Miracle-dz/UniFAR-FTUs huggingface dataset:
SlMYC1 Regulates Type VI Glandular Trichome Formation and Terpene Biosynthesis in Tomato Glandular Cells[OPEN]

The transcription factor SlMYC1 regulates mono- and sesquiterpene biosynthesis differentially in leaf and stem trichomes and is involved in the formation of type VI glandular trichomes in tomato. Tomato (Solanum lycopersicum) glandular trichomes function as biochemical factories that synthesize a diverse array of specialized metabolites. Terpenoids are the most diverse class of plant specialized metabolites, with volatile mono- and sesquiterpenes playing important roles in plant defense. Although the biosynthetic pathways of volatile terpenes in tomato glandular trichomes have been well described, little is known about their regulation. Here, we demonstrate that SlMYC1, a basic helix-loop-helix transcription factor, differentially regulates mono- and sesquiterpene biosynthesis in the type VI glandular trichomes of tomato leaves and stems. SlMYC1 functions as a positive regulator of monoterpene biosynthesis in both leaf and stem trichomes but as a negative regulator of sesquiterpene biosynthesis in stem trichomes. SlMYC1 is also essential for type VI glandular trichome development, as knocking down SlMYC1 led to the production of smaller type VI glandular trichomes at lower densities, and knocking out this gene led to their absence. Our findings reveal a role for SlMYC1 not only in type VI glandular trichome development but also in the regulation of terpene biosynthesis in tomato.
Assisted decision-making and interprofessional collaboration in the care of older people: a qualitative study exploring perceptions of barriers and facilitators in the acute hospital setting

ABSTRACT In recent years, there has been a move toward a more human rights-based approach to the issue of supported and assisted decision-making (ADM) with legislative changes strengthening the formal right for older people to participate in care planning and decision-making. Ireland’s Assisted Decision-Making (Capacity) Act, 2015 breaks from traditional views of capacity to consider the uniqueness of each decision in relation to topic, time and place for those with impaired or fluctuating capacity. This study set out to explore experiences of assisted decision making (ADM) in acute care hospitals in Ireland and to identify the barriers and enablers to ADM for older people and people with dementia from the perspective of different Health and Social Care Professionals (HSCPs) involved in their care. We carried out 26 semi-structured audio-recorded interviews with a convenience sample of HSCPs working in two acute hospitals and subsequently confirmed the results. HSCPs identified several barriers to, and enablers of, ADM in acute hospitals that were categorized into three key themes: Building meaningful engagement with older people and their family carers; barriers and enablers associated with interprofessional collaboration and barriers and enablers associated with the environment. Our findings suggest that despite concrete policy and legislative underpinnings to ADM, this was not always evident in practice and suggests the need for specialized education and training on ADM in practice settings.
The effect of motor and cognitive placebos on the serial reaction time task

Motor learning is a key component of human motor functions. Repeated practice is essential to gain proficiency over time but may induce fatigue. The aim of this study was to determine whether motor performance and motor learning (as assessed with the serial reaction time task, SRTT) and perceived fatigability (as assessed with subjective scales) are improved after two types of placebo interventions (motor and cognitive). A total of 90 healthy volunteers performed the SRTT with the right hand in three sessions (baseline, training and final). Before the training and the final session, one group underwent a motor‐related placebo intervention in which inert electrical stimulation (TENS) was applied over the hand and accompanied by verbal suggestion that it improves movement execution (placebo‐TENS). The other group underwent a cognitive‐related placebo intervention in which sham transcranial direct current stimulation (tDCS) was delivered to the supraorbital area and accompanied by verbal suggestion that it increases attention (placebo‐tDCS). A control group performed the same task without receiving treatment. Overall better performance on the SRTT (not ascribed to sequence‐specific learning) was noted for the placebo‐TENS group, which also reported less perceived fatigability at the physical level. The same was observed in a subgroup tested 24 hr later. The placebo‐tDCS group reported less perceived fatigability, both at the mental and physical level. These findings indicate that motor‐ and cognitive‐related placebo effects differently shape motor performance and perceived fatigability on a repeated motor task.
Characterization of minerals and biogeochemical markers on Mars: A Raman and IR spectroscopic study of montmorillonite

