Miracle-dz/UniFAR-FTUs huggingface dataset:
Current Strategies of Polyploid Plant Genome Sequence Assembly

Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
Surgery vs Radiotherapy in the Management of Biopsy Gleason Score 9-10 Prostate Cancer and the Risk of Mortality

Importance It is unknown how treatment with radical prostatectomy (RP) and adjuvant external beam radiotherapy (EBRT), androgen deprivation therapy (ADT), or both (termed MaxRP) compares with treatment with EBRT, brachytherapy, and ADT (termed MaxRT). Objective To investigate whether treatment of Gleason score 9-10 prostate cancer with MaxRP vs MaxRT was associated with prostate cancer–specific mortality (PCSM) and all-cause mortality (ACM) risk. Design, Setting, and Participants The study cohort comprised 639 men with clinical T1-4,N0M0 biopsy Gleason score 9-10 prostate cancer. Between February 6, 1992, and April 26, 2013, a total of 80 men were consecutively treated with MaxRT at the Chicago Prostate Cancer Center, and 559 men were consecutively treated with RP and pelvic lymph node dissection at the Martini-Klinik Prostate Cancer Center. Follow-up started on the day of prostate EBRT or RP and concluded on October 27, 2017. Exposures Of the 559 men managed with RP and pelvic lymph node dissection, 88 (15.7%) received adjuvant EBRT, 49 (8.8%) received ADT, and 50 (8.9%) received both. Main Outcomes and Measures Treatment propensity score–adjusted risk of PCSM and ACM and the likelihood of equivalence of these risks between treatments using a plausibility index. Results The cohort included 639 men, with a mean (SD) age of 65.83 (6.52) years. After median follow-ups of 5.51 years (interquartile range, 2.19-6.95 years) among 80 men treated with MaxRT and 4.78 years (interquartile range, 4.01-6.05 years) among 559 men treated with RP-containing treatments, 161 men had died, 106 (65.8%) from prostate cancer. There was no significant difference in the risk of PCSM (adjusted hazard ratio, 1.33; 95% CI, 0.49-3.64; P = .58) and ACM (adjusted hazard ratio, 0.80; 95% CI, 0.36-1.81; P = .60) when comparing men who underwent MaxRP vs MaxRT, with plausibility indexes for equivalence of 76.75% for the end point of the risk of PCSM and 77.97% for the end point of the risk of ACM. Plausibility indexes for all other treatment comparisons were less than 63%. Conclusions and Relevance Results of this study suggest that it is plausible that treatment with MaxRP or MaxRT for men with biopsy Gleason score 9-10 prostate cancer can lead to equivalent risk of PCSM and ACM.
How Do Banana Flowers Develop?

Banana flowers form deep within the stem of the banana plant, long before they appear to us. The flowers occur in groups called hands, and the hands are arranged into larger clusters of flowers. Both the number of flowers in a hand and their pattern of development are different between cultivated (supermarket) and wild species of bananas. In supermarket bananas, each hand has many flowers, and the flowers develop in a regular pattern from right to left. In the wild species called the hairy banana, there is no regular pattern of flower formation. Flowers of the hairy banana are never formed in the regular right-to-left manner as found in the supermarket species. This is surprising and illustrates an important point about science: we do not always get the answers we expect. When they are first formed, banana flowers have no parts. They go through a process to form the flower parts that we see. After we describe how this takes place, we give you a project, so you can see how this happens on your own. You will work as a scientist to discover the pattern of development in banana flowers.
Sinorhizobium fredii Strains HH103 and NGR234 Form Nitrogen Fixing Nodules With Diverse Wild Soybeans (Glycine soja) From Central China but Are Ineffective on Northern China Accessions

Sinorhizobium fredii indigenous populations are prevalent in provinces of Central China whereas Bradyrhizobium species (Bradyrhizobium japonicum, B. diazoefficiens, B. elkanii, and others) are more abundant in northern and southern provinces. The symbiotic properties of different soybean rhizobia have been investigated with 40 different wild soybean (Glycine soja) accessions from China, Japan, Russia, and South Korea. Bradyrhizobial strains nodulated all the wild soybeans tested, albeit efficiency of nitrogen fixation varied considerably among accessions. The symbiotic capacity of S. fredii HH103 with wild soybeans from Central China was clearly better than with the accessions found elsewhere. S. fredii NGR234, the rhizobial strain showing the broadest host range ever described, also formed nitrogen-fixing nodules with different G. soja accessions from Central China. To our knowledge, this is the first report describing an effective symbiosis between S. fredii NGR234 and G. soja. Mobilization of the S. fredii HH103 symbiotic plasmid to a NGR234 pSym-cured derivative (strain NGR234C) yielded transconjugants that formed ineffective nodules with G. max cv. Williams 82 and G. soja accession CH4. By contrast, transfer of the symbiotic plasmid pNGR234a to a pSym-cured derivative of S. fredii USDA193 generated transconjugants that effectively nodulated G. soja accession CH4 but failed to nodulate with G. max cv. Williams 82. These results indicate that intra-specific transference of the S. fredii symbiotic plasmids generates new strains with unpredictable symbiotic properties, probably due to the occurrence of new combinations of symbiotic signals.
Pulmonary Embolism Response Teams: A Novel Approach for the Care of Complex Patients With Pulmonary Embolism

