure to traps with the 4‐K lure did not affect female catch, but significantly increased male and total moth catches. These studies demonstrate that codling moth can be trapped effectively in apple under MD without the use of sex pheromone lures. The significant increase in female codling moth catch with the 4‐K lure suggests that efforts to improve spray timings and action threshold determinations as well as mass trapping might be enhanced with this new lure.
Comparative Analysis of C-repeat Binding Factors (CBFs) in Tomato and Arabidopsis

Cold stress is one of the limiting factors of plant production that plants use different mechanisms for cold tolerance. CBF genes play critical role to regulate the cold responsive genes. To better understand of CBF gene functions, the tomato-CBFs and Arabidopsis-CBFs were evaluated using bioinformatics tools, and finally the expression patterns of SlCBF1 gene were analyzed under 10 and 4 ̊C in two contrasting tomato species (Solanum lycopersicum and S. habrochaites). The different cis regulatory elements were observed in promoter region of SlCBF1 and AtCBF1 genes, and ICE1, COR and HOS1 proteins exhibited high interaction with CBFs. The results of Real time PCR of SlCBF1 exhibited that under 10 and 4 ̊C, SlCBF1 was down regulated in cold sensitive tomato genotype while it was slightly up-regulated in cold tolerant genotype at 4 ̊C. The results showed that the SlCBF1 and AtCBF1 genes have differential expression in cold stress.
Developing a dengue forecast model using Long Short Term Memory neural networks method

Background Dengue Fever (DF) is a tropical mosquito-borne disease that threatens public health and causes enormous economic burdens worldwide. In China, DF expanded from coastal region to inner land, and the incidence sharply increased in the last few years. In this study, we conduct the analysis of dengue using the Long Short Term Memory (LSTM) recurrent neural networks. This is an artificial intelligence technology, to develop a precise dengue forecast model. Methodology/Principal Findings The model is developed from monthly dengue cases and local meteorological data of 2005–2018 among top 20 Chinese cities with a record of the highest dengue incidence. The first 13 year data were used to construct the LSTM and to predict the dengue outbreaks in 2018. The results are compared with the estimated dengue cases of other previously published models. Model performance and prediction accuracy were assessed using Root Mean Square Error (RMSE). With the LSTM method, the prediction measurements of average RMSE drop by 54.79% and 34.76% as compared with the Susceptible Infected Recovered (SIR) model and Zero Inflated Generalized Additive Model (ZIGAM). Our results showed that if only local data were used to develop forecast models, the LSTM neural networks would fail to capture the transmission characteristics of dengue virus in areas with fewer dengue cases. Contrarily, transfer learning (TL) can improve the accuracy of prediction of the LSTM neural network model in areas with fewer dengue incidences. Conclusion and significance The LSTM model is beneficial in predicting dengue incidence as compared with other previously published forecasting models. The findings provide a more precise forecast dengue model, which can help the local government and health-related departments respond early to dengue epidemics. Author summary In China, DF is a public health concern that poses a great economic burden on local governments. However, the incidence has sharply increased in recent years with growth in the sub-regions. With this issue, it will be challenging to develop an accurate and timely dengue forecast model. LSTM recurrent neural networks, deep learning methods and virus propagation rules by learning from observational data offer more advantages in predicting the prevalence of infectious disease dynamics than the traditional statistical model. The 2005–2017 data of the top 20 Chinese cities with the highest dengue incidence were used to construct the LSTM model, advantageous in predicting dengue in most cities. Moreover, the model helped to predict the dengue outbreaks in 2018 and used to compare the estimated dengue cases with the RMSE results of other previously published models. A thorough search of the literature shows that this is the first established dengue forecast model using the LSTM method, which is effective in predicting the trend of dengue dynamics.
Outcome of patients > age 40 with Burkitt lymphoma (BL) treated with aggressive chemotherapuetic regimens : Results from the international Burkitt lymphoma collaborative group