Raman spectroscopy is likely to be one of a number of instruments deployed to Mars on future landed missions. The goals of these missions will include characterizing the mineralogy of the rocks and soils, in addition to determining if the planet may be or may have been habitable for life. The astrobiology questions are linked to understanding the aqueous and biogeochemical history of Mars. Clay minerals are studied here because if they are found on Mars they may provide information about the geochemistry of the primary rocks and the aqueous history of the planet. This study compares Raman and IR spectra of the SWy-1, STx-1 and SAz-1 montmorillonites. These samples contain admixtures of organic material, carbonate, amorphous silica and fine-grained quartz, which can all be detected using Raman spectroscopy. Less than 0.1 wt% C as organic material was detected in each of the samples through peaks associated with CC or CH bonds. Carbonate was detected in the Raman spectra for the sample containing 1.65 wt% CO3 but not for 0.15 wt% CO3. Raman spectra exhibit unique bands near 200 and 700 cm−1 that are due to tetrahedral SiO4 in layer silicates and vary depending on the mineral structure. Raman spectra of clay minerals also have unique metal–OH bending vibrations between 840 and 920 cm−1 that provide information about the octahedral cations present. Copyright © 2004 John Wiley & Sons, Ltd.
Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain Gene in albostrians Barley[OPEN]

Leaf variegation in the barley mutant albostrians is caused by mutation of a single CCT–domain containing gene with residual activity, which is directed to the chloroplast. Chloroplasts fuel plant development and growth by converting solar energy into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley (Hordeum vulgare) has greatly broadened the field of chloroplast biology, including the discovery of retrograde signaling. Here, we report identification of the ALBOSTRIANS gene HvAST (also known as Hordeum vulgare CCT Motif Family gene 7, HvCMF7) by positional cloning as well as its functional validation based on independently induced mutants by Targeting Induced Local Lesions in Genomes (TILLING) and RNA-guided clustered regularly interspaced short palindromic repeats-associated protein 9 endonuclease-mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvCMF7 in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvCMF7 is a homolog of the Arabidopsis (Arabidopsis thaliana) CONSTANS, CO-like, and TOC1 (CCT) Motif transcription factor gene CHLOROPLAST IMPORT APPARATUS2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Notably, in barley we localized HvCMF7 to the chloroplast, without any clear evidence for nuclear localization.
Quantitative assessment of SARS‐CoV‐2 RNAemia and outcome in patients with coronavirus disease 2019

The disease spectrum of coronavirus disease 2019 (COVID‐19) varies from asymptomatic infection to critical illness and death. Identification of prognostic markers is vital for predicting progression and clinical practice. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA, known as RNAemia, has been detected in the blood. However, the potential clinical value of SARS‐CoV‐2 RNAemia remains unknown. We, therefore, conducted a meta‐analysis using a random‐effects model to estimate the pooled prevalence of SARS‐CoV‐2 RNAemia as well as summary strength of RNAemia in association with disease severity and unfavorable clinical outcomes. A total of 21 studies involving 2181 patients were included. SARS‐CoV‐2 RNAemia in COVID‐19 patients varied from 9.4% to 74.1%, with a pooled estimate of 34% (95% confidene interval [CI]: 26%–43%). Overall, SARS‐CoV‐2 RNAemia was associated with COVID‐19 severity with odds ratio (OR) of 5.43 (95% CI: 3.46–8.53). In addition, SARS‐CoV‐2 RNAemia was a significant risk factor for unfavorable clinical outcomes (OR = 6.54, 95% CI: 3.82–11.21). The summary OR was 4.28 (95% CI: 2.20–8.33) for intensive care unit (ICU) admission, 11.07 (95% CI: 5.60–21.88) for mortality. Furthermore, RNAemia was also a significant risk factor for invasive mechanical ventilation and multiple organ failure. SARS‐CoV‐2 RNAemia is associated with disease severity, ICU admission, death in COVID‐19, and may serve as a clinical predictor. More prospective trials in evaluating the potential of SARS‐CoV‐2 RNAemia as a prognostic indicator are necessary.
Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis

Abstract We use single-molecule techniques to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ), a system comprised only of the dimeric Ku and Ligase D (LigD). The Ku homodimer alone forms a ∼2 s synapsis between blunt DNA ends that is increased to ∼18 s upon addition of LigD, in a manner dependent on the C-terminal arms of Ku. The synapsis lifetime increases drastically for 4 nt complementary DNA overhangs, independently of the C-terminal arms of Ku. These observations are in contrast to human Ku, which is unable to bridge either of the two DNA substrates. We also demonstrate that bacterial Ku binds the DNA ends in a cooperative manner for synapsis initiation and remains stably bound at DNA junctions for several hours after ligation is completed, indicating that a system for removal of the proteins is active in vivo. Together these experiments shed light on the dynamics of bacterial NHEJ in DNA end recognition and processing. We speculate on the evolutionary similarities between bacterial and eukaryotic NHEJ and discuss how an increased understanding of bacterial NHEJ can open the door for future antibiotic therapies targeting this mechanism.
Comparison of Sepsis Definitions as Automated Criteria

