Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays.
Phylogenetic Revision of Savoryellaceae and Evidence for Its Ranking as a Subclass

Morphology, phylogeny, and molecular clock analyses were carried out on Savoryellaceae in order to understand the placements of taxa in this family. Ascotaiwania and Neoascotaiwania formed a well-supported separate clade in the phylogeny of concatenated partial SSU, LSU, TEF, and RPB2 gene data. These two genera share similar morphological features, especially in their asexual morphs, indicating that they are congeneric. Hence, we synonymize Neoascotaiwania under Ascotaiwania. Ascotaiwania hughesii (and its asexual morph, Helicoon farinosum) and Monotosporella setosa grouped in a clade sister to Pleurotheciales and are excluded from Ascotaiwania which becomes monophyletic. A novel genus Helicoascotaiwania is introduced to accommodate Ascotaiwania hughesii and its asexual morph, Helicoon farinosum. A novel species, Savoryella yunnanensis is introduced from a freshwater habitat in Yunnan Province, China. Comprehensive descriptions and illustrations are provided for selected taxa in this family. In addition, we provide evolutionary divergence estimates for Savoryellomycetidae taxa and major marine based taxa to support our phylogenetic and morphological investigations. The taxonomic placement of these marine-based taxa is briefly discussed. Our results indicate that the most basal group of marine-based taxa are represented within Lulworthiales, which diverged from ancestral Sordariomycetes around 149 Mya (91–209) and Savoryellomycetidae around 213 Mya (198–303).
Genome Analysis of Coxsackievirus A4 Isolates From Hand, Foot, and Mouth Disease Cases in Shandong, China

Coxsackievirus A4 (CVA4) is one of the most prevalent pathogens associated with hand, foot and mouth disease (HFMD), an acute febrile illness in children, and is also associated with acute localized exanthema, myocarditis, hepatitis and pancreatitis. Despite this, limited CVA4 genome sequences are currently available. Herein, complete genome sequences from CVA4 strains (n = 21), isolated from patients with HFMD in Shandong province, China between 2014 and 2016, were determined and phylogenetically characterized. Phylogenetic analysis of the VP1 gene from a larger CVA4 collection (n = 175) showed that CVA4 has evolved into four separable genotypes: A, B, C, and D; and genotype D could be further classified in to two sub-genotypes: D1 and D2. Each of the 21 newly described genomes derived from isolates that segregated with sub-genotype D2. The CVA4 genomes displayed significant intra-genotypic genetic diversity with frequent synonymous substitutions occurring at the third codon positions, particularly within the P2 region. However, VP1 was relatively stable and therefore represents a potential target for molecular diagnostics assays and also for the rational design of vaccine epitopes. The substitution rate of VP1 was estimated to be 5.12 × 10-3 substitutions/site/year, indicative of ongoing CVA4 evolution. Mutations at amino acid residue 169 in VP1 gene may be responsible for differing virulence of CVA4 strains. Bayesian skyline plot analysis showed that the population size of CVA4 has experienced several dynamic fluctuations since 1948. In summary, we describe the phylogenetic and molecular characterization of 21 complete genomes from CVA4 isolates which greatly enriches the known genomic diversity of CVA4 and underscores the need for further surveillance of CVA4 in China.
Fitness of Spontaneous Rifampicin-Resistant Staphylococcus aureus Isolates in a Biofilm Environment

Biofilms of S. aureus accumulate cells resistant to the antibiotic rifampicin. We show here that the accumulation of rifampicin resistant mutants (RifR) in biofilms is not equable but rather is a local event, suggesting that the growth of a few locally emerged mutants is responsible for this. Competition assays demonstrated that, compared to wild-type bacteria, the isolated RifR mutants have a growth advantage in biofilms, but not in planktonic culture. To gain insight into the mechanism of the growth advantage, we tested the involvement of the two-component systems (TCS) that sense and respond to environmental changes. We found that a deletion of SrrAB or NreBC has a drastic effect on the growth advantage of RifR mutants, suggesting the importance of oxygen/respiration responses. All six of the RifR isolates tested showed increased resistance to at least one of the common stresses found in the biofilm environment (i.e., oxidative, nitric acid, and organic acid stress). The RifR mutants also had a growth advantage in a biofilm flow model, which highlights the physiological relevance of our findings.
Ligand Binding Induces Agonistic-Like Conformational Adaptations in Helix 12 of Progesterone Receptor Ligand Binding Domain