BL is considered a highly curable tumor when treated with dose-intensive, multiagent chemotherapy including central nervous system prophylaxis. 60–90% of pediatric and young adult patients (pts) with BL achieve durable remission if treated appropriately. However, the outcome of older adults with BL is more uncertain. We first investigated the SEER database and determined that 57% of reported pts with BL are > age 40. We then performed a systematic review of published manuscripts describing outcome of adult pts (> age 15) with confirmed de novo BL (REAL/WHO defined and confirmed) treated in the modern therapeutic era. Of 33 manuscripts, 17 were excluded due to small sample size ( age 40 for inclusion in a database, and full data is available from 12 manuscripts (10 prospective; 2 retrospective). 470 total adult BL pts ages 15–79 were treated, and 183 (39%) were > age 40. Pts > age 40 had significantly inferior outcomes in 10 of the 12 series. Treatment regimens included intensive short duration therapy (4 series; total N=212; > 40 N=93); ALL-like therapy (6 series; total N=182; > 40 N=62) and ASCT as part of induction therapy (2 series, total N=76; > 40 N=28). The median overall survival at 2 years (OS) for all pts treated with short duration therapy was 71%, and for pts > age 40 was 39%. The OS for all pts treated with ALL-like therapy was 51%, and for pts > age 40 was 40%. Pts > age 40 treated with ASCT as part of induction regimens had somewhat better outcomes (median OS 62%), however this represents a small number of pts who may have been subject to more rigorous selection criteria. We conclude that pts > age 40 with BL are significantly underrepresented in the published clinical trials. Even when these pts are treated with appropriate intensive chemotherapy, the OS is inferior compared to published outcomes in younger pts, and is similar to OS survival historically observed with CHOP chemotherapy alone (40%). Future efforts should evaluate whether BL in older adults has unique biological features. Novel therapeutic regimens, with decreased toxicity, targeting the older majority pts with BL are required.
A novel polyubiquitin chain linkage formed by viral Ubiquitin prevents cleavage by deubiquitinating enzymes

The Baculoviridae family of viruses encode a viral Ubiquitin gene. Although the viral Ubiquitin is homologous to eukaryotic Ubiquitin (Ub), preservation of this gene in the viral genome indicates a unique function that is absent in the host eukaryotic Ub. We report the structural, biophysical, and biochemical properties of the viral Ubiquitin from Autographa Californica Multiple Nucleo-Polyhedrosis Virus (AcMNPV). The structure of viral Ubiquitin (vUb) differs from Ub in the packing of the central helix α1 to the beta-sheet of the β-grasp fold. Consequently, the stability of the fold is lower in vUb compared to Ub. However, the surface properties, ubiquitination activity, and the interaction with Ubiquitin binding domains are similar between vUb and Ub. Interestingly, vUb forms atypical polyubiquitin chain linked by lysine at the 54th position (K54). The K54-linked polyubiquitin chains are neither effectively cleaved by deubiquitinating enzymes, nor are they targeted by proteasomal degradation. We propose that modification of proteins with the viral Ubiquitin is a mechanism to counter the host antiviral responses.
The expression of LjROP4 is required for rhizobial infection in Lotus japonicus

Abstract: Increasing evidence suggests that Rho of plant (ROP) GTPases play important roles in the rhizobium–legume symbiotic nodulation, but the molecular mechanisms of their regulation in symbiosis remain poorly understood. In this study, we showed that ROP4 in Lotus japonicus (LjROP4) is involved in the symbiotic interaction between L. japonicus and Mesorhizobium loti. Tissue expression analysis showed that LjROP4 expressed highly in the root. Histochemical staining analysis showed that after rhizobia inoculation, GUS reporter activity increased in the root vascular bundle, root tip, and lateral root primordia. During nodule development, GUS activity was detected in the cortex of nodule primordia and young nodules. In the mature nodules, GUS activity was detected only in the vascular bundle. Compared with the control, the overexpression of ROP4 and ROP4-CA produced much more pronounced root hair swelling and curling induced by M. loti. The infection event and nodule number noticeably increased, which was consistent with this promotion of root hair deformation. Moreover, RNA interference of LjROP4 produced opposite phenotypes. These data suggest that LjROP4 is required for root hair deformation during rhizobial infection. Thus, our study provides important information about root hair deformation responses induced by nod factors in the early stages of symbiotic interaction.
Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
Morphology and Genetic Diversity of Jabon Putih Seedling from 4 Populations in Sumatra, Nusa Kambangan, Kalimantan, and Sulawesi