Supplemental Digital Content is available in the text. OBJECTIVES: Assess the impact of heterogeneity among established sepsis criteria (Sepsis-1, Sepsis-3, Centers for Disease Control and Prevention Adult Sepsis Event, and Centers for Medicare and Medicaid severe sepsis core measure 1) through the comparison of corresponding sepsis cohorts. DESIGN: Retrospective analysis of data extracted from electronic health record. SETTING: Single, tertiary-care center in St. Louis, MO. PATIENTS: Adult, nonsurgical inpatients admitted between January 1, 2012, and January 6, 2018. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: In the electronic health record data, 286,759 encounters met inclusion criteria across the study period. Application of established sepsis criteria yielded cohorts varying in prevalence: Centers for Disease Control and Prevention Adult Sepsis Event (4.4%), Centers for Medicare and Medicaid severe sepsis core measure 1 (4.8%), International Classification of Disease code (7.2%), Sepsis-3 (7.5%), and Sepsis-1 (11.3%). Between the two modern established criteria, Sepsis-3 (n = 21,550) and Centers for Disease Control and Prevention Adult Sepsis Event (n = 12,494), the size of the overlap was 7,763. The sepsis cohorts also varied in time from admission to sepsis onset (hr): Sepsis-1 (2.9), Sepsis-3 (4.1), Centers for Disease Control and Prevention Adult Sepsis Event (4.6), and Centers for Medicare and Medicaid severe sepsis core measure 1 (7.6); sepsis discharge International Classification of Disease code rate: Sepsis-1 (37.4%), Sepsis-3 (40.1%), Centers for Medicare and Medicaid severe sepsis core measure 1 (48.5%), and Centers for Disease Control and Prevention Adult Sepsis Event (54.5%); and inhospital mortality rate: Sepsis-1 (13.6%), Sepsis-3 (18.8%), International Classification of Disease code (20.4%), Centers for Medicare and Medicaid severe sepsis core measure 1 (22.5%), and Centers for Disease Control and Prevention Adult Sepsis Event (24.1%). CONCLUSIONS: The application of commonly used sepsis definitions on a single population produced sepsis cohorts with low agreement, significantly different baseline demographics, and clinical outcomes.
Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates

A combined plant genetic, biochemical, and structural biology study reveals the molecular basis for diversification of the agriculturally important Methionine-derived glucosinolates in plants. The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis. However, the molecular basis for the evolution of methylthioalkylmalate synthase and its generation of natural product diversity in Brassica is poorly understood. Here, we show that Brassica genomes encode multiple methylthioalkylmalate synthases that have differences in expression profiles and 2-oxo substrate preferences, which account for the diversity of aliphatic glucosinolates across Brassica accessions. Analysis of the 2.1 Å resolution x-ray crystal structure of Brassica juncea methylthioalkylmalate synthase identified key active site residues responsible for controlling the specificity for different 2-oxo substrates and the determinants of side chain length in aliphatic glucosinolates. Overall, these results provide the evolutionary and biochemical foundation for the diversification of glucosinolate profiles across globally cultivated Brassica species, which could be used with ongoing breeding strategies toward the manipulation of beneficial glucosinolate compounds for animal health and plant protection.
Near-Histologic Resolution Images of Cervical Dysplasia Obtained With Gabor Domain Optical Coherence Microscopy

Objective Histopathology is the criterion standard for evaluating cervical squamous intraepithelial neoplasia (dysplasia). In this pilot feasibility study, we examined whether a novel 3-dimensional imaging device using Gabor-domain optical coherence microscopy (GDOCM) could distinguish features of cervical dysplasia comparable with histopathology. Methods A prospective observational pilot study enrolled a small sample of women undergoing loop electrosurgical excision procedure for cervical squamous intraepithelial neoplasia. Fresh ex vivo specimens were imaged with the GDOCM device. Digital images were reviewed by a pathologist who was blinded to the histopathology results. Histopathologic features were then compared with the digital observations. Results Standard histologic features of cervical squamous epithelium and of squamous intraepithelial neoplasia could be observed in GDOCM images. Cervical epithelium, stroma, basement membrane, and squamous papilla could all be identified. Human papillomavirus effects, such as vacuolization and cellular density, were also observed. Conclusions A GDOCM imaging system has the potential to obtain histologic resolution images of the cervix in the evaluation of squamous intraepithelial neoplasia. This pilot study allowed for optimizing the imaging system and paved the way for a future diagnostic accuracy study. The development of this technology could streamline the evaluation of patients at risk for cervical neoplasia.
Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models