Progesterone receptor (PR) is a member of the nuclear receptor (NR) superfamily and plays a vital role in the female reproductive system. The malfunction of it would lead to several types of cancers. The understanding of conformational changes in its ligand binding domain (LBD) is valuable for both biological function studies and therapeutically intervenes. A key unsolved question is how the binding of a ligand (agonist, antagonist, or a selective modulator) induces conformational changes of PR LBD, especially its helix 12. We applied molecular dynamics (MD) simulations to explore the conformational adaptations of PR LBD with or without a ligand or the co-repressor peptides binding. From the simulations, both the agonist progesterone (P4) and the selective PR modulator (SPRM) asoprisnil induces agonistic-like helix 12 conformations (the “closed” states) in PR LBD and the complex of LBD-SPRM is less stable, comparing to the agonist-liganded PR LBD. The results, therefore, explain the partial agonism of the SPRM, which could induce weak agonistic effects in PR. We also found that co-repressor peptides could be stably associated with the LBD and stabilize the LBD in a “semi-open” state for helix 12. These findings would enhance our understanding of PR structural and functional relationships and would also be useful for future structure and knowledge-based drug discovery.
No-Reference Stereoscopic Image Quality Assessment Using Natural Scene Statistics

Stereoscopic image quality assessment is an effective way to evaluate the performance of stereoscopic video systems. However, the most of existing 3D quality assessment methods cant be consistent with the subjective results caused by unconsidered the information of 3D depth or disparity. In this paper, a blind image quality assessment method for stereoscopic images is proposed using deep learning and natural scene statistics. The proposed method is composed of two stages: firstly, the 3D distorted image is classified into symmetrical or asymmetrical distortion using the characteristics of wavelet domain and disparity information of 3D image. The Deep Belief Network (DBNs) is used to classify the wavelet domain features to distortion types. Then, the mapping relationship between the NSS features and 3D image quality is established according to the distortion type. The experiment is tested on the LIVE 3D database which includes both symmetric- and asymmetric-distorted stereoscopic 3D images. Experimental results show that the proposed objective method achieves consistent stereoscopic image quality evaluation results with subjective assessment for various types of distortion, especially show its effectiveness for assessing stereoscopic imagewithcross-distortion.
Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions

Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
Propranolol 0.2% Eye Micro-Drops for Retinopathy of Prematurity: A Prospective Phase IIB Study

Background: Oral propranolol reduces retinopathy of prematurity (ROP) progression, although not safely. Propranolol 0.1% eye micro-drops administered to newborns with stage 2 ROP are well-tolerated, but not sufficiently effective. Methods: A multi-center open-label trial was conducted to assess the safety and efficacy of propranolol 0.2% eye micro-drops in newborns with stage 1 ROP. The progression of the disease was evaluated with serial ophthalmologic examinations. Hemodynamic, respiratory, biochemical parameters, and propranolol plasma levels were monitored. Demographic and perinatal characteristics, co-morbidities and co-intervention incidences, together with ROP progression, were compared with a historical control group in the same centers participating in the trial. Results: Ninety-eight newborns were enrolled and compared with the historical control group. Populations were not perfectly homogeneous (as demonstrated by the differences in the Apgar score and the different incidence rate in surfactant administration and oxygen exposure). The progression to ROP stage 2 or 3 plus was significantly lower than the incidence expected on the basis of historical data (Risk Ratio 0.521, 95% CI 0.297– 0.916). No adverse effects related to propranolol were observed and the mean propranolol plasma level was significantly lower than the safety cut-off of 20 ng/mL. Unexpectedly, three newborns treated with oral propranolol before the appearance of ROP, showed a ROP that was unresponsive to propranolol eye micro-drops and required laser photocoagulation treatment. Conclusion: Propranolol 0.2% eye micro-drops were well-tolerated and appeared to reduce the ROP progression expected on the basis of a comparison with a historical control group. Propranolol administered too early appears to favor a more aggressive ROP, suggesting that a β-adrenoreceptor blockade is only useful during the proliferative phase. Further randomized placebo-controlled trials are required to confirm the current results. Clinical Trial Registration The trial was registered at ClinicalTrials.gov with Identifier NCT02504944 and with EudraCT Number 2014-005472-29.
Spontaneous and Acetylcholine Evoked Calcium Transients in the Developing Mouse Utricle

