Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Selection Traits for Effective Popcorn (Zea mays L. var. Everta) Breeding Under Water Limiting Conditions

Climate change is expected to intensify water restriction to crops, impacting on the yield potential of crops such as popcorn. This work aimed to evaluate the performance of 10 field cultivated popcorn inbred lines during two growing seasons, under well-watered (WW) and water stressed (WS) (ψsoil≥ −1.5 MPa) conditions. Water stress was applied by withholding irrigation in the phenological phase of male pre-anthesis. Additionally, two contrasting inbred lines, P7 (superior line) and L75 (low performer) were compared for grain yield (GY) and expanded popcorn volume (EPV), selected from previous studies, were tested under greenhouse conditions. In the field, no genotype x water condition x crop season (G×WC×CS) interaction was observed, whereas GY (−51%), EPV (−55%) and leaf greenness (SPAD index) measured 17 days after anthesis (DAA) (> −10%) were highly affected by water limitation. In general, root traits (angles, number, and density) presented G×WC×CS interaction, which did not support their use as selection parameters. In relation to leaf senescence, for both WS and WW conditions, the superior inbred lines maintained a stay-green condition (higher SPAD index) until physiological maturity, but maximum SPAD index values were observed later in WW (48.7 by 14 DAA) than in WS (43.9 by 7 DAA). Under both water conditions, negative associations were observed between SPAD index values 15 and 8 days before anthesis DBA), and GY and EPV (r ≥ −0.69), as well as between SPAD index 7, 17, and 22 DAA, and angles of brace root (AB), number of crown roots (NC) and crown root density (CD), in WS (r ≥ −0.69), and AB and CD, in WW (r ≥ −0.70). Lower NC and CD values may allow further root deepening in WS conditions. Under WS P7 maintained higher net photosynthesis values, stomatal conductance, and transpiration, than L75. Additionally, L75 exhibited a lower (i.e., more negative) carbon isotope composition value than P7 under WS, confirming a lower stomatal aperture in L75. In summary, besides leaf greenness, traits related to leaf photosynthetic status, and stomatal conductance were shown to be good indicators of the agronomic performance of popcorn under water constraint.
Factors Associated With In-hospital Mortality of Children With Acute Fulminant Myocarditis on Extracorporeal Membrane Oxygenation

Aim: To analyze the factors associated with in-hospital mortality of children with acute fulminant myocarditis on venoarterial extracorporeal membrane oxygenation (VA-ECMO). Methods: This was a retrospective cohort study using chart reviews of patients diagnosed with acute fulminant myocarditis at the pediatric intensive care unit of two tertiary medical centers between January 1, 2005 and December 31, 2017. The inclusion criteria for this study were: (1) age from 1 month to 18 years; (2) diagnosed with acute myocarditis; (3) cardiogenic shock and need vasoactive-inotropic score ≥20 within 48 h after the use of vasoactive-inotropic agents; and (4) the need for ECMO placement. Results: Thirty-three children with acute fulminant myocarditis who needed ECMO were included. Clinical parameters were retrospectively reviewed. The overall survival rate was 69.6%. Higher levels of pre-ECMO troponin-I and pre-ECMO lactate, and lower post-ECMO left ventricular ejection fraction (LVEF) were significantly associated with in-hospital mortality in univariate analysis. Only higher pre-ECMO lactate and lower post-ECMO LVEF remained as predictors for in-hospital mortality in multivariate analysis. The areas under the curve of pre-ECMO lactate and post-ECMO LVEF in predicting survival were 0.848 (95% CI, 0.697–0.999, p = 0.002) and 0.824 (95% CI, 0.704–0.996, p = 0.01), respectively. A pre-ECMO lactate level of 79.8 mg/dL and post-ECMO LVEF of 39% were appropriate cutoff points to predict mortality. Conclusion: Pre-ECMO lactate level was associated with mortality in children with acute fulminant myocarditis, with an optimal cutoff value of 79.8 mg/dL. After VA-ECMO implantation, post-ECMO LVEF was associated with mortality, with an optimal cutoff value of 39%. The use of LVADs or urgent heart transplantation should be considered if the post-ECMO LVEF does not improve.
Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma

Long non-coding RNAs (lncRNAs) are non-protein-coding RNAs longer than 200 nucleotides. Accumulating evidence demonstrates that lncRNA is a potential biomarker for cancer diagnosis and prognosis. However, there are no prognostic biomarkers and lncRNA models for multiple myeloma (MM). Hence, it is necessary to screen novel lncRNA that can potentially participate in the initiation and progression of MM and consequently construct a risk score system for the disease. Raw microarray datasets were obtained from the Gene Expression Omnibus website. Weighted gene co-expression network analysis and principal component analysis identified 12 lncRNAs of interest. Then, univariate, least absolute shrinkage and selection operator Cox regression and multivariate Cox hazard regression analysis identified two lncRNAs (LINC00996 and LINC00525) that were formulated to construct a risk score system to predict survival. Receiver operating characteristic analysis certificated the superior performance in predicting 3-year overall survival (area under the curve = 0.829). The similar prognostic values of the two-lncRNA signature were also observed in the tested The Cancer Genome Atlas dataset. Furthermore, two other lncRNAs (LINC00324 and LINC01128) were differentially expressed between CD138+ plasma cells from normal donors and MM patients and were verified to be associated with cancer stage in the Gene Expression Omnibus dataset. A lncRNA-mediated competing endogenous RNA network, including 2 lncRNAs, 12 mitochondrial RNAs, and 103 target messenger RNAs, was constructed. In conclusion, we developed a two-lncRNA expression signature to predict the prognosis of MM and constructed a key lncRNA-based competing endogenous RNA network in MM. These lncRNAs were associated with survival and are probably involved in the occurrence and progression of MM.
The Topography of Visually Guided Grasping in the Premotor Cortex: A Dense-Transcranial Magnetic Stimulation (TMS) Mapping Study

Visuomotor transformations at the cortical level occur along a network where posterior parietal regions are connected to homologous premotor regions. Grasping-related activity is represented in a diffuse, ventral and dorsal system in the posterior parietal regions, but no systematic causal description of a premotor counterpart of a similar diffuse grasping representation is available. To fill this gap, we measured the kinematics of right finger movements in 17 male and female human participants during grasping of three objects of different sizes. Single-pulse transcranial magnetic stimulation was applied 100 ms after visual presentation of the object over a regular grid of 8 spots covering the left premotor cortex (PMC) and 2 Sham stimulations. Maximum finger aperture during reach was used as the feature to classify object size in different types of classifiers. Classification accuracy was taken as a measure of the efficiency of visuomotor transformations for grasping. Results showed that transcranial magnetic stimulation reduced classification accuracy compared with Sham stimulation when it was applied to 2 spots in the ventral PMC and 1 spot in the medial PMC, corresponding approximately to the ventral PMC and the dorsal portion of the supplementary motor area. Our results indicate a multifocal representation of object geometry for grasping in the PMC that matches the known multifocal parietal maps of grasping representations. Additionally, we confirm that, by applying a uniform spatial sampling procedure, transcranial magnetic stimulation can produce cortical functional maps independent of a priori spatial assumptions. SIGNIFICANCE STATEMENT Visually guided actions activate a large frontoparietal network. Here, we used a dense grid of transcranial magnetic stimulation spots covering the whole premotor cortex (PMC), to identify with accurate spatial mapping the functional specialization of the human PMC during grasping movement. Results corroborate previous findings about the role of the ventral PMC in preshaping the fingers according to the size of the target. Crucially, we found that the medial part of PMC, putatively covering the supplementary motor area, plays a direct role in object grasping. In concert with findings in nonhuman primates, these results indicate a multifocal representation of object geometry for grasping in the PMC and expand our understanding of how our brain integrates visual and motor information to perform visually guided actions.
Time-Dependent Impairment of Fear Conditioning and Associated Brain Regions After Pilocarpine-Induced Status Epilepticus

Our study aimed to demonstrate time-dependent declarative memory changes and its associated brain regions after status epilepticus (SE) using structural imaging techniques and machine learning methods. Pilocarpine was administrated to establish the SE model. At four different time points after SE (1, 2, 3, and 4 months, respectively), rats were subjected to structural imaging acquisition as well as contextual fear conditioning for the measurement of brain structural changes and declarative memory. Voxel-based morphometry (VBM) analysis were performed. Those significantly different regions were selected as features for training support vector machine (SVM). A linear kernel was chosen for regression of declarative memory. Leave-one-out cross-validation was applied to ensure generalization. Our results showed that the pilocarpine groups displayed the most severely impaired declarative memory at 2 months after SE and improved afterward, but failed to recover to the normal condition at 4 months after SE. The pilocarpine groups showed lower gray matter volumes and larger cerebrospinal fluid (CSF) volumes. After controlling for the total brain volumes, ANOVA demonstrated gray matter volume changes in the CA1 subfield of the hippocampus, primary somatosensory cortex, entorhinal cortex, etc. The combination of VBM and SVM identifies the somatosensory cortex and entorhinal cortex as the correlated brain regions for declarative memory dysfunctions after SE. Our study indicates that compensational mechanisms might be triggered to help with the recovery of memory functions after SE. Structural changes of the somatosensory cortex and entorhinal cortex might be involved in memory impairment after SE.
Structures and Functions of the 3′ Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals

The 3′ untranslated region (3′ UTR) of positive-sense single-stranded RNA [ssRNA(+)] viruses is highly structured. Multiple elements in the region interact with other nucleotides and proteins of viral and cellular origin to regulate various aspects of the virus life cycle such as replication, translation, and the host-cell response. This review attempts to summarize the primary and higher order structures identified in the 3′UTR of ssRNA(+) viruses and their functional roles.
Comprehending Meningioma Signaling Cascades Using Multipronged Proteomics Approaches & Targeted Validation of Potential Markers

Meningiomas are one of the most prevalent primary brain tumors. Our study aims to obtain mechanistic insights of meningioma pathobiology using mass spectrometry-based label-free quantitative proteome analysis to identifying druggable targets and perturbed pathways for therapeutic intervention. Label-free based proteomics study was done from peptide samples of 21 patients and 8 non-tumor controls which were followed up with Phosphoproteomics to identify the kinases and phosphorylated components of the perturbed pathways. In silico approaches revealed perturbations in extracellular matrix remodeling and associated cascades. To assess the extent of influence of Integrin and PI3K-Akt pathways, we used an Integrin Linked Kinase inhibitor on patient-derived meningioma cell line and performed a transcriptomic analysis of the components. Furthermore, we designed a Targeted proteomics assay which to the best of our knowledge for very first-time enables identification of peptides from 54 meningioma patients via SRM assay to validate the key proteins emerging from our study. This resulted in the identification of peptides from CLIC1, ES8L2, and AHNK many of which are receptors and kinases and are difficult to be characterized using conventional approaches. Furthermore, we were also able to monitor transitions for proteins like NEK9 and CKAP4 which have been reported to be associated with meningioma pathobiology. We believe, this study can aid in designing peptide-based validation assays for meningioma patients as well as IHC studies for clinical applications.
Wearable and Stretchable Strain Sensors: Materials, Sensing Mechanisms, and Applications

Recent advances in the design and implementation of wearable resistive, capacitive, and optical strain sensors are summarized herein. Wearable and stretchable strain sensors have received extensive research interest due to their applications in personalized healthcare, human motion detection, human–machine interfaces, soft robotics, and beyond. The disconnection of overlapped nanomaterials, reversible opening/closing of microcracks in sensing films, and alteration of the tunneling resistance have been successfully adopted to develop high‐performance resistive‐type sensors. On the other hand, the sensing behavior of capacitive‐type and optical strain sensors is largely governed by their geometrical changes under stretching/releasing cycles. The sensor design parameters, including stretchability, sensitivity, linearity, hysteresis, and dynamic durability, are comprehensively discussed. Finally, the promising applications of wearable strain sensors are highlighted in detail. Although considerable progress has been made so far, wearable strain sensors are still in their prototype stage, and several challenges in the manufacturing of integrated and multifunctional strain sensors should be yet tackled.
Pre-transplant HLA Antibodies and Delayed Graft Function in the Current Era of Kidney Transplantation

Delayed graft function (DGF) occurs in a significant proportion of deceased donor kidney transplant recipients and was associated with graft injury and inferior clinical outcome. The aim of the present multi-center study was to identify the immunological and non-immunological predictors of DGF and to determine its influence on outcome in the presence and absence of human leukocyte antigen (HLA) antibodies. 1,724 patients who received a deceased donor kidney transplant during 2008–2017 and on whom a pre-transplant serum sample was available were studied. Graft survival during the first 3 post-transplant years was analyzed by multivariable Cox regression. Pre-transplant predictors of DGF and influence of DGF and pre-transplant HLA antibodies on biopsy-proven rejections in the first 3 post-transplant months were determined by multivariable logistic regression. Donor age ≥50 years, simultaneous pre-transplant presence of HLA class I and II antibodies, diabetes mellitus as cause of end-stage renal disease, cold ischemia time ≥18 h, and time on dialysis >5 years were associated with increased risk of DGF, while the risk was reduced if gender of donor or recipient was female or the reason for death of donor was trauma. DGF alone doubled the risk for graft loss, more due to impaired death-censored graft than patient survival. In DGF patients, the risk of death-censored graft loss increased further if HLA antibodies (hazard ratio HR=4.75, P < 0.001) or donor-specific HLA antibodies (DSA, HR=7.39, P < 0.001) were present pre-transplant. In the presence of HLA antibodies or DSA, the incidence of biopsy-proven rejections, including antibody-mediated rejections, increased significantly in patients with as well as without DGF. Recipients without DGF and without biopsy-proven rejections during the first 3 months had the highest fraction of patients with good kidney function at year 1, whereas patients with both DGF and rejection showed the lowest rate of good kidney function, especially when organs from ≥65-year-old donors were used. In this new era of transplantation, besides non-immunological factors, also the pre-transplant presence of HLA class I and II antibodies increase the risk of DGF. Measures to prevent the strong negative impact of DGF on outcome are necessary, especially during organ allocation for presensitized patients.
Eastern Oyster Recruitment Patterns on and Near Natural Reefs: Implications for the Design of Oyster Reef Restoration Projects