Pulmonary embolism represents the third most common cause of cardiovascular death in the United States. Reperfusion therapeutic strategies such as systemic thrombolysis, catheter directed therapies, surgical pulmonary embolectomy, and cardiopulmonary support devices are currently available for patients with high- and intermediate-high–risk pulmonary embolism. However, deciding on optimal therapy may be challenging. Pulmonary embolism response teams have been designed to facilitate multidisciplinary decision-making with the goal to improve quality of care for complex cases with pulmonary embolism. Herein, we discuss the current role and strategies on how to leverage the strengths from pulmonary embolism response teams, its possible worldwide adoption, and implementation to improve survival and change the paradigm in the care of a potentially deadly disease.
Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults

Abstract Background Respiratory syncytial virus (RSV) is an important cause of serious respiratory illness in older adults. Comparison of RSV and influenza infection in hospitalized older adults may increase awareness of adult RSV disease burden. Methods Hospitalized adults aged ≥60 years who tested positive for RSV or influenza between 1 January 2011 and 30 June 2015 were identified from Kaiser Permanente Southern California electronic medical records. Baseline characteristics, comorbidities, utilization, and outcomes were compared. Results The study included 645 RSV- and 1878 influenza-infected hospitalized adults. Patients with RSV were older than those with influenza (mean, 78.5 vs 77.4 years; P = .035) and more likely to have congestive heart failure (35.3% vs 24.5%; P < .001) and chronic obstructive pulmonary disease (COPD) (29.8% vs 24.3%; P = .006) at baseline. In adjusted analyses, RSV infection was associated with greater odds of length of stay ≥7 days (odds ratio [OR] = 1.5; 95% confidence interval [CI], 1.2–1.8; P < .001); pneumonia (OR = 2.7; 95% CI, 2.2–3.2; P < .001); intensive care unit admission (OR = 1.3; 95% CI, 1.0–1.7; P = .023); exacerbation of COPD (OR = 1.7; 95% CI, 1.3–2.4; P = .001); and greater mortality within 1 year of admission (OR = 1.3; 95% CI, 1.0–1.6; P = .019). Conclusions RSV infection may result in greater morbidity and mortality among older hospitalized adults than influenza. Increased recognition of adult RSV disease burden will be important in the evaluation and use of new RSV vaccines and antivirals.
Improved Timeliness of Care for the Underserved: A Potential for Patient Navigation

Citation: Ohlstein JF, Edwards TS, Riley CA, Buell JF, Friedlander PL (2019) Improved Timeliness of Care for the Underserved: A Potential for Patient Navigation. J Otolaryngol Rhinol 5:053. doi. org/10.23937/2572-4193.1510053 Accepted: January 19, 2019: Published: January 21, 2019 Copyright: © 2019 Ohlstein JF, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Journal of Otolaryngology and Rhinology
Biomedical Applications of Graphene-Based Structures

Graphene and graphene oxide (GO) structures and their reduced forms, e.g., GO paper and partially or fully reduced three-dimensional (3D) aerogels, are at the forefront of materials design for extensive biomedical applications that allow for the proliferation and differentiation/maturation of cells, drug delivery, and anticancer therapies. Various viability tests that have been conducted in vitro on human cells and in vivo on mice reveal very promising results, which make graphene-based materials suitable for real-life applications. In this review, we will give an overview of the latest studies that utilize graphene-based structures and their composites in biological applications and show how the biomimetic behavior of these materials can be a step forward in bridging the gap between nature and synthetically designed graphene-based nanomaterials.
Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.
Diphenyl Ethers from a Marine-Derived Aspergillus sydowii