Spontaneous calcium transients are present during early postnatal development in the mouse retina and cochlea, and play an important role in maturation of the sensory organs and neural circuits in the central nervous system (CNS). It is not known whether similar calcium transients occur during postnatal development in the vestibular sensory organs. Here we demonstrate spontaneous intracellular calcium transients in sensory hair cells (HCs) and supporting cells (SCs) in the murine utricular macula during the first two postnatal weeks. Calcium transients were monitored using a genetically encoded calcium indicator, GCaMP5G (G5), at 100 ms-frame−1 in excised utricle sensory epithelia, including HCs, SCs, and neurons. The reporter line expressed G5 and tdTomato (tdT) in a Gad2-Cre dependent manner within a subset of utricular HCs, SCs and neurons. Kinetics of the G5 reporter limited temporal resolution to calcium events lasting longer than 200 ms. Spontaneous calcium transients lasting 1-2 s were observed in the expressing population of HCs at birth and slower spontaneous transients lasting 10-30 s appeared in SCs by P3. Beginning at P5, calcium transients could be modulated by application of the efferent neurotransmitter acetylcholine (ACh). In mature mice, calcium transients in the utricular macula occurred spontaneously, had a duration 1-2 s, and could be modulated by the exogenous application of acetylcholine (ACh) or muscarine. Long-lasting calcium transients evoked by ACh in mature mice were blocked by atropine, consistent with previous reports describing the role of muscarinic receptors expressed in calyx bearing afferents in efferent control of vestibular sensation. Large spontaneous and ACh evoked transients were reversibly blocked by the inositol trisphosphate receptor (IP3R) antagonist aminoethoxydiphenyl borate (2-APB). Results demonstrate long-lasting calcium transients are present in the utricular macula during the first postnatal week, and that responses to ACh mature over this same time period.
Assessment of Glioblastoma Response in the Era of Bevacizumab: Longstanding and Emergent Challenges in the Imaging Evaluation of Pseudoresponse

Glioblastoma is the deadliest primary malignant brain neoplasm, and despite the availability of many treatment options, its prognosis remains somber. Enhancement detected by magnetic resonance imaging (MRI) was considered the best imaging marker of tumor activity in glioblastoma for decades. However, its role as a surrogate marker of tumor viability has changed with the appearance of new treatment regimens and imaging modalities. The antiangiogenic therapy created an inflection point in the imaging assessment of glioblastoma response in clinical trials and clinical practice. Although BEV led to the improvement of enhancement, it did not necessarily mean tumor response. The decrease in the enhancement intensity represents a change in the permeability properties of the blood brain barrier, and presumably, the switch of the tumor growth pattern to an infiltrative non-enhancing phenotype. New imaging techniques for the assessment of cellularity, blood flow hemodynamics, and biochemistry have emerged to overcome this hurdle; nevertheless, designing tools to assess tumor response more accurately, and in so doing, improve the assessment of response to standard of care (SOC) therapies and to novel therapies, remains challenging.
Heart Rate Is a Better Predictor of Cardiorespiratory Fitness Than Heart Rate Variability in Overweight/Obese Children: The ActiveBrains Project