A new empirical approach to model the solvent effects in protein−membrane complexes is proposed. The generalized Born (GB) approximation is extended by including an implicit membrane (IM) in the calculation of the electrostatic contribution to the solvation free energy (GB/IM model). In addition, nonpolar solvation energy terms are calculated on the basis of the solvent-accessible surface approximation including the effect of membrane (SA/IM model). The generalized Born−solvent-accessible surface area (GBSA) model with implicit membrane (GBSA/IM) is implemented in the CHARMm package and is applicable for energy calculations and molecular dynamics simulations. The potential of the new method for studying large molecular systems is demonstrated with the example of two transmembrane proteins, bacteriorhodopsin and rhodopsin. The results show a clear directional asymmetry of the solvation energy during translocation of the proteins through the membrane, which is suggested to be an alternative explanation of t.
Delirium screening tools validated in the context of palliative care: A systematic review

Background: Delirium is a distressing neuropsychiatric disorder affecting patients in palliative care. Although many delirium screening tools exist, their utility, and validation within palliative care settings has not undergone systematic review. Aim: To systematically review studies that validate delirium screening tools conducted in palliative care settings. Design: Systematic review with narrative synthesis (PROSPERO ID: CRD42019125481). A risk of bias assessment via Quality Assessment Tool for Diagnostic Accuracy Studies-2 was performed. Data sources: Five electronic databases were systematically searched (January 1, 1982–May 3, 2020). Quantitative studies validating a screening tool in adult palliative care patient populations were included. Studies involving alcohol withdrawal, critical or perioperative care were excluded. Results: Dual-reviewer screening of 3749 unique titles and abstracts identified 95 studies for full-text review and of these, 17 studies of 14 screening tools were included (n = 3496 patients). Data analyses revealed substantial heterogeneity in patient demographics and variability in screening and diagnostic practices that limited generalizability between study populations and care settings. A risk of bias assessment revealed methodological and reporting deficits, with only 3/17 studies at low risk of bias. Conclusions: The processes of selecting a delirium screening tool and determining optimal screening practices in palliative care are complex. One tool is unlikely to fit the needs of the entire palliative care population across all palliative care settings. Further research should be directed at evaluating and/or adapting screening tools and practices to fit the needs of specific palliative care settings and populations.
Design and Performance of a New Personal Aerosol Monitor

Three particle size fractions of airborne dust are defined in Euro pean and U.S. standards for health-related dust measurements at the workplace: the respirable, the thoracic, and the inhalable fraction. We developed a novel instrument for personal, time-resolved concentration monitoring and sampling of these three fractions. The instrument combines inertial classification, filter sam pling, and photometric aerosol detection. It consists of a two-stage virtual impactor (cut-off diameters of 4 and 10 mu m), three filters, and three light scattering photometers. The virtual impactor serves as a particle size classifier and a coarse particle concentrator. This enrichment compensates for the decreasing particle mass-based photometric sensitivity with increasing particle diameter. The optical sensors are calibrated in-situ via the mass concentrations obtained gravimetrically from the filter samples. The device operates at a flow rate of 3.1 l min. There is strong agreement between the experimentally determined.
The CRISPR revolution and its potential impact on global health security

ABSTRACT Global health security is constantly under threat from infectious diseases. Despite advances in biotechnology that have improved diagnosis and treatment of such diseases, delays in detecting outbreaks and the lack of countermeasures for some biological agents continue to pose severe challenges to global health security. In this review, we describe some of the challenges facing global health security and how genome editing technologies can help overcome them. We provide specific examples of how the genome-editing tool CRISPR is being used to develop new tools to characterize pathogenic agents, diagnose infectious disease, and develop vaccines and therapeutics to mitigate the effects of an outbreak. The article also discusses some of the challenges associated with genome-editing technologies and the efforts that scientists are undertaking to mitigate them. Overall, CRISPR and genome-editing technologies are poised to have a significant positive influence on global health security over the years to come.