Jabon putih (Neolamarckia cadamba) is a widely distributed potential fast-growing species and is thought to be associated with extensive genetic diversity. The aim of the research was to assess the morphological and genetic variation of jabon putih seedling based on AFLP markers. Randomized block design with 4 replications was used to assess seedling morphological variation on 31 families from 4 populations (Kapuas, Kampar, Nusa Kambangan, Pomalaa) based on traits of seedling height, diameter, sturdiness quotient, number of leaves, leaf length, and leaf width at nursery. AFLP Analysis System I Kit by using dry leaf samples from each family was used. Characteristics of jabon putih seedlings had variation among populations and families within population. Genetic variation within population based on morphological traits had the similar trend with result of AFLP analysis. The highest genetic variation was detected in Kapuas population, followed by Pomalaa, Nusa Kambangan, and Kampar populations. Cluster analysis and UPGMA method had 2 cluster and put down most of families from Kapuas in one cluster separated from other families. Based on the genetic similarity analysis, 26 families could be considered as potential families for the establishment of breeding populations. The study has important practical implications for genetic resources management and for future breeding programs of jabon putih.
Forest canopy resists plant invasions: a case study of Chromolaena odorata in sub-tropical Sal (Shorea robusta) forests of Nepal

Invasive Alien Species cause tremendous ecological and economic damage in agriculture, forestry, aquatic ecosystems, and pastoral resources. They are one of the major threats to biodiversity conservation. Understanding the spatial pattern of invasive species and disentangling the biophysical drivers of invasion at forest stand level is essential for managing invasive species in forest ecosystems and the wider landscape. However, forest-level and species-specific information on invasive species abundance and area of extent is largely lacking. In this context, we analysed the cover of one of the world’s worst invasive plant species Chromolaena odorata in Sal (Shorea robusta Gaertn.) forest in central Nepal. Vegetation was sampled in four community-managed forests using 0.01 ha square quadrats, covering forest edge to the interior. Chromolaena cover, floral richness, tree density, forest canopy cover, shrub cover, and tree basal area were measured in each plot. We also estimated the level of disturbance in plots, and calculated distance from the plot to the nearest road. We also explored forest and invasive species management practices in community forests. Chromolaena cover was found to be negatively correlated with forest canopy cover, distance to the nearest road, angle of slope and shrub cover. Canopy cover had the greatest effect on the Chromolaena cover. Chromolaena cover did not show any pattern along native species richness gradients. In conclusion, forest canopy cover is the overriding biotic covariate affecting Chromolaena cover in Sal forests. The practical application of our results in managing Chromolaena in forest ecosystems is discussed.
Postharvest technologies in the ripening of ‘Maçã’ bananas stored in ambient condition