ABSTRACT The spatial relationship between adult eastern oyster Crassostrea virginica populations and recruitment to the benthos of their offspring is not well understood. It is well established that larvae can be widely dispersed, but the relationship between dispersal potential and actual recruitment patterns across the full range of spatial scales involved remains unknown. To explore this relationship, spat collectors were deployed on and near (up to 1 km distance) three natural oyster reefs in New Hampshire in 2014 and 2015. Spat densities on the reefs and within 400 m of the reefs were nearly 10-fold higher than densities more distant. These data do not negate the potential importance of widespread dispersal and recruitment, but they do indicate a surprising level of recruitment very near their likely source. Additional research is needed in other areas to test the generality of the findings and to assess potential causal factors for the observed patterns. The overall implication for choosing sites for oyster reef restoration projects, particularly in recruitment-limited areas, is that they may need to be located much closer to spawning adults than previously thought to maximize the likelihood of adequate natural recruitment and reef development.
Importance of Dietary Changes During the Coronavirus Pandemic: How to Upgrade Your Immune Response

The new coronavirus pandemic continues to spread causing further public health, social, and economic issues. The disparities in the rates of death between countries poses questions about the importance of lifestyle habits and the immune status of populations. An exploration of dietary habits and COVID-19-related death might unravel associations between these two variables. Indeed, while both nutritional excess and deficiency are associated with immunodeficiency, adequate nutrition leading to an optimally functioning immune system may be associated with better outcomes with regards to preventing infection and complications of COVID-19, as well as developing a better immune response to other pathogenic viruses and microorganisms. This article outlines the key functions of the immune system and how macronutrients, micronutrients, and metabolites from the gut microbiome can be essential in the development of an efficient immune system. In addition, the effects of intermittent fasting on the inflammatory state as well as metabolic parameters will be discussed.
Maturity groups and phenology of maize in a rainforest location.

Maturity period is one of the essential characters looked out for by farmers before a maize variety is selected for cultivation. There is need to understand the cause of varietal differences for traits associated with maturity at the seedling and vegetati ve stages of growth in the early and late seasons of the rainforest agro Therefore the objectives of this study were to determine the relationship between maturity groups and their vegetative and reproductive traits, and identify the best trait th determines maturity in maize. Eight maize varieties consisting of 2 varieties per maturity group were planted during 2011 early and late cropping seasons. Data were collected on emergence counts 5, 7, and 9 days after planting (DAP) and dry matter accum 9 DAP to 39 DAP. Data were also collected on flowering, vegetative, reproductive and yield component traits. Emergence percent, emergence index, emergence rate index, growth rate, relative growth rate and yield were calculated from the data collected. Maturity effect was highly significant (P = 0.01) for seedling, vegetative and growth rate traits except emergence rate index, relative growth rate. Significant maturity effect (P = 0.05) was also observed for grain yield. There were no significan t replications and variety within maturity effects. Speed of emergence (EI) of the intermediate to late maturing varieties is the fastest when compare to the early and extra early maturity groups. Emergence %, Emergence Index, growth rate and relative grow th rate had positive correlation with yield. The study indicated that intermediate to late maturity groups emerged faster than the extra early maize maturity groups. Late and intermediate maturity groups had higher dry matter accumulation in comp extra-early and early maturity groups. It was concluded in the study that emergence %, emergence index and days to anthesis and/or silking contributed significantly to maturity classification in maize unlike growth rate (GR), relative growth rate (RGR).
High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.