Six new diphenyl ethers (1–6) along with eleven known analogs were isolated from the ethyl acetate extract of a marine-derived Aspergillus sydowii guided by LC-UV-MS. Their structures were unambiguously characterized by HRESIMS, NMR, as well as chemical derivatization. Compounds 1 and 2 are rare diphenyl ether glycosides containing d-ribose. The absolute configuration of the sugar moieties in compounds 1–3 was determined by a LC-MS method. All the compounds were evaluated for their cytotoxicities against eight cancer cell lines, including 4T1, U937, PC3, HL-60, HT-29, A549, NCI-H460, and K562, and compounds 1, 5, 6, and 8–11 were found to exhibit selective cytotoxicity against different cancer cell lines.
Identification, Expression, and Functional Analysis of the Group IId WRKY Subfamily in Upland Cotton (Gossypium hirsutum L.)

WRKY transcription factors have diverse functions in regulating stress response, leaf senescence, and plant growth and development. However, knowledge of the group IId WRKY subfamily in cotton is largely absent. This study identified 34 group IId WRKY genes in the Gossypium hirsutum genome, and their genomic loci were investigated. Members clustered together in the phylogenetic tree had similar motif compositions and gene structural features, revealing similarity and conservation within group IId WRKY genes. During the evolutionary process, 14 duplicated genes appeared to undergo purification selection. Public RNA-seq data were used to examine the expression patterns of group IId WRKY genes in various tissues and under drought and salt stress conditions. Ten highly expressed genes were identified, and the ten candidate genes revealed distinct expression patterns under drought and salt treatments by qRT-PCR analysis. Among them, Gh_A11G1801 was used for functional characterization. GUS activity was differentially induced by various stresses in Gh_A11G1801p::GUS transgenic Arabidopsis plants. The virus-induced gene silencing (VIGS) of Gh_A11G1801 resulted in drought sensitivity in cotton plants, which was accompanied by elevated malondialdehyde (MDA) content and reduced catalase (CAT) content. Taken together, these findings obtained in this study provide valuable resources for further studying group IId WRKY genes in cotton. Our results also enrich the gene resources for the genetic improvements of cotton varieties that are suitable for growth in stressful conditions.
Ion channels can be allosterically regulated by membrane domains near a de-mixing critical point

&NA; Ion channels are embedded in the plasma membrane, a compositionally diverse two‐dimensional liquid that has the potential to exert profound influence on their function. Recent experiments suggest that this membrane is poised close to an Ising critical point, below which cell‐derived plasma membrane vesicles phase separate into coexisting liquid phases. Related critical points have long been the focus of study in simplified physical systems, but their potential roles in biological function have been underexplored. Here we apply both exact and stochastic techniques to the lattice Ising model to study several ramifications of proximity to criticality for idealized lattice channels, whose function is coupled through boundary interactions to critical fluctuations of membrane composition. Because of diverging susceptibilities of system properties to thermodynamic parameters near a critical point, such a lattice channel's activity becomes strongly influenced by perturbations that affect the critical temperature of the underlying Ising model. In addition, its kinetics acquire a range of time scales from its surrounding membrane, naturally leading to non‐Markovian dynamics. Our model may help to unify existing experimental results relating the effects of small‐molecule perturbations on membrane properties and ion channel function. We also suggest ways in which the role of this mechanism in regulating real ion channels and other membrane‐bound proteins could be tested in the future. &NA; The plasma membrane is close to an Ising critical point, below which it would separate into two phases. Kimchi et al. explore the consequences for ion channel function using a lattice Ising model and find that channel kinetics can be influenced by the proximity of the membrane to a critical point.
“I would have told you about being forgetful, but I forgot”: the experience of cognitive changes and communicative participation after head and neck cancer

Abstract Purpose: Survivors of head and neck cancer have reported difficulties with memory, attention, verbal fluency, and processing speed sometimes persisting years after treatment. Self-perceived cognitive function is an important predictor of communication outcomes in this population. This study explores the lived experience of cognitive changes in survivors of non-nasopharyngeal head and neck cancer and how these changes affect communication in their daily lives. Materials and methods: In the phenomenological tradition, five adult survivors of non-nasopharyngeal head and neck cancer participated in individual semi-structured interviews. The interviews were audio-recorded, transcribed, coded, and summarized into themes. Results: Two major themes emerged: (1) I would have told you about being forgetful, but I forgot; and (2) It’s such a journey that much of it is uncharted. Participants described problems with memory, focus/attention, and task initiation along with slowed processing and language difficulties. These difficulties affected communication at work, socially, and at home. Participants expressed feeling unprepared for the possibility of cognitive changes, not knowing why they were happening or what to do about them. Conclusions: Results of this study have implications for counseling and treatment of individuals with head and neck cancer, as well as advocating for these patients to receive appropriate information and intervention. Implications for rehabilitation Survivors of non-nasopharyngeal head and neck cancer described experiencing problems with memory and focus/attention along with slowed processing and language difficulties. Study participants generally felt both unprepared for the cognitive changes they experienced and, in many ways, unsupported by healthcare providers and others. Rehabilitation professionals should be aware that cognitive changes following medical treatment for head and neck cancer may affect a patient’s ability to learn and follow complex treatment regimens. Rehabilitation professionals can advise and advocate for these patients to receive the appropriate referrals for assessment and treatment of their cognitive symptoms.
Computational approaches for the analysis of RNA–protein interactions: A primer for biologists