Cardiac autonomic function can be quantified through mean heart rate (HR) or heart rate variability (HRV). Numerous studies have supported the utility of different HRV parameters as indicators of cardiorespiratory fitness (CRF). However, HR has recently shown to be a stronger predictor of CRF than HRV in healthy young adults, yet these findings need to be replicated, in other age groups such as children. Therefore, this study aimed: (1) to study the associations between indicators of cardiac autonomic function (HR, standard and corrected HRV parameters) and CRF in overweight/obese children; and (2) to test which of the two indicators (i.e., HR or HRV) is a stronger predictor of CRF. This study used cross-sectional baseline data of 107 overweight/obese children (10.03 ± 1.13 years, 58% boys) from the ActiveBrains project. Cardiac autonomic indicators were measured with Polar RS800CX®. CRF was assessed using a gas analyzer while performing a maximal incremental treadmill test. Correlations and stepwise linear regressions were performed. Mean HR and standard HRV parameters (i.e., pNN50, RMSSD, and SDNN) were associated with CRF (r coefficients ranging from -0.333 to 0.268; all p ≤ 0.05). The association of HR with CRF persisted after adjusting for sex, peak height velocity (PHV), adiposity moderate-to-vigorous physical activity, energy intake and circadian-related variable intradaily variability of activity patterns whilst for HRV parameters (i.e., pNN50, RMSSD, and SDNN) disappeared. Stepwise linear regression models entering HR and all HRV parameters showed that mean HR was the strongest predictor of CRF (β = -0.333, R2 = 0.111, p < 0.001). Standard and corrected HRV parameters did not provide additional value to the coefficient of determination (all p > 0.05). Our findings suggest that HR is the strongest indicator of CRF. It seems that quantification of HRV parameters in time and frequency domain do not add relevant clinical information about the cardiovascular health status (as measured by CRF) in overweight/obese children beyond the information already provided by the simple measure of HR.
Age-Dependent Changes in Transcription Factor FOXO Targeting in Female Drosophila

FOXO transcription factors have long been associated with longevity control and tissue homeostasis. Although the transcriptional regulation of FOXO have been previously characterized (especially in long-lived insulin mutants and under stress conditions), how normal aging impacts the transcriptional activity of FOXO is poorly understood. Here, we conducted a chromatin immunoprecipitation sequencing (ChIP-Seq) analysis in both young (2-week-old) and aged (5-week-old) wild-type female fruit flies, Drosophila melanogaster, to evaluate the dynamics of FOXO gene targeting during aging. Intriguingly, the number of FOXO-bound genes dramatically decreases with age (from 2617 to 224). Consistent to the reduction of FOXO binding activity, many genes targeted by FOXO in young flies are transcriptionally altered with age, either up-regulated (FOXO-repressing genes) or down-regulated (FOXO-activating genes) in adult head tissue. In addition, we show that many FOXO-bound genes in wild-type flies are unique from those in insulin receptor substrate chico mutants. Distinct from chico mutants, FOXO targets specific cellular processes (e.g., actin cytoskeleton) and signaling pathways (e.g., Hippo, MAPK) in young wild-type female flies. FOXO targeting on these pathways decreases with age. Interestingly, FOXO targets in aged flies are enriched in cellular processes like chromatin organization and nucleosome assembly. Furthermore, FOXO binding to core histone genes is well maintained at aged flies. Together, our findings provide new insights into dynamic FOXO targeting under normal aging and highlight the diverse and understudied regulatory mechanisms for FOXO transcriptional activity.
Remembering and Communicating Climate Change Narratives – The Influence of World Views on Selective Recollection

We examine how people remember stories about climate change and how they communicate these stories to others. Drawing on theories of reconstructive memory and cultural theory, we assume that recollection is systematically affected by an individual’s world view as well as by the world view of the target audience. In an experimental study with a Norwegian representative sample (N = 266), participants read a story about three politicians, in which each protagonist was described as holding a specific world view and as trying to tackle climate change with a corresponding strategy (individualistic/free market oriented, hierarchical/technology-oriented, or egalitarian/sustainability-oriented). After 1 day and then after 1 week, participants were asked to retell the story as if to somebody who was characterized as being either an individualist, a hierarchist, or an egalitarian; in addition, a neutral recall control condition without a specified audience was included. Participants’ own world view was assessed and they were classified as endorsing individualism, or hierarchism, or egalitarianism. We hypothesized that retellings would be selectively reconstructed according to the world view of the participant, as well as tuned to the audience’s world view. We assessed the cognitive structure of the recollected story, and, using methods from computational text analysis, we computed similarities among retellings and the original narrative, and among retellings and world views. Results suggest that (i) retellings become less accurate over time, (ii) retelling to an audience with an explicit world view leads to more strongly filtered retellings than recalling without a specified audience, but the filter operates in a non-specific manner with respect to world views, (iii) the cognitive structure of the recollected story shows small but systematic differences concerning the link between story problem and solution as a function of the participant’s and the audience’s world view. No interaction was found between the world view of the participant and that of the audience. Results emphasize the role of world views in communicating climate change, and might help to better understand phenomena such as polarization and echo chamber effects.