The banana is a climacteric fruit with a limited shelf life in the environment and sensitive to storage under refrigeration, necessitating strategies to improve its post harvest conservation. In this sense, the objective of this study was to evaluate the effect of post harvest technologies on the quality and the prolongation of the useful life of ‘Maçã’ bananas during storage in ambient temperature condition (25 oC). The fruits were obtained in physiological maturity in the green color and immersed in the following solutions: distilled water (control), cassava starch, maize starch and 3% calcium chloride for three minutes in addition to the sachets containing 3g KMnO4 for one period of 12 days in ambient condition. The evaluations took place every three days in terms of loss of fresh weight, firmness of peel, starch content, soluble solids, titratable acidity, pH, SS/AT ratio and incidence of rot. The postharvest treatments extended the shelf life of the fruits for 12 days in relation to the nine days of the control treatment. Among the evaluated technologies, the use of sachets of KMnO4 delayed ripening by observing fruits with higher green retention of the peel and pulp firmness, as well as lower fresh mass loss, starch degradation, soluble solids synthesis, ratio SS/AT and incidence of rot during the storage period. Thus, the ethylene absorber based on KMnO4 represents a viable alternative for the preservation of the quality of 'Maçã' bananas during commercialization at room temperature. Key-words: Musa sp. , Ethylene Absorber, Calcium Chloride, Edible Coatings, Fruit Quality
Comparison of Natural Regeneration in Natural Grassland and Pine Plantations across an Elevational Gradient in the Páramo Ecosystem of Southern Ecuador

During the 1980s, reforestation programs using exotic species (Pinus spp.) were established in the páramo ecosystem of Ecuador. The aims of this study were: (1) to compare the natural regeneration between pine plantations (Pi) and natural grassland (NG) across an elevational gradient and (2) to identify the attributes of Pi and soil properties that were influencing herbaceous and woody plant composition and their plant cover. In total, six independent Pinus patula (Schltdl. & Cham. plantations (two per each elevation) were selected and distributed in an elevational range (3200–3400, 3400–3600, 3600–3800 m a.s.l.). Adjacent to Pi, plots in NG were established for recording natural regeneration. Both, namely the attributes and the soil samples, were measured in Pi. The results showed that natural regeneration differs significantly between both types of vegetation. As expected, NG holds more plant diversity than Pi; the elevational range showed a clear tendency that there was more herbaceous richness when elevation range increases, while the opposite was found for woody species. Moreover, attributes of Pi influenced herbaceous and woody vegetation, when saturated hydraulic conductivity (Ksat) in the soil, basal area (BA) and canopy density (CD) increased, herbaceous species richness and its cover decreseased; and when Ksat and the acidity in the soil increased, woody plants richness and its cover decreased. The plantations have facilitated the establishment of shade tolerant species. More studies are needed to evaluate if removal with adequate management of pine plantations can improve the restoration and conservation of the native vegetation of the páramo ecosystem.
Assessing the relationship between diet and size-at-age in Pacific halibut (Hippoglossus stenolepis) using δ13C and δ15N analysis

The ecological mechanisms driving an observed decline in the mean size-at-age of adult Pacific halibut (Hippoglossus stenolepis) in the eastern North Pacific Ocean have yet to be defined. Here, we present the results of a study designed to investigate the relationship between one potential mechanism — diet — and size-at-age using carbon and nitrogen stable isotope analysis. Our results indicate significant differences in the skeletal muscle δ13C and δ15N values between size-at-age categories for each sex, with larger-size-at-age fish consuming diets with higher δ15N values, indicating higher trophic level feeding. Analysis of Bayesian standard ellipse areas showed that for females, intermediate size-at-age categories have the largest dietary range. For males, the largest dietary range was observed in the largest size-at-age category. Our results suggest a size-based stratification in dietary strategy for Pacific halibut with implications for observed declines in size-at-age.
Unsupervised Clusterless Decoding using a Switching Poisson Hidden Markov Model

Spike sorting is a standard preprocessing step to obtain ensembles of single unit data from multiunit, multichannel recordings in neuroscience. However, more recently, some researchers have started doing analyses directly on the unsorted data. Here we present a new computational model that is an extension of the standard (unsupervised) switching Poisson hidden Markov model (where observations are time-binned spike counts from each of N neurons), to a clusterless approximation in which we observe only a d-dimensional mark for each spike. Such an unsupervised yet clusterless approach has the potential to incorporate more information than is typically available from spike-sorted approaches, and to uncover temporal structure in neural data without access to behavioral correlates. We show that our approach can recover model parameters from simulated data, and that it can uncover task-relevant structure from real neural data.