RNA-binding proteins (RBPs) play important roles in the control of gene expression and the coordination of different layers of post-transcriptional regulation. Interactions between certain RBPs and mRNA transcripts are notoriously difficult to predict, as any given protein–RNA interaction may rely not only on RNA sequence, but also on three-dimensional RNA structures, competitive inhibition from other RBPs, and input from cellular signaling pathways. Advanced and high-throughput technologies for the identification of RNA–protein interactions have come to the rescue, but the identification of binding sites and downstream functional effects of RBPs from the resulting data can be challenging. In this review, we discuss statistical inference and machine-learning approaches and tools relevant for the study of RBPs and the analysis of large-scale RNA–protein interaction datasets. This primer is intended for life scientists who are interested in incorporating these tools into their own research. We begin with the demystification of regression models, as used in the analysis of next-generation sequencing data, and progress to a discussion of Hidden Markov Models, which are of particular value in analyzing cross-linking followed by immunoprecipitation data. We then continue with examples of machine learning techniques, such as support vector machines and gradient tree boosting. We close with a brief discussion of current trends in the field, including deep learning architectures.
Recovery of layered tissue optical properties from spatial frequency-domain spectroscopy and a deterministic radiative transport solver

Abstract. We present a method to recover absorption and reduced scattering spectra for each layer of a two-layer turbid media from spatial frequency-domain spectroscopy data. We focus on systems in which the thickness of the top layer is less than the transport mean free path ( 0.1 − 0.8l * ) . We utilize an analytic forward solver, based upon the N’th-order spherical harmonic expansion with Fourier decomposition ( SHEFN ) method in conjunction with a multistage inverse solver. We test our method with data obtained using spatial frequency-domain spectroscopy with 32 evenly spaced wavelengths within λ = 450 to 1000 nm on six-layered tissue phantoms with distinct optical properties. We demonstrate that this approach can recover absorption and reduced scattering coefficient spectra for both layers with accuracy comparable with current Monte Carlo methods but with lower computational cost and potential flexibility to easily handle variations in parameters such as the scattering phase function or material refractive index. To our knowledge, this approach utilizes the most accurate deterministic forward solver used in such problems and can successfully recover properties from a two-layer media with superficial layer thicknesses.
Effects of nicotine and stress exposure across generations in C57BL/6 mice

Abstract Chronic administration of nicotine or exposure to stress can produce long-lasting behavioral and physiological changes in humans and animals alike. Further, the impact of nicotine and stress exposure can be inherited by offspring to produce persistent changes in physiology and behavior. To determine if nicotine and stress interact across generations to influence offspring behavior we exposed F0 male mice to nicotine and F1 male and female mice to chronic unpredictable stress during adolescence. We then measured locomotor sensitization to repeated nicotine injections in the subsequent F2 and F3 generations. Stress exposure alone (F1) did not influence locomotor sensitization in any lineage. However, in the F1 male lineage, F0 nicotine exposure abrogated locomotor sensitization in F2 male and transiently enhanced locomotor sensitization in F2 female offspring. These effects were not passed down to the F3 generations or observed in the F1 female lineage. F1 stress exposure modulated the effects of prior F0 nicotine exposure in a sex-dependent manner. Specifically, stress blunted the nicotine-induced enhancement in locomotor sensitization observed in F2 female offspring of F1 males. The effect of F0 nicotine and F1 stress exposure in females appears to have skipped a generation and enhanced nicotine sensitization only in the F3 generation, and only in females. This novel multigenerational exposure paradigm examining the inheritance of two different environmental exposures demonstrates that nicotine responses can be modified by nicotine and stress exposure from previous generations, and these effects are strongly influenced by sex.